# Patent

## Title
Acid-cleavable linkers exhibiting altered rates of acid hydrolysis

## Abstract

An acid-cleavable peptide linker comprising aspartic acid and proline residues is disclosed. The acid-cleavable peptide linker provides an altered sensitivity to acid-hydrolytic release of peptides of interest from fusion peptides of the formula PEP1-L-PEP2. The inventive linker, L, is described in various embodiments, each of which provides substantially more rapid acid-release of peptides of interest than does a single aspartic acid-proline pair. In an additional aspect, a method of increasing the stability of an acid cleavable linkage to acid hydrolysis is also provided.

## Background
CROSS-REFERENCE TO RELATED APPLICATIONS
This application is a divisional of co-pending U.S. patent application Ser. No. 13/226,610, filed Sep. 7, 2011, which claims benefit of expired U.S. Provisional Patent Application No. 61/413,501, filed Nov. 15, 2010, both of which are incorporated by reference herein in its entirety.


FIELD OF THE INVENTION
The invention relates to the field of protein expression and purification from microbial cells. More specifically, peptide linkers having an altered sensitivity to acid hydrolysis are provided as well as methods of their use.
BACKGROUND OF THE INVENTION
The efficient production of bioactive proteins and peptides has become a hallmark of the biomedical and industrial biochemical industry. Bioactive peptides and proteins are used as curative agents in a variety of diseases such as diabetes (insulin), viral infections and leukemia (interferon), diseases of the immune system (interleukins), and red blood cell deficiencies (erythropoietin) to name a few. Additionally, large quantities of proteins and peptides are needed for various industrial applications including, for example, the pulp and paper and pulp industries, textiles, food industries, personal care and cosmetics industries, sugar refining, wastewater treatment, production of alcoholic beverages and as catalysts for the generation of new pharmaceuticals.
With the advent of the discovery and implementation of combinatorial peptide screening technologies such as bacterial display, yeast display, phage display, ribosome display, and mRNA display technology new applications for peptides having strong affinity for a target surface have been developed. In particular, peptides are being looked to as linkers in biomedical fields for the attachment of diagnostic and pharmaceutical agents to surfaces (see Grinstaff et al, U.S. Patent Application Publication No. 2003-0185870 and Linter in U.S. Pat. No. 6,620,419), as well as in the personal care industry for the attachment of benefit agents to body surfaces such as hair and skin (see commonly owned U.S. Pat. No. 7,220,405, and Janssen et al. U.S. Pat. No. 7,129,326), and in the printing industry for the attachment of pigments to print media (see commonly owned U.S. Patent Application Publication No. 2005-0054752).
In some cases commercially useful proteins and peptides may be synthetically generated or isolated from natural sources. However, these methods are often expensive, time consuming and characterized by limited production capacity. The preferred method of protein and peptide production is through the fermentation of recombinantly constructed organisms, engineered to over-express the protein or peptide of interest. Although preferable to synthesis or isolation, recombinant expression of peptides has a number of obstacles to be overcome in order to be a cost-effective means of production. For example, peptides (and in particular short peptides) produced in a cellular environment are susceptible to degradation from the action of native cellular proteases. Additionally, purification can be difficult, resulting in poor yields depending on the nature of the protein or peptide of interest.
One means to mitigate the above difficulties is the use of genetic chimera for protein and peptide expression. A chimeric protein or “fusion protein” is a polypeptide comprising at least one portion of a desired protein product fused to at least one portion comprising a peptide tag. The peptide tag may be used to assist protein folding, assist in purification, alter polypeptide solubility, protect the protein from the action of degradative enzymes, and/or assist the protein in various transport and targeting processes.
