(en)An L-arabinose inducible expression system comprising a mutant arabinose promoter. This system exhibits an increase in heterologous protein production upon induction with L-arabinose and comprises a mutant araB promoter and an AraC transcription binding region. This system retains the tight regulatory control characteristic of the wild type arabinose operon.

1.ApplicationNumber: US-21227108-A
1.PublishNumber: US-2010068758-A1
2.Date Publish: 20100318
3.Inventor: GRUBER TANJA MARIA
HUANG LISA LIXUAN

4.Inventor Harmonized: GRUBER TANJA MARIA(US)
HUANG LISA LIXUAN(US)

5.Country: US
6.Claims:
(en)An L-arabinose inducible expression system comprising a mutant arabinose promoter. This system exhibits an increase in heterologous protein production upon induction with L-arabinose and comprises a mutant araB promoter and an AraC transcription binding region. This system retains the tight regulatory control characteristic of the wild type arabinose operon.

7.Description:
(en)FIELD OF THE INVENTION
The invention relates generally to the field of recombinant DNA technology and microbial protein expression and specifically to an arabinose inducible expression system comprising a modified araB promoter that is operably-linked to a coding region of interest and wherein the modified araB promoter significantly increases its corresponding protein yield relative to the protein yield of the wild type araB promoter under similar expression conditions.
BACKGROUND OF THE INVENTION
Genetic information encoded in DNA molecules is expressed by a series of steps involving transcription of DNA into mRNA and the subsequent translation of the mRNA into polypeptides or proteins. The expression of the encoded information to form polypeptides is initiated at the promoter site, a region on the DNA molecule to which RNA polymerase binds and initiates transcription.
Recombinant production of proteins and peptides has become a hallmark of the biomedical and industrial biochemical industry. One of the factors influencing the cost of commercial protein/peptide production is the efficient expression of the desired gene product. Factors influencing the efficiency of the process include, but are lot limited to gene dosage (i.e. copy number), promoter strength, and the ability to control expression (i.e. inducibility).
Historically, one means to increase protein production has been the use of multi-copy plasmids. However, the increased metabolic burden placed on the cell often results in a decreased growth rate and plasmid instability. As such, it is desirable to use a strong promoter so that the copy number is minimized. The use of a strong promoter facilitates increased protein production while minimizing the metabolic burden on the host cell (i.e. fewer copies of the gene targeted for expression are required to achieve the same level of protein yield).
The use of strong promoters often requires a level of control when expressing the desired gene product. Uncontrolled constitutive expression often results in undesirable effects on the growth and/or viability of the recombinant host cell. As such, the use of strong, inducible promoters is desired. Preferably, the promoter used is characterized by tightly regulated expression and is induced using a condition or compound that is safe, environmentally friendly, and economical.
The araB gene and its promoter (“araB promoter” also known as the P BAD promoter) are located in the L-arabinose operon. The endogenous L-arabinose operon has been studied in various microorganisms including, but not limited to Escherichia coli, Salmonella typhimurium, and Bacillus subtilis ((Horwitiz et al., Gene (1981) 14:309-319; Lin et al., Gene (1985) 34:111-122; Lin et al. Gene (1985) 34:123-128; Lin et al., Gene (1985) 34: 129-134); Schleif, R., Trends in Genet. (2000) 16(12):559-565; U.S. Pat. No. 5,028,530; and U.S. Pat. No. 6,030,807). The operon is comprised of 3 structural genes (araA, araB, and araD) encoding enzymes responsible for converting L-arabinose to D-xylose-5-phosphate. The gene araA encodes the enzyme arabinose isomerase, responsible for converting arabinose to ribulose. Ribulokinase (encoded by the gene araB) phosphorylates ribulose to make ribulose-5-phosphate. The enzyme ribulose-5-phosphate epimerase (encoded by the gene araD) converts ribulose-5-phosphate to xylulose-5-phosphate, which can be metabolized via the pentose phosphate pathway. The araBAD operon is coordinately controlled by the inducer L-arabinose and the AraC regulatory gene product (Guzman et al., (1995) J. Bacteriol. 177:4121-4130). P BAD based expression systems based are widely used and commercially available from companies such as Invitrogen (Carlsbad, Calif.).
The P BAD expression system is tightly controlled and the inducer, L-arabinose, is safe and economical. However, the wild type araB promoter is not generally considered a strong promoter once induced. As such, use of the currently available P BAD -based expression systems is often unattractive for low cost peptide/protein production where optimal protein yield is desired.
The problem to be solved is to provide an arabinose inducible expression system having the ability to increase protein yield when operably linked to a coding sequence of interest.
SUMMARY OF THE INVENTION
The stated problem has been solved through the discovery of a mutant araB promoter that, when operably-linked to a coding region of interest, improves the yield of the corresponding gene product. The mutant promoter, when operably-linked to an AraC transcription factor binding region, exhibits tightly regulated and inducible expression in an AraC+ microbial host cell.
Several structurally similar mutant araB promoters have been identified. A consensus nucleic acid sequence representative of the conserved structure is provided by SEQ ID NO: 2.
The present mutant araB promoter can be operably linked to additional regulatory elements, which are referred to herein as an “AraC transcription factor binding region”, located upstream—in the 5′ direction— of the present promoter, and which provide the tightly regulated and inducible control associated with commercially available P BAD -based expression systems. Further, a nucleic acid molecule encoding an araB expression system comprises the provided AraC transcription factor binding region operably linked to SEQ ID NO: 2.
Described herein is an arabinose-inducible expression cassette comprising:
a) an AraC transcription factor binding region; b) an araB promoter of SEQ ID NO: 2; and c) a coding region of interest;

wherein the AraC transcription factor binding region, the araB promoter, and the coding region of interest are in operable linkage.
Also described herein is a vector comprising the arabinose-inducible expression cassette.
Typically, the AraC transcription factor is provided by including at least one expressible copy of an araC gene in a recombinant microbial host cell, preferably, on an expression vector. Moreover, a vector comprising the present araB expression system may further comprise an expressible copy of the araC gene.
The AraC transcription factor binding region may comprise nucleic acid sequence SEQ ID NO: 33.
A microbial host cell comprising the present vector is also provided and the vector may comprise at least one transcription terminator, which may comprise SEQ ID NO: 28.
Also described herein are methods to produce a target gene product in a recombinant microbial host cell comprising:
a) providing a recombinant microbial host cell comprising an L-arabinose inducible expression system, said expression system comprising:
i) a nucleic acid molecule encoding a chimeric gene, said chimeric gene comprising at least one copy of the present araB expression system, said araB expression system comprising the araB promoter of SEQ ID NO: 2 operably linked to a coding region of interest encoding a target gene product; ii) at least one expressible copy of an araC gene encoding an AraC regulatory protein;
b) contacting said recombinant microbial host cell with an effective amount of L-arabinose, whereby said chimeric gene is expressed and the target gene product is produced; and c) optionally isolating the target gene product produced in step (b).

Increasing the strength of a promoter is important to reducing the cost of producing a desired gene product. Use of the present araB promoter is particularly attractive when producing small bioactive peptides that typically do not require a specific tertiary structure for activity, i.e. complex folding often associated with larger enzymes. The cost of producing and isolating small peptides is often limited due to their solubility and the endogenous protease activity of the host cell; that is, the small, soluble peptides are often proteolytically degraded. Because of this, it is desirable to produce small peptides in the form of inclusion bodies by producing the peptides as fusion peptides. The fusion peptides are comprised of the small peptide of interest fused to one or more solubility tags (“inclusion body tags”). The present arabinose inducible expression system may be operably linked to a coding region of interest encoding at least one fusion peptide. Preferably, the fusion peptide comprises an inclusion body tag linked to a peptide of interest, wherein the peptide of interest comprises at least one domain having affinity for at least one body surface and is also known as a “body surface-binding peptide”.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 is a plasmid map of plasmid pBAD.GFP. The NcoI-EcoRI, restriction fragment encoding for GFP gene (coding region provided by SEQ ID NO: 6) from plasmid pAcGFP (Clontech, Mountainview, Calif.) was subcloned into the NcoI and EcoRI sites of plasmid pBAD.HisB (Invitrogen, Carlsbad, Calif.; SEQ ID NO: 5) to yield plasmid pBAD.GFP (SEQ ID NO: 8).
FIG. 2 is a CLUSTALW (version 1.83) multiple sequence alignment of 8 selected mutants. The alignment shows that the −10 region of all the sequenced constructs from the library had different sequences (underlined region). The −35 region of all the constructs remains wild type. About half the constructs had deletions around the ribosome binding site (RBS).
FIG. 3 is a CLUSTALW (version 1.83) multiple sequence alignment of various mutant araB promoter sequences and the sequence of the wild type araB promoter. Mutant GFP B1 [“B1”]; (SEQ ID NO: 17) was the brightest mutant sequence accounting for approximately 20% of the brightest cells. Mutants GFP M1 (SEQ ID NO: 18), M2 (SEQ ID NO: 19), and M3 (SEQ ID NO: 20) were less fluorescent than Mutant GFP B1 (SEQ ID NO: 17) but more fluorescent than the wild type araB promoter sequence (SEQ ID NO: 1).
FIG. 4 is a comparative illustration of the various elements found in the araB wild type promoter and mutant araB promoter GFP B1 (“B1”). Regions within each promoter that correlate to sequences associated with proposed functional elements are labeled (“RBS”=ribosome binding site; “−10”=minus ten-like sequence; “−35”=minus thirty five-like sequence; “GFP”=coding region of the green fluorescent protein operably linked to the promoter including the location of the ATG start codon; and “NcoI”=NcoI restriction enzyme recognition sequence).
FIG. 5 is a CLUSTALW (version 1.83) alignment of several mutant araB promoter sequences and the resulting consensus sequence (SEQ ID NO: 2) of the present araB promoter.



