(en)The present invention relates to constructs including one or more nucleic acids encoding two or more oleosin repeat units, and methods of use thereof. The present invention also relates to recombinant polypeptides including two or more oleosin repeat units, and methods of use thereof.

1.ApplicationNumber: US-9075806-A
1.PublishNumber: US-2009133160-A1
2.Date Publish: 20090521
3.Inventor: SCOTT RICHARD WILLIAM
ARCUS VICKERY LAURENCE
ROBERTS NICHOLAS JOHN

4.Inventor Harmonized: SCOTT RICHARD WILLIAM(NZ)
ARCUS VICKERY LAURENCE(NZ)
ROBERTS NICHOLAS JOHN(NZ)

5.Country: US
6.Claims:
(en)The present invention relates to constructs including one or more nucleic acids encoding two or more oleosin repeat units, and methods of use thereof. The present invention also relates to recombinant polypeptides including two or more oleosin repeat units, and methods of use thereof.

7.Description:
(en)The present invention relates to constructs including one or more nucleic acids encoding two or more oleosin repeat units, and methods of use thereof. The present invention also relates to recombinant polypeptides including two or more oleosin repeat units, and methods of use thereof.
Triacylglycerol
Most plants synthesise and store significant amounts of triacylglycerol (TAG) only in developing embryos and pollen cells where it is subsequently utilised to provide catabolizable energy during germination and pollen tube growth. Dicotyledonous plants can accumulate up to approximately 60% of their seed weight as TAG. Ordinarily, this level is considerably lower in the monocotyledonous seeds where the main form of energy storage is carbohydrates (e.g., starch).
The only committed step in TAG biosynthesis is the last one, i.e., the addition of a third fatty acid to an existing diacylglycerol, thus generating TAG. In plants this step is performed by one of three enzymes including: acyl CoA: diacylglycerol acyltransferase (DGAT1); an unrelated acyl CoA: diacylglycerol acyl transferase (DGAT2); and phospholipid: diacylglycerol acyltransferase (PDAT) (Bouvier-Nave et al., 2000; Dahlqvist et al., 2000; Lardizabal et al., 2001; Zou et al., 1999).
Oleosin
Oleosins are specific plant proteins usually found only in seeds and pollen. Their function is to stop oil bodies coalescing during seed and pollen dehiscence. In nature, TAG produced in seeds and pollen form micelles encapsulated by a spherical phospholipid monolayer and one or several species of oleosin proteins. Oil bodies in fruit tissues (such as olives and avocados) do not contain oleosins.
The physiochemical properties of the major oleosins is relatively conserved between plants and is characterised by the following:
15-25 kDa protein corresponding to approximately 140-230 amino acid residues. The protein sequence can be divided almost equally along its length into 4 parts that correspond to a N-terminal hydrophilic region; two centre hydrophobic regions (joined by a proline knot or knob) and a C-terminal hydrophilic region. The topology of oleosin is attributed to its physiochemical properties, which includes a folded hydrophobic core flanked by hydrophilic domains ( FIG. 1 ). This arrangement confers an amphipathic nature to oleosin resulting in the hydrophobic domain being embedded in the phospholipid monolayer (Tzen et al., 1992) while the flanking hydrophilic domains are exposed to the aqueous environment of the cytoplasm ( FIG. 2 ).

Oil Bodies
An oil body that is produced in seed or pollen consists of a droplet of TAG surrounded by a monolayer of phospholipid where the hydrophobic acyl moieties of the phospholipids interact with the encapsulated TAG and the hydrophilic head groups face the cytoplasm. Oil bodies are naturally produced in the seeds and pollen of many plants. Oil bodies can also be generated artificially by combining oleosins, triacylglycerides and phospholipids (Peng et al., 2004).
The outside of the oil body is coated with oleosins which are orientated with their central hydrophobic amino acid domains protruding through the phospholipid monolayer and into the TAG core of the oil body ( FIGS. 2-6 ).
The size of the oil body may be regulated by oleosin imparting a defined curvature; the curvature is dependent on the oleosin::oil ratio as well as the type of oleosin and oil.
Biohydrogenation
It has been demonstrated that the lipid profile of ruminant animal feed in turn influences the lipid profile of meat and dairy products (Demeyer and Doreau, 1999). Different plants have different lipid profiles; by selectively feeding animals only plants with the desired lipid profile it is possible to positively influence the lipid profile of downstream meat and dairy products. In ruminants the final lipid make up of the meat and milk is not only influenced by the dietary lipids but is also heavily influenced by biohydrogenation. Biohydrogenation is the hydrogenation of non-reduced compounds (such as unsaturated fats) by the biota present in the rumen.
Emulsions
Emulsions are produced when one or more liquids that are immiscible (usually due to different polarities and thus different hydrophobicities) in another liquid are uniformly suspended within that liquid, for example when oil droplets are dispersed uniformly in water or water droplets dispersed uniformly in oil. Generation of a relatively stable emulsion requires the use of an emulsifier, which lowers the interfacial tension between the liquids. The stability of an emulsion is generally a measure of what conditions and for how long the uniform dispersion persists. Emulsifiers are commonly used in the food and cosmetic industry; as such the emulsifiers need to have high emulsion stability as well as be safe for consumption and topical application.
It is an object of the present invention to overcome, or at least alleviate, one or more of the difficulties or deficiencies associated with the prior art.
In one aspect the present invention provides a construct including one or more nucleic acids encoding two or more oleosin repeat units. For expression in vegetative plant tissue preferably the construct further includes a nucleic acid encoding a diacylglycerol acryltransferase.
The term “oleosin” as used herein includes any functionally active plant oleosin, including functionally active fragments and variants thereof (e.g., L-oleosin, H-oleosin, steroleosin and caoleosin).
In a preferred embodiment, the oleosin repeat unit may be from white clover or sesame seed, or may be a synthetic or recombinant version of an oleosin repeat unit from white clover or sesame seed.
While Applicants have exemplified the invention using white clover and sesame seed oleosins, the invention is not limited thereto and any functionally active plant oleosin sequence may be used in the constructs of the present invention. The oleosin sequence may be naturally occurring, recombinant or synthetic.
By “repeat units” is meant multiple copies of nucleotide sequences encoding oleosin within a single polynucleotide, or multiple copies of amino acid sequences encoding oleosin within a single polypeptide, which may or may not contain intervening nucleotide or amino acid sequences. The repeat units may be tandem repeats. The repeat units may be homo- or hetero-repeats (homo or heteromeric).
The oleosin repeat units may be linked either directly, for example by direct fusion of the repeats, or by using linking sequences.
In a preferred embodiment of this aspect of the invention linker sequences may be included between the oleosin repeats to facilitate rotation of the oleosin hydrophilic domains relative to each other to form the correct topology. Such linker sequences also facilitate recombinatorial subcloning of sequences encoding desired peptides in between the oleosin repeats, and also facilitate chemical or enzymatic cleavage, for example to destroy the multimeric oleosin chain and/or release the desired peptide from the multimeric oleosin chain.
Thus, the construct may further include nucleotide sequences encoding linking sequences between two or more of the oleosin repeat units. The linking sequences may be short sequences, for example sequences that allow flexibility between the repeat units (act as a flexible hinge) or induce a directional change (act as a directional induction hinge) between the repeats, enable degradation between the oleosin repeat units, for example by peptidases, unrelated peptide sequences that may have bioactive properties, or sites for enzymatic cleavage and or subsequent fusion.
More particularly, the linking nucleotide sequence(s) between the oleosin repeat units may encode the native N- and C-termini of the respective repeats, sequences that code for comparatively short peptides that allow flexibility between the repeats, comparatively short peptides with amino acid residues that induce a directional change in the chain (for example proline), sequences that enable the future targeted cloning of additional sequences between the repeats, sequences that encode for specific targeted peptidase degradation, sequences that encode for bioactive peptides, and/or sequences encoding sites for specific enzymatic cleavage and subsequent fusion, e.g., modified self splicing intein and polymerisation cyclisation (Williams et al., 2005).
The multiple oleosin nucleotide sequences may code for the same oleosin peptide sequence or code for different oleosin peptide sequences. The multiple oleosin nucleotide sequences may code for the same oleosin peptide sequence but use alternate codons in the nucleotide sequence where applicable. This enables the construct to also be used in prokaryotic expression systems that are not non-recombinant minus (rec − ). It also enables the use of oleosins that contain different affinities for the oil body.
In a particularly preferred embodiment of the present invention, the nucleic acid encoding an oleosin repeat unit includes a nucleotide sequence selected from the group consisting of sequences shown in FIGS. 13 , 15 , 17 , 19 , 21 , 23 , 25 , 27 , 31 , 34 , 70 , 72 - 77 and 97 - 106 hereto, and functionally active fragments and variants thereof.
The construct of the present invention includes one or more nucleic acids encoding two or more oleosin repeats, preferably between two or three and twenty oleosin repeats, more preferably between two or three and ten oleosin repeats, most preferably between two or three and five or six oleosin repeats.
The diacylglycerol acyltransferase may be of any suitable type, including functionally active fragments and variants thereof. In a preferred form, the diacylglycerol acyltransferase is selected from the group consisting of DGAT1, DGAT2 and PDAT.
Nucleic acids according to the invention may be full-length genes or part thereof, and are also referred to as “nucleic acid fragments” and “nucleotide sequences” in this specification.
The nucleic acid may be of any suitable type and includes DNA (such as cDNA or genomic DNA) and RNA (such as mRNA) that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases, and combinations thereof.
By “functionally active” in respect of a nucleotide sequence is meant that the fragment or variant (such as an analogue, derivative or mutant) is capable of modifying lipids in a plant. Such variants include naturally occurring allelic variants and non-naturally occurring variants. Additions, deletions, substitutions and derivatizations of one or more of the nucleotides are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 80% identity to the relevant part of the oleosin repeat sequences exemplified herein, more preferably at least approximately 90% identity, most preferably at least approximately 95% identity. Such functionally active variants and fragments include, for example, those having nucleic acid changes that result in conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence. For example, the nucleic acid sequence may be modified to enhance expression without altering the amino acid sequence. Preferably the fragment has a size of at least 30 nucleotides, more preferably at least 45 nucleotides, most preferably at least 60 nucleotides.
By “functionally active” in the context of a polypeptide is meant that the fragment or variant has one or more of the biological properties of oleosin polypeptides. Additions, deletions, substitutions and derivatizations of one or more of the amino acids are contemplated so long as the modifications do not result in loss of functional activity of the fragment or variant. Preferably the functionally active fragment or variant has at least approximately 60% identity to the relevant part of the oleosin polypeptides exemplified herein, more preferably at least approximately 80% identity, most preferably at least approximately 90% identity. Such functionally active variants and fragments include, for example, those having conservative amino acid substitutions of one or more residues in the corresponding amino acid sequence. Preferably the fragment has a size of at least 10 amino acids, more preferably at least 15 amino acids, most preferably at least 20 amino acids.
By “operatively linked” is meant that a regulatory element is capable of causing expression of said nucleic acid in a cell and/or a terminator is capable of terminating expression of said nucleic acid in a cell. Preferably, said regulatory element is upstream of said nucleic acid and said terminator is downstream of said nucleic acid.
By “an effective amount” is meant an amount sufficient to result in an identifiable phenotypic trait in said plant, or a plant, plant seed or other plant part derived therefrom. Such amounts can be readily determined by an appropriately skilled person, taking into account the type of plant, the route of administration and other relevant factors. Such a person will readily be able to determine a suitable amount and method of administration. See, for example, Maniatis et al, Molecular Cloning: A Laboratory Manual, Cold Spring Harbor Laboratory, Cold Spring Harbor, the relevant disclosure of which is incorporated herein by reference.
It will also be understood that the term “comprises” (or its grammatical variants) as used in this specification is equivalent to the term “includes” and should not be taken as excluding the presence of other elements or features.
The construct of the present invention may be a vector. In a preferred embodiment of this aspect of the invention, the vector may include at least one regulatory element, such as a promoter, operatively linked to the nucleic acid. The vector may also include an operatively linked terminator.
The vector may be of any suitable type and may be viral or non-viral. The vector may be an expression vector. Such vectors include chromosomal, non-chromosomal and synthetic nucleic acid sequences, eg. derivatives of plant viruses; bacterial plasmids; derivatives of the Ti plasmid from Agrobacterium tumefaciens , derivatives of the Ri plasmid from Agrobacterium rhizogenes ; phage DNA; yeast artificial chromosomes; bacterial artificial chromosomes; binary bacterial artificial chromosomes; vectors derived from combinations of plasmids and phage DNA. However, any other vector may be used as long as it is replicable, or integrative or viable in the relevant cell.
The regulatory element and terminator may be of any suitable type and may be endogenous to the target cell or may be exogenous, provided that they are functional in the target cell.
Preferably one of the regulatory elements is a promoter. A variety of promoters which may be employed in the vectors of the present invention are well known to those skilled in the art. Factors influencing the choice of promoter include the desired tissue specificity of the vector, and whether constitutive or inducible expression is desired and the nature of the cell to be transformed. Particularly suitable constitutive promoters for use in plants include the Cauliflower Mosaic Virus 35S (CaMV 35S) promoter, the maize Ubiquitin promoter, and the rice Actin promoter. In a preferred embodiment the promoter may be chosen to enable the expression of oleosin in the desired organ, tissue and stage of development.
A variety of terminators which may be employed in the vectors of the present invention are also well known to those skilled in the art. The terminator may be from the same gene as the promoter sequence or a different gene. Particularly suitable terminators for use in plants are polyadenylation signals, such as the CaMV 35S polyA and other terminators from the nopaline synthase (nos) and the octopine synthase (ocs) genes.
The vector, in addition to the regulatory element, the nucleic acid and the terminator, may include further elements necessary for expression of the nucleic acid, in different combinations, for example vector backbone, origin of replication (ori), multiple cloning sites, spacer sequences, enhancers, introns (such as the maize Ubiquitin Ubi intron), antibiotic resistance genes and other selectable marker genes (such as the neomycin phosphotransferase (npt2) gene, the hygromycin phosphotransferase (hph) gene, the phosphinothricin acetyltransferase (bar or pat) gene), and reporter genes (such as green fluorescence protein (GFP), beta-glucuronidase (GUS) gene (gusA)). The vector may also contain a ribosome binding site for translation initiation. The vector may also include appropriate sequences for facilitating correct transcription, amplifying expression, increasing mRNA stability, enhancing protein translation or facilitating accurate translation.
As an alternative to use of a selectable marker gene to provide a phenotypic trait for selection of transformed host cells, the presence of the construct or vector in transformed cells may be determined by other techniques well known in the art, such as PCR (polymerase chain reaction), Southern blot hybridisation analysis, histochemical GUS assays, northern and Western blot hybridisation analyses.
Those skilled in the art will appreciate that the various components of the construct or vector are operatively linked; so as to result in expression of said nucleic acid. Techniques for operatively linking the components of the construct or vector of the present invention are well known to those skilled in the art. Such techniques include the use of linkers, such as synthetic linkers, for example including one or more restriction enzyme sites.
The constructs and vectors of the present invention may be incorporated into a variety of plants, including monocotyledons (such as grasses from the genera Lolium, Festuca, Paspalum, Pennisetum, Panicum and other forage and turfgrasses, corn, rice, sugarcane, oat, wheat and barley) dicotyledons (such as arabidopsis , tobacco, soybean, canola, cotton, potato, chickpea, medics, white clover, red clover, subterranean clover, alfalfa, eucalyptus, poplar, hybrid aspen, and gymnosperms (pine tree)). In a preferred embodiment, the constructs and vectors are used to transform commercial crops that are fed directly to animals.
The constructs and vectors of the present invention may also be incorporated into other eukaryotic expression systems, including yeast, insect and mammalian cells. Thus, repeat oleosins, such as multimeric tandem repeat oleosins, (either homo or hetero repeats) may be generated by recombinant protein expression in eukaryotic expression systems and subsequently purified as functional recombinant oil bodies having the additional properties afforded by the presence of repeat oleosins.
The constructs and vectors of the present invention may also be incorporated into prokaryotic expression systems. Thus, repeat oleosins, such as multimeric tandem repeat oleosins, (either homo or hetero repeats) may be generated by recombinant protein expression in bacteria such as Escherichia coli and subsequently purified and recombined with for example, phospholipids and triacyl glyceride to generate functional recombinant oil bodies with the additional properties afforded by the presence of repeat oleosins.
The constructs and vectors of the present invention may be constructed by any suitable method, including:
Amplification and subsequent cloning of oleosin sequences, for example using PCR with primers designed to publicly available oleosin sequences. For plant based expression clones these may include oleosins amplified from genomic DNA that may also contain introns depending on the clone. For prokaryotic and non-plant eukaryotic expression systems the source of the template for PCR preferably comes from cDNA which will not contain plant introns. Restriction digestion and ligation of oleosin clones that contain suitable inframe restriction sites at both N and C termini. Restriction sites may be added by techniques such as PCR or ligation of sticky ends. Engineering different restriction sites (that correspond to a cloning polylinker sequence) onto the ends of individual oleosin clones, then building up the multimer by a series of digestions and ligations by firstly ligating the polylinker to the 3′ end of the first oleosin clone. Chemically synthesising the complete construct. A combination of the above.

Techniques for incorporating the constructs and vectors of the present invention into cells (for example by transduction, transfection or transformation) are well known to those skilled in the art. For plant cells, techniques include Agrobacterium mediated introduction, electroporation to tissues, cells and protoplasts, protoplast fusion, injection into reproductive organs, injection into immature embryos and high velocity projectile introduction to cells, tissues, calli, immature and mature embryos. The choice of technique will depend largely on the type of cell to be transformed.
Cells incorporating the constructs and vectors of the present invention may be selected, as described above, and then cultured in an appropriate medium to regenerate transformed plants, using techniques well known in the art. The culture conditions, such as temperature, pH and the like, will be apparent to the person skilled in the art. The resulting plants may be reproduced, either sexually or asexually, using methods well known in the art, to produce successive generations of transformed plants.
In a further aspect of the present invention there is provided a plant cell, plant, plant seed or other plant part, including, e.g. transformed with, a construct or vector of the present invention.
The plant cell, plant, plant seed or other plant part may be from any suitable species, including monocotyledons, dicotyledons and gymnosperms. In a preferred embodiment the plant cell, plant, plant seed or other plant part is from a commercial plant that is normally fed directly to animals.
The present invention also provides a plant, plant seed or other plant part derived from a plant cell of the present invention and including a construct or vector of the present invention. The present invention also provides a plant, plant seed or other plant part derived from a plant of the present invention and including a construct or vector of the present invention.
The present invention also provides a eukaryotic cell, such as a yeast, insect or mammalian cell, including, eg. transformed with, a construct or vector of the present invention.
The present invention also provides a prokaryotic cell, eg. a bacteria such E. Coli , including, eg. transformed with, a construct or vector of the present invention.
The present invention also provides a method of producing repeat oleosins in a plant, said method including introducing into said plant a construct or vector of the present invention. By “repeat oleosin” is meant a recombinant polypeptide including two or more oleosin repeat units.
The present invention also provides a method of producing repeat oleosins in a eukaryotic cell, said method including introducing into said eukaryotic cell a construct or vector of the present invention. The method may include the further step of partially or substantially purifying said repeat oleosin from said cell. In a preferred form the repeat oleosin may be partially or substantially purified by the generation of oil bodies. The oil bodies may be produced within the cell, e.g. plant seed.
The present invention also provides a method of producing repeat oleosins in a prokaryotic cell, said method including introducing into said prokaryotic cell a construct or vector of the present invention. The method may include the further steps of partially or substantially purifying said repeat oleosin from said cell. In a preferred form the repeat oleosin may be partially or substantially purified by the generation of oil bodies. The oil bodies may be produced artificially using recombinant oleosin repeats from other expression systems such as E. coli.
The oleosin protein repeats may be purified using affinity chromatography, such as a fused Histidine tag and Ni 2+ resin purification.
The present invention also provides a partially or substantially purified and/or recombinant polypeptide including two or more oleosin repeat units.
The polypeptide may be produced by expression of a construct or vector according to the present invention.
The present invention also provides a lipid encapsulated by a polypeptide according to the present invention.
The oleosin repeat units may be of any suitable type, including functionally active fragments and variants thereof. For example, the oleosin repeat units may be selected from the group consisting of L-oleosin, H-oleosin, steroleosin and caoleosin and functionally active fragments and variants thereof. The oleosin repeats may be tandem repeats. The oleosin repeats may be multimeric tandem repeats. The oleosin repeats may be homo- or hetero-repeats.
In a preferred embodiment, the oleosin repeat unit may be from white clover or sesame seed, or may be a synthetic or recombinant version of an oleosin repeat unit from white clover or sesame seed. However, the invention is not limited thereto and the polypeptide of the present invention may include any functionally active plant oleosin sequence.
The oleosin repeat units may be linked either directly or by linking sequences. Thus, the polypeptide may further include linking sequences between two or more of the oleosin repeat units. The linking sequences may allow flexibility, induce a directional change or enable degradation between the oleosin repeat units.
In a particularly preferred embodiment of the present invention, the oleosin repeat unit includes an amino acid sequence selected from the group consisting of the sequences shown in FIGS. 69 , 70 , 78 - 83 and 107 - 116 hereto, and functionally active fragments and variants thereof.
In another particularly preferred embodiment of the present invention, the oleosin repeat unit is encoded by a nucleotide sequence selected from the group consisting of sequences shown in FIGS. 13 , 15 , 17 , 19 , 21 , 23 , 25 , 27 , 31 , 34 , 70 , 72 - 77 and 97 - 106 hereto, and functionally active fragments and variants thereof.
The recombinant polypeptide of the present invention includes two or more oleosin repeats, preferably between two or three and twenty oleosin repeats, more preferably between two or three and ten oleosin repeats, most preferably between two or three and five or six oleosin repeats.
Applicants have found that that repeat oleosins, such as recombinant multimeric tandem repeat oleosins, (either homo or hetero repeats) may be expressed in the seeds of plants which would mean that the extract would contain a mixture of native oleosins along with the repeat oleosins. If a single species of oleosin multiples are required the repeat oleosins may be expressed in plants in which native oleosin expression has been suppressed, e.g., by mutagenesis, gene silencing or natural selection.
In addition, the repeat oleosins may be coexpressed with a diacylglyerol acyltransferase such as DGAT1 or DGAT2 or PDAT, in plant vegetative organs allowing the generation of emulsion complexes containing substantially only the desired species of oleosin (since oleosins are not normally expressed in the vegetative portions of plants). Thus, co-expression of DGAT1, DGAT2 or PDAT with polyoleosin in the vegetative portions of plants produces oil bodies encapsulated by the polyoleosin.
Furthermore, the repeat oleosins may be expressed and purified from bacteria, such as E. coli , since oleosins are not naturally present in E. coli . Expression of repeat oleosins in some bacteria may require modification of the nucleotide sequence to avoid recombination events occurring in rec − strains.
Applicants have found that use of a series of oleosin repeats generates a recombinant protein with exploitable properties. Linking oleosin units to give homo or hetero multimeric repeats reduces the number of N-termini available for the initiation amino peptidase degradation in the rumen and/or stomach as well as altering the physiochemical characteristics (e.g., the hydrophobic interactions) of the protein and thus broadening the range of emulsification properties. In particular, this has a number of exploitable benefits, including:
Generating a simple method for producing foodstuffs such as meat and milk with health promoting lipid profiles by reducing the degree of biohydrogenation. Allowing for the delivery of fused bioactive peptides to be ingested and delivered intact to the site of absorption. Providing a rapid mechanism to alter the emulsion properties of reconstituted feeds, pharmaceuticals, beauty products etc. Allowing for the delivery of lipid soluble active compounds to be delivered and released in a controlled fashion by topical application. Allowing for the delivery of lipid soluble bioactive compounds to be ingested and delivered intact to the site of absorption.