In many cases it is useful to express a protein or peptide in insoluble form, particularly when the peptide of interest is rather short, normally soluble, and/or subject to proteolytic degradation within the host cell. Production of the peptide in insoluble form both facilitates simple recovery and protects the peptide from undesirable proteolytic degradation. One means to produce the peptide in insoluble form is to recombinantly produce the peptide as part of an insoluble fusion protein by including in the fusion construct, at least one peptide tag (i.e., an inclusion body tag) that induces inclusion body formation. Typically, the fusion protein is designed to include at least one cleavable peptide linker so that the peptide of interest can be subsequently recovered from the fusion protein. The fusion protein may be designed to include a plurality of solubility tags, cleavable peptide linkers, and regions encoding the peptide of interest.
Fusion proteins comprising a peptide tag that facilitate the expression of insoluble proteins are well known in the art. Typically, the tag portion of the chimeric or fusion protein is large, increasing the likelihood that the fusion protein will be insoluble. Examples of large peptides that are typically used include, but are not limited to chloramphenicol acetyltransferase (Dykes et al., Eur. J. Biochem., 174:411 (1988), β-galactosidase (Schellenberger et al., Int. J. Peptide Protein Res., 41:326 (1993); Shen et al., Proc. Nat. Acad. Sci. USA 281:4627 (1984); and Kempe et al., Gene, 39:239 (1985)), glutathione-S-transferase (Ray et al., Bio/Technology, 11:64 (1993) and Hancock et al. (WO94/04688)), the N-terminus of L-ribulokinase (U.S. Pat. No. 5,206,154 and Lai et al., Antimicrob. Agents & Chemo., 37:1614 (1993), bacteriophage T4 gp55 protein (Gramm et al., Bio/Technology, 12:1017 (1994), bacterial ketosteroid isomerase protein (Kuliopulos et al., J. Am. Chem. Soc. 116:4599 (1994), ubiquitin (Pilon et al., Biotechnol. Prog., 13:374-79 (1997), bovine prochymosin (Naught et al., Biotechnol. Bioengineer. 57:55-61 (1998), and bactericidal/permeability-increasing protein (“BPI”; Better, M. D. and Gavit, P D., U.S. Pat. No. 6,242,219). The art is replete with specific examples of this technology, see for example U.S. Pat. No. 6,613,548, describing fusion protein of proteinaceous tag and a soluble protein and subsequent purification from cell lysate; U.S. Pat. No. 6,037,145, teaching a tag that protects the expressed chimeric protein from a specific protease; U.S. Pat. No. 5,648,244, teaching the synthesis of a fusion protein having a tag and a cleavable linker for facile purification of the desired protein; and U.S. Pat. No. 5,215,896; U.S. Pat. No. 5,302,526; and U.S. Pat. No. 5,330,902; and U.S. Patent Application Publication No. 2005-221444, describing fusion tags containing amino acid compositions specifically designed to increase insolubility of the chimeric protein or peptide.
Shorter solubility tags have been developed from the Zea mays zein protein (co-owned U.S. Pat. No. 7,732,569) the Daucus carota cystatin (co-owned U.S. Pat. No. 7,662,913), and an amyloid-like hypothetical protein from Caenorhabditis elegans (co-owned U.S. Pat. No. 7,427,656; each hereby incorporated by reference in their entirety.) The use of short inclusion body tags increases the yield of the target peptide produced within the recombinant host cell.
Aspartic acid-proline linkages can be cleaved using acid treatment. However, the conditions typically used include at least one strong acid, such as HCl or H2SO4, and may require subsequent neutralization with base and may increase the cost of peptide recovery due the amount of salt produced. Further, acid hydrolysis conditions for the intended aspartic acid-proline pair may be accompanied by undesirable hydrolysis at other sites where aspartic acid residues occur or may lead to the deamidation of glutamine or asparagine.
One problem to be solved is to provide peptide linkers that are more sensitive to acid hydrolysis when compared to a single aspartic acid-proline linkage. Increased sensitivity may permit the use of weaker acids, reduce the amount of base that may be needed for neutralization, and may help to protect the peptide of interest from unwanted hydrolysis at other locations within the peptide of interest.
Situations may occur where a peptide or protein of interest contains one or more acid labile aspartic acid-proline linkages where acid hydrolysis is not desired. As such, another problem to be solved is to provide a method to increase the stability of aspartic acid-proline linkages to acid treatment in peptides or proteins wherein acid hydrolysis is undesirable.
SUMMARY OF THE INVENTION
The stated problem has been solved though the discovery of peptide linkers characterized by increased sensitivity to acid hydrolysis when compared to a single aspartic acid-proline (i.e., DP) linkage.
In one embodiment, peptide linkers characterized by greater sensitivity to acid treatment are provided, wherein the peptide linkers comprise an amino acid sequence selected from the group consisting of:










A. DPDP
(SEQ ID NO: 1)



 



B. DPDPDP
(SEQ ID NO: 2)



 



C. DPDPDPDP
(SEQ ID NO: 3)



 



D. DPDPDPP
(SEQ ID NO: 4)



 



E. DPDPPDPP
(SEQ ID NO: 5)



 



F. DPDPPDP
(SEQ ID NO: 6),



and



 



G. DPPDPPDP
(SEQ ID NO: 7),






wherein D is aspartic acid and P is proline.
In a further embodiment, the invention disclosed herein encompasses a fusion peptide according to the structure PEP1-L-PEP2, wherein,
a) PEP1 and PEP2 are independently functional peptides wherein at least one is a peptide of interest (“POI”); and
b) L is an acid-cleavable linker comprising a peptide selected from the group consisting of:










A. DPDP,
(SEQ ID NO: 1)


 



B. DPDPDP,
(SEQ ID NO: 2)


 



C. DPDPDPDP,
(SEQ ID NO: 3)


 



D. DPDPDPP,
(SEQ ID NO: 4)


 



E. DPDPPDPP,
(SEQ ID NO: 5)


 



F. DPDPPDP,
(SEQ ID NO: 6)



and



 



G. DPPDPPDP,
(SEQ ID NO: 7)






wherein D is aspartic acid and P is proline.
The linker, L, provides for increased efficiency of acid release of a peptide from a fusion peptide comprising L. This increase may be defined as the enhancement in acid hydrolysis rate of an intact fusion peptide having a linker of the formula according to the invention when compared to the acid hydrolysis rate of the fusion peptide, PEP1-L-PEP2, having a single DP pair as the linker, L.
In this embodiment, the peptides PEP1 and PEP2 may each be a peptide of interest (i.e., “POI”). Alternatively, one of PEP1 or PEP2 may be an inclusion body tag (i.e., “IBT”) whereas the remaining peptide may be a POI. In the context of the present invention an IBT is a peptide or polypeptide that directs newly synthesized fusion peptide molecules to precipitate or accumulate in insoluble inclusion bodies that can form in recombinant cells expressing heterologous, i.e., foreign, polynucleotides encoding peptides, polypeptides, fusion peptides and the like.
The POI of the fusion peptide may be virtually any peptide or polypeptide. The POI may be one of many targeting peptides that are identifiable by known biopanning methods after their expression in a recombinant bacteriophage. Such targeting peptides have high affinity for various targets of interest, including but not limited to skin, hair, nails, print media, woven or nonwoven fabric, polymers, tooth enamel, tooth pellicle, and clay and the like. POIs may also include antimicrobial peptides, pigment-binding peptides, and cellulose-binding peptides.
Such POIs may have functional applications such as diagnostic markers, pharmaceuticals, stimulators or inhibitors of enzymatic or receptor-mediated processes, and the like. Thus, the fusion peptide comprising the linker L can be employed in an isolation and purification scheme for any POI or polypeptide that can be cleaved from the fusion peptide as a result of being contacted with a sufficiently acidic environment.
In one embodiment, the invention encompasses a method of isolating a peptide of interest (“POI”) from a recombinant cell expressing a heterologous fusion peptide comprising the linker L. The recombinant cell may be any prokaryotic or eukaryotic cell type, including any type of recombinant microbial cell. Preferred recombinant microbial cells include recombinant yeast cells and recombinant bacterial cells. An additional embodiment contemplates taking advantage of the fact that heterologous peptide expression in recombinant cells is often accompanied by the newly synthesized heterologous peptides accumulating in insoluble inclusion bodies within the nucleus or the cytoplasm of the cell. When such insoluble fusion peptides having a POI also comprise the acid-cleavable linker L, it is contemplated herein that acid hydrolysis of L will liberate the POI from the inclusion body, preferably converting it to a more soluble form. The released soluble form of the POI is then more easily separable from remaining inclusion bodies and insoluble remnants thereof.
However, the fusion peptide is equally suitable to embodiments wherein the chemistry of PEP1 and PEP2 result in the synthesis of a soluble fusion peptide that remains soluble in the cytoplasm and does not precipitate or form inclusion bodies. In such cases the acid cleavable linker provides a simple method to separate a soluble POI from the soluble fusion peptide or cleaved fragment thereof.
Thus, an additional embodiment of the invention comprises a method of preparing at least one peptide of interest (“POI”) from a fusion peptide comprising the at least one POI, comprising:
a) providing a recombinant cell synthesizing a fusion peptide having the structure

PEP1-L-PEP2

wherein,

    
    
        i) PEP1 and PEP2 are independently functional peptides wherein at least one is a peptide of interest (“POI”); and
        ii) L is an acid-cleavable linker comprising a peptide selected from the group consisting of:
    
    












A. DPDP,
(SEQ ID NO: 1)


 



B. DPDPDP,
(SEQ ID NO: 2)


 



C. DPDPDPDP,
(SEQ ID NO: 3)


 



D. DPDPDPP,
(SEQ ID NO: 4)


 



E. DPDPPDPP,
(SEQ ID NO: 5)


 



F. DPDPPDP,
(SEQ ID NO: 6)



and



 



G. DPPDPPDP,
(SEQ ID NO: 7)






wherein D is aspartic acid and P is proline; and
b) contacting the fusion peptide with a solution of sufficiently acidic pH so that linker L is cleaved, and
c) isolating the at least one POI.
In an even further embodiment, the invention encompasses a recombinant cell, preferably a microbial cell, and more preferably a bacterial cell that expresses such a fusion peptide. In this context an especially desirable bacterial cell is E. coli. 
Situations may exist where there is a need to increase the stability of a peptide or protein comprising at least one aspartic acid-proline linkage to an acid treatment. As such, a method to increase the stability of an acid cleavable linkage to acid hydrolysis is also provided comprising:

    
    
        a) providing a peptide or protein of interest comprising at least one acid cleavable linkage having the following structure:

XDP;
        
            wherein D is aspartic acid and P is proline and X is any amino acid other than tryptophan or phenylalanine; and
        
        
        b) altering said at least one acid cleavable linkage by substituting X with tryptophan or phenylalanine; whereby the stability of the acid cleavable linkage to acid hydrolysis is increased by the substitution.
    
    