BRIEF DESCRIPTION OF THE BIOLOGICAL SEQUENCES
The following sequences comply with 37 C.F.R. 1.821-1.825 (“Requirements for Patent Applications Containing Nucleotide Sequences and/or Amino Acid Sequence Disclosures—the Sequence Rules”) and are consistent with World Intellectual Property Organization (WIPO) Standard ST.25 (1998) and the sequence listing requirements of the EPC and PCT (Rules 5.2 and 49.5(a-bis), and Section 208 and Annex C of the Administrative Instructions). The symbols and format used for nucleotide and amino acid sequence data comply with the rules set forth in 37 C.F.R. §1.822.
SEQ ID NO: 1 is the nucleic acid sequence of the wild-type araB promoter from pBAD-HisB (Invitrogen).
SEQ ID NO: 2 is the nucleic acid sequence of the consensus sequence of the present mutant araB promoter.
SEQ ID NO: 3 is the nucleic acid sequence of “Primer 1”.
SEQ ID NO: 4 is the nucleic acid sequence of “Primer 2”.
SEQ ID NO: 5 is the nucleic acid sequence of plasmid pBAD-HisB.
SEQ ID NO: 6 is the nucleic acid sequence of the coding region encoding the Green Fluorescence Protein (GFP).
SEQ ID NO: 7 is the amino acid sequence of GFP encoded by plasmid pBAD.GFP.
SEQ ID NO: 8 is the nucleic acid sequence of plasmid pBAD.GFP.
SEQ ID NO: 9 is the nucleic acid sequence of mutant araB promoter “mut1”.
SEQ ID NO: 10 is the nucleic acid sequence of mutant araB promoter “mut2”.
SEQ ID NO: 11 is the nucleic acid sequence of mutant araB promoter “mut3”.
SEQ ID NO: 12 is the nucleic acid sequence of mutant araB promoter “mut4”.
SEQ ID NO: 13 is the nucleic acid sequence of mutant araB promoter “mut5”.
SEQ ID NO: 14 is the nucleic acid sequence of mutant araB promoter “mut6”.
SEQ ID NO: 15 is the nucleic acid sequence of mutant araB promoter “mut7”.
SEQ ID NO: 16 is the nucleic acid sequence of mutant araB promoter “mut8”.
SEQ ID NO: 17 is the nucleic acid sequence of mutant araB promoter GFP.B1 (also referred to herein as “araB1”).
SEQ ID NO: 18 is the nucleic acid sequence of mutant araB promoter GFP.M1.
SEQ ID NO: 19 is the nucleic acid sequence of mutant araB promoter GFP.M2
SEQ ID NO: 20 is the nucleic acid sequence of mutant araB promoter GFP.M3.
SEQ ID NO: 21 is the amino acid sequence of the N-terminus addition associated with promoter araB GFP.B1.
SEQ ID NO: 22 is the nucleic acid sequence of mutant araB promoter GFP.1B (also referred to herein as promoter “ara1b”).
SEQ ID NO: 23 is the nucleic acid sequence of mutant araB promoter GFP.4a (also referred to herein as promoter “ara4a”).
SEQ ID NO: 24 is the nucleic acid sequence of mutant araB promoter GFP.5a (also referred to herein as promoter “ara5a”).
SEQ ID NO: 25 is the nucleic acid sequence of mutant araB promoter GFP.8a (also referred to herein as promoter “ara8a”).
SEQ ID NO: 26 is the nucleic acid sequence of the coding region of the araC gene.
SEQ ID NO: 27 is the amino acid sequence of the AraC protein.
SEQ ID NO: 28 is the nucleic acid sequence of the transcription terminator rrnB T 1 and T 2 .
SEQ ID NO: 29 is the nucleic acid sequence of an O 2 binding site within an araB expression system.
SEQ ID NO: 30 is the nucleic acid sequence an O 1 binding site within an araB expression system.
SEQ ID NO: 31 is the nucleic acid sequence of the CRP protein binding site within an araB expression system.
SEQ ID NO: 32 is the nucleic acid sequence of the AraC I 1 /I 2 binding site within an araB expression system.
SEQ ID NO: 33 is the nucleic acid sequence of an AraC transcription factor binding region located upstream (5′) of an araB promoter. The AraC transcription factor binding region can be operably linked to an araB promoter to form an araB expression system.
SEQ ID NO: 34 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 2.
SEQ ID NO: 35 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 17.
SEQ ID NO: 36 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 22.
SEQ ID NO: 37 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 23.
SEQ ID NO: 38 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 24.
SEQ ID NO: 39 is the nucleic acid sequence of an araB expression system comprising the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 25.
SEQ ID NO: 40 is the nucleic acid sequence of primer “Ara1F”.
SEQ ID NO: 41 is the nucleic acid sequence of primer “Ara1R”.
SEQ ID NO: 42 is the nucleic acid sequence of primer “Ara5F”.
SEQ ID NO: 43 is the nucleic acid sequence of primer “Ara5R”.
SEQ ID NO: 44 is the nucleic acid sequence of primer “Ara8F”.
SEQ ID NO: 45 is the nucleic acid sequence of primer “Ara8R”.
SEQ ID NOs: 46-179 are the amino acid sequences of various hair-binding peptides.
SEQ ID NOs: 175-227 are the amino acid sequences of various skin-binding peptides.
SEQ ID NOs: 228-229 are the amino acid sequences of various nail-binding peptides.
SEQ ID NOs: 230-269 are the amino acid sequences of various teeth-binding peptides.
SEQ ID NO: 270 is the nucleic acid sequence of the Caspase-3 cleavage sequence.
DETAILED DESCRIPTION OF THE INVENTION
The present invention provides an arabinose inducible expression system comprising the present araB promoter (SEQ ID NO: 2). The present arabinose inducible expression system is characterized by a improvement in protein yield in comparison to the commercially available PBAD expression system from which it was derived.
The following definitions are used herein and should be referred to for interpretation of the claims and the specification.
As used herein, the terms “comprises,” “comprising,” “includes,” “including,” “has,” “having,” “contains” or “containing,” or any other variation thereof, are intended to cover a non-exclusive inclusion.
This means a composition, a mixture, process, method, article, or apparatus that comprises a list of elements is not limited to only those elements but may include others not expressly listed or inherent to it. As used herein, “or” refers to an inclusive and an exclusive “or”. For example, a condition A or B is satisfied by any one of the following: A is true (or present) and B is false (or not present), A is false (or not present) and B is true (or present), and both A and B are true (or present).
As used herein, the indefinite articles “a” and “an” preceding an element of the invention do not refer to a specific number of instances of the element within the recited invention. “A” or “an” include one or at least one or “one or more than one”, and the singular word form of the element or component also includes the plural unless the number is obviously meant to be singular.
As used herein, the term “about” refers to modifying the quantity of an ingredient or reactant of the invention or employed refers to variation in the numerical quantity that can occur, for example, through typical measuring and liquid handling procedures used for making concentrates or use solutions in the real world; through inadvertent error in these procedures; through differences in the manufacture, source, or purity of the ingredients employed to make the compositions or carry out the methods; and the like.
“About” also encompasses amounts that differ due to different equilibrium conditions for a composition resulting from a particular initial mixture. Whether or not modified by the term “about”, the claims include equivalents to the quantities.
As used herein, the term “invention” or “present invention” is a non-limiting term and does not refer to any single variation of an invention described herein but encompasses all possible variations described in the specification and defined by the claims.
“Open reading frame” is abbreviated ORF.
“Polymerase chain reaction” is abbreviated PCR.
As used herein, the term “arabinose” refers to L-arabinose as well as all synonyms of compounds classified under CAS # 87-79-9. L-arabinose is used to induce and control expression in the present arabinose expression system.
As used herein, the terms “arabinose expression system”, “arabinose inducible expression system”, and “araB expression system” refers to the combination of genetic elements associated with L-arabinose inducible expression and includes (1) an expressible copy of the araC gene and its corresponding gene product (AraC), (2) suitable regulatory region wherein the AraC transcription regulator can bind and exhibit the tightly-regulated and inducible expression associated with commercially available P BAD -based expression systems, and (3) a promoter, that is, the “arabinose promoter”, capable of promoting transcription when operably-linked to a target coding region of interest.
As used herein, the terms “tightly regulated” and “tightly controlled” refer to an arabinose expression system that is easily modulated and controlled by the presence of an effective concentration of arabinose. Expression activity is dependent upon the presence of an effective concentration of arabinose.
Arabinose operon and expression systems based on the wild type E. coli promoter are well known in the art (Schleif, R., Trends in Genet. (2000) 16:559-565). Expression vectors based on the wild type arabinose expression system are commercially available (for example, PBAD-based expression vectors from Invitrogen). As used herein, the term “wild-type araB promoter” will refer to a nucleic acid molecule having a nucleic acid sequence as provided by SEQ ID NO: 1 (the sequence of the araB promoter used in the commercially available vector pBAD-HisB from Invitrogen (Carlsbad, Calif.)).
As used herein, the term “mutant araB promoter having the consensus sequence of SEQ ID NO: 2” comprises a nucleic acid sequence longer than the wild type araB promoter sequence (SEQ ID NO: 1). The present mutant araB promoter is characterized by the ability to increase peptide production at least a 2-fold, preferably a 5-fold, and most preferably at least a 1 0-fold relative to the amount of protein produced by the wild type araB promoter under substantially identical reaction conditions.
As used herein, the term “AraC” will refer to the transcription factor protein capable of binding to various sites within the arabinose inducible expression system described herein. The araC gene (SEQ ID NO: 26) encodes the AraC protein (SEQ ID NO: 27). The mechanism of AraC transcription factor control of the araBAD operon is well known (Schleif, R., supra). An arabinose inducible expression system comprising the present araB promoter is used in a microbial host cell that produces an effective amount of the AraC protein. The expressible araC gene may be expressed either chromosomally or extrachromosomally, such as by a plasmid. Preferably, the expressible araC gene resides on a vector further comprising the present araB promoter.
As used herein, the term “AraC+” microbial host cell refers to any microbial host cell that produces an effective amount of the AraC protein.
As used herein, the terms “effective amount of AraC” or “effective concentration of AraC” refers to that amount or concentration of AraC regulatory protein within the microbial host that inhibits transcription of the araB promoter system in the absence of an effective amount of L-arabinose.
As used herein, the terms “effective amount of L-arabinose” or “effective concentration of L-arabinose” refers to the amount or concentration of L-arabinose that induces expression of the heterologous gene. The amount of L-arabinose added to the culture medium may vary but typically provides an L-arabinose concentration ranging from 0.00002% to 20%, preferably 0.002% to 2%, and most preferably about 0.01% to 0.5%. It is well known in the art to determine the effective amount or concentration of AraC and L-arabinose required to inhibit or promote expression using the present araB promoter system (Guzman et al., supra).
As used herein, the term “operon” refers to a combination of elements including a gene encoding a peptide and the control region which regulates that expression.
As used herein, the term “operator” refers to a DNA sequence capable of interacting with a specific transcription factor, thereby controlling the function of the adjacent gene(s).
As used herein, the term “promoter” refers to a DNA sequence within the control region at which RNA polymerase binds and initiates transcription of the adjacent gene(s), that is, coding regions/target sequences. The present promoter may also include a start codon that introduces a small N-terminal addition to the coding region of interest so long as the function of the gene product encoded by the coding region is retained. Alternatively, the present promoter need not include such a start codon.
As used herein, the term “arabinose promoter” or “araB promoter” refers to a region of DNA known to bind RNA polymerase and initiate transcription and will typically include the region spanning from just upstream (5′) the −35 sequence upstream of the actual ribosomal binding site and downstream and up to, but not including, the target coding region. One of skill in the art will recognize that the −35 region will typically include all or a portion of the I 1 /I 2 AraC binding site (SEQ ID NO: 32). As shown and defined herein, the present arabinose promoter sequence may include an alternative start codon upstream of the target coding region which may add a short N-terminal extension to the resulting peptide. It is well known in the art to determine if the short N-terminal extension adversely affects the target coding sequence gene product.
The consensus sequence of the present mutant araB promoter is provided as SEQ ID NO: 2. As described herein, structurally similar versions of the present mutant araB promoter that do not add a short N-terminal extension to the desired gene product retained the characteristic increase in relative protein yield. The present araB promoter may comprise a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 17, 22, 23, 24, and 25.
As used herein, the term “AraC transcription factor binding region” refers to regulatory regions upstream (5′) of the present araB promoter which aid in the binding of the transcription factor AraC when inhibiting transcription. This region can include the O 1 (SEQ ID NO: 30) and O 2 (SEQ ID NO: 29) sites as well as the CRP (cAMP receptor protein; also known a “CAP”) binding site (SEQ ID NO: 31). An AraC transcription factor binding region as exemplified herein is SEQ ID NO: 33.
As used herein, the terms “araB promoter control system”, “araB promoter system”, “araB expression system”, and the “arabinose inducible expression system comprising the present promoter” refer to a nucleic acid molecule encoding the AraC transcription factor binding region operably linked to the present mutant araB promoter. The araB promoter system may comprise the AraC transcription factor binding region (SEQ ID NO: 33) operably linked to the consensus sequence of the present araB mutant promoters (SEQ ID NO: 2), resulting in SEQ ID NO: 34. Differently, the araB promoter system may comprise a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 34, 35, 36, 37, 38, and 39 or from the group consisting of SEQ ID NOs: 35, 36, 37, 38, and 39.
As used herein, the term “heterologous gene” refers to a gene that is foreign, i.e. originating from a donor different from the host or a chemically synthesized or modified gene and can include a donor of a different species form the host. The gene typically encodes for polypeptides ordinarily not produced by the organism susceptible to transformation.
As used herein, the term “isolated nucleic acid molecule” refers to a polymer of RNA or DNA that is single- or double-stranded, optionally containing synthetic, non-natural or altered nucleotide bases. An isolated nucleic acid molecule in the form of a polymer of DNA may be comprised of one or more segments of cDNA, genomic DNA or synthetic DNA.