Applicants have found that by the use of repeat oleosins, such as recombinant multimeric tandem repeat oleosins (either homo or hetero repeats) the stability of an oil body may be regulated. The incorporation of amino acid residues between the oleosin repeats may be desirable to allow sufficient flex between the repeats, to influence the curvature of the oil body, to control the direction of the repeats relative to each other, to incorporate bioactive peptides, to provide sites for directed proteolytic degradation, or to provide sites for specific enzymatic cleavage and subsequent fusion, e.g., modified self splicing intein and polymerisation cyclisation (Williams et al., 2005).
Thus, the present invention also provides a mechanism for the delivery of bioactive peptides that may be fused between the repeats or at the end of the repeats.
The present invention also provides a mechanism for allowing free rotation between the repeats or for directing the orientation of the repeats relative to each other by incorporating linking sequences between the repeats.
The size of the suspended particles contributes to the stability of the suspension and the amount of material that may be suspended and this allows the emulsification properties to be tailored for the application. By altering the number of oleosin repeats in a peptide sequence (preferably using recombinant technologies) oleosins with different emulsification properties may be generated. These may confer enhanced stabilities in terms of, for example, temperature stability, pH stability and/or altered particle size. In turn this broadens the number of compounds that may be emulsified, as well as expanding the applications of the emulsifications, for example, by extending their stability and the amount of compounds that may be emulsified.
In a further aspect the present invention provides a method of manipulating lipids in a plant, said method including introducing into said plant a construct including one or more nucleic acids encoding two or more oleosin repeat units.
Manipulation of lipids includes, but is not limited to, alteration of emulsification properties, including stability of suspension and amount of material that may be suspended, alteration of physiochemical properties, including hydrophobic interactions, and altering the degree of biohydrogenation.
In a preferred embodiment, the present invention provides a method of altering stability of an oil body in a plant, said method including modifying an oleosin in said plant to include two or more oleosin repeat units. This may in turn alter the ratio of oleosin to oil in said oil body.
Reduction of Biohydrogenation
In ruminants, biohydrogenation is the hydrogenation of non-reduced compounds (such as unsaturated fats) with hydrogen from rumen biota. Applicants have engineered oleosin to generate oil bodies containing unsaturated fats in the TAG (surrounded by a phospholipid monolayer) encapsulated by the oleosin repeats of the present invention. This may be less susceptible to the process of biohydrogenation in the rumen before it passes into the intestine for absorption. While applicants do not wish to be restricted by theory, it is thought that a chain of oleosin units would have fewer N-termini per unit of oleosin available for amino peptidase degradation (the main form of protein degradation in the rumen). In turn this would reduce the degree of oleosin degradation and therefore reduce the loss of oil body integrity and subsequently reduce the degree of biohydrogenation of the unsaturated fats in the TAG. In turn this would lead to an increase in the level of unsaturated fats reaching the site of adsorption in the intestine. In turn this would lead to a change in the fatty acid profile of foodstuffs such as milk and meat products from the animal eating such a product.
Thus, the present invention provides a method of altering biohydrogenation of a lipid, said method including encapsulating said lipid in a recombinant polypeptide including two or more oleosin repeat units.
The present invention also provides a method of protecting unsaturated lipids from biohydrogenation, said method including incorporating said unsaturated lipids into an oil body including a recombinant polypeptide including two or more oleosin repeat units.
Delivery of Fused Bioactive Peptides Orally and Topically
Applicants have engineered restriction sites between the oleosin repeats to enable insertion of a frame coding sequence (such as those encoding bioactive peptides that would normally be susceptible to degradation in the intestines). While applicants do not wish to be restricted by theory it is thought that a chain of oleosin units would have enhanced stability in the digestive acid conditions of the stomach as well as fewer N-termini per unit of oleosin available for amino peptidase degradation (the main form of protein degradation in the rumen). Thus a peptide inserted between multimeric oleosin tandem repeats is afforded a degree of protection from degradation by digestive acidic conditions and aminopeptidases. In turn this would reduce the degree of active peptide degradation in the stomach and rumen. In turn this would lead to higher levels of active peptides reaching the site of adsorption in the intestine. In turn this would lead to an increased absorption of bioactive peptides by the organism. The degree of protection may be altered by the position of the bioactive peptide in the oleosin chain, the nature of the oleosins in the chain, and/or the amino acid sequences joining the oleosins and bioactive peptides.
Thus, the present invention provides a method of delivering a bioactive peptide, to animals including humans, said method including inserting said peptide at the N- or C-terminus of a series of two or more oleosin repeat units or between two or more oleosin repeat units to produce a recombinant polypeptide and administering said recombinant polypeptide to said animal.
Preferably, the bioactive peptides are delivered orally or topically. The bioactive peptides may be delivered to the intestine. The bioactive peptides may be delivered by timed release, eg. sustained release or delayed release.
The present invention also provides a partially or substantially purified or recombinant polypeptide including two or more oleosin repeat units and further including one or more bioactive peptides.
The bioactive peptide may be inserted at the N- or C-terminus of a series of two or more oleosin repeat units or between two or more oleosin repeat units.
The recombinant polypeptide may be produced by expression of a construct or vector according to the present invention.
Thus, the present invention also provides a construct including one or more nucleic acids encoding two or more oleosin repeat units and further including one or more nucleic acids encoding bioactive peptides.
Delivery of Encapsulated Bioactive Peptides and Other Compounds Orally and Topically
Polyoleosin provides a mechanism for the development and delivery of compounds such as therapeutic and prophylactic drugs, including drugs for internal parasites in humans and animals and bioactive peptides; and organisms such as health promoting bacteria (e.g., lactobacillus ) by encapsulation of the compound or organism within the oil body. In particular, it provides a mechanism for delivering bioactive peptides through the rumen and into the digestive system, substantially without loss of bioactivity. This issue currently represents a major hurdle for the development of bioactives for internal parasites in rumens. Polyoleosins thus facilitate development of bioactive drug development and delivery.
In addition, polyoleosin has a similar application in the delivery of encapsulated bioactives in cosmetics, eg. creams and may be applied epidermally, for example to wounds or skin problems. Polyolesin may also have applications for controlled release in dermal applications.
Thus, the present invention also provides a method of delivering compounds and/or organisms to animals including humans, said method including encapsulation said compound or organism in an oil body including two or more oleosin repeat units and administering said oil body to said animal.
Preferably the compound is a therapeutic or prophylactic drug or a bioactive peptide or protein.
Preferably the organism is a bacterium, more preferably a health promoting bacterium such as lactobacillus.
Preferably the compound or organism is delivered orally or topically. The compound or organism may be delivered to the intestine. The compound or organism may be delivered by timed release eg. sustained release or delayed release.
Emulsification and Encapsulation of Bioactives
Repeat oleosins, such as recombinant multimeric tandem repeat oleosins (either homo or hetero repeats), may be used to tailor emulsion complexes and to encapsulate bioactive compounds that may exist in the emulsion. By the use of repeat oleosins, the stability of an oil body may be tailored by oleosin. The size of the suspended particles contributes both to the stability of the suspension and the amount of material that may be suspended. By altering the number of oleosin repeats in a peptide sequence (preferably using recombinant technologies) oleosins with different emulsification properties are generated. These confer enhanced stabilities in terms of, for example, temperature and pH stability and altered particle size. In turn this broadens the number of compounds that may be emulsified as well as expanding the applications of the emulsifications.
Polyoleosin allows the manufacturer to tailor the emulsification properties by altering the number of oleosin repeats. The majority of processed foods utilise emulsifiers of some form or another. In addition, polyoleosins may be utilised in the cosmetics industry. The oil based encapsulation mechanism provides an ideal delivery mechanism for any compound, notably bioactives for dermal application.
Accordingly, in a further aspect the present invention provides a method of altering the emulsification properties of an oleosin, said method including recombinantly producing the oleosin with two or more oleosin repeat units.
Altering the emulsification properties of the oleosin may include altering temperature and/or pH stability and/or size of oil bodies including the oleosin.
The present invention also provides a recombinant oleosin with altered emulsification properties, said oleosin including two or more oleosin repeat units.
The recombinant polypeptide may be produced by expression of a construct or vector according to the present invention.
Thus, in the polypeptides of the present invention tandem oleosins may be fused directly or by small linking (eg. hinge) sequences. The polypeptides may contain fused bioactive peptides either at the terminal ends of the repeats or located between the repeats.
Such polyoleosins may be used to deliver encapsulated products/compounds/proteins that do not have to be fused to the oleosin peptides but rather are generated during the process of creating oil bodies or AOBs.
Polyoleosins may also be used to deliver bioactive peptides either encapsulated within oil bodies, AOBs or fused to the ends of oleosin repeats or fused between the repeats.
Polyoleosins used for emulsification or delivery or protection of compounds may be tailored by changing the number of oleosin tandem repeats rather than simply being the fusion of a peptide of insert fused between two oleosin repeats.
The present invention will now be more fully described with reference to the accompanying Examples and drawings. It should be understood, however, that the description following is illustrative only and should not be taken in any way as a restriction on the generality of the invention described above.



IN THE FIGURES
FIG. 1 . Kyte and Doolittle hydrophobic plot (window=17) of a typical oleosin sequence.
FIG. 2 . Oil body showing topology of oleosin single peptide chains.
FIG. 3 . Oil body showing topology of dimeric oleosin repeat peptide chains joined by unique peptide linkers.
FIG. 4 . Oil body showing topology of trimeric oleosin repeat peptide chains joined by unique peptide linkers.
FIG. 5 . Oil body showing topology of tetrameric oleosin repeat peptide chains joined by unique peptide linkers.
FIG. 6 . Oil body showing topology of pentameric oleosin repeat peptide chains joined by unique peptide linkers.
FIG. 7 . Typical Kyte and Doolittle hydrophobicity plot (window=17) of homo or hetero pentameric oleosin tandem repeat containing unique inter oleosin peptide liners.
FIG. 8 . pBLUESCRIPT II SK MCS sequence and translated amino acid sequence. With the exception of EcoRV all other restriction sites are not present in either the white clover oleosin clone or the Gateway PCR entry vector pENTR/D • and XXX=codon not part of a restriction site.
FIG. 9 . Standard layout of primers and PCR products to generate white clover polyoleosin constructs.
FIG. 10 . Map of pENTR/D-TOPO.
FIG. 11 . Map of pCR2.1-TOPO.
FIG. 12 . Map of pOLE01-MC.
FIG. 13 . Sequence of the oleosin coding region in pOLE01-MC (Seq ID No. 29). CACC =GATEWAY™ adapter, XXXX=oleosin sequence, XXXXXX=restriction enzyme site—included in primer, TGA =stop codon.
FIG. 14 . Map of pOLE02-MC.
FIG. 15 . Sequence of the oleosin coding region in pOLE02-MC (Seq ID No. 30). XXXX=oleosin sequence, XXXXXX=restriction enzyme site—included in primer, XXXXXX=codons for extra amino acids—included in primer.
FIG. 16 . Map of pOLE03-MC.
FIG. 17 . Sequence of the oleosin coding region in pOLE03-MC (Seq ID No. 31). XXXX=oleosin sequence, XXXXXX=restriction enzyme site—included in primer, XXXXXX=codons for extra amino acids—included in primer.
FIG. 18 . Map of pOLE04-MC.
FIG. 19 . Sequence of the oleosin coding region in pOLE04-MC (Seq ID No. 32). XXXX=oleosin sequence, XXXXXX=restriction enzyme site—included in primer, XXXXXX=codons for extra amino acids—included in primer.
FIG. 20 . Map of pOLE05-MC.
FIG. 21 . Sequence of the oleosin coding region in pOLE05-MC (Seq ID No. 33). XXXX=oleosin sequence, XXXXXX=restriction enzyme site—included in primer, XXXXXX=codons for extra amino acids—included in primer.
FIG. 22 . Map of pOLE06-MC.
FIG. 23 . Sequence of the oleosin coding region in pOLE06-MC (Seq ID No. 34). XXXX=GATEWAY™ adapter sequence, XXXX=oleosin sequence, XXXXXX=base pairs encoding for additional amino acids—included in primer, XXXX =polylinker sequence,









FIG. 24 . Map of pOLE07-MC.
FIG. 25 . Sequence of the oleosin coding region in pOLE07-MC (Seq ID No. 35). XXXX=GATEWAY™ adapter sequence, XXXX=oleosin sequence, XXXXXX=base pairs encoding for additional amino acids—included in primer, XXXX =polylinker sequence,









FIG. 26 . Map of pOLE08-MC.
FIG. 27 . Sequence of the oleosin coding region in pOLE08-MC (Seq ID No. 36). XXXX=GATEWAY™ adapter sequence, XXXX=oleosin sequence, XXXXXX=base pairs encoding for additional amino acids—included in primer, XXXX =polylinker sequence,









FIG. 28 . Agarose gel of HindIII/ClaI digested pOLE04-MC and pOLE08-MC. Dotted boxes outline the regions excised for extraction from gel.
FIG. 29 . Map of pOLE09-MC.
FIG. 30 . Agarose gel results from checking pOLE09-MC.
Expected Sizes:
Clone 7
NcoI/XhoI—2.6 kb and 1.3 kb NcoI/SpeI/XhoI—2.6 kb, 1.3 kb & 57 bp NotI/XhoI—2.6 kb, 697 bp, & 643 bp XhoI—3.9 kb
Clone 9
NcoI/XhoI—two bands at ˜2.6 kb clones C9.1-C9.3 correct NcoI/SpeI/XhoI—2.6 kb & two bands at ˜1.3 kb clones C9.1-C9.3 correct NotI/XhoI—2.6 kb, 1.9 kb & 643 bp clones C9.1-C9.3 correct XhoI—5.2 kb clones C9.1-C9.3 correct


Clones 9.1-9.3 all showed the correct/expected sizes for pOLE09-MC.
The region in the pOLE09-MC cassette containing the newly inserted oleosin was then sequenced.
FIG. 31 . Sequence of pOLE09-MC, confirming the addition of the oleosin from pOLE04-MC into pOLE08-MC. Sequence was obtained by sequencing across the last oleosin in pOLE09-MC into the original pOLE08-MC vector. All mismatches were checked back to the original electropherogram to confirm errors were due to software misreads.
FIG. 32 . Map of pOLE10-MC.
FIG. 33 . Agarose gel analysis of a restriction enzyme digested pOLE10-MC clone, compared to pOLE09-MC.
Expected Sizes:







Clone 9











XhoI/PstI
−4.5 kb and 650 bp
correct


PstI
−5.1 kb
correct


SalI/PstI
−4.5 kb and 650 bp
correct























Expected Sizes:







Clone 10











XhoI/PstI
−4.5 kb and 1.2 kb
correct


PstI
−5.7 kb
correct


SalI/PstI
−5.1 kb and 650 bp
correct























Both pOLE09-MC and pOLE10-MC clones were found to be correct when analysed by restriction digests.
The region in the pOLE10-MC cassette containing the newly inserted oleosin was then sequenced using the M13-Reverese primer (five clones sequenced and found to match the predicted sequence.
FIG. 34 . Sequence of pOLE10-MC, confirming the addition of the oleosin from pOLE05-MC, into pOLE09-MC. Sequence was obtained via sequencing into the fifth pOLE10-MC and back across into pOLE09-MC. FIG. 35 . Map of pRSh1.
FIG. 36 . Map of pRS12.
FIG. 37 . EcoRI digest of C6 and C7 clones in pRSH1.
Expected Sizes:









Clone 6-pRSH1
10,349 bp, 3084 bp, 725 bp and 566 bp
clones 1, 3,



&4 correct

Clone 7-pRSH1
10,349 bp, 3084 bp, 1352 bp and
clones 1, 2,


566 bp
&3 correct

pRSH1
11,525 bp, 3084 bp, 566 bp and 463 bp.


















FIG. 38 . EcoRI digest of C8 clones in pRSH1.
Expected Sizes:









Clone 8-pRSH1
10,349 bp, 3084 bp, 1973 bp and 566 bp
clones 2-8



correct

pRSH1
11,525 bp, 3084 bp, 566 bp and 463 bp.
















FIG. 39 . EcoRI digest of C9 and C10 clones in pRSH1.
Expected Sizes:









Clone 9-pRSH1
10,970 bp, 3084 bp, 1973 bp and
clones 1, 2, &


566 bp
4 correct

Clone 10-pRSH1
11,594 bp, 3084 bp, 1973 bp and
clones 1, 2, &


566 bp
4 correct.

















FIG. 40 . BamHI digest of C9 and C10 clones in pRSH1.
Expected Sizes:









Clone 9-pRSH1
10826 bp, 4400 bp and 1367 bp
clone correct

Clone 10-pRSH1
10826 bp, 4400 bp and 1991 bp
clone correct

pRSH1
10826 bp, 3279 bp, 830 bp and 703 bp.
















FIG. 41 . EcoRI digest of DGAT1 clones in pRSH1.
Expected Sizes:









DGAT1-pRSH1
10700 bp, 3084 bp,
clones 1-3 correct


1232 bp and 566 bp

pRSH1
11525 bp, 3084 bp,
FIG. 42. EcoRV digest of


566 bp and 463 bp.
C6 clones in pRS12.

















Expected Sizes:









C6-pRS12
9131 bp, 7424 bp and 3762 bp
clones 2, 3, 5, &8 correct

pRS12
13810 bp and 7424 bp.















FIG. 43 . Restriction digest of DGAT1 and C7 clones in pRS12.
Expected Sizes:










DGAT1-pRS12
SpeI
14437 bp, 3833 bp
clones 1 &2



and 2908 bp
correct

C7-pRS12
SpeI
14437 bp, 2908 bp, 2724 bp
clones 1 &2



and 878 bp
correct

pRS12
SpeI
14437 bp, 3889 bp



and 2908 bp

DGAT1-pRS12
BamHI
17039 bp
clones 1 &2



and 4139 bp
correct

C7-pRS12
BamHI
16683 bp, 4139 bp
clones 1 &2



and 125 bp
correct

pRS12
BamHI
15562 bp, 4139 bp, 830 bp



and 703 bp.

























FIG. 44 . Restriction digest of C8, C9 and C10 clones in pRS12.
Expected Sizes:










C8-pRS12
SpeI
14437 bp, 2908 bp, 2724 bp
clones 1 &2



and 1499 bp
correct

C9-pRS12
SpeI
14437 bp, 2908 bp, 2724 bp
clones 2 &3



and 2120 bp
correct

C10-pRS12
SpeI
14437 bp, 2908 bp, 2744 bp
clones 1-3



and 2724 bp
correct

pRS12
SpeI
14437 bp, 3889 bp



and 2908 bp

C8-pRS12
BamHI
16683 bp, 4139 bp
clones 1 &2



and 746 bp
correct

C9-pRS12
BamHI
16683 bp, 4139 bp
clones 2 &3



and 1367 bp
correct

C10-pRS12
BamHI
16683 bp, 4139 bp
clone 1 . . .



and 1991 bp
correct

pRS12
BamHI
15562 bp, 4139 bp, 830 bp



and 703 bp.





























FIG. 45 . Restriction digest of C8, C9 and C10 clones in pRS12.
Expected Sizes:










C10-pRS12
BamHI
16683 bp, 4139 bp and 1991 bp
clones . . . 2 &




3 correct

C8-pRS12
EcoRV
10382 bp, 7424 bp and 3762 bp
clones 1 &




2 correct

C9-pRS12
EcoRV
10382 bp, 7424 bp and 4383 bp
clones 2 &




3 correct

C10-pRS12
EcoRV
10382 bp, 7424 bp and 5007 bp
clones 1-3




correct

pRS12
SpeI
14437 bp, 3889 bp and 2908 bp

pRS12
BamHI
15562 bp, 4139 bp, 830 bp



and 703 bp

pRS12
EcoRV
13810 bp and 7424 bp.

























FIG. 46 . A representative diagram of the pRSh1 binary vector containing oleosin multimers.
FIG. 47 . A representative diagram of the pRS12 binary vector containing oleosin multimers.
FIG. 48 . Plasmid map for the expression vector p17NON (N terminal oleosin, in pDEST17).
FIG. 49 . Plasmid maps for the expression vectors p42CON (N terminal oleosin in pET DEST42).
FIG. 50 . Characterisation of p17NON by PCR analysis.
Expected Sizes: NT −505 bp
All plasmids appear to contain an insert of the expected size
This amplification confirms the presence of the N terminal oleosin gene in the pDEST17 plasmid→p17NON
FIG. 51 . Characterisation of p42CON by PCR analysis.
Expected Sizes: NT −561 bp
NT#1 appears to contain a slightly larger insert.