BRIEF DESCRIPTION OF THE FIGURES
FIG. 1 shows the relative rates of acid cleavage of an intact fusion peptide having a DP cleavage site (“DP1”), a DPDP cleavage site (“DP2”; SEQ ID NO: 1), a DPDPDP cleavage site (“DP3”; SEQ ID NO: 2) or a DPDPDPDP cleavage site (“DP4”; SEQ ID NO: 3).
FIG. 2 shows a plot of the halftime, t1/2, of acid hydrolysis performed at about 70° C. as a function of the number of DP pairs in the acid cleavable linker.
FIG. 3 demonstrates the effect on acid hydrolysis rates of an intact fusion peptide having an amino acid substitution in the position immediately to the amino terminal side of the aspartic acid residue of a single DP linker; i.e., an aspartic acid-proline pair.
FIG. 4 demonstrates the effect on acid hydrolysis rates of an intact fusion peptide having an amino acid substitution in the position immediately to the carboxy terminal side of the proline residue of a single DP linker; i.e., an aspartic acid-proline pair.
FIG. 5 demonstrates the effect on rates of acid hydrolysis of an intact fusion peptide of having additional proline residues included in the acid cleavable linker “DP3”; DP3 (SEQ ID NO: 2), PP1 (SEQ ID NO: 4), PP2 (SEQ ID NO: 5) and PP3 (SEQ ID NO: 6).
FIG. 6 demonstrates the effect on rates of acid hydrolysis of an intact fusion peptide of placing additional proline residues within the acid cleavable linker “DP3”; DP3 (SEQ ID NO: 2), PP2 (SEQ ID NO: 5) and PP4 (SEQ ID NO: 7). See Table 2 for each corresponding linker sequence.
FIG. 7 demonstrates the effect of different acidic conditions on the rate of acid hydrolysis of an intact fusion peptide comprising the acid cleavable linker DP1, DP3, PP2 or PP3 (SEQ ID NO: 5) at approximately 70° C. See Table 2 for each corresponding linker sequence.
FIG. 8 demonstrates the effect of different acidic conditions on the rate of acid hydrolysis of an intact fusion peptide having either the acid cleavable linker DP3 (SEQ ID NO: 2) or PP2 (SEQ ID NO: 5) at reduced temperature of 50° C. See Table 2 for each corresponding linker sequence.
FIG. 9 demonstrates the effect of different acidic conditions on the extent of acid hydrolysis of an intact fusion peptide KSI(C4E).DP.HC353 having the acid cleavable linker DP. Maximum cleavage is obtained after 4 h at pH 2 and 80° C. Arrows indicate the full length fusion (F), HC353 (H) and KSI(C4E) (K).
FIG. 10 demonstrates the effect of different acidic conditions on the extent of acid hydrolysis of an intact fusion peptide KSI(C4E).DPDPPDPP.HC353 having the acid cleavable linker DPDPPDPP. Maximum cleavage is obtained after only 1 h at pH 2 and 80° C., at 60° C. for 4 h at pH 2 or at pH 4 for 4 hr and at 80° C. Arrows indicate the full length fusion (F), HC353 (H) and KSI(C4E) (K).
FIG. 11 demonstrates the effect of different acidic conditions on the extent of acid hydrolysis of an intact fusion peptide KSI(C4E).DPPDPPDP.HC353 having the acid cleavable linker DPPDPPDP. Maximum cleavage is obtained after only 90 min 4 h at pH 2 and 80° C., at 70° C. for 4 h at pH 2 or at pH 3 for 4 h and at 80° C. Arrows indicate the full length fusion (F), HC353 (H) and KSI(C4E) (K).
FIG. 12 demonstrates the effect of different acidic conditions on the extent of acid hydrolysis of an intact fusion peptide KSI(C4E).DPDPDP.HC353 having the acid cleavable linker DPDPDP. Maximum cleavage is obtained after only 120 min 4 h at pH 2 and 80° C., at 70° C. for 4 h at pH 2 or at pH 3 for 4 h and at 80° C. Arrows indicate the full length fusion (F), HC353 (H) and KSI(C4E) (K).



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 (2009) 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 NOs: 1-7 are the amino acid sequences of various embodiments of the present acid-cleavable linkers.
SEQ ID NOs: 8-25 are the polynucleotide sequences of the primers, oligonucleotides and plasmids used in preparing the polynucleotides encoding recombinant fusion peptides INK101, INK101DP, INK101DP2, INK101DP3, and INK101DP4.
SEQ ID NO: 26 is the amino acid sequence of the core acid-cleavable peptide, INK101DP.
SEQ ID NOs: 27-102 are primer sequences for performing mutagenesis of the immediately amino- and carboxy-terminal neighboring amino acids of the DP pair in INK101DP.
SEQ ID NOs: 103-110 are mutagenesis primer sequences that direct the insertion of additional proline residues into the acid-cleavable linker of INK101DP3.
SEQ ID NOs: 111-235 are amino acid sequences of various target-specific binding peptides as provided in Table 1 below:








TABLE 1





SEQ ID NOs:
Target Specificity







111-121
Hair


122-132
Skin


133-134
Finger/toe nail


135-143
Tooth (pellicle)


144-154
Tooth (enamel)