As used herein, the terms “coding region”, “coding sequence”, “target coding region”, and “coding region of interest” refers to a DNA molecule having a DNA sequence that encodes a desired gene product. The coding region of interest is operably linked to the present araB promoter system (i.e. forming a chimeric gene) for L-arabinose induced expression. The coding region typically includes the start codon encoding the first amino acid of the desired gene product. In one embodiment, the present promoter may introduce a start codon 5′ to the target coding region, that is, a start codon in addition to the start codon in the target coding region, which is in-frame with the coding region and introduces a small N-terminal addition to the target gene product.
As used herein, the terms “gene product”, “target gene product”, “target coding region gene product”, and “peptide of interest” refer to the desired peptide/protein product encoded by the target coding region. The gene product optionally includes a small N-terminal addition. e.g. 22 amino acids encoded by a promoter region providing an additional start codon so long as the activity/function of the gene product is not adversely affected. Moreover, the target gene product need not include such an N-terminal addition, that is i.e. the promoter region does not include a start codon 5′. The target gene product may include any peptide/protein product including, but not limited to proteins, fusion proteins, enzymes, peptides, polypeptides, and oligopeptides. The target gene product may be a fusion peptide comprising at least one inclusion body tag and at least one target surface-binding peptide. The target surface-binding peptide may be a body surface-binding peptide. The body surface-binding peptide may be selected from the group consisting of hair-binding peptides, skin-binding peptides, nail-binding peptides, and teeth-binding peptides. The body surface-binding peptide may comprise at least one peptide selected from the group consisting of hair-binding peptides having an amino acid sequence as provided by SEQ ID NOs: 46-179, skin-binding peptides having an amino acid sequence as provided by SEQ ID NOs: 175-227, nail-binding peptides having an amino acid sequence as provided by SEQ ID NOs: 228-229, and teeth-binding peptides having an amino acid sequence as provided by SEQ ID NOs: 230-269.
As used herein, the term “body surface-binding peptide” refers to a peptide having high affinity (less than 10 −5 M Kd or less than 10 −5 MB 50 ) for a body surface. Examples of body surfaces include, but are not limited to hair, skin, nail, and oral cavity surfaces (teeth, pellicle, gum, tongue, etc.). The body surface-binding peptides are typically used to couple a personal or health care agent to the body surface. These agents include colorants, conditioners, antimicrobials, etc.). Means to identify suitable body-surface binding peptides are well known in the art and may include biopanning techniques such as phage display, bacterial display, yeast display, ribosome display, and mRNA-display, etc. The body surface-binding peptide may be empirically-generated.
As used herein, the term “hair” refers to human hair, eyebrows, and eyelashes.
As used herein, the term “skin” refers to human skin, or substitutes for human skin, such as pig skin, VITRO-SKIN® and EPIDERM™ and refers to a body surface generally comprising a layer of epithelial cells and may additionally comprise a layer of endothelial cells.
As used herein, the term “nails” refers to human fingernails and toenails.
As used herein, the term “pigment” refers to an insoluble, organic or inorganic colorant.
As used herein, “HBP” means hair-binding peptide. An HBP is a peptide that binds with high affinity (less than 10 −5 M Kd) to human hair. Examples of hair binding peptides have been reported (U.S. patent application Ser. No. 11/074473 to Huang et al.; Int'l App. Pub. No. WO 0179479; U.S. Pat. App. No. 2002/0098524 to Murray et al.; U.S. Pat. App. Pub. No. 2003/0152976 to Janssen et al.; Int'l App. Pub. No. WO 04048399; U.S. Pat. App. Pub. No. 2007/0067924; and U.S. Pat. App. Pub. No. 2007/0249805) and are provided in Table A.
As used herein, “SBP” refers to and is an abbreviation for skin-binding peptide. A SBP is a peptide that binds with high affinity (less than 10 −5 M Kd) to human or mammalian skin. Examples of skin binding peptides are provided in Table A and have been reported in U.S. patent application Ser. No. 11/069858 to Buseman-Williams; Int'l App. Pub. No. WO 2004/000257 to Rothe et. al.; and U.S. Pat. App. Pub. No. 2007/0249805.
As used herein, “NBP” refers to and is an abbreviation for nail-binding peptide. A NBP is a peptide that binds with high affinity (less than 10 −5 M Kd) to human. Examples of nail binding peptides are provided in Table A and have been reported in U.S. Pat. App. Pub. No. 2007/0249805.
As used herein, “TBP” refers to and is an abbreviation for teeth-binding peptide. A TBP is a peptide that binds with high affinity (less than 10 −5 M Kd) to mammalian or human tooth enamel or tooth pellicle, which is a glycoprotein naturally found on the surface of mammalian teeth. Examples of teeth-binding peptides are provided in Table A and have been reported in U.S. patent application Ser. No. 11/877,692.
As used herein, an “antimicrobial peptide” refers to a peptide having the ability to kill microbial cell populations. See U.S. Pat. App. Pub. No. 2007/0249805.
As used herein, the term “inclusion body tag”, abbreviated as “IBT” and refers to a polypeptide that facilitates formation of inclusion bodies when fused to a peptide of interest. The peptide of interest is typically soluble within the host cell and/or host cell lysate when not fused to an inclusion body tag. Fusion of the peptide of interest to the inclusion body tag produces a fusion protein that agglomerates into intracellular bodies, also called inclusion bodies, within the host cell. The fusion protein comprises a portion having an inclusion body tag and a peptide/protein of interest. The polypeptide/protein of interest may be separated from the inclusion body tags using cleavable peptide linker elements. See U.S. patent application Ser. Nos. 11/641936, 11/641273, and 11/782836.
As used herein, “cleavable linker elements”, “peptide linkers”, and “cleavable peptide linkers” are used interchangeably and refer to cleavable peptide segments typically found between inclusion body tags and the peptide of interest. After the inclusion bodies are separated and/or partially-purified or purified from the cell lysate, the cleavable linker elements can be cleaved chemically and/or enzymatically to separate the inclusion body tag from the peptide of interest. The fusion peptide may also include a plurality of regions encoding one or more peptides of interest separated by one or more cleavable peptide linkers. The peptide of interest can then be isolated from the inclusion body tag, if necessary.
The inclusion body tag(s) and the peptide of interest may exhibit different solubilities in a defined medium, typically aqueous, thereby facilitating separation of the inclusion body tag from the peptide of interest. Preferably, the inclusion body tag is insoluble in an aqueous solution while the protein/polypeptide of interest is appreciably soluble in an aqueous solution. The pH, temperature, and/or ionic strength of the aqueous solution can be adjusted to facilitate recovery of the peptide of interest. In a preferred embodiment, the differential solubility between the inclusion body tag and the peptide of interest occurs in an aqueous solution having a pH of 5 to 10 and a temperature range of 15° C. to 50° C. The cleavable peptide linker may be from 1 to about 50 amino acids, preferably from 1 to about 20 amino acids in length. An example of an enzymatically cleavable peptide linker is provided by SEQ ID NO: 270 (Caspase-3 cleavage sequence). In a preferred embodiment, the cleavable linker is an acid cleavable aspartic acid—proline dipeptide (D-P) moiety. The cleavable peptide linkers may be incorporated into the fusion proteins using any number of techniques well known in the art.
As used herein, the term “operably linked” refers to the association of two or more nucleic acid molecules having known function on a single nucleic acid fragment so that the function of one is affected by the presence of the other. For example, a promoter is operably linked with a coding sequence when it is capable of affecting the expression of that coding sequence, that is when the coding sequence is under the transcriptional control of the promoter. “Operably linked” may include the association of the present promoter sequence with well characterized upstream (5′) regulatory elements associated with AraC-based transcription control of the L-arabinose operon/expression system. A non-limiting example would be operably linking the present promoter sequence of SEQ ID NO: 2 downstream of a DNA region associated with AraC transcription factor binding and regulatory control (for example, SEQ ID NO: 33 comprising the O 2 region (SEQ ID NO: 30) and all and/or portions of the CRP receptor protein binding site (SEQ ID NO: 31) and portion of the I 1 /I 2 region (SEQ ID NO: 32) not encompassed by the 5′ region of the present araB promoter as defined by SEQ ID NO: 2). Chimeric genes may be provided by operably linking (in a 5′ to 3′ direction) a nucleic acid molecule encoding the AraC transcription factor binding region to the present araB promoter which is further operably linked to a coding region of interest. Such a chimeric gene may further comprise a transcription terminator sequence operably linked to the 3′ end of the coding region of interest. The transcription terminator sequence may be the rrnB T1 and T2 terminator provided by SEQ ID NO: 28.
“Operably linked” may also refer to the products of chimeric genes, such as fusion proteins. As such, “operably linked” refers to the linking of an inclusion body tag to a peptide of interest to be produced and recovered. The inclusion body tag is “operably linked” to the peptide of interest if upon expression the fusion protein is insoluble and accumulates in inclusion bodies in the expressing host cell.
As used herein, the terms “fusion protein”, “fusion peptide”, “chimeric protein”, and “chimeric peptide” are interchangeable and refer to a polymer of amino acids (peptide, oligopeptide, polypeptide, or protein) comprising at least two portions, each portion comprising a distinct function. A first portion of the fusion peptide may comprise at least one inclusion body tag and a second portion of the fusion peptide may comprise at least one peptide of interest. The fusion protein may additionally include at least one cleavable peptide linker that facilitates chemical and/or enzymatic cleavage and separation of the inclusion body tag(s) and the peptide(s) of interest.
Means to prepare the present promoters are well known in the art as disclosed in Stewart et al., Solid Phase Peptide Synthesis, Pierce Chemical Co., Rockford, Ill., 1984; Bodanszky, Principles of Peptide Synthesis, Springer-Verlag, New York, 1984; and Pennington et al., Peptide Synthesis Protocols, Humana Press, Totowa, N.J., 1994. Preferably, the present promoters and the corresponding chimeric genes, expression cassettes, and vectors may be prepared using recombinant DNA and molecular cloning techniques.
As used herein, the terms “polypeptide” and “peptide” are interchangeable and refer to a polymer of two or more amino acids joined together by a peptide bond, wherein the peptide is of unspecified length, thus, peptides, oligopeptides, polypeptides, and proteins are included within the present definition. This term also includes post expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. Also included are peptides containing one or more analogues of an amino acid or labeled amino acids and peptidomimetics.
As used herein, the terms “protein of interest”, “polypeptide of interest”, “peptide of interest”, “targeted protein”, “target gene product”, “target coding region gene product” “targeted polypeptide”, “targeted peptide”, “expressible protein”, and “expressible polypeptide” are interchangeable and refer to a bioactive protein, polypeptide, or peptide that is targeted for expression using the present araB promoter system.
As used herein, the terms “bioactive” or “peptide of interest activity” refer to the activity or characteristic associated with the peptide and/or protein of interest. The bioactive peptides may be used as, for example, curative agents for diseases (e.g., insulin, interferon, interleukins, anti-angiogenic peptides (U.S. Pat. No. 6,815,426); polypeptides that bind to defined cellular targets such as receptors, channels, lipids, cytosolic proteins, and membrane proteins; peptides having antimicrobial activity; peptides having an affinity for a particular material (e.g., hair-binding polypeptides, skin-binding polypeptides, nail-binding polypeptides, cellulose-binding polypeptides, polymer-binding polypeptides, clay-binding polypeptides, silica-binding polypeptides, carbon nanotube-binding polypeptides and peptides that have an affinity for particular animal or plant tissues) for targeted delivery of benefit agents.
As used herein, the term “benefit agent” refers to a molecule that imparts a desired functionality to the complex for a defined application. The benefit agent may be the peptide of interest itself or may be one or more molecules bound to, either covalently or non-covalently, or associated with, the peptide of interest wherein the binding affinity of the targeted polypeptide is used to selectively target the benefit agent to the targeted material. The targeted polypeptide comprises at least one region having an affinity for at least one target material (e.g., biological molecules, polymers, hair, skin, nail, other peptides, etc.) and at least one region having an affinity for the benefit agent (e.g., pharmaceutical agents, pigments, conditioners, dyes, fragrances, etc.). Examples of benefits agents may include, but are not limited to, conditioners for personal care products, pigments, dye, fragrances, pharmaceutical agents (e.g., targeted delivery of cancer treatment agents), diagnostic/labeling agents, ultraviolet light blocking agents (i.e., active agents in sunscreen protectants), and antimicrobial agents (e.g., antimicrobial peptides).
As used herein, the term “inclusion body” refers to an intracellular amorphous deposit comprising aggregated protein found in the cytoplasm of a cell. Small peptides are typically soluble with the host cell and/or cell lysates can be fused to one or more inclusion body tags to facilitate formation of an insoluble fusion protein. In an alternative embodiment, the peptide may be partially insoluble in the host cell, but produced at relatively lows levels where significant inclusion body formation does not occur. As such, the formation of inclusion bodies will enhance peptide yield.
“Codon degeneracy” refers to the nature in the genetic code permitting variation of the nucleotide sequence without affecting the amino acid sequence of an encoded polypeptide. Accordingly, the instant invention relates to any nucleic acid fragment that encodes the present amino acid sequences. The skilled artisan is well aware of the “codon-bias” exhibited by a specific host cell in usage of nucleotide codons to specify a given amino acid. Therefore, when synthesizing a gene for improved expression in a host cell, it is desirable to design the gene such that its frequency of codon usage approaches the frequency of preferred codon usage of the host cell.
The term “amino acid” refers to the basic chemical structural unit of a protein or polypeptide. The following abbreviations are used herein to identify specific amino acids:













Three-Letter
One-Letter


Amino Acid
Abbreviation
Abbreviation





Alanine
Ala
A


Arginine
Arg
R


Asparagine
Asn
N


Aspartic acid
Asp
D


Cysteine
Cys
C


Glutamine
Gln
Q


Glutamic acid
Glu
E


Glycine
Gly
G


Histidine
His
H


Isoleucine
Ile
I


Leucine
Leu
L


Lysine
Lys
K


Methionine
Met
M


Phenylalanine
Phe
F


Proline
Pro
P


Serine
Ser
S


Threonine
Thr
T


Tryptophan
Trp
W


Tyrosine
Tyr
Y


Valine
Val
V


Miscellaneous (or as defined in
Xaa
X


the present application)







































As used herein, the term “gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ sequences) and following (3′ sequences) the coding sequence. “Native gene” refers to a gene as found in nature with its own regulatory sequences “Chimeric gene” refers to any gene that is not a native gene, comprising regulatory and coding sequences that are not found together in nature. Accordingly, a chimeric gene may comprise regulatory sequences and coding sequences that are derived from different sources, or regulatory sequences and coding sequences derived from the same source, but arranged in a manner different than that found in nature. The term “foreign” gene refers to a gene not normally found in the host organism, but that is introduced into the host organism by gene transfer. Foreign genes can comprise native genes inserted into a non-native organism, or chimeric genes.
As used herein, the term “coding sequence” refers to a DNA sequence that encodes for a specific amino acid sequence. “Suitable regulatory sequences” refer to nucleotide sequences located upstream (5′ sequences), within, or downstream (3′ sequences) of a coding sequence, and which influence the transcription, RNA processing or stability, or translation of the associated coding sequence. Regulatory sequences may include promoters, promoter systems (i.e., the promoter region and additional transcription factor binding sites upstream of the promoter required for inducible, controlled expression), enhancers, ribosomal binding sites, translation leader sequences, introns, polyadenylation recognition sequences, RNA processing site, effector binding sites, and stem-loop structures. One of skill in the art recognizes that selection of suitable regulatory sequences will depend upon host cell and/or expression system used.
As used herein, the term “genetic construct” refers to a series of contiguous nucleic acids useful for modulating the genotype or phenotype of an organism. Non-limiting examples of genetic constructs include but are not limited to a nucleic acid molecule, and open reading frame, a gene, an expression cassette, a vector, a plasmid and the like.
As used herein, the term “transformation” refers to the transfer of a nucleic acid fragment into the genome of a host organism. As used herein, the host cell's genome is comprised of chromosomal and extrachromosomal (e.g., plasmid) genes. Host organisms containing the transformed nucleic acid fragments are referred to as “transgenic” or “recombinant” or “transformed” organisms.
As used herein, the term “host cell” refers to cell which has been transformed or transfected, or is capable of transformation or transfection by an exogenous polynucleotide sequence.
As used herein, the terms “plasmid” or “vector” refer to an extrachromosomal element often carrying genes which are not part of the central metabolism of the cell, and usually in the form of circular double-stranded DNA molecules. Such elements may be autonomously replicating sequences, genome integrating sequences, phage or nucleotide sequences, linear or circular, of a single- or double-stranded DNA or RNA, derived from any source, in which a number of nucleotide sequences have been joined or recombined into a unique construction which is capable of introducing a promoter fragment and DNA sequence for a selected gene product along with appropriate 3′ untranslated sequence into a cell. “Expression cassette” refers to a specific vector containing a foreign gene and having elements in addition to the foreign gene that allow for enhanced expression of that gene in a foreign host.
Standard recombinant DNA and molecular cloning techniques used herein are well known in the art and are described by Sambrook, J., and Russell, D., Molecular Cloning: A Laboratory Manual, Third Edition, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, N.Y. (2001) (hereinafter “Sambrook”); and by Silhavy, T. J., Bennan, M. L. and Enquist, L. W., Experiments with Gene Fusions, Cold Spring Harbor Laboratory Cold Press Spring Harbor, N.Y. (1984); and by Ausubel, F. M. et al., Current Protocols in Molecular Biology, published by Greene Publishing Assoc. and Wiley-Interscience ( 1987).
araB Operon and L-arabinose Inducible Expression Systems
The endogenous L-arabinose operon has been studied in various microorganisms including, but not limited to Escherichia coli, Salmonella typhimurium, and Bacillus subtilis ((Horwitiz et al., Gene (1981) 14:309-319; Lin et al., Gene (1985) 34:111-122; Lin et al. Gene (1985) 34:123-128; Lin et al., Gene (1985) 34: 129-134); Schleif, R. Trends in Genet. (2000) 16:559-565; U.S. Pat. No. 5,028,530; and U.S. Pat. No. 6,030,807). The operon is comprised of 3 structural genes (araA, araB, and araD) encoding enzymes responsible for converting L-arabinose to D-xylose-5-phosphate. The gene araA encodes the enzyme arabinose isomerase, responsible for converting arabinose to ribulose. Ribulokinase (encoded by the gene araB) phosphorylates ribulose to make ribulose-5-phosphate. The enzyme ribulose-5-phosphate epimerase (encoded by the gene araD) converts ribulose-5-phosphate to xylulose-5-phosphate, which can be metabolized via the pentose phosphate pathway. The araBAD operon is coordinately controlled by the inducer L-arabinose and the AraC regulatory gene product (Guzman et al., (1995) J. Bacteriol. 177:4121-4130). P BAD -based expression systems developed from a wild type araBAD operon (i.e. pBAD expression vectors) are widely used and commercially available from companies such as Invitrogen (Carlsbad, Calif.).
The regulatory control elements and the underlying control mechanism of P BAD -based expression systems have been extensively studied (Schleif, R., 2000, supra). The araC gene product (AraC) is a transcription factor that, as a homodimer, acts to both positively and negatively influence transcription of the araB promoter. In the absence of L-arabinose, the AraC dimer binds to the O 2 and I 1 binding sites, forming a DNA loop that inhibits transcription. The I 1 half site overlaps with the −35 region of the wild type araB promoter.
In the presence of an effective concentration of L-arabinose, the AraC acts to stimulate transcription. Upon binding to L-arabinose, the AraC dimer releases its association with the O 2 binding site, forming an association with the I 1 /I 2 half sites, that is the I 1 /I 2 region that partially overlaps with the −35 region of the present promoter sequence. Release of the DNA loop and subsequent association of the AraC dimer with the I 1 /I 2 region stimulates transcription.
The sensitivity of the araB operon is also influenced by the level of cyclic AMP in the cell, which in turn influences the level of cAMP receptor protein (CRP, also referred to as “CAP”). A cyclic AMP receptor protein binding site (CRP binding site) is upstream of, and partially overlaps with, the I 1 /I 2 region. In the presence of glucose, catabolic repression of the araB expression system is observed. Conversely, increased levels of cAMP promote binding of CRP to the CRP binding site. Binding of CRP to the CRP binding site in combination with L-arabinose induction is required for maximum transcription activity.
The araB promoter region described herein generally spans a portion of the araB expression system that encompasses a region starting immediately upstream and adjacent to the start codon of the coding region targeted for expression through the −35 region (encoding a portion of the I 1 /I 2 half sites). One of skill in the art can operably link the present mutant araB promoter sequence (SEQ ID NO: 2) to a nucleic acid molecule comprising the upstream AraC transcription factor binding sites, e.g., O 2 as well as other regulatory elements associated with L-arabinose induction. The upstream region encompassing the AraC transcription factor binding site(s) may include at least one O 2 site (SEQ ID NO: 29), at least one O 1 site (SEQ ID NO: 30), at least one CRP binding site (SEQ ID NO: 31), and the remaining portion of the I 1 /I 2 region not included in the 5′ end of the araB promoter sequence (SEQ ID NO: 2), where each of the elements are appropriately spaced to facilitate effective AraC regulated L-arabinose induction. Preferably, the upstream AraC transcription factor binding region comprises SEQ ID NO: 33.
The mutant araB promoter region may have the consensus sequence provided by SEQ ID NO: 2. The mutant araB promoter region may comprise a nucleic acid molecule having a sequence selected from the group consisting of SEQ ID NOs: 17, 22, 23, 24, and 25.
The mutant araB promoter region described herein may be operably linked to an upstream (5′ to the present mutant araB promoter sequence; SEQ ID NO: 2) AraC transcription factor binding region. Or, in an L-arabinose inducible expression system, the araB promoter system, may comprise an AraC transcription factor binding region operably linked to the present araB promoter sequence. Preferably, the araB promoter system comprises the AraC transcription factor binding region of SEQ ID NO: 33 operably linked to SEQ ID NO: 2. The araB promoter system comprising the present araB promoter is provided by SEQ ID NO: 34. In addition, the present araB promoter system may comprise a nucleic acid molecule having a nucleic acid sequence selected from the group consisting of SEQ ID NOs: 34, 35, 36, 37, 38, and 39.
The present araB promoter can be used to construct chimeric genes, expression cassettes, and expression vectors as well as host cells comprising such constructs. For example, a chimeric expression cassette may be provided comprising
i) a nucleic acid molecule encoding an L-arabinose inducible expression system, said L-arabinose inducible expression system comprising an AraC transcription factor binding region operably linked to the an araB promoter having a nucleic acid sequence of SEQ ID NO: 2;
ii) a coding region of interest operably linked to the nucleic acid molecule of (i).
In addition, a vector comprising the chimeric expression cassette may be provided. In such a vector, it is preferred that an expressible copy of the araC gene be included.
Microbial host cells comprising the present vectors are also provided. Examples of host strains include, but are not limited to bacterial species such as Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. The preferred host cells may be bacterial host cells, such as an Enterobacteriaceae or selected from the genera consisting of Escherichia, Salmonella, and Bacillus. Preferably, the host strain is Escherichia coli.
The microbial cell comprising the present araB promoter expression system requires an effective amount of intracellular AraC protein to act as a transcriptional regulator. A microbial host cell comprising an effective amount of AraC will be referred to an “AraC+” microbial host cell. The AraC protein can be provided by an expressible copy of araC anywhere within the transformed microbial host cell. Preferably, the transformed microbial host cell comprises an expressible copy of the araC gene on a vector and more preferably, the expressible copy of the araC gene in located on the same vector as the present araB promoter expression system. The present vector preferably comprises an araC gene comprising an O 1 region (SEQ ID NO: 30; a binding site for AraC that represses transcription of the araC promoter (Pc) (Schleif, R., supra). In addition, the araC gene may be located on the same expression vector and transcribed in opposite orientation relative to the araB promoter expression system ( FIG. 1 ).
Expressible Peptides of Interest
As used herein, the terms “expressible peptides of interest”, “expressible protein of interest”, and “target gene product” refer to the desired peptide/protein product encoded by the coding region of interest. The target gene product may optionally include a small N-terminal addition (e.g. 22 amino acids) encoded by a promoter region providing an additional start codon so long as the activity/function of the gene product is not adversely affected. Alternatively, the target gene product need not include a small N-terminal addition, that is, the promoter region does not include a start codon 5′). The target gene product may include any peptide/protein product including, but not limited to peptides, polypeptides, proteins, fusion peptides/proteins, and enzymes. The target gene product may be a fusion peptide comprising at least one inclusion body tag and at least one target surface-binding peptide.
Body Surface-Binding Peptides
The target surface-binding peptide may be a body surface-binding peptide (See Table A). As defined herein, body surface-binding peptides refer to peptide sequences that specifically bind with high affinity to a specific body surface including, but not limited to hair, nails, skin, and the tissues of the oral cavity (gums, teeth, etc.), for example, the body surface-binding peptides may be selected from the group consisting of hair-binding peptides, skin-binding peptides, nail-binding peptides, and teeth-binding peptides.
Phage display has been used to identify various body surface-binding peptides. For example, peptides having an affinity for a body surface have been described in (U.S. Pat. Nos. 7,220,405 and 7,285,264; U.S. Pat. App. Pub. Nos. 2005/0226839, 2005/0249682, 2007/0065387, 2007/0067924, 2007/0196305, 2007/0110686, 2006/0073111, and 2006/0199206; U.S. patent application Ser. No.11/877,692; U.S. patent applicaiton Pub. Ser. No. 11/939583; and Int'l Pat. App. Pub. No. WO2004048399)
Examples of various body surface-binding peptides are provided in Table A.





TABLE A



Examples of Body Surface-Binding Peptides







Body

SEQ



Surface
Amino Acid Sequence
ID NO:
Reference



Hair
RVPNKTVTVDGA
46
US 2005/0226839





US 7,220,405



Hair
DRHKSKYSSTKS
47
US 2005/0226839




US 7,220,405



Hair
KNFPQQKEFPLS
48
US 2005/0226839




US 7,220,405



Hair
QRNSPPAMSRRD
49
US 2005/0226839




US 7,220,405



Hair
TRKPNMPHGQYL
50
US 2005/0226839




US 7,220,405



Hair
KPPHLAKLPFTT
51
US 2005/0226839




US 7,220,405



Hair
NKRPPTSHRIHA
52
US 2005/0226839




US 7,220,405



Hair
NLPRYQPPCKPL
53
US 2005/0226839




US 7,220,405



Hair
RPPWKKPIPPSE
54
US 2005/0226839




US 7,220,405



Hair
RQRPKDHFFSRP
55
US 2005/0226839




US 7,220,405



Hair
SVPNKXVTVDGX
56
US 2005/0226839




US 7,220,405



Hair
TTKWRHRAPVSP
57
US 2005/0226839




US 7,220,405



Hair
WLGKNRIKPRAS
58
US 2005/0226839




US 7,220,405



Hair
SNFKTPLPLTQS
59
US 2005/0226839




US 7,220,405



Hair
SVSVGMKPSPRP
60
US 2005/0226839




US 7,220,405



Hair
DLHTVYH
61
US 2005/0226839




U5 7,220,405



Hair
HIKPPTR
62
US 2005/0226839




U5 7,220,405



Hair
HPVWPAI
63
US 2005/0226839




US 7,220,405



Hair
MPLYYLQ
64
US 2005/0226839




US 7,220,405



Hair
HLTVPWRGGGSAVPFYSHSQI
65
US 2005/0226839


TLPNH

US 7,220,405



Hair
GPHDTSSGGVRPNLHHTSKKE
66
US 2005/0226839


KRENRKVPFYSHSVTSRGNV

US 7,220,405



Hair
KHPTYRQ
67
US 2005/0226839




US 7,220,405



Hair
HPMSAPR
68
US 2005/0226839




US 7,220,405



Hair
MPKYYLQ
69
US 2005/0226839




US 7,220,405



Hair
MHAHSIA
70
US 2005/0226839




US 7,220,405



Hair
AKPISQHLQRGS
71
US 2005/0226839




US 7,220,405



Hair
APPTPAAASATT
72
US 2005/0226839




US 7,220,405



Hair
DPTEGARRTIMT
73
US 2005/0226839




US 7,220,405



Hair
LDTSFPPVPFHA
74
US 2005/0226839




US 7,220,405



Hair
LDTSFHQVPFHQ
75
US 2005/0226839




US 7,220,405



Hair
LPRIANTWSPS
76
US 2005/0226839




US 7,220,405



Hair
RTNAADHPAAVT
77
US 2005/0226839




US 7,220,405




US 2007/0065387



Hair
SLNWVTIPGPKI
78
US 2005/0226839




US 7,220,405



Hair
TDMQAPTKSYSN
79
US 2005/0226839




US 7,220,405



Hair
TIMTKSPSLSCG
80
US 2005/0226839




US 7,220,405



Hair
TPALDGLRQPLR
81
US 2005/0226839




US 7,220,405



Hair
TYPASRLPLLAP
82
US 2005/0226839




U5 7,220,405



Hair
AKTHKHPAPSYS
83
US 2005/0226839




U5 7,220,405



Hair
TDPTPFSISPER
84
US 2005/0226839




US 7,220,405



Hair
SQNWQDSTSYSN
85
US 2005/0226839




US 7,220,405



Hair
WHDKPQNSSKST
86
US 2005/0226839




US 7,220,405



Hair
LDVESYKGTSMP
87
US 2005/0226839




US 7,220,405



Hair
NTPKENW
88
WO2004048399



Hair
NTPASNR
89
WO2004048399



Hair
PRGMLST
90
WO2004048399



Hair
PPTYLST
91
WO2004048399



Hair
TIPTHRQHDYRS
92
WO2004048399



Hair
TPPTHRL
93
WO2004048399



Hair
LPTMSTP
94
WO2004048399



Hair
LGTNSTP
95
WO2004048399



Hair
TPLTGSTNLLSS
96
WO2004048399



Hair
TPLTKET
97
WO2004048399



Hair
KQSHNPP
98
WO2004048399



Hair
QQSHNPP
99
WO2004048399



Hair
TQPHNPP
100
WO2004048399



Hair
STNLLRTSTVHP
101
WO2004048399



Hair
HTQPSYSSTNLF
102
WO2004048399



Hair
SLLSSHA
103
WO2004048399



Hair
QQSSISLSSHAV
104
WO2004048399



Hair
NASPSSL
105
WO2004048399



Hair
HSPSSLR
106
WO2004048399



Hair
K H/R/N SHHTH
107
WO2004048399



Hair
E H/R/N SHHTH
108
WO2004048399



Hair
SHHTHYGQPGPV
109
WO2004048399



Hair
LESTSLL
110
WO2004048399



Hair
DLTLPFH
111
US 2007/0065387



Hair
RTNAADHP
112
US 2007/0067924



Hair
IPWWNIRAPLNA
113
US 2007/0067924



Hair
EQISGSLVAAPWEGEGER
114
US 11/877,692



Hair
PKRGRHKRPKRHKGGGTPPE
115
US 11/877,692


LLHGAPRSC



Hair
LDTSFHQVPFHQKRKRKD
116
US 11/877,692



Hair
EQISGSLVAAPWKRKRKD
117
US 11/877,692



Hair
TPPELLHGDPRSKRKRKD
118
US 11/877,692



Hair
NTSQLSTEGEGED
119
US 11/877,692



Hair
TPPELLHGDPRSC
120
US 2007/0067924



Hair
HINKTNPHQGNHHSEKTQRQ
121
US 11/939583



Hair
HAHKNQKETHQRHAA
122
US 11/939583



Hair
HEHKNQKETHQRHAA
123
US 11/939583




US 7,285,264



Hair
HNHMQERYTEPQHSPSVNGL
124
US 11/939583



Hair
THSTHNHGSPRHTNADA
125
US 2007/0196305



Hair
GSCVDTHKADSCVANNGPAT
126
US 11/939583



Hair
AQSQLPDKHSGLHERAPQRY
127
US 11/939583



Hair
AQSQLPAKHSGLHERAPQRY
128
US 11/939583



Hair
AQSQLPEKHSGLHERAPQRY
129
US 11/939583



Hair
TDMMHNHSDNSPPHRRSPRN
130
US 11/939583



Hair
TPPELAHTPHHLAQTRLTDR
131
US 11/939583



Hair
RLLRLLRLLRLL
132
US 11/939583



Hair
TPPELLHGEPRS
133
US 11/939583



Hair
TPPELLHGAPRS
134
US 7,285,264



Hair
EQISGSLVAAPW
135
US 2005/0226839

(normal


US 7,220,405

and

bleached)