All others appear to contain an insert of the expected size
This amplification confirms the presence of the N-terminal oleosin gene in the pET DEST42 plasmid→p42CON
FIG. 52 . Expression analysis by SDS PAGE of 6HON. N=Non-induced
I=Induced <=putative expressed 6HON expected size 6HON=14.7 kD.
FIG. 53 . Inclusion body analysis by SDS PAGE of the 6HONpeptide. N=Non induced, I=Induced, <=putative expressed 6HON, expected size 6HON=14.7 kD
*=putative expressed 6HOC expected size 6HOC=12.8 kD
FIG. 54 . Trial scale Nickel column purification analysis by SDS PAGE of 6HON. <=putative expressed 6HON expected size 6HON=14.7 kD.
Samples loaded as equivalent volumes.
FIG. 55 . Large scale Nickel purification analysis by SDS PAGE of 6HON. Expected size of 6HON=14.7 kD.
FIG. 56 . Concentration of 6HON. Volume of each eluted fraction was approximately 1 mL.
FIG. 57 . SDS-PAGE/immunoblot screened against anti oleosin N terminal antibody. Run on 18% SDS PAGE gel, 90 min 150V. 1° and 2° antibody diluted in 20 mL PBS. 1° antibody=1:2000 (10 μL). 2° antibody=1:5000 (4 μL) anti rabbit Ig, Horseradish Peroxidase linked whole antibody from donkey.
Lanes 4, 5, and 6 contained 1.8, 6.9, and 4.7 ng purified 6HON, respectively. Antibody appears to bind to 17OF (Lane 2), 17OC (Lane 3) and a number of peptides present in the extract from clover seed. Reason for binding to 17OC unclear, but may be due to similarities in 6×His tag and neighbouring regions.
FIG. 58 . Coomassie and subsequent immunoblot analysis of oil bodies extracted from clover seed. Arrow indicates expected size of clover seed oleosin (20 kDa).
L=Ladder; A & B=duplicate oil body extracts from clover seed.
FIG. 59 . PCR analysis of Agrobacterium colonies transformed with oleosin clone plasmids.
Lane A=AgR6; B=AgR 7; C=AgR 8; D=AgR9; E & F=AgR10; G, H, I=AgR 7; J, K, L=AgR 8; M, N, O=AgR 9; P=untransformed LBA4404; Q and R=AgR 7 plasmid DNA; S=1 Kb plus ladder
FIG. 60 . Effect of Basta on regeneration from hypocotyl (top) and cotyledon explants (bottom).
FIG. 61 . Growth of Basta resistant and sensitive shoots from DGAT co cultivated explants on 5 mg/L Basta.
FIG. 62 . PCR for the bar gene on putative transgenic shoots.
Lanes A and N 1 Kb plus ladder; lanes B and C DNA from AgR 6 shoots; lanes D and E DNA from AgR 7 shoots; lanes F and G DNA from AgR 8 shoots; lanes H and I DNA from AgR 9 shoots; lanes J and K DNA from AgR 10 shoots; lane L AgR 7 plasmid DNA; lane M blank
FIG. 63 . PCR for the Bar and oleosin gene.
Top panel ═PCR for bar gene, Bottom panel ═PCR with the same DNA using oleosin clone specific primers












Lanes
A = 1kb plus ladder;
B F = pRSH1 C6 plants;



G = pRSH1 C6 plasmid;
H = blank;



I L = pRSH1 C7 plants;
M = pRSH1 C7 plasmid;



N = blank;
O R = pRSH1 C8 plants;



S = pRSH1 C6 plasmid;
T = 1kb plus ladder



















FIG. 64 . RT PCR for oleosin from pRSH1 C6 transgenic shoots.
Lanes A and N=1 Kb plus ladder;
B F=reverse transcriptase treated RNA from pRSH1 C6 plants; G K RNASE treated RNA from pRSH1 C6 plants; L=pRSH1 C6 plasmid DNA; M blank

FIG. 65 . Northern blot analysis of 5 μg total RNA from Lotus japonicus hairy roots transformed with 1, 2, 3, 4 or 5 oleosin repeats.
Probed with 25 ng random primed 5 μCi 32P labelled oleosin cDNA.
Positive controls: +=4 pg; +=20 pg (arrows in ladder lane); oleosin gene (PCR product).
Line in single oleosin lanes indicates main transcript size detected (approximately 1.4 Kb);
Line in tandem oleosin construct lanes indicates main transcript size detected (approximately 2 Kb);
Line in trimeric oleosin construct lanes indicates main transcript size detected (approximately 2.7 Kb);
Line in tetrameric oleosin construct lanes indicates main transcript size detected (approximately 3.4 Kb);
Line in pentameric construct lanes indicates main transcript size detected (approximately 4 Kb);
Small black arrows indicate oleosin hybridising transcripts of aberrant size.
FIG. 66 . Schematic diagram of the synthetic sesame seed polyoleosin construct. The sequence was generated using optimised codons selected for expression and elevated GC content, randomised between the repeats with elevated mRNA stability, cryptic splice sites removed, UBQ10 intron, Kozak, tetranucleotide stop codon and restriction sites added.
FIG. 67 . Arabidopsis thaliana UBQ10 intron modifications.
A. Modified Arabidopsis thaliana UBQ10 intron (3′ splice site modified to be PstI as per Rose and Beliakoff, 2000) (Seq ID No. 44).

B. Comparison of the modified UBQ10 intron (Seq ID No. 44) with the original sequence from Norris et al., (1993) (Seq ID No. 45). Consensus=Seq ID No. 46.

FIG. 68 . NetGene2 graphical output prediction of splicing of the synthetic sesame seed polyoleosin construct. The GC content had been elevated, cryptic splice sites had been manually removed, and the Arabidopsis thaliana UBQ10 intron had been added.
FIG. 69 . Alignment of the translated sequences of 6 tandem repeats of the original sesame seed oleosin (without linkers) (Seq ID No. 47) with the 6 tandem repeats containing random assignment of the appropriate degenerate codons, GC optimised and modified linkers (with the intron removed) (Seq ID No. 48). Consensus=Seq ID No. 49.
The alignment shows the oleosin peptide sequences of each repeat are identical, also there is no change between the randomised codons sequences with and without intron.
FIG. 70 . Nucleic acid (Seq ID No. 50) and amino acid (Seq ID No. 51) Sequence and feature map of the synthetic sesame seed hexameric polyoleosin with randomised optimal degenerate codons, enriched GC content, enhanced mRNA stability, engineered restriction sites (also optimised for codon usage) and modified UBQ10 intron.
Key: attL sites (bold); engineered restriction sites and linkers (italics); oleosin repeats (grey box, white letters); double stop codon to ensure no read through due to amber codon (bold, underline); tetra-nucleotide stop codon (black box, white letter); UBQ10 intron (grey box, black letters); −20 to −11 from original cDNA (underline); −10 to −1 modified Joshi et al (1997) consensus sequence (bold, italics, underline).
FIG. 71 . Vector map of the synthetic sesame seed polyoleosin construct in PCR Script.
FIG. 72 . Nucleotide sequence of clone synthesised by GENEART AG containing 6 tandem Sesame seed oleosin repeats with randomised degerate codons (Seq ID No. 52).
FIG. 73 . Feature map of the nucleotide sequence of the identical triple oleosin repeats synthesised by GENEART AG (Seq ID No. 53).
FIG. 74 . Feature map of nucleotide sequence of pET29+Ole6-6×His (Seq ID No. 54).
FIG. 75 . Feature map of nucleotide sequence of pET29+Ole2-6×His (Seq ID No. 55).
FIG. 76 . Feature map of nucleotide sequence of pET29+Ole4-6×His (Seq ID No. 56).
FIG. 77 . Feature map of nucleotide sequence of pET29+Ole5-6×His (Seq ID No. 57).
FIG. 78 . Peptide sequence of: pET29+Ole6-6×His (Seq ID No. 58).
FIG. 79 . Peptide sequence of: pET29+Ole2-6×His (Seq ID No. 59).
FIG. 80 . Peptide sequence of: pET29+Ole4-6×His (Seq ID No. 60).
FIG. 81 . Peptide sequence of: pET29+Ole5-6×His (Seq ID No. 61).
FIG. 82 . Peptide sequence of: pUCOle3+(Seq ID No. 62).
FIG. 83 . Peptide sequence of: p29Ole (Seq ID No. 63).
FIG. 84 . Whole gel elution results from prokaryotic expression and purification of sesame seed oleosin.
A. Preliminary analysis of 1×−6× AOBs by SDS-PAGE separation.
Small arrows indicate expected sizes of 4×, 5× and 6× oleosin (rectangular boxes). Large arrows indicate bands of putative polyoleosin protein corresponding to 1×, 2, and 3× oleosins (oval boxes). Expected molecular weights are shown in brackets.
B. Coomassie stained SDS-PAGE gel after whole gel elution (39C_sesame_oleosin_AOBs.doc).
L K =BioRad Kaleidoscope Standards (cat# 161-0324) Pre=Coomassie stained slice of acrylamide gel prior to elution =expected size of oleosin.
FIG. 85 . SDS-PAGE analysis of fractions from Ni-affinity purification of prokaryotically expressed denatured sesame seed oleosin (48C_sesame_oleosin_His_pur.doc).
PI=Post Induction SPL=Supernatant, Post Lysis L=Lysate FT=Flow Through L S =BioRad Prestained SDS-PAGE Standards, Low Range (cat# 161-0305) # A & # B =Fraction number from either column A or B. =expected size of oleosin.
FIG. 86 . Analysis of rabbit anti-sesame seed oleosin antiserum by immunoblot and silver staining. Analysis of antibody titre and specificity.
LK=BioRad Kaleidoscope Standards (cat# 161 0324) 11=3 ng of 1 A 21=13 ng 1 A 31=27 ng 1 A 41=132 ng 1 A 51=663 ng 1 A S1 & S2=sesame seed extract C=clover seed extract 12=3 ng of 1B 22=14 ng 1B 32=29 ng 1B 42=143 ng 1B I=crude post-induction sample LP=BioRad Precision Plus Standard (cat# 161 0363). □=expected size of oleosin. Overflow of the standards can be seen in lanes 11 and I.
The rabbit raised antibodies show a high affinity for the affinity purified recombinant oleosin, detecting down to at least 3 ng. The antibodies also show high specificity, with no cross-reactivity against soluble seed proteins and low cross-reactivity to bacterial proteins (lane 1).
FIG. 87 . Visualisation of emulsification layer containing artificial oil bodies (AOBs) after first (top) and second (bottom) rounds of sonication.
FIG. 88 . SDS-PAGE/immunoblot analysis of AOB 1×, 2×, 3×, 4× and 6× oleosin.
For analysis of the 6× polyoleosin two samples were loaded per lane. N =non-induced negative control.
FIG. 89 . Analysis of AOBs containing 1×-6× Sesame seed polyoleosin proteins by SDS/urea-Gradient PAGE/SafeStain.
FIG. 90 . SDS, urea-PAGE/immunoblot of AOB Analysis of 1×-6× AOBs by SDS/urea-PAGE/SafeStain.
Small arrow indicates expected position of 6× oleosin (rectangular box). Large arrows indicate bands of putative polyoleosin protein corresponding to 1×, 2, 3×, 4×, and 5× oleosins (oval boxes). Expected molecular weights are shown in brackets.
FIG. 91 . Microscopic analysis of AOB containing a different number of oleosin repeats. Size of AOBs when prepared with polyoleosins containing increasing numbers of repeating oleosin units.
FIG. 92 . Effect of polyoleosin on the stability over time of AOB containing a different number of oleosin repeats after 7 days at 4° C. AOBs were prepared with different polyoleosins containing increasing numbers of repeating oleosin units. Vector control AOBs were prepared using inclusion bodies from E. coli containing a vector control.
FIG. 93 . Microscopic analysis of size of AOB containing a different number of oleosin repeats after heat treatment at 90° C. for 15 min.
FIG. 94 . Heat stability of emulsification layers (containing AOB) in relation to the number of repeat oleosin units.
FIG. 95 . Microscopic analysis of AOB containing a different number of oleosin repeats after incubation in different pH buffers.
FIG. 96 . SDS-PAGE/immunoblot (A) and Coomassie (B) analysis of prokaryotically produced recombinant polyoleosin purified by Artificial Oil Body or Ni 2+ affinity column.
FIG. 97 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh1-PSP1 (CaMV35S driving 1 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 64).
FIG. 98 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh1-PSP3 (CaMV35S driving 3 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 65).
FIG. 99 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh1-PSP4 (CaMV35S driving 4 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 66).
FIG. 100 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh1-PSP6 (CaMV35S driving 6 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 67).
FIG. 101 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh3-PSP1 ( Arabidopsis oleosin seed promoter driving 1 oleosin repeat with the UBQ10 intron in the first repeat) (Seq ID No. 68).
FIG. 102 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh3-PSP3 ( Arabidopsis oleosin seed promoter driving 3 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 69).
FIG. 103 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh3-PSP4 ( Arabidopsis oleosin seed promoter driving 4 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 70).
FIG. 104 . Feature map of nucleotide sequence of attB flanking regions, single oleosin clone and UBQ10 in pRSh3-PSP6 ( Arabidopsis oleosin seed promoter driving 6 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 71).
FIG. 105 . Feature map of nucleotide sequence of attB flanking regions, identical oleosin clones in pRSh1-Ole3+ (CaMV35s promoter driving 3 identical oleosin tandem repeats; no intron) (Seq ID No. 72).
FIG. 106 . Feature map of nucleotide sequence of attB flanking regions, identical oleosin clones in pRSh1-Ole3+ ( Arabidopsis oleosin seed promoter driving 3 identical oleosin tandem repeats; no intron) (Seq ID No. 73).
FIG. 107 . Peptide sequence of: pRSh1-PSP1 (CaMV35S driving 1 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 74).
FIG. 108 . Peptide sequence of: pRSh1-PSP3 (CaMV35S driving 3 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 75).
FIG. 109 . Peptide sequence of: pRSh1-PSP4 (CaMV35S driving 4 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 76).
FIG. 110 . Peptide sequence of: pRSh1-PSP6 (CaMV35S driving 6 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 77).
FIG. 111 . Peptide sequence of: pRSh3-PSP1 ( Arabidopsis oleosin seed promoter driving 1 oleosin repeat with the UBQ10 intron in the first repeat) (Seq ID No. 78).
FIG. 112 . Peptide sequence of: pRSh3-PSP3 ( Arabidopsis oleosin seed promoter driving 3 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 79).
FIG. 113 . Peptide sequence of: pRSh3-PSP4 ( Arabidopsis oleosin seed promoter driving 4 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 80).
FIG. 114 . Peptide sequence of: pRSh3-PSP6 ( Arabidopsis oleosin seed promoter driving 6 oleosin tandem repeats with the UBQ10 intron in the first repeat) (Seq ID No. 81).
FIG. 115 . Peptide sequence of: pRSh1-Ole3+ (CaMV35s promoter driving 3 identical oleosin tandem repeats; no intron) (Seq ID No. 82).
FIG. 116 . Peptide sequence of: pRSh3-Ole3+ ( Arabidopsis oleosin seed promoter driving 3 identical oleosin tandem repeats; no intron) (Seq ID No. 83).
FIG. 117 . SDS-PAGE/immunoblot showing production of Sesame seed polyoleosin in Arabidopsis thaliana seeds. Analysis of oil bodies from transgenic Arabidopsis thaliana seeds over expressing varying tandem repeats of the sesame seed oleosin.
FIG. 118 . SDS-PAGE/Coomassie showing crude protein extracts from Arabidopsis thaliana wild type seeds and transgenic seeds expressing Sesame seed polyoleosin.
FIG. 119 . Picture of relative recombinant protein levels in Arabidopsis oil bodies and effects of different Sesame seed polyoleosin lengths on emulsification thicknesses after heating. SDS-PAGE/immunoblot analysis and emulsification stability analysis of oil bodies from transgenic Arabidopsis thaliana over expressing varying tandem repeats of the sesame seed oleosin and the increase in heat stability of the emulsification layers extracted from these transformants. The reduction in oleosin repeat numbers correlates with a decrease in the emulsification layer remaining after 24 hr at 90° C., where the thickest emulsification can be seen from plants expressing the hexameric polyoleosin construct.
FIG. 120 . Picture of heating effect on emulsification thicknesses of transgenic Arabidopsis oil bodies expressing different polyoleosins. Heat stability analysis of the emulsification layers from transformants expressing 1, 3 or 6 oleosin repeats. The reduction in oleosin repeat numbers correlates with a decrease in the emulsification layer remaining after 24 hr at 90° C., where the thickest emulsification can be seen from plants expressing the hexameric polyoleosin construct. At 0 hrs through to 24 hrs at 90° C. the higher the number of oleosin repeats correlates with a thicker emulsification layer. After 58 hrs at 90° C. the oil bodies from the wild type arabidopsis has been reduced to a very thin layer with a small ring of emulsion deposited on the tube above the remaining aqueous phase. In comparison, the ring of emulsion remaining in the transformant samples is much greater.



EXAMPLES
Example 1
White Clover Polyoleosin Construction
We have generated a dimeric, trimeric, tetrameric and a pentameric homo white clover oleosin tandem repeat construct and placed these into plant binary vectors for plant transformation. The following is a description of the methods used to generate the constructs. It should be noted that the oleosin sequence used is for example only. Any oleosin sequence or combinations of oleosins, steroleosins and caoleosins and oleosin linking sequences could be used.
Overview of Experimental Approach to Generation of White Clover Oleosin Repeats
Five oleosin clones (Pole01-MC to pOLE05-MC), containing suitable restriction sites, were prepared for the subsequent generation of constructs containing oleosin repeats. In this description clones pOLE01-MC to pOLE05-MC were used to prepare monomer, dimer, trimer, tetramer and pentamer oleosin repeat constructs, pOLE06-MC to pOLE10-MC respectively. The pBLUESCRIPT polylinker ( FIG. 8 ) was used in the preparation of pOLE01-MC to provide the multiple restriction sites required to build the oleosin repeat constructs.
Standard Method of Generating Restriction Enzyme/White Clover Oleosin Cassette
PCR products were produced using a proof-reading polymerase to amplify the existing oleosin open reading frame (609 bases) of an oleosin clone containing no SacI, XbaI, SpeI, BamHI, SmaI, PstI, EcoRI, HindIII Bsp1061, SalI or XhoI sites. For each cassette unique primers were designed to amplify the oleosin sequence and add specific flanking restriction sites ( FIG. 9 ). Additional base pairs coding for specific amino acids were also included between the restriction site and oleosin priming sequence. In the polyoleosin peptide these amino acids could be expected to act as spacer arms enabling the individual oleosins to be separated from each other, reducing the chances of any misfolding occurring.
The oleosin PCR product to generate pOLE01-MC was then TOPO cloned into the pENTR/D-TOPO vector with the primary purpose of maintaining the flanked oleosin sequence. The oleosin PCR product to generate pOLE02, 03, 04, 05-MC was then TOPO cloned into the pCR2.1-TOPO vector with the primary purpose of maintaining the flanked oleosin sequence. Maps of the vectors used for cloning, pENTR/D-TOPO and pCR2.1-TOPO are shown in FIGS. 10 and 11 , respectively.
The new construct was transformed into competent E. coli cells and plated out for single colonies. Individual colonies were cultured and the purified plasmid from these cultures was analysed by digestion with a range of suitable restriction enzymes. If no suitable colonies were identified then this process was repeated. Those colonies/plasmid preps that produced predicted patterns by restriction enzyme digestion were then sequenced across the cassette containing the oleosin insert and the resulting data compared against the predicted sequence for the construct/plasmid.
The construction of constructs pOLE01-MC to pOLE05-MC is summarised below, based on the method outlined above. Each cassette was fully sequenced after construction, with all sequences being confirmed as correct.
We have generated polyclonal antibodies to a number of white clover oleosin fragments, the generation and characterisation of these antisera is summarised below.
pOLE01-MC









In the forward primer XXXX represents an oleosin specific primer that has a 5′ end beginning with the first ATG site in the open reading frame.
In the reverse primer XXXX represents an oleosin specific primer that has a 5′ end complementary to the sequence for last codon in the open reading frame.
(2) Outline of PCR Product
CACC ▪▪▪▪▪▪SacI/XhoI/









cloned into pENTR/D-TOPO to generate pOLE01-MC

▪▪▪▪▪▪ Oleosin ORF sequence

CACC pENTR/D-TOPO adapter sequence

SacI/XhoI Engineered restriction sites, each site adds 6 base pairs










Stop Codon
A map of pOLE01-MC is shown in FIG. 12 . The sequence of pOLE01-MC is shown in FIG. 13 .
pOLE02-MC






(3) Primer design





(Seq ID No. 3)






Forward primer
TCTAGAGGTACTXXXXXXXXXXXXXXXXXX







(Seq ID No. 4)






Reverse primer
ACTAGTAGTACCXXXXXXXXXXXXXXXXXX


























In the forward primer XXXX represents an oleosin specific primer that has a 5′ end beginning with the first ATG site in the open reading frame.
In the reverse primer XXXX represents an oleosin specific primer that has a 5′ end complementary to the sequence for last codon in the open reading frame.
Outline of PCR Product
XbaI/GGTACT▪▪▪▪▪▪GGTACT/SpeI cloned into pCR2.1-TOPO to generate pOLE02-MC

▪▪▪▪▪▪ Oleosin ORF sequence

GGTACT Extra bases to code for glycine and threonine.