155-161
Antimicrobial


162-172
Clay


173-185
Calcium carbonate


186-192
Polypropylene


193-201
Polytetrafluoroethylene


202-208
Polyethylene


209-214
Nylon


215-217
Polystyrene


218-221
Cellulose acetate


222-225
Carbon black


226-230
Cromophtal yellow


231-235
Sunfast magenta









SEQ ID NOs: 236-249 are the amino acid sequences of peptides that function as inclusion body tags (IBTs).
SEQ ID NO: 250 is plasmid PLX121 that provides for expression of the INK101DP peptide.
SEQ ID NO: 251 is the sequence of the polynucleotide encoding the INK101DP peptide.
SEQ ID NO: 252 is the amino acid sequence of solubility tag KSI(C4E).
SEQ ID NO: 253 is the amino acid sequence of the peptide of interest HC353.
SEQ ID NO: 254 is the nucleic acid sequence of plasmid pLD001.
SEQ ID NO: 255 is the nucleic acid sequence encoding fusion peptide KSI(C4E).DP.HC353.
SEQ ID NO: 256 is the amino acid sequence of fusion peptide KSI(C4E).DP.HC353.
SEQ ID NO: 257 is the nucleic acid sequence of primer 353.DP3 UP.
SEQ DI NO: 258 is the nucleic acid sequence of primer 353.DP3 DOWN.
SEQ ID NO: 259 is the nucleic acid sequence encoding fusion peptide KSI(C4E).DPDPDP.HC353.
SEQ ID NO: 260 is the amino acid sequence of fusion peptide KSI(C4E).DPDPDP.HC353.
SEQ ID NO: 261 is the nucleic acid sequence of primer PP2 HC353 UP.
SEQ DI NO: 262 is the nucleic acid sequence of primer PP2 HC353 DOWN.
SEQ ID NO: 263 is the nucleic acid sequence encoding fusion peptide KSI(C4E).DPDPPDPP.HC353.
SEQ ID NO: 264 is the amino acid sequence of fusion peptide KSI(C4E).DPDPPDPP.HC353.
SEQ ID NO: 265 is the nucleic acid sequence of primer 353 PP4 UP.
SEQ ID NO: 266 is the nucleic acid sequence of primer 353 PP4 DOWN.
SEQ ID NO: 267 is the nucleic acid sequence encoding fusion peptide KSI(C4E).DPPDPPDP.HC353.
SEQ ID NO: 268 is the amino acid sequence of fusion peptide KSI(C4E).DPPDPPDP.HC353.
Several of the peptides listed above and the methods by which they were identified and prepared have been previously described in detail in U.S. Patent Application Publication Nos. U.S. 2009-0048428 and U.S. 2005-0054752, both of which are hereby incorporated by reference.
Persons of ordinary skill in the art will readily appreciate that the foregoing non-limiting listing of distinct classes of peptides is provided for illustrative purposes only, as examples of the scope of distinct sets of targeting peptides that may be incorporated into a fusion peptide of the formula PEP1-L-PEP2 wherein L is an acid-cleavable linker encompassed by the invention disclosed herein.
DETAILED DESCRIPTION OF THE INVENTION
The following definitions are used herein and should be referred to for interpretation of the claims and the specification. Unless otherwise noted, all U.S. patents and U.S. Patent Applications referenced herein are incorporated by reference in their entirety.
As used herein, the articles “a”, “an”, and “the” preceding an element or component of the invention are intended to be nonrestrictive regarding the number of instances (i.e., occurrences) of the element or component. Therefore “a”, “an”, and “the” should be read to include one or at least 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 “comprising” means the presence of the stated features, integers, steps, or components as referred to in the claims, but that it does not preclude the presence or addition of one or more other features, integers, steps, components or groups thereof. The term “comprising” is intended to include embodiments encompassed by the terms “consisting essentially of” and “consisting of”. Similarly, the term “consisting essentially of” is intended to include embodiments encompassed by the term “consisting of”.
As used herein, the term “about” modifying the quantity of an ingredient or reactant 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. The term “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.
Where present, all ranges are inclusive and combinable. For example, when a range of “1 to 5” is recited, the recited range should be construed as including ranges “1 to 4”, “1 to 3”, “1-2”, “1-2 & 4-5”, “1-3 & 5”, and the like.
As used herein, the term “isolated nucleic acid molecule” is 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 term “pigment” refers to an insoluble, organic or inorganic colorant.
As used herein, the term “hair” as used herein refers to human hair, eyebrows, and eyelashes.
As used herein, the term “skin” as used herein refers to human skin, or substitutes for human skin, such as pig skin, VITRO-SKIN® and EPIDERMTTM. Skin, as used herein, will refer 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” as used herein refers to human fingernails and toenails.
As used herein, “PBP” means polymer-binding peptide. As used herein, the term “polymer-binding peptide” refers to peptide sequences that bind with high affinity to a specific polymer (U.S. Pat. No. 7,427,656). Examples include peptides that bind to polyethylene (SEQ ID NO:202-208), polypropylene (SEQ ID NOs: 186-192), polystyrene (SEQ ID NOs: 215-217), Nylon (SEQ ID NOs: 209-214), and poly(tetrafluoroethylene) (SEQ ID NOs: 193-201).
As used herein, “HBP” means hair-binding peptide. As used herein, the term “hair-binding peptide” refers to peptide sequences that bind with high affinity to hair. The hair-binding peptide may be comprised of a single hair-binding domain or multiple binding domains wherein at least one of the binding-domains binds to hair (i.e. multi-block peptides). Examples of hair binding peptides have been reported (U.S. patent application Ser. No. 11/074,473 to Huang et al.; WO 0179479; U.S. Patent Application Publication No. 2002/0098524 to Murray et al.; Janssen et al., U.S. Patent Application Publication No. 2003/0152976 to Janssen et al.; WO 2004048399; U.S. application Ser. No. 11/512,910, and U.S. patent application Ser. No. 11/696,380). Examples of hair-binding peptides are provided as SEQ ID NOs: 111-121.
As used herein, “SBP” means skin-binding peptide. As used herein, the term “skin-binding peptide” refers to peptide sequences that bind with high affinity to skin. Examples of skin binding peptides have also been reported (U.S. patent application Ser. No. 11/069,858 to Buseman-Williams; Rothe et. al., WO 2004/000257; and U.S. patent application Ser. No. 11/696,380). Skin as used herein as a body surface will generally comprise a layer of epithelial cells and may additionally comprise a layer of endothelial cells. Examples of skin-binding peptides are provided as SEQ ID NOs: 122-132.
As used herein, “NBP” means nail-binding peptide. As used herein, the term “nail-binding peptide” refers to peptide sequences that bind with high affinity to nail. Examples of nail binding peptides have been reported (U.S. patent application Ser. No. 11/696,380). Examples of nail-binding peptides are provided as SEQ ID NOs: 133-134.
As used herein, an “antimicrobial peptide” is a peptide having the ability to kill microbial cell populations (U.S. Pat. No. 7,427,656). Examples of antimicrobial peptides are provided as SEQ ID NOs: 155-161.