Hair
NEVPARNAPWLV
136
US 2005/0226839

(bleached)


US 7,220,405



Hair
NSPGYQADSVAIG
137
US 2005/0226839

(bleached)


US 7,220,405



Hair
AKPISQHLQRGS
138
US 2005-0226839

(bleached)


US 7,220,405



Hair
LDTSFPPVPFHA
139
US 2005/0226839

(bleached)


US 7,220,405



Hair
SLNWVTIPGPKI
140
US 2005/0226839

(bleached)


US 7,220,405



Hair
TQDSAQKSPSPL
141
US 2005/0226839

(bleached)


US 7,220,405



Hair
KELQTRNVVQRE
142
US 2005/0226839

(bleached)


US 7,220,405



Hair
QRNSPPAMSRRD
143
US 2005/0226839

(bleached)


US 7,220,405



Hair
TPTANQFTQSVP
144
US 2005/0226839

(bleached)


US 7,220,405



Hair
AAGLSQKHERNR
145
US 2005/0226839

(bleached)


US 7,220,405



Hair
ETVHQTPLSDRP
146
US 2005/0226839

(bleached)


US 7,220,405



Hair
KNFPQQKEFPLS
147
US 2005/0226839

(bleached)


US 7,220,405



Hair
LPALHIQRHPRM
148
US 2005/0226839

(bleached)


US 7,220,405



Hair
QPSHSQSHNLRS
149
US 2005/0226839

(bleached)


US 7,220,405



Hair
RGSQKSKPPRPP
150
US 2005/0226839

(bleached)


US 7,220,405



Hair
THTQKTPLLYYH
151
US 2005/0226839

(bleached)


US 7,220,405



Hair
TKGSSQAILKST
152
US 2005/0226839

(bleached)


US 7,220,405



Hair
TAATTSP
153
US 2005/0226839

(normal


US 7,220,405

and

bleached)



Hair
LGIPQNL
154
US 2005/0226839

(bleached)


US 7,220,405



Hair
THSTHNHGSPRHTNADAGNP
155
US 2007/006S387

(Conditioner


US 2007/01 96305

resistant)



Hair
QQHKVHHQNPDRSTQDAHHS
156
US 2007/0196305

(Conditioner

resistant)



Hair
HHGTHHNATKQKNHV
157
US 2007/0196305

(Conditioner

resistant)



Hair
STLHKYKSQDPTPHH
158
US 2007/0196305

(Conditioner

resistant)



Hair
SVSVGMKPSPRP
159
US 2007/0196305

(Conditioner

resistant)



Hair
TPPTNVLMLATK
160
US 2006/0073111

(shampoo

resistant)



Hair
TPPELLHGDPRS
161
US 2006/0073111

(shampoo

resistant)



Hair
NTSQLST
162
US 2007/0067924

(shampoo


US 7,285,264

resistant)



Hair
STLHKYKSQDPTPHH
163
US 2007/0196305

(conditioner

resistant)



Hair
GMPAMHWIHPFA
164
US 2006/0073111

(shampoo


US 7,285,264

and

conditioner

resistant)



Hair
HDHKNQKETHQRHAA
165
US 2006/0073111

(shampoo


US 7,285,264

and

conditioner

resistant)



Hair
HNHMQERYTDPQHSPSVNGL
166
US 2006/0073111

(shampoo


US 7,285,264

and

conditioner

resistant)



Hair
TAEIQSSKNPNPHPQRSWTN
167
US 2006/0073111

(shampoo


US 7,285,264

and

conditioner

resistant)



Hair
P-NTSQLST (hair-binding
168
US 11/939583

(multiple
peptide)-GGG (spacer)-

binding
RTNAADHPKC (hair-binding

domains)
peptide)-GGG (spacer)-


NTSQLST (hair-binding


peptide)-GGG (spacer)-


RTNAADHPKC (hair-binding


peptide)-GGG (spacer)-


NTSQLST (hair-binding


peptide)-GGG (spacer)-


RTNAADHPKC (hair-binding


peptide)



Hair
P-RTNAADHPAAVT (hair-
169
US 11/939583

(multiple
binding peptide)-GGGCGGG

binding
(spacer)-RTNAADHPAAVT

domains)
(hair-binding peptide)-


GGGCGGG (spacer)-


RTNAADHPAAVT (hair-binding


peptide)-GGGC (spacer)



Hair
P-RTNAADHPAAVT (hair-
170
US 11/939583

(multiple
binding peptide)-GGGCGGG

binding
(spacer)-IPWWNIRAPLNA (hair-

domains)
binding peptide)-GGGCGGG


(spacer)-DLTLPFH (hair-binding


peptide)-GGGC (spacer)



Hair
P-RTNAADHP (hair-binding
171
US 11/939583

(multiple
peptide)-GGG (spacer)-

binding
TPPELLHGDPRSKC (hair-

domains)
binding peptide)-GGG (spacer)-


RTNAADHP (hair-binding


peptide)-GGG (spacer)-


TPPELLHGDPRSKC (hair-


binding peptide)-GGG (spacer)-


RTNAADHP (hair-binding


peptide)-GGG (spacer)-


TPPELLHGDPRSKC (hair-


binding peptide)



Hair
P-TPPTNVLMLATK (hair-
172
US 11/939583

(multiple
binding peptide)-GGG (spacer)-

binding
RTNAADHPKC (hair-binding

domains)
peptide)-GGG (spacer)-


TPPTNVLMLATK (hair-binding


peptide)-GGG (spacer)-


RTNAADHPKC (hair-binding


peptide)-GGG (spacer)-


TPPTNVLMLATK (hair-binding


peptide)-GGG (spacer)-


RTNAADHPKC (hair-binding


peptide)



Hair
P-RTNAADHP (hair-binding
173
US 11/939583

(multiple
peptide)-GGG (spacer)

binding
TPPTNVLMLATKKC (hair-

domains)
binding peptide)-GGG (spacer)-


RTNAADHP (hair-binding


peptide)-GGG (spacer)-


TPPTNVLMLATKKC (hair-


binding peptide) GGG (spacer)-


RTNAADHP (hair-binding


peptide)-GGG (spacer)-


TPPTNVLMLATKKC (hair-


binding peptide)



Hair
PG (Spacer)-IPWWNIRAPLNA
174
US 11/939583

(multiple
(hair-binding peptide)- GAG

binding
(spacer)-

domains)
IPWWNIRAPLNA (hair-binding


peptide)-


GGSGPGSGG (spacer)-


NTSQLST (hair-binding peptide)-


GGG (spacer)-


NTSQLST (hair-binding peptide)-


GGPKK (spacer)



Hair and
KRGRHKRPKRHK
175
US 2007/0065387

skin


US 2007/0110686

(Empirical)


US 2007/0067924



Hair and
RLLRLLR
176
US 2007/0065387

skin


US 2007/0110686

(Empirical)



Hair and
HKPRGGRKKALH
177
US 2007/0065387

skin


US 2007/0110686

(Empirical)



Hair and
KPRPPHGKKHRPKHRPKK
178
US 2007/0065387

skin


US 2007/0110686

(Empirical)



Hair and
RGRPKKGHGKRPGHRARK
179
US 2007/0065387

skin


US 2007/0110686

(Empirical)



Skin
TPFHSPENAPGS
180
US 11/877,692




US 2005/0249682



Skin
TPFHSPENAPGSK
181
US 2007/0110686



Skin
TPFHSPENAPGSGGGS
182
US 2007/0110686



Skin
TPFHSPENAPGSGGGSS
182
US 2007/0110686



Skin
TPFHSPENAPGSGGG
184
US 2007/0110686



Skin
FTQSLPR
185
US 11/877,692




US 2005/0249682



Skin
KQATFPPNPTAY
186
US 11/877,692




US 2005/0249682




WO2004048399



Skin
HGHMVSTSQLSI
187
US 11/877,692




US 2005/0249682




WO2004048399



Skin
LSPSRMK
188
US 11/877,692




US 2005/0249682




WO2004048399



Skin
LPIPRMK
189
US 2005/0249682




WO2004048399



Skin
HQRPYLT
190
US 2005/0249682




WO2004048399



Skin
FPPLLRL
191
US 2005/0249682




WO2004048399



SKIN
QATFMYN
192
WO2004048399



SKIN
VLTSQLPNHSM
193
WO2004048399



Skin
HSTAYLT
194
WO2004048399



Skin
APQQRPMKTFNT
195
WO2004048399



Skin
APQQRPMKTVQY
196
WO2004048399



Skin
PPWLDLL
197
WO2004048399



Skin
PPWTFPL
198
WO2004048399



Skin
SVTHLTS
199
WO2004048399



Skin
VITRLTS
200
WO2004048399



Skin
DLKPPLLALSKV
201
WO2004048399



Skin
SHPSGALQEGTF
202
WO2004048399



Skin
FPLTSKPSGACT
203
WO2004048399



Skin
DLKPPLLALSKV
204
WO2004048399



Skin
PLLALHS
205
WO2004048399



Skin
VPISTQI
206
WO2004048399



Skin
YAKQHYPISTFK
207
WO2004048399



Skin
HSTAYLT
208
WO2004048399



Skin
STAYLVAMSAAP
209
WO2004048399



Skin
SVSVGMKPSPRP
210
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
TMGFTAPRFPHY
211
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
NLQHSVGTSPVW
212
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
QLSYHAYPQANHHAP
213
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
NQAASITKRVPY
214
US 2006/0199206

(Body

Wash

Resistant)



Skin
SGCHLVYDNGFCDH
215
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
ASCPSASHADPCAH
216
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
NLCDSARDSPRCKV
217
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
NHSNWKTAADFL
218
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
GSSTVGRPLSYE
219
US 2006/0199206

(Body

Wash

Resistant)



Skin
SDTISRLHVSMT
220
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
SPLTVPYERKLL
221
US 2006/0199206

(Body

Wash

Resistant)



Skin
SPYPSWSTPAGR
222
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
VQPITNTRYEGG
223
US 2006/0199206

(Body

Wash

Resistant)



Skin
WPMHPEKGSRWS
224
US 2006/0199206

(Body

Wash

Resistant)



Skin
DACSGNGHPNNCDR
225
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Skin
DHCLGRQLQPVCYP
226
US 2006/0199206

(Body

Wash

Resistant)



Skin
DWCDTIIPGRTCHG
227
US 11/877,692

(Body


US 2006/0199206

Wash

Resistant)



Fingernail
ALPRIANTWSPS
228
US 2005/0226839




US 7,220,405



Fingernail
YPSFSPTYRPAF
229
US 2005/0226839

and Hair


US 7,220,405



Tooth
AHPESLGIKYALDGNSDPHA
230
US 11/877,692

(pellicle)



Tooth
ASVSNYPPIHHLATSNTTVN
231
US 11/877,692

(pellicle)



Tooth
DECMEPLNAAHCWR
232
US 11/877,692

(pellicle)



Tooth
DECMHGSDVEFCTS
233
US 11/877,692

(pellicle)



Tooth
DLCSMQMMNTGCHY
234
US 11/877,692

(pellicle)



Tooth
DLCSSPSTWGSCIR
235
US 11/877,692

(pellicle)



Tooth
DPNESNYENATTVSQPTRHL
236
US 11/877,692

(pellicle)



Tooth
EPTHPTMRAQMHQSLRSSSP
237
US 11/877,692

(pellicle)



Tooth
GNTDTTPPNAVMEPTVQHKW
238
US 11/877,692

(pellicle)



Tooth
NGPDMVQSVGKHKNS
239
US 11/877,692

(pellicle)



Tooth
NGPEVRQIPANFEKL
240
US 11/877,692

(pellicle)



Tooth
NNTSADNPPETDSKHHLSMS
241
US 11/877,692

(pellicle)



Tooth
NNTWPEGAGHTMPSTNIRQA
242
US 11/877,692

(pellicle)



Tooth
NPTATPHMKDPMHSNAHSSA
243
US 11/877,692

(pellicle)



Tooth
NPTDHIPANSTNSRVSKGNT
244
US 11/877,692

(pellicle)



Tooth
NPTDSTHMMHARNHE
245
US 11/877,692

(pellicle)



Tooth
QHCITERLHPPCTK
246
US 11/877,692

(pellicle)



Tooth
TPCAPASFNPHCSR
247
US 11/877,692

(pellicle)



Tooth
TPCATYPHFSGCRA
248
US 11/877,692

(pellicle)



Tooth
WCTDFCTRSTPTSTSRSTTS
249
US 11/877,692

(pellicle)



Tooth
APPLKTYMQERELTMSQNKD
250
US 11/877,692

(enamel)



Tooth
EPPTRTRVNNHTVTVQAQQH
251
US 11/877,692

(enamel)



Tooth
GYCLRGDEPAVCSG
252
US 11/877,692

(enamel)



Tooth
LSSKDFGVTNTDQRTYDYTT
253
US 11/877,692

(enamel)



Tooth
NFCETQLDLSVCTV
254
US 11/877,692

(enamel)



Tooth
NTCQPTKNATPCSA
255
US 11/877,692

(enamel)