A map of pOLE02-MC is shown in FIG. 14 . The sequence of pOLE02-MC is shown in FIG. 15 .
pOLE03-MC






Primer design





(Seq ID No. 5)






Forward primer
CCCGGGGGTACTXXXXXXXXXXXXXXXXXX







(Seq ID No. 6)






Reverse primer
CTGCAGAGTACCXXXXXXXXXXXXXXXXXX


























In the forward primer XXXX represents an oleosin specific primer that has a 5′ end beginning with the first ATG site in the open reading frame.
In the reverse primer XXXX represents an oleosin specific primer that has a 5′ end complementary to the sequence for last codon in the open reading frame.
Outline of PCR Product
SmaI/GGTACT▪▪▪▪▪▪GGTACT/PstI cloned into PCR2.1-TOPO to generate pOLE03-MC

▪▪▪▪▪▪ Oleosin ORF sequence

GGTACT Extra bases to code for glycine and threonine

A map of pOLE03-MC is shown in FIG. 16 . The sequence of pOLE03-MC is shown in FIG. 17 .
pOLE04-MC






(4) Primer design





(Seq ID No. 7)






Forward primer
AAGCTTGGTACTXXXXXXXXXXXXXXXXXX







(Seq ID No. 8)






Reverse primer
ATCGATAGTACCXXXXXXXXXXXXXXXXXX


























In the forward primer XXXX represents an oleosin specific primer that has a 5′ end beginning with the first ATG site in the open reading frame.
In the reverse primer XXXX represents an oleosin specific primer that has a 5′ end complementary to the sequence for last codon in the open reading frame.
Outline of PCR Product
HindIII/GGTACT▪▪▪▪▪▪GGTACT/Bsp1061 cloned into pCR2.1-TOPO to generate pOLE04-MC
▪▪▪▪▪▪ Oleosin ORF sequence

GGTACT Extra bases to code for glycine and threonine

A map of pOLE04-MC is shown in FIG. 18 . The sequence of pOLE04-MC is shown in FIG. 19 .
pOLE05-MC






(5) Primer design





(Seq ID No. 9)






Forward primer
GTCGACGGTACTTCTXXXXXXXXXXXXXXXXXX







(Seq ID No. 10)






Reverse primer
CTCGAGXXXXXXXXXXXXXXXXXX


























In the forward primer XXXX represents an oleosin specific primer that has a 5′ end beginning with the first ATG site in the open reading frame.
In the reverse primer XXXX represents an oleosin specific primer that has a 5′ end complementary to the sequence for last codon in the open reading frame.
Outline of PCR Product
SalI/GGTACTTCT▪▪▪▪▪▪XhoI cloned into pCR2.1-TOPO to generate pOLE05-MC
▪▪▪▪▪▪ Oleosin ORF sequence

GGTACTTCT Extra bases to code for glycine, threonine and serine

A map of pOLE05-MC is shown in FIG. 20 . The sequence of pOLE05-MC is shown in FIG. 21 .
pOLE06-MC
pOLE01-MC and pBLUESCRIPT were digested using SacI and XhoI. The pBLUESCRIPT fragment was ligated into the open pOLE01-MC vector to form pOLE06-MC ( FIG. 22 ). The sequence of pOLE06-MC is shown in FIG. 23 .
CACC ▪SacI/••••••/XbaI/SpeI/BamHI/SmaI/PstI/EcoRI/EcoRV/HindIII/Bsp106/•/SalI/XhoI/









CACC pENTR/D-TOPO adapter sequence

▪ Oleosin ORF sequence

SacI to XhoI Restriction sites within pBLUESCRIPT

• amino acids encoded within the MCS but not corresponding to a restriction site










Stop Codon
Confirmation of the addition of the polylinker was carried out via digestion with SacI, XhoI, XbaI, BamHI, SmaI, PstI, EcoRI, HindIII and SalI. The pOLE06-MC cassette was then sequenced.
pOLE07-MC
pOLE06-MC was digested using XbaI and pOLE02-MC was digested with XbaI and SpeI, the resulting fragments were ligated together to form pOLE07-MC ( FIG. 24 ). The sequence of pOLE07-MC is shown in FIG. 25 .
CACC ▪SacI/••••••/XbaI/••/▪/••/SpeI/BamHI/SmaI/PstI/EcoRI/EcoRV/HindIII/Bsp106I/•/SalI/XhoI/









CACC pENTR/D-TOPO adapter sequence

▪ Oleosin ORF sequences

SpeI to XhoI Restriction sites within pBLUESCRIPT

• amino acids encoded within the MCS but not corresponding to a restriction site










Stop Codon
Confirmation of the generation of pOLE07-MC was carried via XbaI/EcoRI, PstI, and HindIII/PstI digests. In order to gain a complete sequence of the clone, an LR reaction was performed to transfer the pOLE07-MC cassette into pET-DEST42. The pOLE07-MC cassette was then sequenced.
pOLE08-MC
pOLE07-MC and pOLE03-MC were digested using SmaI and PstI, then the required fragments were ligated together to form pOLE08-MC ( FIG. 26 ). The sequence of pOLE08-MC is shown in FIG. 27 .
CACC ▪SacI/••••••/XbaI/••/▪/••/SpeI/BamHI/SmaI/••/▪/••/PstI/EcoRI/EcoRV/HindIII/Bsp106I/•/SalI/XhoI/









CACC pENTR/D-TOPO adapter sequence

▪ Oleosin ORF sequences

PstI to XhoI Restriction sites within pBLUESCRIPT

• amino acids encoded within the MCS but not corresponding to a restriction site










Stop Codon
Confirmation of the generation of pOLE08-MC was carried out via PstI/NcoI, NotI/XhoI and BamHI digests. In order to gain a complete sequence of the clone, the pOLE08-MC oleosin cassette was transferred into pET-DEST42 by an LR reaction. The cassette was then sequenced and the sequence of the polylinker, and the pOLE03-MC oleosin fragment ligated into pOLE07-MC.
pOLE09-MC
pOLE08-MC containing the oleosin trimer, was digested using HindIII and ClaI (ClaI is an isoschizomer of Bsp106I), and pOLE04-MC was digested with HindIII and ClaI (Table 1), the resulting fragments were gel purified ( FIG. 28 ). The digests were purified from the agarose gel using the QIAGEN QIAquick Gel Extraction Kit. The HindIII/ClaI digested oleosin isolated from pOLE04-MC was then cloned into the HindIII/ClaI linearised pOLE08-MC vector (table 2) to generate pOLE09-MC ( FIG. 29 ).
CACC ▪SacI/••••••/XbaI/••/▪/••/SpeI/BamHI/SmaI/••/▪/••PstI/EcoRI/EcoRV/HindIII/••/▪/••ClaI/•/SalI/XhoI/









CACC pENTR/D-TOPO adapter sequence

▪ Oleosin ORF sequences

ClaI to XhoI Restriction sites within pBLUESCRIPT

• amino acids encoded within the MCS but not corresponding to a restriction site










Stop Codon






TABLE 1



Table describing the components used in the restriction enzyme

digest to produce the linearised pOLE08-MC vector and the

oleosin insert/fragment from pOLE04-MC






4
8





10

μL
pOLE04-MC


10
μL
pOLE08-MC

1
1
μL
HindIII (Roche)

1
1
μL
ClaI (Roche)

2
2
μL
Buffer B (Roche)

6
6
μL
sH 2 O

20
20
μL
Total volume



After 2.5 h at 37° C. added






1
1
μL
Phosphatase (Roche, CAP, 20 U/uL)





Incubated for a further 30 min at 37° C.












































TABLE 2



Table describing the components used in the ligation of the

linearised pOLE08-MC vector and the oleosin insert/fragment

from pOLE04-MC to produce pOLE09-MC.









Ct8
Ct4
1:1
1:3
1:6













3.5

3.5
3.5
3.5
μL
pOLE08-MC HindIII/ClaI







linearised vector


8
2
6
12
μL
Oleosin HindIII/ClaI fragment







from

4
4
4
4
4
μL
Ligase buffer

1
1
1
1
1
μL
T4 DNA Ligase (Roche)

11.5
7
9.5
5.5

μL
sH 2 0

20
20
20
20
20.5
μL
Total volume



Incubated at 11° C. overnight.
































5 μL of each of the above ligation reactions were then transformed into E. coli DH5α to allow screening for correct pOLE09-MC plasmids.
Confirmation of the generation of pOLE09-MC was carried via agarose gel/ethidium bromide analysis of the NcoI/XhoI, NcoI/SpeI/XhoI, XhoI, and NotI/XhoI digests ( FIG. 30 ).
In order to gain a complete sequence of the clone, the pOLE09-MC oleosin cassette was transferred into pET-DEST42 by an LR reaction. The cassette was then sequenced ( FIG. 31 ).
pOLE10-MC
Due to poor restriction enzyme digestion efficiency when digesting the oleosin tetramer pOLE09-MC with SalI, pOLE09-M was digested using only XhoI (Table 3). SalI generated ends that are compatible with XhoI generated ends and thereby the SalI/XhoI generated fragment was ligated into the XhoI linearised vector. pOLE05-MC was digested with SalI and XhoI and the resulting oleosin fragment was ligated with pOLE09-MC (table 3) to form pOLE10-MC ( FIG. 32 ).
CACC ▪SacI/••••••/XbaI/••/▪/••/SpeI/BamHI/SmaI/••/▪/••PstI/EcoRI/EcoRV/HindIII/••/▪/••ClaI/•/SalI/••/▪XhoI/









CACC pENTR/D-TOPO adapter sequence

▪ Oleosin ORF sequences

ClaI to XhoI Restriction sites within pBLUESCRIPT

• amino acids encoded within the MCS but not corresponding to a restriction site










Stop Codon






TABLE 3



Table describing the components used in the restriction enzyme digest

to produce the linearised oleosin tetramer pOLE09-MC vector

and the oleosin insert/fragment from pOLE05-MC.








5
9




x3
x2





6

μL
pOLE05-MC (midipreped DNA)



6
μL
pOLE09-MC (midipreped DNA)


1
2
μL
XhoI (Roche)


1
x
μL
SalI (Roche)


2
2
μL
Buffer H (Roche)


10
10
μL
s H 2 O


20
20
μL
Total volume






After 2.5 h at 37° C. added








—
1
μL
Phosphatase (Roche, CAP, 20U/uL)





Incubated for a further 30 min at 37° C.






































The digests were purified from the agarose gel using the QIAGEN QIAquick Gel Extraction Kit. The XhoI/SalI digested oleosin isolated from pOLE05-MC was then cloned into the XhoI linearised pOLE09-MC vector (Table 4) to generate pOLE10-MC.





TABLE 4



Table describing the components used in the ligation of the linearised

pOLE09-MC vector and the oleosin insert/fragment from pOLE05-MC

to produce pOLE10-MC.








Ct9
Ct5
1:3
1:9












3
6
3
3
μL
pOLE09-MC XhoI/Sa/I linearised vector



3
9
μL
Oleosin XhoI/Sa/I fragment from






pOLE05-MC

1
1
1
1
μL
Ligase buffer

4
4
4
4
μL
T4 DNA Ligase (Roche)

12
9
9
3
μL
sH 2 0

20
20
20
20.5
μL
Total volume



Incubated at 11° C. overnight.































5 μL of each of the above ligation reactions were then transformed into E. coli DH5α to allow screening for correct pOLE10-MC plasmids. Confirmation of the generation of pOLE10-MC was carried via PstI/XhoI, PstI and SalI/PstI restriction enzyme digests. One clone was selected for detailed agarose/ethidium bromide gel analysis, and compared to pOLE09-MC digested with the same enzymes ( FIG. 33 ).
In order to gain a complete sequence of the clone, the pOLE10-MC oleosin cassette was transferred into pET-DEST42 by an LR reaction. The cassette was then sequenced ( FIG. 34 ).
Generation of Binary Constructs
Clones pOLE06-MC through to pOLE10-MC were generated as GATEWAY™ entry vectors. The following is a description of subsequent LR reactions performed to transfer the oleosin constructs into two plant binary vectors, pRSh1 (Table 5 and FIG. 35 ) and pRS12 (Table 5 and FIG. 36 ).
TABLE 5 Table describing the components between the left and right borders of two plant binary vectors used to transform the multimeric oleosin repeats into plants. Bacterial Plant Construct Plasmid Cassette Selectable Selectable Name Type Design Marker Marker pRSh1 Plant binary CaMV35s::attR1::GW::attR2::OCS3′ Spectinomycin r BASTA r pRS12 Plant binary CaMV35s::attR1::GW::attR2::OCS3′ Spectinomycin r Kanamycin r & GFP expression Key: attR1 GATEWAY ™ recombination site attR2 GATEWAY ™ recombination site CaMV35s Cauliflower mosaic virus promoter sequence GFP Jelly Fish Green Fluoresence Protein sequence GW GATEWAY ™ destination cassette OCS3′ Octapine Synthase Terminator sequence
Overview of Experimental Approaches Used to Clone White Clover Oleosin Repeats and DGAT1 into pRSH1.

Linerasing the Entry Clones
When cloning into pRSH1, linearising the entry clone seemed to make the reaction more efficient. 2 μg of each of the six constructs were digested in 20 μL volumes with the enzyme Alw441 (Roche) which cuts once in the back bone of PENTRD™. Digests were cleaned up using the QIAGEN QIAquick PCR Purification Kit.™.
LR reactions were set up between pRSH1 with pOLE06-MC to pOLE10-MC as well as with DGAT1 as per Table 6.





TABLE 6



LR reactions for cloning oleosin repeats and DGAT1 into pRSH1.










Rxn 1
Rxn 2
Rxn 3
Rxn 4
Rxn 5
Rxn 6

Component
C6
C7
C8
C9
C10
DGAT1











Linear entry
5.55
5.55
5.55
5.55
5.55
5.55

clone

pRSH1
0.2
0.2
0.2
0.2
0.2
0.2

(1.5 μg/μL)

LR Clonase ™
2
2
2
2
2
2

(μL)

LR Rxn
2
2
2
2
2
2

mix ™ (μL)

Topoisomerase
0.25
0.25
0.25
0.25
0.25
0.25

(μL)

H 2 O (μL)
—
—
—
—
—
—

Total (μL):
10
10
10
10
10
10



C6 = pOLE06-MC etc.



































The LR reactions were incubated overnight at 25° C., and were then transformed into E. coli DH5α. Four colonies were picked for each of the constructs C6-pRSH1, C7-pRSH1, C9-pRSH1 & C10-pRSH1, eight colonies were picked for C8-pRSH1 and three colonies for DGAT1-pRSH1.
Restriction Enzyme Digests to Screen Colonies
Plasmid DNA was extracted from clones, and purified plasmid was analysed by restriction digest using the following protocol:








μL
Component








2
Plasmid DNA (construct in pRSH1)

1
EcoRI (Roche)

2
Buffer H (Roche)

15
s H 2 O

20
Total volume
























Incubated at 37° C. for 2 hours.
Digests were analysed by agarose/ethidium bromide gel electrophoresis and are shown in FIGS. 37-39 .
Due to difficulties distinguishing between the two constructs C9-pRSH1 and C10-pRSH1 with the EcoRI digest clone1 of C9-pRSH1 and clone2 of C10-pRSH1 were digested with BamHI to determine if both constructs were correct. Digests were analysed by agarose/ethidum bromide gel electrophoresis and are shown in FIGS. 40-41 .
Overview of Experimental Approaches Used to Clone White Clover Oleosin Repeats and DGAT1 into pRS12.
Linearising the Binary Plasmid
When cloning into pRS12, linearising the binary plasmid rather than the entry clone seemed to make the reaction more efficient. 2 μg of pRS12 was digested in a 20 μL reaction volume with the enzyme SmaI (Roche), which makes a single cut between the GATEWAY™ att recombination sites in pRS12. The digest was cleaned up using phenol:chloroform:isoamyl alcohol (25:24:1 v/v) and then chloroform. 100% recovery of DNA was assumed from this cleanup method.
LR reactions were set up between pRS12 with pOLE06-MC to pOLE10-MC as well as with DGAT1 as per Table 7.





TABLE 7



For LR cloning oleosin repeats and DGAT1 into pRS12.










Rxn 1
Rxn 2
Rxn 3
Rxn 4
Rxn 5
Rxn 6

Component
C6
C7
C8
C9
C10
DGAT1











Linear entry
1
1
1
1
1
1

clone

pRS12
0.2
0.2
0.2
0.2
0.2
0.2

(2 μg/μL)

LR Clonase ™
2
2
2
2
2
2

(μL)

LR Rxn
2
2
2
2
2
2

mix ™ (μL)

Topoisomerase
0.25
0.25
0.25
0.25
0.25
0.25

H 2 O (μL)
5.3
5.3
5.3
5.3
5.3
5.3

Total (μL):
10
10
10
10
10
10



C6 = pOLE06-MC etc.


































The LR reactions were incubated overnight at 25° C., and were then transformed into E. coli DH5α. Twelve colonies were picked for analysis from the C6-pRS12 construct, two colonies from C7-pRS12, two from C8-pRS12, three from C9-pRS12, three from C10-pRS12, and two from DGAT1-pRS12.
Restriction Enzyme Digests to Screen Colonies
Plasmid DNA was extracted from clones, and purified plasmid was analysed by restriction digest using the following protocol:








μL
Component








2
Plasmid DNA (construct in pRS12)

1
Restriction enzyme (Roche)

2
Buffer (Roche)

15
s H 2 O

20
Total volume
























Incubated at 37° C. for 2 hours.
Digests were analysed by agarose/ethidium bromide gel electrophoresis and are shown in FIGS. 42-45 .
Representative maps of a pRSH1 binary vector containing white clover oleosin multimers is shown in FIG. 46 .
Representative maps of a pRS12 binary vector containing white clover oleosin multimers is shown in FIG. 47 .
Generation of Polyclonal Antibodies to White Clover Oleosin
Cloning of N-Terminal Region of White Clover Oleosin Into the pDEST17 and pET-DEST42 Expression Vectors
The N-terminal region of oleosin was cloned into the pENTR-D vector, to produce the construct pEON. The N-terminal region of oleosin was transferred into the pDEST17 and pET-DEST42 vectors (Invitrogen) by the LR reaction to produce the constructs p17NON ( FIG. 48 ) and p42CON ( FIG. 49 ), which were then transformed into E. coli DH5α. p17NON was designed to express the N-terminal oleosin peptide with an N-terminal 6×His tag (6HON). The p42CON was designed to express the N-terminal oleosin peptides with a C-terminal 6×His tag (ON6H).
Plasmid DNA purified from the putative constructs was analysed by PCR using T7 and T7t primers (as marked on the maps in FIG. 48 and FIG. 49 ), to determine if the terminal regions were present ( FIG. 50 and FIG. 51 ).
Plasmid DNA from lines p42CON-2 and p17NON-1 were transformed into E. coli strains BL21 and BL21-Al for protein expression.
(b) Sequence Analysis of Putative p17NON and p42CON
The p17NON and p42CON plasmid lines were sequenced from the 5′ and 3′ ends using T7 and T7t primers, respectively. The sequences obtained showed that the N-terminal regions of oleosin had been cloned in frame into both the pDEST17 and pET-DEST42 vectors.
Expression of Tagged Peptides
Example of Standard Culture and Induction Protocol
10 mL LB Amp100 broths were inoculated with expression construct in E. coli BL21-AI and incubated overnight at 37° C. 220 rpm. The next day duplicate 10 mL LB Amp100 broths were inoculated with 500 μL of the overnight cultures (to give OD 600 =0.05-0.1). All cultures were incubated for approximately three hours at 37° C. 220 rpm, until OD 600 =0.5-0.7 was reached. One set of the duplicate cultures was induced by the addition of 20% Arabinose to a final concentration of 0.2% and IPTG (isopropyl β-D-thiogalactopyranoside) to a final concentration of 1 mM. The second set of duplicate cultures was used as the non-induced negative controls, and therefore nothing was added to these cultures. All cultures were then incubated overnight at 37° C. 220 rpm. 1 mL aliquots were removed from each culture and prepared for SDS-PAGE analysis (Table 8).





TABLE 8



Standard prokaryotic induction protocol.








1° broth
10 mL LB Amp100 broths

1° inoculation
Colony picked from plate by toothpick

1° incubation
Overnight at 37° C. 220 rpm

conditions

2° broth
10 mL LB Amp100 broths (in duplicate)

2° inoculation
500 μL of the overnight cultures (to give OD600 = 0.05-0.1)

2° incubation
Approximately three hours at 37° C. 220 rpm, until OD600 = 0.5-0.7

conditions

Induction
+ve - 20% Arabinose to a final concentration of 0.2% and IPTG


(isopropyl β-D-thiogalactopyranoside) to a final concentration of 1 mM


−ve - nothing added to non-induced negative control cultures

Induction incubation
Overnight at 37° C. 220 rpm

conditions

Additional
This may include harvesting and lysing cells

preparation

Analysis
1 mL aliquots were removed from each culture and prepared for


SDS-PAGE analysis





































Purification of Tagged White Clover Oleosin Peptides
HIS-Select Nickel Affinity Gel (Sigma) was used to purify the oleosin 6×HIS tagged proteins under denaturing conditions (Table 9 shows the buffers used).
Denaturing Buffers






TABLE 9



Buffers used to purify tagged white clover oleosin.





Final vol. (mL)










Final
100
100
100


Stock
conc
EQUIL'N
WASH
ELUTION


(M)
(M)
BUFFER
BUFFER
BUFFER












PO
mL
0.25
0.1
40
40
40

Urea
g

6
36 g
36 g
36 g

(Mr = 60.06)

NaCl
mL
5
0.3
6
6
6

Imidazole
mL
2
0.005
0.25

Imidazole
mL
2
0.02

1

Imidazole
mL
2
0.25


12.5







pH
5M HCl
8.0
8.0
8.0








































Example of Standard Large Scale Purification Protocol
1.5 mL of HIS-Select Nickel Affinity Gel was transferred to a chromatography column. The affinity gel was washed with two volumes of deionized water and then equilibrated with three volumes of equilibration buffer. The clarified crude extract was loaded onto the column at a flow rate of 2 to 10 column volumes/hour. After the extract was loaded, the column was washed with wash buffer at a flow rate of about 10 to 20 column volumes/hour. The 6×His tagged protein was eluted from the column using 3 to 10 column volumes of elution buffer at a flow rate of 2 to 10 column volumes/hour. Fractions were collected continuously and assayed for the target protein using Bradford's protein assay.
N-Terminal Fragment of White Clover Oleosin
Induction of p17NON and the Expression of 6HON (Oleosin N-Terminal with N-6×His tag)





TABLE 10



Large scale induction protocol.








1° broth
10 mL LB Amp100 broths

1° inoculation
p17NON in E. coli BL21-Al, colony picked from plate by toothpick

1° incubation
Overnight at 37° C. 220 rpm

conditions

2° broth
10 mL LB Amp100 broths

2° inoculation
500 μL of the overnight cultures (to give OD600 = 0.05-0.1)

2° incubation
Approximately three hours at 37° C. 220 rpm, until OD600 = 0.5-0.7

conditions

Induction
20% Arabinose to a final concentration of 0.2% and IPTG (isopropyl


β-D-thiogalactopyranoside) to a final concentration of 1 mM

Induction incubation
Overnight at 37° C. 220 rpm

conditions

Analysis
1 mL aliquots were removed from each culture and prepared for


SDS-PAGE analysis (FIG. 52)


































Inclusion Body Preparation of 6HON For Purification






TABLE 11



Inclusion body preparation for E. coli expressed white clover oleosin.