As used herein, “cellulose acetate-binding peptide” refers to a peptide that binds with high affinity to cellulose acetate. Examples of cellulose acetate-binding peptides are provided as SEQ ID NOs: 218-221.
As used herein, “clay-binding peptide” refers to a peptide that binds with high affinity to clay (U.S. patent application Ser. No. 11/696,380). Examples of clay-binding peptides are provided as SEQ ID NOs: 162-172.
As used herein, “calcium carbonate-binding peptide” refers to a peptide that binds with high affinity to calcium carbonate. Examples of calcium carbonate-binding peptides are provided as SEQ ID NOs: 173-185.
As used herein, “tooth-pellicle-binding peptide” refers to a peptide that binds with high affinity to the proteinaceous tooth pellicle layer that lies external to the enamel. Examples of tooth pellicle-binding peptides are provided as SEQ ID NOs: 135-143.
As used herein, “tooth-enamel-binding peptide” refers to a peptide that binds with high affinity to the enamel of the tooth. Examples of tooth enamel-binding peptides are provided as SEQ ID NOs: 144-154.
As used herein, “pigment-binding peptide” refers to a peptide that binds with high affinity to pigment particles of various types. Examples of pigment-binding peptides are peptides that bind to carbon black (SEQ ID NOs: 222-225), Cromophtal yellow (SEQ ID NOs: 226-230) and Sunfast Magenta (SEQ ID NOs: 231-235).
As used herein, the term “operably linked” refers to the association of nucleic acid sequences on a single nucleic acid fragment so that the function of one is affected by 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 (i.e., that the coding sequence is under the transcriptional control of the promoter). In a further embodiment, the definition of “operably linked” may also be extended to describe the products of chimeric genes, such as fusion peptides. As such, “operably linked” will also refer 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 as inclusion bodies in the expressing host cell.
Means to prepare the present peptides are well known in the art (see, for example, 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). The various components of the fusion peptides (inclusion body tag, peptide of interest, and the cleavable linker/cleavage sequence) described herein can be combined using carbodiimide coupling agents (see for example, Hermanson, Greg T., Bioconjugate Techniques, Academic Press, New York (1996)), diacid chlorides, diisocyanates and other difunctional coupling reagents that are reactive to terminal amine and/or carboxylic acid groups on the peptides. However, chemical synthesis is often limited to peptides of less than about 50 amino acids length due to cost and/or impurities. In a preferred embodiment, the biological molecules described herein are prepared using standard recombinant DNA and molecular cloning techniques.
As used herein, the terms “polypeptide” and “peptide” will be used interchangeably to 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. In one aspect, this term also includes post expression modifications of the polypeptide, for example, glycosylations, acetylations, phosphorylations and the like. Included within the definition are, for example, peptides containing one or more analogues of an amino acid or labeled amino acids and peptidomimetics. In a preferred embodiment, the present IBTs are comprised of L-amino acids.
As used herein, the term “bioactive” or “peptide of interest activity” refers to the activity or characteristic associated with the peptide and/or protein of interest. The bioactive peptides may be used in a variety of applications including, but not limited to curative agents for diseases (e.g., insulin, interferon, interleukins, anti-angiogenic peptides (U.S. Pat. No. 6,815,426), and polypeptides that bind to defined cellular targets (with the proviso that the peptide of interest is not an antibody or the Fab fragment of an antibody) such as receptors, channels, lipids, cytosolic proteins, and membrane proteins, to name a few), peptides having antimicrobial activity, peptides having an affinity for a particular material (e.g., hair binding polypeptides, skin binding polypeptides, nail binding polypeptides, tooth enamel-binding polypeptides, pellicle-binding peptides, cellulose binding polypeptides, polymer binding polypeptides, clay binding polypeptides, silicon binding polypeptides, carbon nanotube binding polypeptides, and peptides that have an affinity for particular animal or plant tissues) for targeted delivery of benefit agents. The peptide of interest is typically no more than 300 amino acids in length, preferably less than 200 amino acids in length, and most preferably less than 100 amino acids in length. In a preferred embodiment, the peptide of interest is a peptide selected from a combinatorially generated library wherein the peptide is selected based on a specific affinity for a target substrate.
As used herein, the “benefit agent” refers to a molecule that imparts a desired functionality to a complex involving the peptide of interest for a defined application. 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 targeted polypeptide is used to selectively target the benefit agent to the targeted material. In another embodiment, 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, clays, other peptides, etc.) and at least one region having an affinity for the benefit agent (e.g., pharmaceutical agents, pigments, conditioners, dyes, fragrances, etc.). In another embodiment, the peptide of interest comprises a plurality of regions having an affinity for the target material and a plurality of regions having an affinity for the benefit agent. In yet another embodiment, the peptide of interest comprises 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 of different. Examples of benefits agents may include, but are not limited to conditioners for personal care products, pigments, dyes, 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), to name a few.
“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 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.
As used herein, the term “solubility” refers to the amount of a substance that can be dissolved in a unit volume of a liquid under specified conditions. In the present application, the term “solubility” is used to describe the ability of a peptide (inclusion body tag, peptide of interest, or fusion peptides) to be resuspended in a volume of solvent, such as a biological buffer. In one embodiment, the peptides targeted for production (“peptides of interest”) are normally soluble in the cell and/or cell lysate under normal physiological conditions. Fusion of one or more inclusion body tags (IBTs) to the target peptide results in the formation of a fusion peptide that is insoluble under normal physiological conditions, resulting in the formation of inclusion bodies. In one embodiment, the peptide of interest is insoluble in an aqueous medium having a pH range of 5-12, preferably 6-10; and a temperature range of 5° C. to 50° C., preferably 10° C. to 40° C.
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