Tooth
PSEPERRDRNIAANAGRFNT
256
US 11/877,692

(enamel)



Tooth
THNMSHFPPSGHPKRTAT
257
US 11/877,692

(enamel)



Tooth
TTCPTMGTYHVCWL
258
US 11/877,692

(enamel)



Tooth
YCADHTPDPANPNKICGYSH
259
US 11/877,692

(enamel)



Tooth
AANPHTEWDRDAFQLAMPPK
260
US 11/877,692

(enamel)



Tooth
DLHPMDPSNKRPDNPSDLHT
261
US 11/877,692

(enamel)



Tooth
ESCVSNALMNQCIY
262
US 11/877,692

(enamel)



Tooth
HNKADSWDPDLPPHAGMSLG
263
US 11/877,692

(enamel)



Tooth
LNDQRKPGPPTMPTHSPAVG
264
US 11/877,692

(enamel)



Tooth
NTCATSPNSYTCSN
265
US 11/877,692

(enamel)



Tooth
SDCTAGLVPPLCAT
266
US 11/877,692

(enamel)



Tooth
TIESSQHSRTHQQNYGSTKT
267
US 11/877,692

(enamel)



Tooth
VGTMKQHPTTTQPPRVSATN
268
US 11/877,692

(enamel)



Tooth
YSETPNDQKPNPHYKVSGTK
269
US 11/877,692

(enamel)
















































































































































































































































































































































































































































































































































































































































































































































































The body surface-binding peptide may be selected from the group consisting of hair-binding peptides, skin-binding peptides, nail-binding peptides, and teeth-binding peptides. The body surface-binding peptide may be selected from the group consisting of hair-binding peptides (SEQ ID NOs: 46-179 and 229), skin-binding peptides (SEQ ID NOs. 175-227), nail-binding peptides (SEQ ID NOs. 228-229), and teeth-binding peptides (SEQ ID NOs. 230-269).
Production of Fusion Peptides Comprising at Least One Inclusion Body Tag
The present araB expression system can be operably linked to any coding region of interest. The resulting chimeric gene is transformed and expressed in an appropriate microbial host cell, typically in the form of an expression vector. Induction with an effective amount of L-arabinose is used to produce the desired gene product.
The desired gene product is a small bioactive peptide of interest that is appreciably soluble in the host cell and/or host cell liquid lysate under normal physiological conditions. The peptides of interest are preferably, generally short (<50 amino acids in length) and difficult to produce in sufficient amounts due to proteolytic degradation. Fusion of the peptide of interest to at least one inclusion body forming tags creates a fusion peptide that is insoluble in the host cell and/or host cell lysate under normal physiological conditions. Production of the peptide of interest is typically increased when expressed and accumulated in the form of an insoluble inclusion body as the peptide is generally more protected from proteolytic degradation. Furthermore, the insoluble fusion protein can be easily separated from the host cell lysate using centrifugation or filtration.
The length of the peptide of interest may vary as long as (1) the peptide is appreciably soluble in the host cell and/or cell lysate, and/or (2) the amount of the targeted peptide produced is significantly increased when expressed in the form of an insoluble fusion peptide/inclusion body; that is, expression in the form of a fusion protein protect the peptide of interest from proteolytic degradation. Typically the peptide of interest is less than 200 amino acids in length, preferably less than 100 amino acids in length, more preferably less than 75 amino acids in length, even more preferably less than 50 amino acids in length, and most preferably less than 25 amino acids in length.
The function of the peptide of interest is not limited by the present method and may include, but is not limited to, bioactive molecules that act as curative agents for diseases, such as insulin, interferon, interleukins, peptide hormones, anti-angiogenic peptides, and peptides that bind to and affect defined cellular targets such as receptors, channels, lipids, cytosolic proteins, and membrane proteins (see U.S. Pat. No. 6,696,089); peptides having an affinity for a particular material, such as biological tissues, biological molecules, hair-binding peptides (see U.S. patent application Ser. No. 11/074473; Int'l Pat. App. No. WO 0179479; U.S. Pat. App. Pub. No. 2002/0098524; U.S. Pat. App. Pub. No. 2003/0152976; Int'l Pat. App. No. WO 04048399; U.S. Pat. App. Pub. No 2007/0067924; and U.S. Pat. App. Pub. No. 2007/0249805), skin-binding peptides (see U.S. Pat. No. 7,309,482; Int'l. Pat. App. No. WO 2004/000257; and U.S. Pat. App. Pub. No. 2007/0249805), nail-binding peptides (see U.S. Pat. App. Pub. No. 2007/0249805), cellulose-binding peptides, polymer-binding peptides (see U.S. Pat. App. Pub. Nos. 2007/0141629, 2007/0264720, 2008/0207872, 2007/0141628, and 2007/0261775), clay-binding peptides, silica-binding peptides, and carbon nanotube binding peptides) for targeted delivery of at least one benefit agent (see U.S. patent application Ser. No. 10/935642; U.S. patent application Ser. No. 11/074473; and U.S. Pat. App. Pub. No. 2007/0249805).
The peptide of interest may comprise at least one body surface-binding peptide selected from the group of hair-binding peptides, skin-binding peptides, nail-binding peptides, antimicrobial peptides, and polymer-binding peptides. The peptide of interest may be selected from the group consisting of a hair-binding peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs 46 to 179 (SEQ ID NOs: 168-174 are examples of hair binding-domains comprising multiple hair-binding peptides coupled together by short spacers), a skin-binding peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 175 to 227, a nail-binding peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs: 228 and 229, and a teeth-binding peptide comprising an amino acid sequence selected from the group consisting of SEQ ID NOs. 230 to 269.
Typically, the fusion peptide should be insoluble in an aqueous matrix at a temperature of 10° C. to 50° C., preferably 10° C. to 40° C. The aqueous matrix typically comprises a pH range of 5 to 12, preferably 6 to 10, and most preferably 6 to 8. The temperature, pH, and/or ionic strength of the aqueous matrix can be adjusted to obtain the desired solubility characteristics of the fusion peptide/inclusion body.
As used herein, the term “benefit agent” refers to a molecule that imparts a desired functionality to a target material, such as hair, skin, etc., (see U.S. patent application Ser. No. 10/935642; U.S. patent application Ser. No. 11/074473; and U.S. patent application Ser. No. 11/696380 for a list of typical benefit agents such as conditioners, pigments/colorants, fragrances, etc.). The benefit agent may be a peptide of interest itself or may be one or more molecules bound to, (covalently or non-covalently, or associated with, the peptide of interest wherein the binding affinity of the peptide of interest is used to selectively target the benefit agent to the targeted material. The peptide of interest may comprise at least one region having an affinity for at least one target material, e.g., biological molecules, polymers, hair, skin, nail, other peptides, etc., and at least one region having an affinity for the benefit agent, e.g., pharmaceutical agents, antimicrobial agents, pigments, conditioners, dyes, fragrances, etc. The peptide of interest may comprise a plurality of regions having an affinity for the target material and a plurality of regions having an affinity for one or more benefit agents. Moreover, the peptide of interest may comprise at least one region having an affinity for a targeted material and a plurality of regions having an affinity for a variety of benefit agents wherein the benefit agents may be the same or different. Examples of benefits agents include, but are not limited to, conditioners for personal care products, pigments, dye, fragrances, pharmaceutical agents (e.g., targeted delivery of cancer treatment agents), diagnostic/labeling agents, ultraviolet light blocking agents (i.e., active agents in sunscreen protectants), and antimicrobial agents (e.g., antimicrobial peptides).
Cleavable Peptide Linkers
The use of cleavable peptide linkers is well known in the art. Fusion peptides comprising at least one inclusion body tag will typically include at least one cleavable sequence separating the inclusion body tag from the peptide of interest. The cleavable sequence facilitates separation of the inclusion body tag(s) from the peptide(s) of interest. The cleavable sequence may be provided by a portion of the inclusion body tag and/or the peptide of interest (e.g., inclusion of an acid cleavable aspartic acid—proline moiety). The cleavable sequence preferably includes in the fusion peptide at least one cleavable peptide linker between the inclusion body tag and the peptide of interest.
Means to cleave the peptide linkers are well known in the art and may include chemical hydrolysis, enzymatic cleavage agents, and combinations thereof. One or more chemically cleavable peptide linkers are included in the fusion construct to facilitate recovery of the peptide of interest from the inclusion body fusion protein. Examples of chemical cleavage reagents include cyanogen bromide, which cleaves methionine residues; N-chloro succinimide, iodobenzoic acid or BNPS-skatole [2-(2-nitrophenylsulfenyl)-3-methylindole], which cleaves tryptophan residues; dilute acids, which cleave at aspartyl-prolyl bonds, and hydroxylamine, which cleaves at asparagine-glycine bonds at pH 9.0. See Gavit, P. and Better, M., J. Biotechnol., 79:127-136 (2000); Szoka et al., DNA, 5(1):11-20 (1986); and Walker, J. M., The Proteomics Protocols Handbook, 2005, Humana Press, Totowa, N.J. One or more aspartic acid—proline acid cleavable recognition sites (i.e., a cleavable peptide linker comprising one or more D-P dipeptide moieties) may preferably be included in the fusion protein construct to facilitate separation of the inclusion body tag(s) form the peptide of interest. The fusion peptide may include multiple regions encoding peptides of interest separated by one or more cleavable peptide linkers.
Moreover, one or more enzymatic cleavage sequences may be included in the fusion protein construct to facilitate recovery of the peptide of interest. Proteolytic enzymes and their respective cleavage site specificities are well known in the art. Preferably, the proteolytic enzyme is selected to specifically cleave only the peptide linker separating the inclusion body tag and the peptide of interest. Examples of enzymes useful for cleaving the peptide linker include, but are not limited to Arg-C proteinase, Asp-N endopeptidase, chymotrypsin, clostripain, enterokinase, Factor Xa, glutamyl endopeptidase, Granzyme B, Achromobacter proteinase I, pepsin, proline endopeptidase, proteinase K, Staphylococcal peptidase I, thermolysin, thrombin, trypsin, and members of the Caspase family of proteolytic enzymes (e.g. Caspases 1 -10) (Walker, J. M., supra). An example of a cleavage site sequence is provided by SEQ ID NO: 270 (Caspase-3 cleavage site; Thornberry et al. J. Biol. Chem., 272:17907-17911 (1997) and Tyas et al., EMBO Reports, 1 (3):266-270 (2000)).
Typically, the cleavage step occurs after the insoluble inclusion bodies and/or insoluble fusion peptides are isolated from the cell lysate. The cells can be lysed using any number of means well known in the art, such as mechanical and/or chemical lysis. Methods to isolate the insoluble inclusion bodies/fusion peptides from the cell lysate are well known in the art, such as, centrifugation, filtration, and combinations thereof. Once recovered from the cell lysate, the insoluble inclusion bodies and/or fusion peptides can be treated with a chemical or enzymatic cleavage agent to cleave the inclusion body tag from the peptide of interest. The fusion protein and/or inclusion body may be diluted and/or dissolved in a suitable solvent prior to treatment with the cleavage agent. Alternatively, the cleavage step may be omitted if the inclusion body tag does not interfere with the activity of the peptide of interest.
After the cleavage step, preferably, the peptide of interest can be separated and/or isolated from the fusion protein and the inclusion body tags based on a differential solubility of the components. Parameters such as pH, salt concentration, and temperature may be adjusted to facilitate separation of the inclusion body tag from the peptide of interest. The peptide of interest may be soluble while the inclusion body tag and/or fusion protein is insoluble in the defined process matrix, typically aqueous. Alternatively, the peptide of interest may be insoluble while the inclusion body tag is soluble in the defined process matrix.
In an optional embodiment, the peptide of interest may be further purified using any number of well known purification techniques in the art such as ion exchange, gel purification techniques, and column chromatography (see U.S. Pat. No. 5,648,244).
Transformation and Expression
Given the mutant araB promoter system described herein and a coding region of interest, one of skill in the art can construct chimeric genes and/or expression vectors suitable for use in an appropriate expression host.
Typically, the vector or cassette contains sequences directing transcription and translation of the relevant chimeric gene, a selectable marker, and sequences allowing autonomous replication or chromosomal integration. As used herein, the present mutant araB promoter (SEQ ID NO: 2) is operably linked to a coding sequence encoding a peptide or protein of interest. The present araB promoter may be used to drive expression chromosomally or extrachromosomally, i.e. in vector based expression. The present arabinose inducible expression system comprising the mutant araB promoter is used to direct expression of a chromosomally-integrated heterologous gene. In addition, the present arabinose inducible expression system comprising the mutant araB promoter may be used to direct expression on an autonomously replicating vector, such as a plasmid). Additional 5′ and 3′ regulatory elements may be included to further aid in transcription initiation and/or transcriptional termination.