1° broth
5 mL LB Amp100 broths

1° inoculation
p17NON in E. coli BL21-AI

1° incubation
Overnight at 37° C. 220 rpm

conditions

2° broth
50 mL LB Amp100 broths

2° inoculation
3.5 mL of the overnight cultures (to give OD600 = 0.05-0.1)

2° incubation
Approximately three hours at 37° C. 220 rpm, until OD600 = 0.5-0.7

conditions

Induction
20% Arabinose to a final concentration of 0.2% and IPTG (isopropyl


β-D-thiogalactopyranoside) to a final concentration of 1 mM

Induction incubation
Overnight at 37° C. 220 rpm

conditions

Additional
The induced cells were collected by centrifugation and resuspended in

preparation
1/10 culture volume of buffer (50 mM Tris-HCl pH 8.0, 2 mM EDTA).


Lysozyme was added to a concentration of 100 μg/mL, 1/10 volume of


1% Triton X-100 was then added, mixed gently and incubated at 30° C.


for 15 minutes. DNA was sheared by sonication and the insoluble


protein fraction was separated from the soluble fraction by


centrifugation.

Analysis
1 mL aliquots were removed from each culture and prepared for


SDS-PAGE analysis (FIG. 53)









































Nickel Affinity Chromatography to Purify 6HON
HIS-Select Nickel Affinity Gel (Sigma) was used to purify the 6HON under denaturing conditions (as described above).
A trial scale purification of 6HON was carried out using a 2 mL sample from the insoluble protein fraction (as described above). The isolated 6HON was visualised using SDS-PAGE ( FIG. 54 ).
Large Scale Purification of 6HON






TABLE 12



Large scale preparation for prokaryotically produced white clover oleosin for

antibody generation.








1° broth
5 mL LB Amp100 broths

1° inoculation
p17NON in E. coli BL21-AI

1° incubation
Overnight at 37° C. 220 rpm

conditions

2° broth
500 mL LB Amp100 broths

2° inoculation
50 mL of the overnight cultures (to give OD600 = 0.05-0.1)

2° incubation
Approximately three hours at 37° C. 220 rpm, until OD600 = 0.5-0.7

conditions

Induction
20% Arabinose to a final concentration of 0.2% and IPTG (isopropyl


β-D-thiogalactopyranoside) to a final concentration of 1 mM

Induction incubation
Overnight at 37° C. 220 rpm

conditions

Additional
The induced cells were collected by centrifugation and resuspended in

preparation
1/10 culture volume of buffer (50 mM Tris-HCl pH 8.0, 2 mM EDTA).


Lysozyme was added to a concentration of 100 μg/mL, 1/10 volume of


1% Triton X-100 was then added, mixed gently and incubated at 30° C.


for 15 minutes. DNA was sheared by sonication and the insoluble


protein fraction was separated from the soluble fraction by


centrifugation.

Analysis
1 mL aliquots were removed from each culture and prepared for


SDS-PAGE analysis










































HIS-Select Nickel Affinity Gel was used to purify 6HON under denaturing conditions (as described above). A large scale purification of 6HON was carried out using the 500 mL sample (induced as described above). The purified 6HON was visualised using SDS-PAGE ( FIG. 55 ) and the concentration of the eluted protein was estimated using a Bradford's protein assay, and found to be approximately 0.72, 2.74 and 1.89 mg/mL, for Elutions 1, 2 and 3 respectively ( FIG. 56 ).
Generation of Rabbit Anti-White Clover Oleosin Antisera
Immunisation of Rabbit
66 μL of Elution 2 (see Large scale purification of 6HON, above), containing 250 μg purified protein, was mixed with 433 μL PBS. This was passed to the Massey University Small Animals Unit for immunisation of a rabbit (male, ID# 124, Massey University Animal Ethics Committee (MUAEC) approval number 04/28). 25 days after the primary immunisation the first boost was administered (66 μL of Elution 2, containing 250 μg purified protein, mixed with 433 μL PBS), and the second boost was given 46 days after the primary immunisation (128 μL of Elution 1, containing 250 μg purified protein, mixed with 372 μL PBS).
Preparation of Rabbit Anti-White Clover Oleosin Antisera
53 days after the primary immunisation approximately 3 mL of blood was taken from the rabbit and placed at 4° C. for approximately 16 h. To separate the serum the blood was centrifuged at 1500×g 20 min 4° C. The serum (1.5 mL) was transferred to a fresh tube and stabilised with 0.25% Phenol in PBS and 0.01% Methiolate.
Assaying Titre and Specificity of Rabbit Anti-White Clover Oleosin Antisera by SDS-PAGE Immunoblot Analysis
The samples outlined in Table 13 were analysed by SDS-PAGE immunoblot analysis using the anti oleosin N terminal antibody ( FIG. 57 ).





TABLE 13



Samples used to determine titre and specificity of polyclonal rabbit anti-white

clover oleosin antisera.








Lane
ID
Load
Oleosin
Induced
Expressed










1
FLA-BL21_AI, E. coli
1 μL
6HOF
−
−

2
FLA-BL21_AI, E. coli
1 μL
6HOF
+
+

3
17C-2-BL21_AI, E. coli
1 μL
6HOC
+
+

4
Elu1, 1:200, pure
1 μL
6HON, 1.8 ng
+
+

5
Elu2, 1:200, pure
1 μL
6HON, 6.9 ng
+
+

6
Elu3, 1:200, pure
1 μL
6HON, 4.7 ng
+
+

8
clover seed extract
0.1 μL
1.6 μg total protein

9
clover seed extract
1 μL
16 μg total protein

10
clover seed extract
5 μL
80 μg total protein

































Using Rabbit Anti-White Clover Oleosin Antisera to Detect Oleosin in Clover Seed Oil Bodies
We checked to see if the antibodies were capable of detecting full-length oleosin. Early analysis of the antibodies on crude clover seed protein extracts had shown that the antibodies were able to be used to detect a protein of the expected size when clover seed oil body extracts were analysed by Immunoblot analysis ( FIG. 58 ).
Results from the immunoblot showed that the anti-oleosin N-terminal antibodies could be used to specifically detect a ˜20 kDa protein—the expected size of the clover oleosin protein.
Overview of Experimental Approaches Used to Transform Plants with White Clover Polyoleosin Clones.

Transformation of Brassica oleracea with White Clover Polyoleosin and DGAT1 Constructs

A total of 12 constructs were transformed into Brassica oleracea (Table 14. These were all transferred into Agrobacterium tumefaciens strain LBA4404 via the freeze-thaw method described in Christey and Braun (2004). Colonies were selected on LB medium containing 100 ml/l streptomycin and 100 ml/l spectinomycin. PCR analysis for the BAR gene was used to confirm plasmid presence in Agrobacterium colonies.





TABLE 14



Summary of constructs placed into Brassica oleracea .






Construct
C&F code
Genes
Marker



pRSH1-C6
AgR 6
35S-oleosin monomer
35S-BAR

pRSH1-C7
AgR 7
35S-oleosin dimer
35S-BAR

pRSH1-C8
AgR 8
35S-oleosin trimer
35S-BAR

pRSH1-C9
AgR 9
35S-oleosin tetramer
35S-BAR

pRSH1-C10
AgR 10
35S-oleosin pentamer
35S-BAR

pRSH1-At DGAT
DGAT
35S-Arab. DGAT
35S-BAR

pRSh4

Arab. oleosin seed
35S-BAR



promoter + GUSi

pRSh6

oleosin seed prom. +
35S-BAR



oleosin monomer

pRSh7

oleosin seed prom. +
35S-BAR



oleosin dimer

pRSh8

oleosin seed prom. +
35S-BAR



oleosin trimer

pRSh9

oleosin seed prom. +
35S-BAR



oleosin tetramer

pRSh10

oleosin seed prom. +
35S-BAR



oleosin pentamer






































Plant Material and Transformation
For these experiments a rapid cycling (RC) B. oleracea line, DH1012, selected for high regeneration and transformation ability by Sparrow et al. (2004) was used. Seeds were germinated in vitro as described in Christey et al. (1997). Hypocotyl and cotyledonary petiole explants from 4-5 day-old seedlings were co-cultivated briefly with a culture of Agrobacterium grown overnight in LB medium containing antibiotics prior to 1:10 dilution in antibiotic-free minimal medium (7.6 mM (NH 4 ) 2 SO 4 , 1.7 mM sodium citrate, 78.7 mM K 2 HPO 4 , 0.33M KH 2 PO 4 , 1 mM MgSO 4 , 0.2% sucrose) with growth for a further 4 hrs. Explants were cultured on Murashige-Skoog (MS; Murashige and Skoog, 1962) based medium with B5 vitamins and 2.5 mg/L BA. After 3 days co-cultivation, explants were transferred to the same medium with 300 mg/L Timentin (SmithKline Beecham) and subsequently placed on selection medium with 2.5 mg/L Basta. Green shoots were transferred to hormone-free Linsmaier-Skoog based medium (LS; Linsmaier and Skoog, 1965) containing 5 mg/L Basta and solidified with 10 gm/L Danisco Standard Agar. Explants were cultured in tall Petri dishes (9 cm diameter, 2 cm tall) sealed with Micropore (3M) surgical tape. Shoots were cultured in clear plastic tubs (98 mm, 250 ml, Vertex). All culture manipulations were conducted at 25° C. with a 16 h/day photoperiod, provided by Cool White fluorescent lights (20 μE/m 2 /s).
Determination of Selective Levels of Basta
Hypocotyl and cotyledon explants from 4 day-old seedlings were cultured on LSN medium containing 2.5 mg/L BAP and 300 mg/L Timentin and 5 different levels of Basta (0, 2.5, 5, 10 and 25 mg/L) to determine the appropriate level to use for selection in co-cultivation experiments.
To determine the selective level of Basta for maintenance of in vitro shoots, small healthy apical cuttings were transferred to tall pots of hormone-free LSn containing either 2.5 or 5 mg/L Basta.
Conformation of Brassica oleracea Transformation by PCR
DNA was isolated from leaves of in vitro shoots using the rapid method described in Christey and Braun (2004). PCR was conducted to test for the presence of the bar gene using the primers baran (5′-tcagatctcggtgacgggcagg-3′) (Seq ID No. 11) and barse (5′-atgagccaagaacgacgcccgg-3′) (Seq ID No. 12) to produce a 551 bp product. PCR conditions were: 94° C. for 30 sec, 65° C. for 30 sec and 72° C. for 30 sec over 40 cycles.
PCR was conducted on Bar positive samples to check for the presence of the oleosin clones using the primers outlined in Table 15. PCR conditions were: 94° C. for 30 s, 45° C. for 30 s and 68° C. for 30 s for 30 cycles. A 650 bp product was expected.
TABLE 15 Primers used for oleosin PCR. Primer name Sequence Sequence IDs AgR 6 forward CACCATGGCACAACCT SEQUENCE ID NO. 13 CAAGTT AgR 7 forward GCTCCACCGCG SEQUENCE ID NO. 14 AgR 6/7 reverse TCCACTAGTTCTAG SEQUENCE ID NO. 15 AgR 8 forward CTAGAACTAGTGGAT SEQUENCE ID NO. 16 AgR 8 reverse TCCTGCAGAGTAC SEQUENCE ID NO. 17 AgR 9 forward GTACTCTGCAGGA SEQUENCE ID NO.18 AgR 9 reverse ATACGATAGTAC SEQUENCE ID NO. 19 AgR 10 forward CTATCGATACCGTCG SEQUENCE ID NO. 20 AgR 10 reverse CTCGAGTGTTGATCTC SEQUENCE ID NO. 21 TTAGCTTC
Conformation of White Clover Polyoleosin Construct Gene Expression in Brassica oleracea Transformants by RT-PCR

RNA was isolated from plants using the Concert™ small scale isolation reagent (Invitrogen). DNA was digested using Turbo DNase (Ambion). For RT-PCR the primers described in Table 15 were used to amplify the transcribed region. Reactions were performed on RNA samples using the Superscript™ III (Invitrogen) Reverse Transcriptase, with the RT step performed at 50° C. followed by PCR.
Agrobacterium Transformation
PCR for the Bar gene was used to confirm the presence of the oleosin-containing plasmids in Agrobacterium colonies ( FIG. 59 ). Two BAR positive colonies from each transformation event were selected for storage at −80° C. in glyercols and used in subsequent explant co-cultivation experiments.
Determination of Selective Levels of Basta
The results of the explant selection experiment confirmed that use of 2.5 mg/L Basta was suitable for use as the selection level for subsequent co-cultivation experiments. After 2-4 weeks on this level rare shoot regeneration was noted ( FIG. 60 ). In contrast, in vitro shoot cuttings showed some development on 2.5 mg/L Basta with root development apparent on some. In contrast, after 4-5 weeks on 5 mg/L Basta cuttings turned brown with no root development. This level was used in subsequent experiments for growth of putative transgenic shoots.
Selection of Transgenic Shoots
At least 150 explants were co-cultivated with each construct (Table 16). Three to four weeks after co-cultivation rare small green shoots were apparent. Putative Basta resistant shoots were excised and transferred to hormone-free media containing 5 mg/L Basta. In vitro shoot and root growth on Basta-containing medium confirmed plants were transgenic. Transgenic plants were healthy with good shoot and root development and normal phenotype. In contrast, Basta sensitive cuttings showed little development ( FIG. 61 ). Transgenic shoots were obtained mainly from hypocotyl explants with only rare transgenic shoots obtained from cotyledon explants. While the overall transformation rate was only 1.2%, there was a lot of variation between both experiments and explants, with some combinations producing over 5% transformation in some experiments.





TABLE 16



Summary of PCR positive shoots.







No. explants
No. PCR +



cocultivated
ve for BAR








Construct
cotyledon
hypocotyl
cotyledon
hypocotyl
Total










pRSH1-C6
70
90
0
6
6

pRSH1-C7
170
110
1
3
4

pRSH1-C8
390
190
2
2
4

pRSH1-C9
390
190
0
4
4

pRSH1-C10
250
120
3
7
10

At DGAT
416
195
0
8
8

pRSh4
200
120
2
2
4

pRSh6
100
50
0
0
0

pRSh7
110
30
0
1
1

pRSh8
110
50
1
2
3

pRSh9
110
50
0
0
0

pRSh10
110
50
1
0
1

Total
2426
1245
10
35
45









































Conformation of Transformation by PCR
Shoots growing on 5 mg/L Basta that were still green and showing good root development after at least two subcultures had DNA extracted and PCR performed for the bar gene. Over 250 shoots were analysed with 45 confirmed as having the bar gene (20%) (Table 10). PCR analysis confirmed the presence of the Bar gene in all plants that had shown good growth on selective levels of Basta in vitro. PCR for the Bar gene produced a 551 bp fragment ( FIG. 62 ). PCR analysis of Bar positive shoots for the oleosin gene indicated that not all plants contain the oleosin gene as well ( FIG. 63 ).
Transgenic shoots were obtained for 10 of the 12 constructs in Table 14. Most constructs had at least 4 independent transgenic shoots but no transgenic shoots were obtained for pRSh6 and pRSh9. Negative shoots were retained on 5 mg/L Basta in case they were false negatives and re-tested if they remained green with roots. Generally PCR negative shoots showed Basta sensitivity symptoms in subsequent subculture rounds suggesting negative PCR results were genuine. For all transgenic lines 1-2 pots of clonal cuttings remain in vitro. All lines appeared healthy with good root and shoot development and normal phenotype.
Conformation of Expression by RT-PCR
RT-PCR analysis confirmed expression of the oleosin construct in 4 out of 5 lines tested ( FIG. 64 ).
Transformation of Lotus japonicus with Agrobacterium rhizogenes

Northern Analysis of RNA Extracted from Hairy Roots

Northern blot analysis was performed on transformed Lotus japonicus hairy roots (see below) to confirm the expression of the polyoleosin constructs. The blot was probed with 32 P labeled, random primed, white clover oleosin cDNA ( FIG. 65 ). The Northern blot analysis shows that the constructs are transcribed. In each case it appears that transcription has finished close to the 3′ end of the OCS terminator where a single oleosin transcript and the terminator are roughly 1.5 kb in length. It is clear that the transcript from the single oleosin is highly expressed in the majority of the single oleosin transformants. Each additional oleosin repeat resulted in the increase in the transcript size by the appropriate amount (˜650b). As such that the sizes are as follows 1.4 kb, 2 kb, 2.7 kb, 3.4 kb and 4 kb for the oleosin monomer, dimer, trimer, tetramer and pentamer, respectively. The level of transcript accumulated appears to be inversely proportional to the number of oleosin repeats. Furthermore, the transformants containing either the oleosin monomer or dimer did not have any transcripts of unexpected size hybridising to the oleosin probe, whereas the transformants containing the oleosin trimer, tetramer or pentamer had a number of additional hybridising bands. In the majority of cases the bands were considerably larger than the expected size, frequently >4.4 kb, and in only one case did the hybridising band appear to be smaller than the predicted transcript. Since the extra bands only appear in lines transformed with the trimeric or larger oleosin repeats, we have assumed that these bands represent aberrantly processed oleosin RNA, and in many cases the processing appears to have failed to terminate transcription.
Transformation of Lotus japonicus with Agrobacterium rhizogenes (A4T)
Protocol
Day 1


Scarify lotus seeds using p220 wet/dry sand paper
Sterilise seeds by rotating for 20 min in 10 mL sterilisation soln:
7 mL 100% ethanol 1 mL 30% H 2 O 2 2 mL H 2 O

Wash 3 times in sterile H 2 O
Place seeds on 1% water agar plates
Wrap plates in tinfoil (dark) and germinate at 25° C. for 2 days
Streak TY agar plate with Agrobacterium rhizogenes (A4T) glycerol stock and grow overnight @ 28° C.


Day 2


Inoculate 50 mL YEB culture broth with colony from A4T plate and grow overnight @ 28° C. shaking (220 rpm)


Day 3


Make Agrobacterium competent cells and transform with binary plasmid containing gene of interest, plate on TY agar plates and grow for 2 days at 28° C. (refer: Transformation of Agrobacterium )
Transfer germinated seeds to ½ B5 media, approx 10 across each plate, roots pointing down.
Tape plates together, grow vertically on lab bench.


Day 5


Pick colonies from Agrobacterium plates into 10 mL TY-spectomycin broths and grow at 28° C. shaking (220 rpm) for 2 days.


Day 6


Perform PCR on Agrobacterium broths to check for desired gene.


Day 7


Inoculate Lotus japonicus plants by dipping a sterile scalpel into the Agrobacterium broth and cutting off the root. After inoculation tape plates together, wrap in tinfoil and leave overnight on lab bench


Day 8


Unwrap plates and grow for 2 days vertically on lab bench


Day 9


Transfer plants to MS (CRO) media containing the antibiotic cephotaximine, 10 across a plate. Grow vertically on lab bench.
Roots can be viewed (for GFP) under a Microscope 10-20 days later.


Media
½ B5 Media (No Sucrose)









0.0425
g
NaH 2 PO 4 •2H 2 0

0.625
g
KN0 3

0.0335
g
(NH 4 ) 2 S0 4

0.0625
g
MgS0 4 •2H 2 0

0.01
g
Ferric EDTA

0.025
g
Myo-Inositol

0.25
mL
Stock A

0.25
mL
Stock B

0.25
mL
Stock C

0.25
mL
Stock D























Adjust pH to 5.5 with 0.2M KOH or 0.2M HC 1-6
6 g Agar

Make up to 500 mL with sterile H20
MS(CRO) Media










50
mL
MS Macro Stock

5
mL
MS Macro Stock

5
mL
MS Fe (EDTA) Stock

1
mL
B5B Vitamins stock

30
g
Sucrose

100
mg
Myo-Inositol

8
g
Phytagel agar



pH to 5.7 with NaOH

Final volume = 1000 mL




















MS Macro Stock










33
g
NH 4 NO 3

38
g
KNO 3

8.8
g
CaCl 2 •2H 2 O

3.4
g
KH 2 PO 4

7.4
g
MgSO 4 •7H 2 O



Final volume = 1000 mL

















MS Fe (EDTA) Stock









4 g
Ferric EDTA (Fe Na Ethylene diaminetetra acetic)



Final volume = 500 mL













MS Micro Stock










1.24
g
H 3 BO 3

4.46
g
MnSO 4 •4H 2 0

1.72
g
ZnSO 4 •7H 2 0

0.166
g
KI

0.05
g
Na 2 MoO 4 •2H 2 0

0.005
g
CuSO 4 •5H 2 0

0.005
g
CoCl 2 •6H 2 0



Final volume = 1000 mL



















B5 Vitamin Stock












0.1 g
Nicotinic Acid


1.0 g
Thiamine HCl


0.1 g
Pyridoxine HCl






Final volume = 100 mL






1 mL
aliquots into eppendorfs





Store at −20° C.
























Notes
Transformation of Lotus:


This protocol includes the transformation of Agrobacterium which sometimes is just being grown from glycerols. Also is written as for GFP—if for PPT resistant plants then on day 9 (or just when roots are visible) we transfer to selective plates. Usually 4 plants (roots only) per plate. Once selection has taken place (either GFP or PPT) individual roots are transferred to individual plates. Supposedly we transfer all or some of the tissue to a new plate each month. Once we are growing root portions only the plates are kept horizontal, sealed and in darkness, usually in the 25 C room.

Transformation of Agrobacterium rhizogenes (A4T)

1. Streak a TY agar plate with Agrobacterium rhizogenes (A4T) glycerol stock and grow 28° C. overnight.
2. Inoculate 50 mL of YEB broth with a colony from Agrobacterium plate and grow at 28° C., shaking (220 rpm) until OD 600 is approx 0.5 (16 h)
3. Centrifuge cells for 15 min @ 400 rpm, discard supernatant and resuspend in 10 mL of 0.15M NaC 1-4
4. Centrifuge cells for 10 min @ 4000 rpm, discard supernatant, and resuspend in 1 mL of ice-cold 20 mM CaCl 2
5. Aliquot 200 μL of cells into an eppendorf tube, add 5 μg of DNA and incubate on ice for 30 min.
6. With what is left of the 1 mL aliquot 186 μL of cells and 14 μL of DMSO into eppendorf tubes and freeze in liquid N 2 then store at −70° C.
7. After incubation on ice for 30 mins freeze the DNA/cells in liquid N 2 for 1 min.
8. Thaw in a 37° C. waterbath
9. Repeat steps 7 & 8
10. Add 1 mL of YEB broth and incubate cells for 4 h @ 28° C. with gentle shaking
11. Plate cells on TY agar containing spectomycin and grow for 2 days @ 28° C.
12. Pick colonies from the Agrobacterium plates into 10 mL TY broths containing spectomycin and grow for 2 days @ 28° C., shaking at 220 rpm.