Any naturally-occurring amino acid
Xaa
X


(or as defined by the formulas


described herein)









“Gene” refers to a nucleic acid fragment that expresses a specific protein, including regulatory sequences preceding (5′ non-coding sequences) and following (3′ non-coding 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 (including coding regions engineered to encode fusion peptides) 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. A “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′ non-coding sequences), within, or downstream (3′ non-coding 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, 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, a plasmid and the like.
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); 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., Short Protocols in Molecular Biology, 5th Ed. Current Protocols and John Wiley and Sons, Inc., N.Y., 2002.
As used herein, the terms “fusion peptide”, “fusion protein”, “chimeric protein”, and “chimeric peptide” can be used interchangeably and refer to a polymer of amino acids (peptide, oligopeptide, polypeptide, or protein) comprising at least two portions, each portion comprising a distinct functionally independent peptide. In a fusion peptide wherein a first peptide PEP1 and a second peptide, PEP2, are both directly and covalently bound to an acid cleavable linker, L, through peptide bonds, a result of acid cleavage of the acid cleavable peptide linker, L, will be to disrupt the covalent bond between PEP1 and PEP2 rendering them soluble but no longer covalently joined. The result is that PEP1 and PEP2 would be separable by conventional biochemical methodology.
As used herein, the term “heterologous” refers to peptides and polypeptides that are not naturally encoded by a cell's genome, but are programmed to be synthesized by a cell that has been recombinantly engineered by standard gene transfer methods. As used herein, the term heterologous encompasses the fusion peptides of the invention, which are encoded by expression vectors that are introduced into the desired cell type. As used herein, a recombinant cell, a recombinant microbial cell, a recombinant yeast cell and a recombinant bacterial cell are cells that have been genetically or recombinantly engineered to synthesize the heterologous fusion peptides of the invention. In some cases, the synthesis of a heterologous peptide or polypeptide may be the result of the infection of a cell by either a eukaryotic virus or a prokaryotic bacteriophage.
In one embodiment, the invention encompasses a method of isolating a peptide of interest (“POI”) from a recombinant cell expressing a heterologous fusion peptide comprising the linker L. The recombinant cell may be any prokaryotic or eukaryotic cell type, including microbial cells. Preferred recombinant microbial cells include recombinant yeast and recombinant bacterial cells. An additional embodiment contemplates taking advantage of the fact that heterologous peptide expression in recombinant cells is often accompanied by the newly synthesized heterologous fusion peptides accumulating in insoluble inclusion bodies within the nucleus or the cytoplasm of the cell. When such insoluble fusion peptides having a POI also comprise the acid-cleavable linker L, it is contemplated herein that acid hydrolysis of L will liberate the POI from the inclusion body, preferably to a more soluble form. The released soluble form of the POI is then more easily separable from remaining inclusion bodies and insoluble remnants thereof.
As used herein, an “inclusion body” is an insoluble intracellular deposit of aggregated heterologous polypeptide(s) found in the cytoplasm or nucleus of a recombinant prokaryotic or eukaryotic cell. In a preferred embodiment the inclusion body is found in a recombinant microbial cell. In an even more preferred embodiment the recombinant microbial cell is a recombinant yeast cell or a recombinant bacterial cell. In a further preferred embodiment the recombinant bacterial cell is a recombinant Escherichia coli. 
As used herein, the term “solubility tag” or “inclusion body tag,” i.e., “IBT,” will refer to a peptide or polypeptide that facilitates formation of inclusion bodies when fused to a peptide of interest. The peptide of interest is preferably 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 an inclusion body tag produces a fusion protein that accumulates into intracellular bodies (inclusion bodies) within the host cell.
Peptides of interest that are typically soluble within 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 of interest 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 increase peptide production. In a further embodiment, fusion of the peptide of interest to one or more inclusion body tags (IBTs) increases the amount of protein produced in the host cell. Formation of the inclusion body facilitates simple and efficient purification of the fusion peptide from the cell lysate using techniques well known in the art such as centrifugation and filtration. In another embodiment, the inclusion body tag comprises an effective number of cross-linkable cysteine residues useful for separating the IBT from the peptide of interest (post cleavage into a mixture of peptide fragments) with the proviso that the peptide of interest is devoid of cysteine residues. The fusion protein typically includes one or more cleavable peptide linkers used to separate the protein/polypeptide of interest from the inclusion body tag(s). The cleavable peptide linker is designed so that the inclusion body tag(s) and the protein/polypeptide(s) of interest can be easily separated by cleaving the linker element. The peptide linker can be cleaved chemically (e.g., acid hydrolysis) or enzymatically (i.e., use of a protease/peptidase that preferentially recognizes an amino acid cleavage site and/or sequence within the cleavable peptide linker).