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary but is most preferably included. The termination control region comprises the rrnB T 1 and T 2 terminators as provided by SEQ ID NO: 28.
Preferred host cells are microbial hosts that can be found broadly within the fungal or bacterial families and which grow over a wide range of temperature, pH values, and solvent tolerances. It is contemplated that any bacteria, yeast, or filamentous fungi can be suitable hosts for expression of the present nucleic acid molecules encoding the fusion peptides. Transcription, translation, and the protein biosynthetic apparatus are universal genetic processes. Because of this, large-scale microbial growth and functional gene expression may utilize a wide range of simple or complex carbohydrates, organic acids and alcohols, i.e. methanol, saturated hydrocarbons such as methane or carbon dioxide in the case of photosynthetic or chemoautotrophic hosts. However, the functional genes may be regulated, repressed or depressed by specific growth conditions, which may include the form and amount of nitrogen, phosphorous, sulfur, oxygen, carbon or any trace micronutrient including small inorganic ions. In addition, the regulation of functional genes may be achieved by the presence or absence of specific regulatory molecules added to the culture and not typically considered nutrient or energy sources. Growth rate may also be an important regulatory factor in gene expression. Examples of host strains include, but are not limited to bacterial species such as Salmonella, Bacillus, Acinetobacter, Zymomonas, Agrobacterium, Erythrobacter, Chlorobium, Chromatium, Flavobacterium, Cytophaga, Rhodobacter, Rhodococcus, Streptomyces, Brevibacterium, Corynebacteria, Mycobacterium, Deinococcus, Escherichia, Erwinia, Pantoea, Pseudomonas, Sphingomonas, Methylomonas, Methylobacter, Methylococcus, Methylosinus, Methylomicrobium, Methylocystis, Alcaligenes, Synechocystis, Synechococcus, Anabaena, Thiobacillus, Methanobacterium, Klebsiella, and Myxococcus. The preferred host cells may be bacterial host cells, such as an Enterobacteriaceae or selected from the genera consisting of Escherichia, Salmonella, and Bacillus. Preferably, the host strain is Escherichia coli.
Fermentation Media
Fermentation media must contain suitable carbon substrates. Suitable substrates may include, but are not limited to, monosaccharides such as glucose and fructose, oligosaccharides such as lactose or sucrose, polysaccharides such as starch or cellulose or mixtures thereof and unpurified mixtures from renewable feedstocks such as cheese whey permeate, cornsteep liquor, sugar beet molasses, and barley malt. L-arabinose is used to induce the present arabinose inducible expression system. As such, L-arabinose is typically not included in the fermentation media until expression of the desired chimeric gene (encoding the peptide or protein of interest) is desired. L-arabinose can be added at any time during the fermentation, although it is often preferable to induce expression only after a desired cell density/mass is achieved in the fermentor. It is contemplated that the source of carbon utilized in the present invention may encompass a wide variety of carbon containing substrates and will only be limited by the choice of organism. Preferred carbon substrates include glucose, fructose, and sucrose.
In addition to a carbon source, fermentation media may or must contain other components suitable and/or necessary for the growth of the cultures and promotion of the expression of the present fusion peptides. These are known to those skilled in the art and include minerals, salts, cofactors, buffers, etc.
Culture Conditions
Suitable culture conditions can vary and depend on the chosen production host and are generally known in the art. Typically, cells are grown at a temperature in the range of about 25° C. to about 40° C. in an appropriate medium. Suitable growth media in the present invention are common commercially prepared media such as Luria Bertani (LB) broth, Sabouraud Dextrose (SD) broth or Yeast medium (YM) broth. Other defined or synthetic growth media may also be used and the appropriate medium for growth of the particular microorganism will be known by one skilled in the art of microbiology or fermentation science. The use of agents known to modulate catabolite repression directly or indirectly, e.g., cyclic adenosine 2′:3′-monophosphate, may also be incorporated into the fermentation medium.
Suitable pH ranges for the fermentation are typically between pH 5.0 to pH 9.0, where pH 6.0 to pH 8.0 is preferred.
Fermentation may be performed under either aerobic or anaerobic conditions whereas aerobic conditions are generally preferred.
Industrial Batch and Continuous Fermentations
Classical batch fermentation is a closed system where the composition of the medium is set at the beginning of the fermentation and not subject to artificial alterations during the fermentation. Thus, at the beginning of the fermentation the medium is inoculated with the desired organism or organisms, and fermentation is permitted to occur without adding anything to the system. Typically, a “batch” fermentation is batch with respect to the addition of carbon source and attempts are often made at controlling factors such as pH and oxygen concentration. In batch systems the metabolite and biomass compositions of the system change constantly up to the time the fermentation is stopped. Within batch cultures cells moderate through a static lag phase to a high growth log phase and finally to a stationary phase where growth rate is diminished or halted. If untreated, cells in the stationary phase will eventually die. Cells in log phase generally are responsible for the bulk of production of end product or intermediate.
A variation on the standard batch system is the Fed-Batch system. Fed-Batch fermentation processes are also suitable in the present invention and comprise a typical batch system with the exception that the substrate is added in increments as the fermentation progresses. Fed-Batch systems are useful when catabolite repression is apt to inhibit the metabolism of the cells and where it is desirable to have limited amounts of substrate in the media. Measurement of the actual substrate concentration in Fed-Batch systems is difficult and is therefore estimated on the basis of the changes of measurable factors such as pH, dissolved oxygen and the partial pressure of waste gases such as CO 2 . Batch and Fed-Batch fermentations are common and well known in the art and examples may be found in Thomas D. Brock in Biotechnology: A Textbook of Industrial Microbiology, Second Edition (1989) Sinauer Associates, Inc., Sunderland, Mass. (hereinafter “Brock”), or Deshpande, Mukund V., Appl. Biochem. Biotechnol., (1992) 36:227-234.
Although the present invention is performed in batch mode it is contemplated that the method would be adaptable to continuous fermentation methods. Continuous fermentation is an open system where a defined fermentation medium is added continuously to a bioreactor and an equal amount of conditioned media is removed simultaneously for processing.
Continuous fermentation generally maintains the cultures at a constant high density where cells are primarily in log phase growth.
Continuous fermentation allows for the modulation of one factor or any number of factors that affect cell growth or end product concentration. For example, one method will maintain a limiting nutrient such as the carbon source or nitrogen level at a fixed rate and allow all other parameters to moderate. In other systems a number of factors affecting growth can be altered continuously while the cell concentration, measured by media turbidity, is kept constant. Continuous systems strive to maintain steady state growth conditions and thus the cell loss due to the medium being drawn off must be balanced against the cell growth rate in the fermentation. Methods of modulating nutrients and growth factors for continuous fermentation processes as well as techniques for maximizing the rate of product formation are well known in the art of industrial microbiology and a variety of methods are detailed by Brock, supra.
It is contemplated that the present invention may be practiced using either batch, fed-batch or continuous processes and that any known mode of fermentation would be suitable.
One of skill in the art will recognize that typically any amount, concentration, or other value or parameter that is given either as a range, preferred range, or a list of upper preferable values and lower preferable values, is to be understood as specifically disclosing all ranges formed from any pair of any upper range limit or preferred value and any lower range limit or preferred value, regardless of whether ranges are separately disclosed. Where a range of numerical values is recited herein, unless otherwise stated, the range is intended to include the endpoints thereof, and all integers and fractions within the range. It is not intended that the scope of the invention be limited to the specific values recited when defining a range.
EXAMPLES
The present invention is further illustrated by the following Examples, which indicate preferred aspects of the invention. From the above discussion and these Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the spirit and scope thereof, can make various changes and modifications of the invention to adapt it to various uses and conditions.
The meaning of abbreviations used is as follows: “min” means minute(s), “h” means hour(s), “μL” means microliter(s), “mL” means milliliter(s), “L” means liter(s), “nm” means nanometer(s), “mm” means millimeter(s), “cm” means centimeter(s), “μm” means micrometer(s), “mM” means millimolar, “M” means molar, “mmol” means millimole(s), “μmol” means micromole(s), “pmol” means picomole(s), “g” means gram(s), “μg” means microgram(s), “mg” means milligram(s), “g” means the gravitation constant, “rpm” means revolutions per minute, “DTT” means dithiothreitol, “OD 600 ” means optical density at a 600 nm wavelength, “GFP” means green fluorescent protein; “nm” mean nanometer, “amp” means ampicillin; “LB” means Luria-Bertani broth or lysogeny broth; “FACS” means fluorescence activated cell sorter; “RFU” means relative fluorescence units, “wt” means wild type; and “cat#” means catalog number.
General Methods
Standard recombinant DNA and molecular cloning techniques used in the Examples are well known in the art and are described by Sambrook and Russell, (supra); Silhavy et al., (supra); and Ausubel et al., (supra).
Materials and methods suitable for the maintenance and growth of bacterial cultures are also well known in the art. Techniques suitable for use in the following Examples may be found in Manual of Methods for General Bacteriology, Phillipp Gerhardt, R. G. E. Murray, Ralph N. Costilow, Eugene W. Nester, Willis A. Wood, Noel R. Krieg and G. Briggs Phillips, eds., American Society for Microbiology, Washington, DC., 1994, or in Brock (supra). All reagents, restriction enzymes and materials used for the growth and maintenance of bacterial cells were obtained from BD Diagnostic Systems (Sparks, Md.), Invitrogen (Carlsbad, Calif.), Life Technologies (Rockville, Md.), QIAGEN (Valencia, Calif.) or Sigma-Aldrich Chemical Company (St. Louis, Mo.), unless otherwise specified.
Example 1
Construction of Mutant araB Promoter Library
Typically, strong E. coli promoters share significantly more sequence homology with the consensus −35 and −10 regions of the strong E. coli promoters (in Biochemistry, Voet, D. & Voet. J. G., 1990, John Wiley & Sons, Inc., Hoboken, N.J., pp. 855-858; 1 st edition). The araB promoter is a medium strength promoter. Its −10 promoter sequence (TACTGT) is significantly different from the consensus −10 region (TATAAT) of stronger E. coli promoters. This difference is believed to lead to lower gene expression levels depending on the sequence context of the 5′ end sequence of the gene. One strategy of improving the araB promoter strength is to change the −10 promoter sequence of araB into that of the consensus sequence. An alternative approach is to introduce randomization at the −10 promoter region, while keeping the −35 promoter region unchanged as it overlaps with the binding site of the transcriptional regulator AraC.
AraC is the transcriptional regulator for the araB promoter that activates transcription of araB gene in the presence of L-arabinose, and represses the transcription in the absence of L-arabinose (Guzman et al., J Bacteriol. 177(14):4121-4130 (1995) and U.S. Pat. No. 5,028,530 to Lai et al.). The araB promoter is also regulated by catabolite repression. In order to provide a reporter plasmid for the improvement selection of stronger araB mutant promoters, a reporter plasmid pBAD.GFP was constructed ( FIG. 1 ; SEQ ID NO: 8). Green Fluorescent Protein (Aequorea coerulescens GFP; SEQ ID NO: 7) was used as a reporter gene product expressed from a plasmid in E. coli. The NcoI-EcoRI restriction fragment encoding for GFP gene (SEQ ID NO: 6) from plasmid pAcGFP (Clontech, Mountainview, Calif.) was subcloned into the NcoI and EcoRI sites of plasmid pBAD.HisB (Invitrogen, Carlsbad, Calif.; SEQ ID NO: 5) to yield plasmid pBAD.GFP ( FIG. 1 ; SEQ ID NO: 8).
The E. coli strain TOP10 (Invitrogen, Carlsbad, Calif.) transformed with pBAD.GFP (strain DPD5146) was induced with 0.2% L-arabinose overnight in LB media with 100 μg/mL ampicillin, and an induction of fluorescence intensity was detected using the Perkin Elmer HTS7000Plus bioassay plate reader (Perkin Elmer, Boston, Mass.), with excitation wavelength at 485 nm and emission wavelength at 535 nm (pBAD.GFP(−)=no L-arabinose added (control); pBAD.GFP(+)−1=0.2% L-arabinose added at inoculation; and pBAD.GFP(+)−2=0.2% L-arabinose added at mid-log growth phase). The results are provided in Table 1.