Agrobacterium transformed with a binary vector are prepared for infiltration by plating or spreading a bacterial lawn on the appropriate plate with appropriate antibiotics (although Rifampicin is not normally included). The Agrobacterium should be grown at 28° C. for 2-3 days.
Clover Seed Oilbody Purification
Buffers for Oilbody Extraction
Buffer A










4
mL
500 mM NaPhosphate Buffer, pH 7.5

41.1
g
sucrose



Final volume = 200 mL (with dH 2 O)














Buffer D










1
mL
500 mM NaPhosphate Buffer, pH 7.5

17.1
g
sucrose

23.4
g
NaCl



Final volume = 200 mL (with dH 2 O)















Detergent Washing Solution









0.4 mL
10% Tween 20 (0.1%)

20 mL
Floating Buffer (½x Buffer D)



Final volume = 40 mL (with dH 2 O)














Procedure
1. Weigh 2 g of clover seed. 2. Homogenate the seed in ˜20 mL of Buffer A with sand in a mortar and pestle. 3. Transfer to two 15 mL Falcon tubes and centrifuge 3200×g 10 min RT. 4. Transfer upper aqueous phase and any floating material to two 15 mL Falcon tubes and add 1 mL Buffer D. 5. Resuspend the oil bodies thoroughly by sonication Power-1 Duty Cycle-100% 5×30 sec. 6. Centrifuge 10,000 rpm 10 min RT. 7. Transfer upper/floating oil-body layer at the top with a bended spatula to 2 mL microfuge tubes containing 1.5 mL of Detergent Washing Solution. 8. Resuspend the oil bodies thoroughly by sonication Power-1 Duty Cycle-100% 5×30 sec. 9. Centrifuge 10,000 rpm 10 min RT. 10. Transfer upper/floating oil-body layer at the top with a bended spatula to 2 mL microfuge tubes containing 1.5 mL of Buffer A. 11. Resuspend the oil bodies thoroughly by sonication Power-1 Duty Cycle-100% 5×30 sec. 12. Centrifuge 10,000 rpm 10 min RT. 13. Transfer upper/floating oil-body layer at the top with a bended spatula to 2 mL microfuge tubes containing 500 μL of Buffer A. 14. Resuspend the oil bodies thoroughly by vortexing and prepare samples for SDS-PAGE analysis.

RNA Isolation from Plants Using the QIAGEN RNeasy Kit


RNA was isolated from Agrobacterium tumefaciens infected N. benthamiana leaves and Agrobacterium rhizogenes infected L. japonicus roots using the RNeasy Plant Mini Kit (QIAGEN, Hilden, Germany). Approximately 0.1 g of tissue was removed from the plant, placed into a 1.5 mL microcentrifuge tube, frozen in liquid nitrogen and ground to a fine powder using a stainless steel rod. 450 μL RLT Buffer (guanidinium isothiocyanate) and 4.5 μL β-mercaptoethanol were added and the mixture vortexed vigorously until the sample thawed then for a further 30 sec. The lysate was transferred onto a QIAshredder spin column (lilac), fitted in a 2 mL collection tube (supplied) using a 1 mL pipette with the end of the tip cut off to prevent blockages. The mixture was spun in microfuge for 2 min at 13000 rpm. The filtrate was transferred to a 1.5 mL centrifuge tube taking care not to disturb the debris in collection tube. 225 μL Absolute Ethanol (0.5 vols.) was added and mixed immediately by pipetting. The filtrate/ethanol mix, and any precipitate, was decanted onto the RNeasy mini spin column (pink) which had been fitted in a 2 mL collection tube (supplied). The mixture was spun in a microfuge for 15 sec at 13000 rpm. The filtrate was then discarded, but the column and collection tube were retained for the next step. To column was washed by loading on 700 μL RW1 Buffer then spun in a microfuge for 15 sec at 13000 rpm. The filtrate was discarded, and 500 μL RPE Buffer was loaded onto the column, which was then spun in a microfuge for 15 sec at 13000 rpm. Again, the filtrate was discarded and another 500 μL RPE Buffer was loaded onto the column and spun for 15 sec at 13000 rpm. The filtrate was discarded, and the column was spun for an additional min at 13000 rpm to thoroughly dry the column. Next the column was carefully removed from the collection tube, avoiding the carry-over of ethanol/wash buffer. The RNeasy column was then placed into a fresh 1.5 mL collection tube (supplied) and 30 μL RNase-free H 2 O was added onto the column. The column was spun in a microfuge for 60 sec at 13000 rpm to elute the RNA. The RNA was stored at −20° C. until required.
RT-PCR
cDNA synthesis.
Expand Reverse Transcriptase, Roche, cat#1785826, supplied with 5× Buffer and DTT.









8.5-9.5
μL
Total RNA (1 μg recommended)

either 2
μL
10 μM gene specific reverse primer

or 1
μL
Oligo(dT) 12-18 @ 100 pmoles/μL



Total volume 10.5 μL (with RNase-free sterile H 2 O)















Denatured RNA and primer for 10 min at 65° C.
Immediately cooled on ice.
Added respective reagents separately to each tube in the following order (no cocktail):









4
μL
5 x Expand reverse transcriptase buffer (first-strand) (1×)

2
μL
100 mM DTT (10 mM)

2
μL
10 mM dNTP Mix (dATP + dCTP + dGTP + dTTP, Roche



cat#1581295; 1 mM)

0.5
μL
RNase Inhibitor (Roche, cat#799017, 40 U/μL; 20U)

1
μL
Expand Reverse Transcriptase (Roche cat#11 785 834 001;



50 U/μL; 50U)



Total volume 20 μL(with RNase-free sterile H 2 O)



















Mixed and pulse spun.
Incubated at 43° C. for 45-60 min.
Quenched on ice.
Used immediately.
First Round PCR Reaction.










5
μL
cDNA

1
μL
10 mM dNTP Mix (dATP + dCTP + dGTP + dTTP, Roche



cat#1581295; 200 μM)

0.3
μL
25 μM Forward primer (150 nM)

0.3
μL
25 μM Reverse primer (150 nM)

5
μL
10x PCR reaction buffer with MgCl 2 (Roche cat#1 647 679; 1×)

1
μL
Taq DNA Polymerase (Roche cat#1 647 679; 1 U/μL; 1U)



Total volume 50 μL (with sH 2 O)



















First Round PCR Amplification.














95° C.
2:00

1 cycle


95° C.
0:30


58° C.
0:30
{close oversize brace}
30 cycles


72° C.
2:30


72° C.
7:00

1 cycle



















Northern Analysis of RNA
4 pg pMC6 (Clone 6) used as template.
Amplified using pMC1 (Clone 1) forward and reverse primers and standard Taq reaction.
Extracted bands purified using QIAGEN Gel Purification kit.
Product quantified to 55 ng/μL.
Formaldehyde Gels
***All water should be sourced fresh from the still.
10× MOPS/EDTA Buffer
(A) 52.3 g MOPS (Free Acid, Mr=209, 500 mM)
Adjust pH to 7.0 with 10N NaOH.
Final vol 250 mL.
(B) 1.86 g EDTA (Na salt, Mr=372, 10 mM, or 1 mL 500 mM EDTA in 500 mL)
Adjust pH to 7.5 with 10 N NaOH.
Final vol 250 mL
Add 250 mL MOPS to 250 mL EDTA to obtain correct final concentrations.
Store in the dark at room temperature.
The buffer may yellow with age or autoclaving but this will not affect buffering capacity.
Buffer A
300 μL 10×MOPS/EDTA Buffer
Final vol 1 mL.
Formaldehyde/Formamide









89 μL
AR Formaldehyde (37-40%)

250 μL
Formamide (TOXIC. Fumehood and Gloves)















Gel Loading Buffer












400 mg
Sucrose


320 μL
Buffer A





Mix to dissolve then add






















5 mg
Xylene cyanol

5 mg
Bromophenol blue



Mix to dissolve. Add






















178 μL
AR Formaldehyde (37-40%) (TOXIC. Fumehood and Gloves)

500 μL
Formamide (TOXIC. Fumehood and Gloves)



Store in 100 μL aliquots at −20° C.














Running Buffer (=1×MOPS/EDTA)









225 mL
10× MOPS/EDTA Buffer



Total vol = 2.25 L













Sample Preparation










30
μg
RNA (as a dry pellet)

5.5
μL
Buffer A



Resuspend RNA. Add





12
μL
Formamide/Formaldehyde (TOXIC. Fumehood and Gloves)



Heat to 70° C. (heating block) for 10 min then quench on ice.





Add 4.5
μL
Gel Loading Buffer





Load onto submerged gel.

































Pouring Formaldehyde Gel
Prepare gel tray by wiping out with ethanol and taping both ends with a double layer of masking tape.











250
200
125
mL
Final vol.

2.5
2.0
1.25
g
Agarose

25
20
12.5
mL
10x MOPS/EDTA Buffer

180
144
90
mL
H 2 O



For today's work 2 gels 150 × 100 mm prepared with 30-tooth combs in each.
















Mix in a 500 mL flask and dissolve in microwave. Stir while cooling.
All of following steps should be done in the fumehood:










Add 45 mL
36 mL
22.5 mL
AR Formaldehyde (37-40%)














Mix and pour into prepared gel tray, with comb in place.
Allow to set for 30-45 min.
Cover with Running Buffer, load and run initially at 50V for 15 min to get samples into gel, then turn voltage down to 12V and run overnight.
Northern Blot
20×SSC










175.3
g
AR NaCl (=3M)

88.2
g
AR Sodium citrate (=0.3M)



Adjust pH to 7.0














Total Volume 1 L
This Northern Blot method uses the flow of buffer DOWN through a gel then a nylon membrane to transfer denatured RNA from the gel onto the membrane. Based on the design of the Schleicher & Schuell TurboBlotter.
1. Two 3 cm stacks of interfolded paper hand towels (Hygenex Royale, 245×270 mm, cat#2170360) were placed side-by-side in a plastic tray 2. Two sheet of 3 mM paper, cut to 220×160 mm were placed on top, followed by one sheet pre-wetted in 10×SSC. 3. The nylon membrane (Hybond-XL (Amersham; cat no: RPN303S) was cut to 220×160 mm, pre-wetted with dH 2 O, rinsed for 1 min in 10×SSC, and finally placed onto the stack. 4. The gel was removed from the gel plate and washed for 20 min in 10×SSC. 5. The washed gel was then placed onto the membrane ensuring that no bubbles were trapped between the gel and the membrane. Note care was taken to ensure that the gel was positioned correctly as transfer may be initiated as soon as the gel comes into contact with the membrane. 6. Three sheets of pre-wetted 3 mM paper, cut to 230×170 mm, were layered onto the stack. Again ensuring that no bubbles were trapped between the layers. 7. Finally the pre-wetted 3 mM wick, cut to ˜800×180 mm, was placed across the stack, with each end folded over and submerged in 100 mL 20×SSC, which was in containers at the side of the blot/stack.
NOTE 1. The wick was kept flat at all times (i.e. the containers were long enough so that the wick did not have to be crammed in). 2. The sides of the containers were only 1-2 cm high so that the capillary action could easily draw the 20×SSC up and out of the reservoirs.


Next Day




1 The blot was carefully taken apart down to the gel. A soft leaded pencil was pushed through the wells, and used to mark the position of each well on the membrane.
2. The RNA crosslinked to the membrane using a
3. The membrane was then placed between two sheets of dry 3 mM paper and allowed to dry.
4. Finally the membrane was wrapped in Gladwrap and stored at 4° C. overnight.




Labelling the Probes
RadPrime DNA Labeling System (Invitrogen, Cat. No.: 18428-011)








1.
Denature 25 ng DNA dissolved in 19 μL of sterile distilled water


or TE in a microcentrifuge tube by heating for 5 min in a boiling


water bath; then immediately cool on ice

2.
Perform the following additions on ice:









1
μL
500 μM dATP



1
μL
500 μM dGTP



1
μL
500 μM dTTP



20
μL
2.5X Random Primers Solution



5
μL
[α-32P]dCTP (3000 Ci/mmol. 10 mCi/mL,





approximately 50 μCi)


To
49
μL
with dH 2 O




3.
Pulse spin

4.
Mix briefly, add









1
μL
Klenow Fragment




5.
Mix gently but thoroughly

6.
Pulse spin

7.
Incubate at 37° C. for 10 min







8.
Add
5
μL
Stop Buffer














































Purifying the Probe.
ProbeQuant G-50 Micro Columns, Amersham Biosciences, cat#27-5335-01.
1. Loosen the lid of the column and snap off the seal at the bottom. 2. Place the column into a 1.5 mL microcentrifuge tube. 3. Spin at 735×g for 1 min to remove the liquid. 4. Place the column into a fresh 1.5 mL microcentrifuge tube. 5. Layer the labelled probe onto the column. 6. Spin at 735×g for 2 min (unincorporated nucleotides, dyes, and salts will remain on the column). 7. The purified labelled probe will collect in the microfuge tube. 8. Denature the labelled DNA by heating to 95-100° C. for 5 min and snap-cool on ice. 9. Pulse spin. 10. Immediately add into Pre/Hybridisation Solution in tubes (do not place directly onto blot).

Probing Blots
20×SSC










175.3
g
AR NaCl (=3M)

88.2
g
AR Sodium citrate (=0.3M)



Adjust pH to 7.0

Total volume 1 L















Pre/Hybridisation Solution.
(from: Church G M & Gilbert W. 1984 , Genomic Sequencing, Proc. Natl. Acad. Sci. USA ).









12.5
mL
1M NaHPO 4 Buffer pH 7.2 (250 mM)

20
mL
H 2 O

100
μL
0.5 M EDTA (1 mM)

17.5
mL
20% SDS (7%)

0.5
g
BSA (1%)



Final volume ~50 mL.

















Pre-wet blots in 2×SSC before placing in hybridisation oven tubes.
Pre-hybridise in 45 mL Pre/Hybridisation Solution at 65° C. for 2 h.
Add denatured probe (see above) to the Pre/Hybridisation Solution and hybridise at 65° C. overnight.
Washing Blots
2× Wash Buffer









50 mL
20 × SSC (2 × SSC)

2.5 mL
20% SDS (0.1% SDS)



Final volume = 500 mL.














1× Wash Buffer.









25 mL
20 × SSC (1 × SSC)

2.5 mL
20% SDS (0.1% SDS)



Final volume = 500 mL.














0.2× Wash Buffer.









5 mL
20 × SSC (0.2 × SSC)

2.5 mL
20% SDS (0.1% SDS)



Final volume = 500 mL.














0.1× Wash Buffer.









2.5 mL
20 × SSC (0.1 × SSC)

2.5 mL
20% SDS (0.1% SDS)



Final volume = 500 mL.














Wash Filters




2× Wash Buffer 2×15 min at 65° C. (˜200 mL per hybridisation tube).
1× Wash Buffer 2×15 min at 65° C. (˜200 mL per hybridisation tube).
0.2× Wash Buffer 2×15 min at 65° C. (˜200 mL per hybridisation tube).
0.1× Wash Buffer 2×5 min at 65° C. (˜200 mL per hybridisation tube).




Seal membranes in thin plastic bag, check counts using Geiger counter, and expose to X-ray film with intensifying screen at −70° C., overnight (if ˜20 counts per second) or longer depending on signal intensity after washing.
Blots were exposed for 3 days.
Example 2
Synthetic Sesame Seed Polyoleosin Construction
Background
We designed a synthetic sesame seed oleosin with tandem repeats for expression in both E. coli as well as plants (e.g., Arabidopsis and Lotus ). It should be noted that the oleosin sequence used is for example only. Any oleosin sequence or combinations of oleosins, steroleosins and caoleosins and oleosin linking sequences could be used. The original sesame seed oleosin nucleotide sequence and translated peptide sequence are from a sesame seed oleosin, GenBank clone AF091840 (Tai et al., 2002). The codons were optimised for both E. coli and Arabidopsis expression. Each repeat used randomised degenerate codons to code for the specific amino acid sequence thus ensuring that the repeats will not be rearranged by non rec − bacteria such as Agrobacterium tumefaciens or Agrobacterium rhizogenes . The construct was designed so that it can be relatively simply subcloned from the original backbone (pUC57) into both pET29a and various plant binary vectors. In order to allow simple restriction digestion and re-ligation to reduce the number of repeats as well as to enable us to paste in future peptides between the repeats we engineered restriction sites between them.
The design allows various numbers of tandem repeats to be easily transferred into pET29a and to perform simple digestions on the original clone to remove different numbers of inserts then transfer to binary vectors. This included a NcoI site on each end of the sesame oleosin to place it into pET29a which gives the peptide an N-terminal S*Tag and thrombin cleavage site and a C-terminal His.Tag. For transfer to plant binary vectors we designed an attL1 site to the 5′ end and an attL2 site to the 3′ end, these are compatible for with our GATEWAY plant binary constructs built in house.
Unique restriction sites (Eco47 μl, DraI, MluNI, SacI, SalI, EcoRI, HindIII, ScaI, HpaI, Alw44I) were also engineered between the repeats to allow future additions of peptides between the repeats. A single oleosin repeat can be generated by XhoI digestion and re-ligation. Similarly, constructs for a dimeric, trimeric and tetrameric oleosin repeats can be generated by digestion and re-ligation with ClaI, BstXI and NdeI respectively. These can then be transferred to chosen binary vectors via the LR reaction. If the intron is not required then this can be removed after transfer to the binary. NotI sites flanked the ORF of the complete clone to allow sub-cloning into pART binary vectors if necessary.
We have mainly concentrated on constructs using cauliflower mosaic virus 35S promoter (CaMV35S), a well-characterized over-expression promoter. It is expected that polyoleosin expression will only be seen in the seeds of transformed plants where triglyceride will be present (de Boer and Somerville, 2001). We have also created a binary vector containing the Arabidopsis oleosin promoter; this can also be utilised for discreet polyoleosin expression in the seed.
In addition we created several alternative trimeric oleosin-repeat constructs, In E. coli , we have had success expressing a trimer of direct repeats of the sesame oleosin that was successfully expressed by Dr. Bocky Chi-Chung Peng (Peng et al., 2004). We created two binary vectors (CaMV35S and Oleosin promoters) containing this direct repeat trimer. These constructs have been transformed into Arabidopsis.
Codon Analysis
We compared the codon usage by both E. coli and Arabidopsis (Table 17). From this we were able to identify codons that were not suitable for use in this construct; these included the following:











Arg
AGG


Arg
AGA


Arg
CGG


Arg
CGA


Arg
CGC


Ile
ATA


Leu
CTA


stop
TAG






















These codons were removed from the codon Table, the remaining codons were placed in a spread sheet which randomised the possibilities still available for each amino acid. Thus, while the codon usage was randomised the peptide sequence for the sesame seed oleosin was conserved. The randomisation was repeated 6 times, one for each oleosin repeat. An alignment of these sequences showed that the homology dropped to approximately 75% between each repeat and the drop in homology was generally distributed evenly across the whole sequence.





TABLE 17



Comparison of E. coli and A. thaliana codon usage.

















































































































































































































































Each number represents the proportion that codon is used to code for the respective amino acid. Codons in grey were not used in the polyoleosin construct since they coded for the respective amino acid less than 10% of the time in either organism. Codons in bold and underlined were removed to raise the GC content and to remove cryptic splice sites and mRNA degradation signals (ATTTA).
Selection and Location of Restriction Sites Between Oleosin Repeats
Restriction sites were inserted as linkers between the repeats. The sites were chosen to allow the subcloning of different combinations of oleosin repeats; they also allowed for the generation of 8 amino acid linkers between each repeat to allow for free rotation etc. Linkers with undesirable codons were not used.
The multiple cloning sites of both pUC57 and pET29a allowed the design of a sub-cloning strategy using multiple placements of the following restriction sites within the polyoleosin construct.
















Bst XI
Cla I
Pst I
Nco I
Nde I
Not I
Xho I















The randomised oleosin repeats were checked for these sites and alternative codons were then used to eliminate the sites when discovered.
Unique Restriction Sites
We also engineered unique Eco47 III, Dra I, Mlu NI, Sac I, Sal I, Sca I, Hpa I, Alw44I sites between different repeats. These have been included to allow future additions of peptides between the repeats.
Not I Sites
Not I sites flank the ORF of the complete clone. This is to allow sub-cloning into pART binary vectors if necessary.
A schematic diagram of the construct is shown in FIG. 66 .
Optimisation for: Improving Translation Efficiency; Increasing RNA Stability; Correct Splicing.
Tetranucleotide Stop Codon.
Brown et al., (1990) reported that there was an increasing number of reports where the tri-nucleotide stop codons do not signal the termination of protein synthesis; they found that the signals UAA(A/G) and UGA(A/G) are the preferred stop codons in eukaryotes. Hence we have added an A to the 3′ end of the second stop codon (TGA) in our construct.
mRNA Degradation Signal
Beelman and Parker (1995) reported the degradation signal ATTTA (AUUUA) can destabilize transcripts in plants as well as animals. The proposed construct ORF originally had 7 ATTTA sites. These were predominantly caused by the sequence coding for isoleucine followed by a tyrosine residue. The ATTTA sites were removed by changing the relevant isoleucine codons to ATC. Re-analysis of the splice sites after the removal of the ATTTA sites showed that fewer regions were predicted to be introns (partially determined by the GC content).
pOly T
The original proposed construct ORF would have had 27 TTTT sites and 12 TTTTT sites.
To reduce the number of these regions the phenylalanine codon TTT was removed and replaced by TTC; in one case the site was eliminated by moving the engineered DraI site to the 5′ end of the Mlu NI site. Combined these changes reduced the number of TTTT sites to 14 and the number of TTTTT sites to 1.
Plant Intron Insertion
The insertion of a recognised plant intron into an expression construct frequently results in a significantly enhanced expression of the construct in planta; this is termed Intron Mediated Enhancement (Rose 2004 and references therein). The sequence and position of the intron is important in terms of expression enhancement with the highest gains obtained by placing the Arabidopsis thaliana ubiquitin10 (UBQ10) intron within the first 250 bases or so of the 5′ end of the transcript (Rose, 2002; 2004 and references therein). Rose and Beliakoff (2000) found that utilising a PstI site was a useful way to insert introns. This was achieved by engineering a PstI site to the 5′ end of the intron and by modifying the existing 3′ end of the intron to contain a PstI site, from this they were able to add or delete functional introns wherever a PstI site existed in the gene or cDNA.
Vector NTI identified approximately 4 PstI sites within the proposed polyoleosin construct with the closest to the 5′ end occurring approximately 500 bases downstream. All these sites were eliminated using various combinations of degenerate codons and a new PstI site was engineered at position 300 using the degenerate codons. This places the intron in the first oleosin repeat and therefore enables the generation of all truncated versions with the intron (see Sub-Cloning Strategy below). Using the UBQ10 intron sequence (Norris et al., 1993) we engineered the 3′ end to include a PstI site; the comparison with the original sequence is shown in FIG. 67 .
The new polyoleosin construct (containing the intron) was then analysed by NetGene2 (Hebsgaard et al., 1996; Brunak et al., 1991, web site address http://www.cbs.dtu.dk/services/NetGene2/) to confirm that the engineered intron would be predicted to be spliced correctly. This analysis revealed that not only would the UBQ10 be spliced out correctly but there were also high confidence cryptic donor and acceptor sites that would likely result in aberrant splicing. The putative cryptic splice sites were either eliminated wherever possible or reduced in confidence by using alternative redundant codons. The analysis was repeated and showed that the only high confidence donor and acceptor sites remaining were flanking the engineered UBQ10 intron (NetGene 2 results of both the polyoleosin prior to cryptic splice site removal and polyoleosin with intron and cryptic splice sites removed are shown below); it was predicted that the splicing would remove only the intron and would leave the construct in frame. The analysis showed that a number of regions did not appear to be coding regions and as such may be susceptible to some aberrant splicing. To further reduce the possibility of cryptic splicing we then modified the GC content of the construct (see GC content below).
GC Content
Oleosins with optimised and randomised codons; no ATTTA sites or TTT were still found to have relatively low GC content compared to the original sequence. To increase the GC content the additional codons were removed: ATT, AAT, TTA, CTT; this raised the GC content to close to the original content (Table 18).
The repeats were linked using the previously engineered linking regions. These sequences were modified to remove all but the first Pst I sites in the first oleosin repeat and the removal of an Xho site in the second oleosin repeat. In our construct the ORF has no ATTTA or TTTT sites. Furthermore, when the sequence was re-analysed by NetGene2 the only predicted intron splice site in the ORF was the UBQ10 intron engineered into the PstI site and the % identity of the repeats increased from an average of 74.8% identical to 79.1% identical.
NetGene2 was used to predict the splicing of the proposed construct. The results indicated that the RNA should only be spliced at the acceptor and donor sites of the UBQ10 intron (Table 19 and FIG. 68 ).
Conformation of Sequence
The coding sequence of the complete ORF (after splicing) was then checked against a heptameric repeat of the original oleosin translated sequence and found to be identical over the oleosin coding regions ( FIG. 69 ).
The sequence and feature map of the proposed construct is shown in FIG. 70 and the vector map is shown in FIG. 71 .
Sub-Cloning Strategy.
Plant Intron Removal
The intron is designed to be removed by Pst I digestion, fragment removal and re-ligation. However, due to the presence of a Pst I site in the multiple cloning site of pUC57 it would be necessary to perform a partial digestion to remove this fragment. It would be preferable to attempt this at least once in order to generate full length clones with and without the intron in the initial cloning vector. Alternatively the full length clones can be transferred to expression vectors prior to Pst I digestion as detailed above.
Transfer to E. coli Expression Vector pET29a and Generation of Different Number of Repeats.
Transfer the complete clone via partial NcoI digestion then re-ligation into pET29a. The intron can then be removed by Pst I digestion and re-ligation. Full Nco I digestion of the original clone then transfer to pET29a will also yield two trimeric oleosin clones, one will contain the intron. All NcoI digests going into pET29a will have to also be checked for orientation, as this step is not directional. Following intron removal in pET29a a single oleosin repeat can be generated by Xho I digestion and re-ligation. Similarly, constructs for a dimeric, trimeric and tetrameric oleosin repeats can be generated by digestion and re-ligation with Cla I, Bst Xl and Nde I respectively.
Transfer to pRS Series of GATEWAY Adapted Binary Vectors and Generation of Different Number of Repeats.
A single oleosin repeat can be generated by Xho I digestion and religation. Similarly, constructs for a dimeric, trimeric and tetrameric oleosin repeats can be generated by digestion and re-ligation with Cla I, Bst Xl and Nde I respectively. These can then be transferred to chosen binary vectors via the LR reaction. If the intron is not required then this can be removed after transfer to the binary vector or by partial digestion in pUC57.





TABLE 18



Comparison of GC content of each synthetic oleosin repeat and the original

oleosin sequence.






Original
Oleosin Repeat Number










Construct Design
Oleosin
1
2
3
4
5
6



Oleosins with initial selection of optimised
60.9%
54%
54%
53%
57%
56.8%
53.8%

and randomised codons; no ATTTA sites or TTT

codons

Oleosins with initial selection of optimised
60.9%
58.7%
59.1%
59.8%
60.5%
59.5%
57.7%

and randomised codons; no ATTTA sites or TTT

codons and additionally no ATT, AAT, TTA or

CTT codons





































TABLE 19



NetGene2 tabulated output prediction of splicing in polyoleosin after manual

removal of cryptic splice sites plus the addition of the UBQ10 intron and enriched GC

content. The predicted cryptic splice site at position 97 was ignored since this is in the

attL1 site and is not part of the transcribed region.

With Intron, optimised codons, enriched GC content, RNA stability

modifications



Donor splice sites, direct strand











5′ exon intron

pos 5′->3′
phase
strand
confidence
3′



332
2
+
1.00
GTACCTGCAG{circumflex over ( )}GTAAATTTCT H





Acceptor splice sites, direct strand











5′ intron exon

pos 5′->3′
phase
strand
confidence
3′



97
1
+
0.90
AAAAAAGCAG{circumflex over ( )}GCTCCGCGGC

635
1
+
1.00
TGATCTGCAG{circumflex over ( )}TCATCACAAT H





Branch points, direct strand







acceptor
branch


5′ A

pos 5′->3′
pos 5′->3′
strand
score
3′



97
52
+
−2.41
CAACAAATTGATAAGCAATG

635
617
+
−3.71
GATTAATCTGAGTTTTTCTG























































Prokaryotic Expression Constructs.
Three sesame seed oleosin direct repeat constructs were used to generate the prokaryotic expression constructs ( FIGS. 66 , 72 and 73 ). One clone provided by Dr Bocky Peng (Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227) contained a single oleosin clone using the cDNA nucleotide sequence obtained from the sesame seed oleosin clone as reported by Peng et al., (2004). A second clone generated synthetically by GENEART AG contained 3 identical tandem repeats of the cDNA nucleotide sequence obtained from the sesame seed oleosin clone ( FIG. 73 ); each repeats was linked with a nucleotide sequence encoding glycine-glycine-glycine-glycine-serine-glycine-glycine-glycine-glycine-serine (GGGGSGGGGS) (Seq ID No. 22). The third clone was the synthetic sesame seed oleosin hexameric repeat generated by GENEART AG ( FIG. 66 ). Combinations of the GENEART AG synthesised clones including the prokaryotic specific constructs and the plant optimised construct were used to generate prokaryotic expression vectors in the Novagen pET29 backbone containing between 1 to 6 repeats of the oleosin transcript ( FIGS. 74-83 ).
The first new synthetic oleosin clone was designed around the sesame seed oleosin minus the six C terminal amino acids but a different C terminal linker to the 6×His tag. Successful expression of this clone in the pET29a vector would indicate that a specific C terminal linker amino acid sequence is not essential for successful expression. The design of the linker also allows for many different oleosin sequences/repeats to be cloned into the 3′ region of the clone, including components of the existing synthetic oleosin sequence with altered codons.
In the synthetic sesame seed oleosin identical triplicate nucleotide repeat clone ( FIGS. 73 and 83 ), the linker sequence between each unit in the repeat has a repetitive amino acid motif of GGGGSGGGGS, which is designed to allow free movement of each unit in relation to the other units. The C terminal sequence is also be the same as C terminal sequence from the protein expressed by p29Ole, i.e., the single sesame seed oleosin construct. A summary of the constructs and their design is listed in Table 20.





TABLE 20



Constructs in the pET29 (Novagen) backbone for sesame seed polyoleosin

expression in E. coli .








Number




of



sesame



seed

Construct

oleosin
Source of

name
Purpose
repeats
repeats



p29Ole
prokaryotic expression
1
original cDNA (FIG. 83)

p29Ole2-6xHis
prokaryotic expression
2
triplet identical repeats from GENEART AG




clone (FIG. 73)

p29PS3a
prokaryotic expression
3
first 3 randomised codon repeats from




GENEART AG (FIG. 70)

p29PS3b
prokaryotic expression
3
second 3 random repeats from GENEART AG




(FIG. 70)

p29Ole3+
prokaryotic expression
3
Triplet identical repeats from GENEART AG




(FIG. 73)

p29Ole4-6xHis
prokaryotic expression
4
Original cDNA and triplicate identical repeats




from GENEART AG (FIG. 73)

p29Ole5-6xHis
prokaryotic expression
5
Triplicate identical repeats from GENEART AG




(FIG. 73)

p29Ole6-6xHis
prokaryotic expression
6
randomised codon repeats from GENEART AG




(FIG. 70)









































Generation of Polyclonal Antibodies to Sesame Seed Oleosin
Culture and Induction of Expression System
A 50 mL LB broth, supplemented with 50 μg/L kanamycin (Kan50), was inoculated with a loop of pET29 (containing the nucleotide sequence encoding a single sesame seed oleosin with a C-terminal His tag) culture from a plate and incubated 37° C. 200 rpm overnight (16 h). The following day 6 mL aliquots of the overnight culture were used to inoculate 2×125 mL LB Kan50 broths in 1 L conical flasks (initial OD600=0.16). The cultures were incubated 37° C. 200 rpm for ˜2 h (OD 600 =0.6) and IPTG was added to a final concentration of 0.24 mg/mL (1 mM). The induced cultures were returned to incubate at 37° C. 200 rpm for a further 4 h. The cultures were transferred to 250 mL centrifuge pots and spun at 4000×g 4° C. for 10 min (5000 rpm, Sorvall, SS34 rotor).
The supernatant was discarded and the remaining cells were lysed by adding 10 mL of B PER® Reagent (Novagen) to the pellet and vortexing/pipetting up and down until the cell suspension was homogeneous. The lysed culture was then incubated with gentle mixing for 20 min. Soluble proteins were separated from insoluble proteins by centrifugation at 12,000×g 4° C. for 25 min (13,400 rpm, microfuge). The supernatant was discarded (i.e. retained insoluble proteins in pellet). To increase the purity of the inclusion bodies, 5 mL B PER® Reagent+200 μg/mL lysozyme was added to the pellet, which was then vortexed/pipetted up and down to resuspend. The mixture was then incubated at RT for 5 min, then spun at 12,000×g 4° C. for 25 min (13,400 rpm, microfuge). The supernatant was discarded (i.e. retained insoluble proteins in pellet, pellet very diffuse) and pellet/dissolved inclusion bodies was resuspended in 4 mL Binding Buffer (100 mM NaPO 4 , pH8.0, 500 mM NaCl, 6M urea and 10 mM imidazole). To remove debris the mixture was spun at 12,000×g 4° C. for 15 min (13,400 rpm, microfuge).
Ni-Agarose Purification and Concentration of His-Tagged Recombinant Protein
2 mL aliquots of Invitrogen Ni agarose slurry was placed into two empty columns (A and B) and spun in a hand-operated centrifuge to remove storage buffer. To equilibrate the columns 3×4 mL Binding Buffer was passed through the columns, spinning in the hand-operated centrifuge between each equilibration. The lysate was added to the column and the Ni agarose was gently resuspended into the lysate. The columns were incubated at RT for 10 min with gentle end-over-end mixing then spun in a hand-operated centrifuge to remove post bind filtrate. To remove non-bound proteins the columns were washed 3×4 mL Wash Buffer (100 mM NaPO 4 , pH8.0, 500 mM NaCl, 6M urea and 50 mM imidazole), spinning in a hand-operated centrifuge between each wash. Note that the Wash Buffer previously contained 25 mM imidazole the higher concentration (50 mM) was found to increase the purity of the His-tagged target protein in the eluted fractions. Finally, fractions were eluted in the following sequential volumes of Elution Buffer (100 mM NaPO 4 , pH8.0, 500 mM NaCl, 6M urea and 250 mM imidazole), with spinning in a hand-operated centrifuge between each fraction: 1 mL (fraction 1), 2 mL (fraction 2), 1 mL (fraction 3), 1 mL overnight (fraction 4).
200 μL of fraction 3A and 3B was removed and put aside, fractions 1A, 2A, and the remainder of fraction 3A were pooled as were fractions 1B, 2B, and the remainder of fraction 3B giving approximately 2.5 mL each. Each pool was placed into a spin concentrator with a 10 kD molecular weight cut off. The concentrators were spun 3181×g 4° C. for 60 min. The concentrate was transferred to a fresh tube and the membrane washed with 2×100 uL of the respective retained Fraction 3, the washes were then added to the concentrate.
Whole Gel Elution/Purification of Target Protein
Whole gel elution was performed using the Bio Rad Mini Whole Gel Eluter as per manufacturers instructions. A denaturing elution buffer was used (250 mM Tris, 125 mM boric acid, 0.1% SDS, check final pH=8.7) and the gel was eluted at 85 mA (constant) for 25 min.
The whole gel elution technique was used to increase the purity of a sample of Ni 2+ agarose purified recombinant sesame oleosin. Table 21 outlines the loss of recombinant protein that occurred at each stage of the purification process.





TABLE 21



Protein losses during the whole gel elution procedure.









Total





Protein
Volume
Remaining


Following . . .
(μg)
(μL)
(%)











Ni-agarose column
4106
830
100


Concentration
978
60
24


Whole gel elution
272
3000
7


Concentration
83
70
2






























Following the whole gel elution the gel ( FIG. 84 ) and cellophane (not shown) were Coomassie stained to try to identify where the loss had occurred.
An intense band of the same molecular weight as the oleosin could be seen both in the gel and on the cellophane. This indicated that the region of the gel containing the oleosin had not been completely over one of the slots in the whole gel eluter, and only an estimated 40% of the target protein was actually eluted from the gel. The presence of oleosin on the cellophane membrane suggested that the oleosin was either precipitating out at high concentrations or the oleosin was binding to the cellophane, which is possible given the hydropathic clusters within the protein.
Ni Agarose Chromatography Affinity Purification
Following the failure of the whole gel elution another culture was prepared and passed through two Ni2+ agarose affinity columns (A and B) and washed at a high stringency (50 mM imidazole). Eluted fractions were analysed by Coomassie stained SDS PAGE ( FIG. 85 ) and the protein concentration of fractions 1A and 1B was measured using the Bradford's Assay (Table 22).





TABLE 22



Protein concentration of selected fractions from Ni 2+ agarose

purification.


















Final
Final






uL in

vol.
amt.

Sample
Read 1
Read 2
Average
ug
rxn
ug/uL
(uL)
(ug)



1A
0.584
0.583
0.584
2.65
1
2.65
400
1060

1B
0.608
0.605
0.608
2.86
1
2.86
400
1146

























Raising Antibodies in Rabbits
The first injection was prepared by mixing equal amount of Freunds Complete Adjuvant and the solution containing 265 μg of the target protein, to a maximum final volume of 0.5 mL. The injection was then administered into multiple sites across the back of the neck and shoulder area of the rabbit. Booster shots containing 77 μg of the target protein were delivered 3 4 weeks after the primary. Then 10-14 days later a test bleed of ˜3 mL was removed for preliminary analysis.
Bleeds were normally stored overnight at 4° C. The following day this was spun at 1500×g 4° C. for 5 min. Clear serum was removed from the top of the clot and initially stored as 200 μL aliquots at 20° C. After thawing, phenol and methiolate was added to the serum (to a final concentration of 0.25% and 0.01% respectively)
Analysis of Rabbit Anti-Sesame Seed Oleosin Antiserum
Four SDS PAGE gels were prepared and loaded identically with samples containing varying amounts of affinity purified oleosin (first fractions from columns A and B). The gels were run out and three were used for immunoblot analysis and one was silver stained.
Serum from the test sample was prepared as described above for the rabbit anti-white clover oleosin antisera and used at 1:200 and 1:1000 dilutions (in TBS-Tween) to screen two of the immunoblots. The remaining immunoblot was screened with a 1:200 dilution (in TBS-Tween) of a chicken anti oleosin antibody raised by Professor Jason Tzen (Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan 40227). Results from the immunoblot analysis and silver staining are shown in FIG. 86 .
Expression and Analysis of 1×-6× Polyoleosin in E. coli

Preparation of E. coli Expression Lines

100 μL competent E. coli Rosetta cells were transformed with 2.5 μL plasmid DNA. Samples were then incubated on ice for 20 min; heat shocked 42° C. 1 min; cooled rapidly on ice 2 min; and incubated with the addition of 900 μL LB broth at 37° C. 60 min 1400 rpm (Thermomixer). Pelleted cells were spread on LB Kan50 plates and incubated at 37° C. overnight.
Preparation of Artificial Oil Bodies (AOBs)
The primary methods for investigating the properties of the putative triple sesame polyoleosin protein was to compare with the single sesame recombinant protein in terms of:
AOB size AOB stability over time and at various temperatures and pH values Stability of AOBs in the rumen

Day 1
10 mL LB Kan50 broth toothpick inoculated with original colony from p29Ole3+(8b) and p29Ole, then incubated at 37° C. overnight.
Day 2
5 mL overnight culture inoculated into a 100 mL LB Kan50 broth (500 mL flask). Incubated 37° C. 150 min. Induced with 400 μL 250 mM IPTG, incubated 37° C. 3 h.
Each culture was transferred to 2×50 mL Falcon tubes and cells pelleted by centrifugation 10 min 4° C. 3200×g. Pellet resuspended in 4 mL B Per Reagent (Pierce) and incubated to lyse (RT 20 min, gentle end-over-end mixing).
Insoluble protein pelleted by centrifugation 20 min 4° C. 3200×g. Supernatant discarded and pellets resuspended in 2 mL Oilbody Buffer (total vol.; 50 mM NaPO 4 pH8.0, 50 mM NaCl) and stored at −20° C.
Day 3
Samples removed from −20° C. and thawed. 2×500 μL each prep mixed with 4.5 mL Oilbody Buffer and either 200 μL(A) or 500 μL(B) of purified sesame oil (remaining 1 mL of each prep returned to −20° C.).
Samples were then sonicated (Sonics & Materials Vibra˜Cell VC600, 600 W, 20 kHz; ⅛″ tapered micro-tip probe) on ice at Power 4, 80% pulse, 1×90 sec (probe heated up at this setting); followed by Power 4, 50% pulse, 2×180 sec. After incubation on ice for 90 min the samples were again sonicated on ice at Power 4, 50% pulse, 2×180 sec.
To concentrate the AOBs the samples were spun 10 min 4° C. 3200×g and the lower phase decanted off from under upper oilbody phase. Oilbodies were then mixed in 5 mL Oilbody Buffer and completely resuspended by sonication at Power 4, 50% pulse, 1×180 sec. The AOBs were then stored at 4° C. until required for subsequent analysis.
Alternatively, pellets from 20 mL induced cultures of 1×6× polyoleosin lines were resuspended in 1 mL Oilbody Buffer and sonicated (Sonics & Materials Vibra˜Cell VC600, 600 W, 20 kHz; ⅛″ tapered micro tip probe) off/on ice at:









Pulse
Time
Power



100
20
3

100
20
3

100
20
3

100
20
3



















The mixture was then spun in a microfuge 4° C. 10 min 14,000×g (14,500 rpm), the supernatant discarded and 1 mL Oilbody Buffer added to the pellets. 10 μL Purified Sesame Oil added to 240606 samples and 50 μL Purified Sesame Oil added to 210606 samples. Sonicated:









Pulse
Time
Power



100
20
3

100
20
3

100
20
3

100
10
5



















Spun in a microfuge 4° C. 15 min 14,000×g (14,500 rpm). None of the samples had formed AOBs. Supernatant discarded and 1 mL Oilbody Buffer added to pellets. 50 μL Purified Sesame Oil added to all 240606 and 210606 samples, including those that had already formed AOBs (white layer). Sonicated:









Pulse
Time
Power



100
15
5

100
15
5

100
15
5

100
15
5



















Spun in a microfuge 4° C. 15 min 14,000×g (14,500 rpm). The supernatant was transferred to a fresh 1.5 mL tube, and the supernatant and AOBs were stored at 4° C. overnight.
It can be seen by the formation of two layers that (AOB layer=upper), all samples form AOBs including the negative controls ( FIG. 87 ), which consist of induced E. coli Rosetta strain containing the pET22 vector. However, the AOBs formed using non-oleosin E. coli proteins are unstable and rapidly breakdown and coalesce ( FIG. 92 ).
Alternative methods to prepare artificial oil bodies can also be used including varying the oil/buffer/protein emulsion via different proportions or different oils and buffers. It is also possible to vary the ultrasonic energy required or to dispense with the requirement for ultrasonication via use of other disruptive methods such as vortexing and the use of organic solvents to purify the polyoleosin prior to use.
Analysis of the Purity of Polyoleosins from AOBs
750 μL Oilbody Buffer added to AOBs, then sonicated:









Pulse
Time
Power



100
15
5
















30 μL of each sample was mixed with an equal volume of SDS GLB [@ 2×SDS], and the remaining AOBs were stored at 4° C. Protein denatured in boiling water bath for 5 min. Samples loaded onto 12% SDS PAGE [@ 2×SDS] gel at 15 μL per lane for the supernatant (S) and 2.5 μL per lane for the AOBs (A). Run at 150V 75 min. After electrophoresis gels were transferred to PVDF membrane for subsequent immunoblot analysis with rabbit anti-oleosin antibodies ( FIG. 88 ). Alternatively samples were loaded onto a 4-15% gradient SDS-PAGE (with no stacking gel) and after electrophoresis gels were stained with SafeStain (Invitrogen) ( FIG. 89 ). Earlier attempts to analyse artificial oil bodies from bacteria by SDS-PAGE showed that varying portions of the 3×, 4×, 5× and 6× samples do not run into the gel, and stop at the stacking/separating gel interface. As it was possible that the polyoleosin proteins with higher numbers of repeats were forming high molecular weight aggregates. This problem is partially alleviated by using SDS/urea denaturing PAGE (Table 23) and visualised using SafeStain ( FIG. 90 ).