TABLE 1





Relative Fluorescence

Strain
Relative Fluorescence Units
Units









pBAD.GFP(−)
653
857

(control)

pBAD.GFP(+)-1
1552
1756

(early log phase)

pBAD.GFP(+)-2
2419
2623

(mid log phase)



























As expected for typical gene expression in E. coli, a higher level of GFP fluorescence was detected when the culture was induced at mid log growth phase vs. early log phase.
An araB promoter mutant library was constructed by synthesizing two complementary oligonucleotides encompassing the wild type araB promoter (SEQ ID NO: 1) sequence.






primer 1:





(SEQ ID NO: 3)





5′-gatcctacctgacgctttttatcgcaactctc NNNNNN ttctccata




cccgttttttgggctaacaggaggaattaaccatg-3′



primer 2:




(SEQ ID NO: 4)





5′-catggttaattcctcctgttagcccaaaaaacgggtatggagaa NNN




NNN gagagttgcgataaaaagcgtcaggtag-3′.






























“N” indicates randomized positions which are equal mixtures of G,A,T, and C nucleotides) The two oligonucleotides, when annealed, contain a BamHI overhang at the 5′ end, and a NcoI site containing blunt end at the 3′ end. This fragment can be ligated into pBAD.GFP plasmid (SEQ ID NO: 8) at the BamHI (upstream of araB promoter) and NcoI (at ATG start codon) sites. The blunt end at NcoI site generated additional diversity for varying the distance between ribosomal binding site (RBS) and the ATG start codon.
The ligation mixture for the araB promoter mutant library was used to carry out transformation. A Fluorescence Activated Cell Sorter (FACS) was used to identify and select clones with stronger fluorescence intensity. Increased fluorescence (i.e. amount of GFP produced) allowed the detection of araB promoter mutants characterized by their ability to improved protein production level by monitoring fluorescence.
Example 2
Transformation and Quality Control of the Library
The ligation mix of the library was transformed into electro-competent E. coli TOP10 cells (Invitrogen) and plated on LB/ampicillin plates (100 μg/mL). Approximately 20,000 colonies were obtained. In order to test whether mutations were actually introduced into the -10 region of the promoter, eight random constructs were selected for sequencing. The eight colonies were inoculated into 3 mL of LB-ampicillin broth (10 g/L bacto-tryptone, 5 g/L bacto-yeast extract, 10 g/L NaCl, 100 mg/L ampicillin; pH 7.0). Plasmid DNA was extracted with the Qiagen miniprep kit (Qiagen, Valencia, Calif.) and the DNA sequence was determined.
FIG. 2 shows that the −10 region of the 8 sequenced mutant promoter constructs (SEQ ID NOs: 9-16) from the library had different sequences (underlined region) in comparison to the wild type (wt) starting sequence. The −35 region of all the constructs remained wild type. About half the constructs had deletions around the ribosome binding site (RBS), which was expected based on the initial cloning strategy (Example 1).
The mixed library of 20,000 colonies were transferred from the LB/Amp plates and resuspended in LB/Ampicillin (100 μg/mL). Glycerol was added to 15% (v/v) and the cells frozen at −80° C.
Example 3
Use of a Fluorescence Activated Cell Sorter (FACS) to Identify Mutants with Increased Expression
An aliquot of the library of mixed constructs was inoculated in LB/Amp (100 μg/mL), grown up to OD 600 of 0.3, and induced with 0.2% arabinose for about 4 hours. E. coli TOP10 cells comprising the wild type arabinose promoter sequence (SEQ ID NO: 1) in the pBAD.GFP vector were grown up in the same manner to serve as controls.
The cells were analyzed with a fluorescence activated cell sorter (FACS; FACSVantage™ SE system; BD Biosciences, San Jose, Calif.), using a 488 nm laser. The E. coli TOP10 cells served as a negative control and were used to set up the parameters of the FACS and to set the boundaries for the subsequent gating of the cells. Fluorescence was measured at an emitted wavelength of 530 nm (±15 nm). E. coli TOP cells not transformed to express GFP (i.e. no fluorescence) served as a negative control.
FACS measurement of the TOP10 cells expressing the GFP protein under the control of the wild type araB promoter (SEQ ID NO: 1) were measured after induction. The measured fluorescence from the wild type araB driven expression of GFP was used to set a baseline fluorescence to measure the effect of the araB promoter mutations on GFP production. Cells having an increased fluorescence relative to the cells expressing GFP from the wild type promoter were selected and isolated for sequence analysis (i.e. “positive” hits).
Approximately 96% of the cells from the mutant promoter library fell into the ‘negative’ gating region (no significant increase in fluorescence relative to the observed fluorescence of cells expressing the wild type araB promoter). Approximately 1.6% fell into the ‘intermediate’ gating (slight increase in fluorescence relative to the wild type araB driven GFP expression), and about 0.04% of cells into the ‘positive’ gating (significantly higher fluorescence measured).
Approximately 1.6 million cells were sorted into the ‘intermediate’ bin, and approximately 36,000 cells in the ‘positive’ bin. These two populations were grown up overnight in LB/Amp medium (100 μg/mL). An aliquot of each was used to start a new 3-mL culture in LB/Amp medium, grown to OD 600 of 0.3, and induced with 0.2% L-arabinose for 4 hours. After letting the GFP mature for about 8 hours, a second round of FACS analysis/sorting was performed.
Results from the Second Round of FACS Enrichment
Approximately 56,000 cells from gate ‘P3’ (i.e. the top 0.3% of fluorescing cells) were sorted. This population was grown up overnight on LB/Amp plates (100 μg/mL). Fifty (50) colonies were picked and grown up in 3-mL LB/Amp medium to OD 600 of 0.3 and induced with 0.2% L-arabinose for 4 hours. After letting the GFP mature for approximately 8 hours, the cells were checked for fluorescence under a fluorescence microscope. About 20% of the cells were markedly brighter than the rest.
Example 4
Sequence Analysis of Promoter Mutants
The sequence of each araB mutant from the 50 colonies picked in Example 3 were determined to identify the mutations that give rise to higher fluorescence of the cells due to higher levels of expressed GFP. The brightest fraction of cells, which consisted of about 20% of the population, all contained the same promoter mutation (Mutant “GFP-B1”; SEQ ID NO: 17). An additional three mutations were identified that yielded intermediate brightness, similar to cells with pBAD.GFP (denoted as mutants GFP-M1 (SEQ ID NO:18), GFP-M2 (SEQ ID NO: 19), and GFP-M3 (SEQ ID NO: 20)), as determined visually by fluorescence microscopy.
The sequence of mutant promoter GFP-B1 (a.k.a. “B1”) was identical for all the very bright constructs that were identified. GFP-M1, GFP-M2, and GFP-M3 were only represented once in the samples that were sequenced ( FIG. 3 ). The sequence shown in this alignment includes sequences upstream of the promoter region up to, but not including the ATG start codon of GFP. The coding sequence of GFP was wild type in all cases, ruling out the possibility that the increased fluorescence is due to a mutation in GFP itself.
Two main features become apparent from FIG. 3 : (1) the −10 sequence is different in all constructs, and (2) there is an insertion of about 75 bases (bold type) after the RBS in constructs GFP-B1 and GFP-M3. This duplication has high sequence similarity to the region encompassing the promoter region and its flanking sequences.
Example 5
Fluorescence Assay of Mutant Clones GFP-B1 and GFP-M2
Two clones from the initial FACS experiment (Example 3) were selected for further analysis using a fluorescence plate reader (Perkin Elmer HTS7000Plus bioassay plate reader; PerkinElmer Life and Analytical Sciences, Waltham, Mass.). E. coli TOP10 cells transformed with pBAD.GFP (wt), pBAD.GFP-B1 and pBAD.GFP-M2 (comprising SEQ ID NO: 19) were grown in LB, 100 μg/mL ampicillin and induced at mid log growth phase by 0.2% L-arabinose overnight. Two hundred microliters of each cell culture was transferred to a 96-well plate in duplicates, and the fluorescence signal was measured at excitation wavelength at 485 nm and emission wavelength at 535 nm. The fluorescence intensity was normalized to OD 600 levels to 1 (measured absorbance in same instrument at 595 nm) (Table 2).







TABLE 2





Relative Fluorescence Intensity (RFU)








Clones
LB
LB, 0.2% arabinose
LB, 0.2% glucose











Wild type
230
827
162


GFP-B1
232
9697
383


GFP-M2
234
576
271



























Results:
The clone comprising the GFP-B1 mutant araB promoter (SEQ ID NO: 17) was the brightest clone, its fluorescence intensity was about 10× higher compared to wild type (SEQ ID NO: 1) araB-GFP clone. The GFP expression in mutant GFP-B1 is low in the absence of arabinose, or in the presence of glucose. This indicates that GFP-B1 mutant is tightly controlled by arabinose, and is subjected to catabolite repression (similar to the tightly regulated expression control observed in wild type araB promoter). Another clone from the FACS selection, GFP-M2, did not show improved fluorescence when analyzed using a fluorescence plate reader. The increased fluorescence associated with the promoter activity of mutant araB promoter GFP-B1 was confirmed.
Example 6
N-Terminal Sequencing of the Protein Product
Analysis of the GFP-B1 promoter (SEQ ID NO: 17) sequence shows that there are two potential translational start sites, one being the start site of the wild type GFP protein, the other the first ATG after the RBS (see FIG. 6 ). The introduced ATG start codon is in frame with the second ATG start codon (the start codon in the coding region for the wild type GFP protein). In order to determine which one is used in the cell, the N-terminal sequence of the over expressed product was determined. The cells transformed with plasmid pBAD.GFP-B1 (B1) were grown up to OD 600 of 0.3 and induced for 3 hours. An aliquot was run on a NUPAGE® 4-12% Bis-Tris gel (Invitrogen) and transferred to a PVDF (polyvinylidene difluoride) membrane. The blot was stained with COOMASSIE® Blue R-250 (Invitrogen), and the band of interest excised and submitted to N-terminal sequencing using Edman chemistry. The N-terminal sequence obtained (MVPDAFYRNSL; SEQ ID NO: 21) corresponds to the first ATG codon (located right after the ribosomal biding site (RBS) and 5′ to the wild type GFP start codon) being used. Thus, mutant araB promoter GFP-B1 (SEQ ID NO: 17) adds an additional 24 amino acids to the N-terminus of the over expressed protein.
Example 7
Analysis of the araB Mutant Promoter B1
In order to gain more insights into what features of the araB B1 mutant promoter are responsible for the increased production of GFP, the fluorescence of various mutant constructs was compared.
A comparison of the wild type araB promoter (SEQ ID NO: 1) versus the mutant araB B1 promoter of SEQ ID NO: 17 indicates that the mutant promoter comprises a general duplication of a promoter-like region as shown in FIG. 4 . The sequence of the −10 region of the first promoter element is not identical to the sequence of the −10 region of the second promoter element in the mutant B1 promoter. No discernable ribosomal binding sequence could be identified in the duplicated motif of araB mutant promoter B1.
Example 8
Preparation of Various Additional Mutant Promoters Derived from the Wild-Type araB Promoter or the Mutant araB Promoter B1
Various additional mutant promoter sequences were prepared using primer pairs for targeted modification to either the wild type araB promoter or the mutant araB promoter B1 (Example 7). The following PCR conditions were used unless otherwise noted.
QuickChange PCR was used according to the manufacturer's instructions (Stratagene, La Jolla, Calif.)







PCR Protocol:




Temperature
Time



95° C.
30 sec

95° C.
30 sec

55° C.
10 min (repeated 17 times)

68° C.
10 min

68° C.
10 min

4° C.
hold























The products from the PCR reactions were gel purified. Constructs were transformed into E. coli TOP10 electro-competent cells.
A. Preparation of Mutant araB Promoter by Removing the ATG Start Codon in Mutant B1
A derivative of mutant promoter B1 (SEQ ID NO: 17) was prepared by removing the ATG start codon so that a GFP fusion product was not formed. Using mutant araB promoter B1 (SEQ ID NO: 17) as a template, several sets of primers were used to prepare a modified version of mutant promoter B1 lacking the ATG start codon (ATG→ATC). (Table 3; mutant promoter Ara1b; “1b”)
B. Preparation of Mutant Promoter ara4a by Replacing the First −10 Sequence of the Promoter by the −10 Wild Type Sequence
A derivative of mutant promoter B1 was prepared by introducing the wild type −10 sequence into the first −10 hexamer of the mutant B1 sequence. This was achieved by cloning the NcoI fragment (about 100 nucleotides) of mutant promoter B1 into the wild type sequence, yielding sequence mutant promoter ara4a (SEQ ID NO: 23)
C. Preparation of Mutant Promoter ara5a by Replacing the NcoI Site that Contains the Start Codon of GFP, with an NdeI Site.
Using mutant araB promoter B1 (SEQ ID NO: 17) as a template, two primers were used to prepare a modified version of mutant promoter B1 by replacing the NcoI site that contains the start codon of GFP, with an NdeI site (Table 3; mutant promoter Ara5a; “5a”).
D. Preparation of Mutant Promoter ara8a by Having Two Different −10 Regions Compared to Mutant B1.
Using mutant araB promoter GFP-M2 (SEQ ID NO: 19) as a template, two primers were used to prepare a modified version of mutant promoter B1 to result in a sequence that contains two different −10 sequences. (Table 3; mutant promoter Ara8a; “8a”).










TABLE 3







Resulting



Primer
Primer Sequence
Modification
Mutant Promoter

Template Used
Name
(SEQ ID NO.)
Introduced
(SEQ ID NO:)



Mutant B1
Ara1F
gaggaattaaccatcgta
Change
Ara1b


(SEQ ID NO: 17)

cctgacgc
ATG to ACT
(SEQ ID NO: 22)



(SEQ ID NO: 40)
in mutant B1

Mutant B1
Ara1R
gcgtcaggtacgatggtt

(SEQ ID NO: 17)

aattcctc
(SEQ ID NO: 41)



Mutant B1
Ara5F
ggctaacagaaatcatat
Mutated
Ara5a

(SEQ ID NO: 17)

ggtgagcaagggc
NcoI to
(SEQ ID NO: 24)



(SEQ ID NO: 42)
NdeI in

Mutant B1
Ara5R
gcccttgctcaccatatga
construct

(SEQ ID NO: 17)

tttctgttagcc



(SEQ ID NO: 43)



Mutant GFP-M2
Ara8F
ccatacccgttttttggcta
Put
Ara8a

(SEQ ID NO: 19)

acagaaataccatggtg
duplicated
(SEQ ID NO: 25)



agcaagggcgcc
sequence



(SEQ ID NO: 44)
back in frame.

Mutant GFP-M2
Ara8R
ggcgcccttgctcaccat
Results in same

(SEQ ID NO: 19)

ggtatttctgttagccaaa
sequence as



aaacgggtatgg
mutant B1, except



(SEQ ID NO: 45)
for different −10




sequences.








































Summary of All the Constructs and Their Fluorescence:
All plasmid constructs were transformed into E. coli Top10. Cells were grown in 3 mL LB (+100 μg/mL Ampicillin) overnight. New 3-mL growths were grown to OD 600 of about 0.3, induced with 0.2% L-arabinose and grown for 4 hours. OD 600 and fluorescence were measured and values below represent fluorescent units per one OD equivalent of cells.
Measurement of fluorescence: Perkin Elmer HTS7000Plus bioassay plate reader, with excitation wavelength at 485 nm and emission wavelength at 535 nm. Subtracted background fluorescence and normalized OD levels to 1 (measured absorbance in same instrument at 595 nm).
Table 4 shows the fluorescence (Relative fluorescence units; RFU) of various araB mutant promoters vs. the wild type araB promoter control when operably linked to a GFP fluorescent reporter.





TABLE 4



GFP Fluorescence of Various Mutant Promoters vs. The

Wild Type araB Promoter









Measured
Percent Increase


Promoter
SEQ ID
Fluorescence 1,2
in Fluorescence
Fold

ID.
NO.
(RFU)
vs. wild type 1
difference 1









Wild type
1
366
NA
NA

araB

500

promoter

344



Mean = 403



S.D. = 69

B1
17
3166
750
8.5



3420



3692



Mean = 3426



S.D. = 215

ara1B
22
3741
829
9.3

ara4A
23
2846
620
7.2



2956



Mean = 2901



S.D. = 55

ara5A
24
2115
425
5.2

ara8A
25
8378
1980
21

M2
19
369
−0.25
1



434



Mean = 402



S.D. = 32.5



1 = Mean value used for comparison to average value for wild type fluorescence. Fluorescence is proportional to the amount of GFP present.

2 = normalized per 1 OD 600 of cells after subtracting out background.















































A CLUSTALW sequence alignment (version 1.83) was performed using mutant araB promoters B1, ara1B, ara4A, ara5A, and ara8a to generate a consensus mutant araB promoter sequence ( FIG. 5 ). The araB promoter consensus sequence is provided as SEQ ID NO: 2.