TABLE 23



Recipe for SDS/urea denaturing PAGE.




SDS/urea Separating Gel
SDS/urea Stacking Gel










2.5
mL
4x Tris-SDS Separating Buffer
5
mL
2x Tris-SDS Stacking Buffer

3
mL
40% Acrylamide
1.25
mL
40% Acrylamide

4.8
g
Urea (Mr = 60, 8 M final conc.)
4.8
g
Urea (Mr = 60, 8 M final conc.)




Made to 10 mL with H 2 O
Made to 10 mL with H 2 O

pH adjusted to 8.8 with conc. HCl
pH adjusted to 6.8 with 1 M HCl








10
μL
TEMED
10
μL
TEMED






100
μL
10% APS
Washed top of polymerised separating gel with




200 μL aliquots.







100
μL
10% APS





* Rinsed wells immediately before loading samples *











































AOB Properties
5 μL aliquots of AOBs were placed on a microscope slide and observed at 1000× magnification ( FIG. 91 ). When observed under the microscope the 1× oleosin AOBs appeared to be the smallest, and as the number of oleosin repeats increased the average size of the AOBs increased; up to the 3× polyoleosin, when AOB size appeared to remain similar for the 3×, 4×, 5× and 6× polyoleosin.
It is likely that significantly more single oleosin was used to make AOB than any of the multimeric tandem repeat proteins. This would explain the comparatively small size of the 1× oleosin AOB size.
AOB Stability Over Time
A 50 μL aliquot of AOBs was transferred to a 250 μL PCR tube and incubated at 4° C. for 168 h. 5 μL aliquots of the AOBs were then placed on a microscope slide and observed at 1000× ( FIG. 92 ). AOB generated from vector control protein extracts showed almost complete coalescence of the oil. After 168 h the size of the AOB in the samples containing recombinant oleosins was inversley related to the number of oleosin repeats. In other words the AOB containing single chain oleosin units were on average larger than those containing 3 linked oleosin units that in turn were on average larger than those containing 6 linked oleosin units ( FIG. 92 ). Thus the long-term stability of the emulsification can be tailored by altering the number of oleosin repeats used to generate the AOB.
AOB Heat Stability
A 50 μL aliquot of AOBs was transferred to a 250 μL PCR tube and incubated either at 70° C. for 4 h, or at 90° C. for 15 min in a PCR machine. To clearly define the amount of intact AOBs remaining, the tubes were spun 10 min 4° C. 3200×g (4000 rpm, Eppendorf 5810R centrifuge, A 4 62 swing out rotor). 5 μL aliquots of the AOBs were then placed on a microscope slide and observed at 1000× ( FIG. 93 ).
Although there did not appear to be much difference in the size of the different AOBs after heat treatment, a large proportion of the AOBs formed with the 1× and 2× polyoleosins had coalesced ( FIG. 93 ) to form large pools of oil. Those AOBs that were observed from samples formed with the 3× polyoleosin were of relatively the same size as before the heat treatment, but had formed a very thick emulsion. Some coalescence was observed in the 4× and 5× AOBs, but no large pools of oil were observed ( FIG. 93 ). With the 6× polyoleosin there was no change in the size of the AOBs, nor was there any evidence of coalescence ( FIG. 93 ). Thus the heat stability of the emulsification can be tailored by altering the number of oleosin repeats used to generate the AOB.
In addition, thickness of the emulsion layer remaining after heat treatment was correlated with an increase in oleosin repeat number ( FIG. 94 ). Thus the stability of the emulsification at elevated temperatures can be tailored by altering the number of oleosin repeats used to generate the AOB.
Stability of AOB with Different Polyoleosins at pH 3.5, 8.0 and 10.5
A large number of proteins have been found experimentally to have different optimum pH of maximal stability where pH influences the folding and the net charge of the proteins. We tested for stability of AOBs generated with different polyoleosins at pH 3.5, 8.0 and 10.5.
Buffers: 50 mM Sodium Phosphate pH 8,100 mM NaC 1-50
50 mM Glycine-HCl pH 3.5 50 mm Glycine-NaOH pH 10.5

AOBs were generated using 1, 2, 3 or 6 polyoleosins; the negative control consisted of AOBs generated using inclusion bodies generated from E. coli containing an empty expression vector. Each preparation was sonicated to evenly suspend them in buffer containing 50 mM sodium phosphate pH 8, 100 mM NaCl. A 25 μl suspension of each polyoleosin-oil body was aliquot into microtubes containing 75 μL of the buffers at different pH. The tubes were incubated at room temperature (˜22° C.) with every 5 minutes interval of 15 seconds vigorously shaking (˜1,400 rpm) using a Thermomixer. After approximately 4 hours, samples were taken (˜4 μL) and dropped on glass slice for microscoping at 1000× magnification.
After 4 hours at room temperature the negative control AOBs were beginning to coalesce at both pH3.5 and 10.5; while no coalescence of the negative control was seen at pH8 the AOBs were no longer spherical ( FIG. 95 ). The AOBs containing 1 oleosin repeat appeared to be unstable at both pH3.5 and 10.5 but were stable at pH8.0. In comparison, AOBs containing 2 or more oleosin repeats were relatively stable at both pH 8.0 and 3.5. At pH 10.5 the AOBs containing 2 or more oleosin repeats were still visible but appeared to be smaller than those in lower pH buffers ( FIG. 95 ). Some precipitation/aggregation of the emulsification was noted in the preparations containing 2 or more oleosin repeats at pH 10.5.
Comparison of Purification of Oleosin by AOB Generation Versus Affinity Purification
Prokaryotically produced polyoleosins were purified by either AOB generation or Ni 2+ affinity column. These samples were analysed by both SDS-PAGE/immunoblot or Coomassie stain or SafeStain ( FIG. 96 ). This demonstrates that both methods can be used for polyoleosin purification.
Transformation of Arabidopsis thaliana with Polyoleosin Constructs Under the Control of the CaMV35s Construct or the Arabidopsis Oleosin Seed Promoter.
A range of plant binary vectors containing from 1 to 6 oleosin repeats were created using the synthetic sequences generated by GENEART AG ( FIGS. 66 , 70 , 71 & 72 ) and two plant binary vectors containing either the CaMV35s promoter or the Arabidopsis oleosin seed promoter (Table 24 and FIGS. 97-116 ).





TABLE 24



Summary of constructs generated for expression of polyoleosin in plants.












UBQ10






intron

Construct
Plant

Oleosin
in first
Selectable

name
promoter
Terminator
cassette
repeat
marker



pRSh1-PSP1
CaMV35s
ocs3′
1 oleosin,
yes
Spectinomycin &




randomised

Basta




degenerarte




codons

pRSh1-PSP3
CaMV35s
ocs3′
3 oleosins,
yes
Spectinomycin &




randomised

Basta




degenerate




codons

pRSh1-PSP4
CaMV35s
ocs3′
4 oleosins,
yes
Spectinomycin &




randomised

Basta




degenerate




codons

pRSh1-PSP6
CaMV35s
ocs3′
6 oleosins,
yes
Spectinomycin &




randomised

Basta




degenerate




codons

pRSh3-PSP1
Oleosin
ocs3′
1 oleosin,
yes
Spectinomycin &


seed

randomised

Basta




degenerate




codons

pRSh3-PSP3
Oleosin
ocs3′
3 oleosins,
yes
Spectinomycin &


seed

randomised

Basta




degenerate




codons

pRSh3-PSP4
Oleosin
ocs3′
4 oleosins,
yes
Spectinomycin &


seed

randomised

Basta




degenerate




codons

pRSh3-PSP6
Oleosin
ocs3′
6 oleosins,
yes
Spectinomycin &


seed

randomised

Basta




degenerate




codons

pRSh1-Ole3+
CaMV35s
ocs3′
3 oleosins,
no
Spectinomycin &




identical

Basta




nucleotides




codons



























































Analysis of Agrobacterium Plasmid Preps
Agrobacterium tumefaciens (strain GV3101) was transformed using the freeze thaw method. 5 μg of plasmid was added to 250 μL of competent GV3101 cells and incubated on ice for 30 min. The cells were then frozen in liquid nitrogen for 1 min and thawed in a 37° C. water bath for 1 min. This process was repeated once then 1 mL LB broth was added to the cell mix. Following incubation at 28° C. for 4-6 h, the cells were pelleted, resuspended in 100 μL LB and plated (20 μL and 50 μL) onto LB Spec.
Transformed colonies were visualised on LB spec plates after approximately 48 h and single colonies were re streaked on LB spec to ensure the use of single colonies. From these new plates, single colonies were selected and plasmid preps obtained by using 8-10 mL of overnight culture in a modified QIAGEN Mini Prep protocol. Quantification of the preps was by NanoDrop spectrophotometer, and as yields were typically low, the presence of the construct in Agrobacterium was detected by PCR.
Primers
pRSh1-PSP4:






(Seq ID No. 23)






35S(3′end)Fwd
5′ GAC ACG CTC GAG GAA TTC GGT ACC







(Seq ID No. 24)






UBQ10IntRev
5′ GAT GGT GAT GAC TGC AGA TCA GAA
























Product size=609 bp

pRSh1-PSP6:













UBQ10IntFwd





(Seq ID No. 25)







5′ CGA TTA ATC TGA GTT TTT CTG ATC TGC AGT CA






PolySes3R




(Seq ID No. 26)







5′ CGA TCA CCG TTC CGG CCA ATG TC





























Product size=889 bp




The pRSh1-PSP4 primers could be used on any of the 35S promoter polyoleosin constructs.
Cycle
94° C./2 min
(94° C./30 seq; 63° C./30 sec; 72° C./1 min)×30
72° C./7 min
Primers
pRSh3-PSP4 and pRSh3-PSP6:






(Seq ID No. 27)






OlePro
5′ GAC ACG TGA CTT CTC GTC TCC TT







(Seq ID No. 28)






UBQ10IntRev
5′ GAT GGT GAT GAC TGC AGA TCA GAA
























Product size=722 bp




In theory, these primers will detect any of the plant polyoleosin constructs containing the oleosin promoter. The constructs were thoroughly checked by restriction digestion and sequencing when purified from E. coli . The positive controls were the respective pRSh3-PSP4 and pRSh3-PSP6 plasmid preps from E. coli.
Cycle
94° C./2 min
(94° C./30 sec; 63° C./30 sec; 72° C./45 sec)×30
72° C./7 min
Transformation of Arabidopsis thaliana var Columbia with Polyoleosin Binary Constructs









Columbia plants were transformed using the floral dip method. The efficiency of this process can vary depending on a number of variables, including the construct itself, the health and floral development stage of the plant and the strain of Agrobacterium . For some constructs, two variations on the floral dip method were employed in order to try and optimise infiltration effectiveness.
One method involved dipping the entire plant or pot of plants (Full-dip) into Agrobacterium culture suspended in a solution of 5% (w/v) sucrose and 10 mM magnesium chloride, pH 5.7. Prior to dipping, Silwet L77 (a silicone polyether copolymer) was added to the culture solution to aid infiltration. Plants could be dipped up to three times, at a frequency of no more than once per week. We now have some idea of the efficiency of our full dip method using the polyoleosin constructs, which looks to be about 0.05 0.1%. This indicates that 1 g of T1 seed (approx 50,000 seed) should yield 25 herbicide resistant plants. One batch of 200 dipped plants should yield between 2 g and 5 g of seed.
The alternative method involved dropping Agrobacterium culture, suspended in the floral dip solution described above, onto individual flowers using a sterile transfer pipette (Floral drop). The rationale here was to avoid the entire plant being covered in Agrobacterium , thus aiding plant recovery. Florets were infiltrated as often as every second day and up to four times in total.
The seed collected from these transformation events represent T1 seed, which were germinated and sprayed with Basta herbicide in order to select transformed T1 plants. The total number of plants subjected to either of these methods with the different constructs is summarised in Table 25.





TABLE 25



Summary of Arabidopsis transformations completed with the polyoleosin

monomeric, trimeric, tetrameric and hexameric polyoleosin constructs.














Approx number of
Method of

Batch Number
Construct
Promoter
Terminator
Resistance
plants treated
transformation











GH 22083
pRSh1-PSP1
CaMV 35S
ocs3′
Spec/Basta
200
Full-dip

GH 22242
pRSh1-PSP1
CaMV 35S
ocs3′
Spec/Basta
60
Floral drop

GH 22243

GH 22082
pRSh1-PSP3
CaMV 35S
ocs3′
Spec/Basta
200
Full-dip

GH 22244
pRSh1-PSP3
CaMV 35S
ocs3′
Spec/Basta
60
Floral drop

GH 22188

GH 22446
pRSh1-PSP4
CaMV 35S
ocs3′
Spec/Basta
200
Full dip

GH 22017
pRSh1-PSP6
CaMV 35S
ocs3′
Spec/Basta
300
Full dip

GH 22150

GH 22171-2
pRSh1-PSP6
CaMV 35S
ocs3′
Spec/Basta
60
Floral drop

GH 22209-10

GH 22447
pRSh3-PSP4

Arabidopsis

ocs3′
Spec/Basta
200
Full dip




oleosin


GH 22286
pRSh3-PSP6

Arabidopsis

ocs3′
Spec/Basta
300
Full dip

GH 22430


oleosin


GH 22196
pRSh3-PSP6

Arabidopsis

ocs3′
Spec/Basta
60
Floral drop




oleosin


GH 22646
pRSh1-Ole3+
CaMV 35S
ocs3′
Spec/Basta
200
Full dip

GH 22485
pRSh3-Ole3+

Arabidopsis

ocs3′
Spec/Basta
200
Full dip




oleosin














































PCR Testing of Herbicide Resistant T1 Plants
T1 seed from batch GH 22017 (Table 25) was collected and 1 g of seed germinated. Spraying with Basta herbicide resulted in approximately 20 herbicide resistant plants. These plants were also tested by PCR on genomic DNA. Genomic DNA was extracted from the rosette leaves of selected plants once they were of a suitable size. Extraction was carried out using the QIAGEN DNeasy mini kit protocol and 100 ng genomic DNA was used as PCR template. Two primer pairs were used to detect different areas of the polyoleosin insertion, thus giving information as to whether any gross rearrangements occurred during integration of the construct into the plant genome.
Plants Transformed with Tandem Repeats of Identical Nucleotide Sesame Seed Oleosin Transcripts.
The concern with using a construct containing repeating units of exactly the same sequence, as is the case with the Ole3+ constructs, is that non rec − bacteria such as Agrobacterium may utilise their natural recombination mechanism to rearrange the sequence each time a new generation of bacteria is grown. Most laboratory strains of E. coli have the rec mutation to prevent this phenomenon. The PCR results go some way towards investigating this possibility, by using 2 sets of primers at each end of the repeating unit structure in the constructs. This suggests the constructs are intact after one round of sub-culturing. An additional check is to digest the plasmid preps from Agrobacterium with restriction enzymes and check the banding pattern obtained. The plasmid prep yield from Agrobacterium is typically too low to be able to perform digests, so the prep of clone #1 from each construct was used to transform E. coli TOP10 cells by heatshock. Plasmid preps were prepared by overnight culture of three single colonies and extraction using the Qiagen mini-prep kit. The preps were analysed by three restriction enzymes the correct banding pattern is observed for all the clones tested. This result indicates that the Ole3+ constructs are intact in the Agrobacterium with no rearrangement. In the white clover constructs (discussed above), aberrent RNA species were only found to be expressed in Lotus japonicus roots when the number of identical white clover oleosin repeats was greater than 3. This could be due to rearrangements occurring in the Agrobacterium prior to plant transformation or during the process of stable integration into the plant geneome.
An additional check of integrity is to sequence through the repeating units of the E. coli preps from TOP10 cells transformed with plasmid obtained from Agrobacterium . We have sequenced through 90% of the repeating units and for the sequence completed, the construct sequence matches with the expected database sequence.
The possibility of rearrangement is potentially greater as the Agrobacterium integrates its T-DNA into the plant genome. We have no control over this event, so can only check for rearrangement events in the genomic DNA of herbicide resistant plants once they have been identified.
Analysis of Arabidopis thaliana Seeds Expressing Sesame Seed Oleosin.
Protein Expression
The herbicide resistant Arabidopsis seeds (T1) from the floral dip and full dip plants (T0) were allowed to self and set seed (T2). Seeds were collected from plants as the sliques matured (i.e., turned brown and became dry). Seeds were separated from the sliques and all seeds from 1 plant were pooled. Given the method of transformation the T2 seeds consist of segregating populations. It could be expected that for a single insertion event the T2 seed will demonstrate a 3:1 segregation pattern for a dominant trait (as would be expected for protein expression under the CaMV35s promoter). This would consist of 25% homozygous, 50% hemizygous and 25% wild type (untransformed).
Immunoblot Analysis of Arabidopsis thaliana Oil Bodies Containing Sesame Seed Oleosin.
T2 seeds from approximately 10 individual transformation events for each construct were analysed for protein expression. Seed lots for analysis were chosen based on the total amount of seed collected per plant.
Weigh out 25 mg of seed collected from 1 plant; combine with approximately 100 mg of dried, clean sand and 500 μL buffer A (600 mM Sucrose in 10 mM Sodium Phosphate buffer, pH 7.5).
Grind to a paste using mortar and pestel.
Recover maximum volume using pipette.
Rinse mortar and pestel 2× with 500 μL buffer A.
Combine extract and rinse in eppendorf tube, spin at 13 k rpm for 5 minutes.
Quickly recover the majority of the aqueous layer (bottom layer) using a piptette and transfer to a fresh tube.
Recover overlying oil layer by piptette after tilting the tube horizontally; transfer to a fresh tube.
To both fractions (aqueous and oil layer) add buffer A to a final volume of 500 μL; mix by pipetting.
Mix with equal volumes of loading buffer, vortex, boil for 5 minutes and analyse by SDS-PAGE/immunoblot using rabbit anti-sesame seed oleosin antiserum as the primary antibody ( FIG. 117 ).
The rabbit anti-sesame seed oleosin antiserum showed no binding with extracts from wild type plants. Immunoreactive protein of the expected size was detected in the plants transformed with the polyoleosin constructs including the monomeric, trimeric and tetrameric constructs (dimeric and tetrameric transformants were not included) ( FIG. 117 ). The SDS-PAGE/immunoblot analysis demonstrates that the constructs can be expressed and translated and that the protein is of the expected molecular weight, it accumulates in the seed and is targeted to the oil bodies in the correct manner. The T2 seed populations screened here contained segregating populations, hence it could be reasonably anticipated that even higher levels of expression would exist in homozygous plants as well perhaps in transgenic plants yet to be analysed. The presences of the immunoreactive band at the molecular weight of the monomeric sesame seed oleosin in all extracts from plants transformed with the polyoleosin trimer and polyoleosin hexamer suggests that either some protein cleavage is occurring or that some of the transcript is only translated as far as the first oleosin repeat before being terminated. The ratio of monomer to either trimer or hexamer is relatively low indicating that the level of accumulation of the monomer is also low.
SDS-PAGE/Coomassie analysis of the crude protein extracts from seeds of the same samples shows that the level of recombinant protein in the hemizygous transgenic plants is too low to be detected by Coomassie stain in the background of native proteins ( FIG. 118 ).
Properties of Sesame Seed Polyoleosin Expressed in Arabidopsis thaliana Seeds.
Heat Stability
Oil bodies from two wild type, pRSh1-PSP1, pRSh1-PSP3 and pRSh1-PSP6 Arabidopsis transformants were compared for heat stability. 25 mg of seed from each plant was ground separately in a mortar and pestle containing xxμL oil body extraction buffer (10 mM Sodium Phosphate buffer containing 600 mM sucrose)). This was transferred to a microfuge tube, the mortar and pestle was rinsed a further two times with 500 μL of oil body extraction buffer, combined with the original extract and the volumes were made up to 500 μL with oil body extraction buffer. The tubes were spun at 13 k rpm for 10 minutes and photographed ( FIG. 119 ). Each sample showed a thin layer (containing the oil bodies) floating on the surface of extraction buffer. 400 μL of the oil body extraction buffer was removed using a protein gel loading tip attached to an eppendorf. Small aliquots of oil body extraction buffer were used to resuspend the oil layer and removed to a new 2 ml eppendorf tube. The oil body layers were made up to the same final volume (approximately 500 μL with oil body extraction buffer and resuspended fully by pipetting. 50 μL of the suspension was loaded into PCR tubes and capped; 50 μL was stored at 4° C. The PCR tubes were heated at 90° C. for 2, 4, 24 and 58 hrs. At each time point the tubes were removed from the heating block, spun for 10 minutes at 13 k rpm to separate the suspensions and photographed ( FIG. 120 ). The reduction in oleosin repeat numbers correlates with a decrease in the emulsification layer remaining after 24 hr at 90° C., where the thickest emulsification can be seen from plants expressing the hexameric polyoleosin construct. The reduction in oleosin repeat numbers correlates with a decrease in the emulsification layer remaining after 24 hr at 90° C., where the thickest emulsification can be seen from plants expressing the hexameric polyoleosin construct. At 0 hrs through to 24 hrs at 90° C. the higher the number of oleosin repeats correlates with a thicker emulsification layer. After 58 hrs at 90° C. the oil bodies from the wild type arabidopsis has been reduced to a very thin layer with a small ring of emulsion deposited on the tube above the remaining aqueous phase. In comparison, the ring of emulsion remaining in the transformant samples is much greater ( FIG. 120 ). Thus the stability of the emulsification derived from seed extracts at elevated temperatures can be tailored by altering the number of oleosin repeats used to transform the plant.
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Reference to any prior art in the specification is not, and should not be taken as, an acknowledgement or any form of suggestion that this prior art forms part of the common general knowledge in Australia or any other jurisdiction.
Finally, it is to be understood that various alterations, modifications and/or additions may be made without departing from the spirit of the present invention as outlined herein.