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.
As used herein, “acid-cleavable linker,” “acid-labile linker,” “acid-cleavable peptide,” and “acid cleavage site” may be used interchangeably and refers to a peptide that displays at least one acid-cleavable peptide bond under the conditions specified herein. The linker function of the acid-cleavable peptide is based on the fact that the linker is covalently bonded to at least two peptides, PEP1 and PEP2 wherein the at least two peptides are either identical or distinct from each other. Cleaving the linker, L, results in the breaking of a peptide bond, e.g., the bond between an aspartic acid and a proline residue or between two proline residues. The result would be that PEP1 and PEP2 would no longer be covalently joined.
In one embodiment, the acid-cleavable linker is bonded at either its carboxy terminus or amino terminus to an inclusion body tag (“IBT”) and a peptide of interest (“POI”) at the opposite terminus. Schematically, this may be represented according to the structural formula PEP1-L-PEP2, where either PEP1 or PEP2 may be either an IBT or POI and L represents an acid-cleavable linker.
In a further embodiment of PEP1-L-PEP2, both PEP1 and PEP2 are POIs. In such an embodiment, the fusion peptide is likely to be soluble, as would be the cleaved forms of PEP1 and PEP2. In an additional embodiment, wherein both PEP1 and PEP2 are POIs, it may unexpectedly arise that the fusion peptide is insoluble in the recombinant cell. This is likely to arise when either of the POIs unexpectedly functions as an IBT. In such cases, the acid-cleavage and peptide isolation may proceed as in the case where one of either PEP1 or PEP2 is a known IBT peptide.
In the context of the present invention, the term “isolate” or “isolated” refers to separating a given peptide or cellular component (e.g., inclusion body) from other cellular proteins, structures, components, debris, molecules, and the like, without any inference of having achieved a specific degree of purity. For illustration purposes, isolating a fusion peptide, POI or an inclusion body may arise when a mixture of components comprising a fusion peptide, POI or inclusion body is submitted to one or more process steps resulting in an enrichment of the fusion peptide, inclusion body or POI over the starting mixture of components. Isolating any given component separates it from some, but not necessarily all components of a cell homogenate, lysate or extract. Put another way, the term “isolated” may refer to either a purified component or a partially purified component. In the latter, no degree of purity should be inferred. Similarly, the term “separated” or “separating” and the like can be used interchangeably with “isolated” and “isolating,” as well as other similarly used terms.
In the context of the claimed invention the term “solution of sufficiently acidic pH” refers to any aqueous or organic liquid having a pH value that is sufficiently low to cleave the acid-cleavable linker L. These include organic solvents, water, or any saline, or buffered saline, or growth medium having a pH value that is sufficiently low to cleave the acid-cleavable linker L. A solution of sufficiently acidic pH encompasses solutions that are formulated to lower the intracellular pH of intact cells, the pH of the environment of disrupted or solubilized cells, or any mixture of cellular components, in order to promote the cleavage of linker L within the fusion peptide PEP1-L-PEP2.
A “POI” (i.e., protein of interest) is any peptide having one or more activities or functions that render it of interest to persons of ordinary skill in the art. Accordingly, the POI can possess any kind of functionality including, but not limited to, receptors, ligands, enzymes, diagnostic markers, cellular or viral structural components and the like. The term “independently functional” indicates that a POI or IBT demonstrates its activities or functions without participation by, or interaction with, an additional component of the fusion peptide PEP1-L-PEP2. Thus, for example, after hydrolytic release from either a soluble or insoluble fusion peptide, a POI will demonstrate its relevant properties, activities or functions under the proper conditions.
As used herein, a non-POI portion of the fusion peptide PEP1-L-PEP2 is what remains of the fusion peptide after the POI is removed by acid cleavage. Thus, in some instances, the non-POI portion of the fusion peptide could be represented by the IBT alone, or the IBT fused to a portion of the cleaved linker L. When the fusion peptide is insoluble, the non-POI portion of the fusion peptide refers to the insoluble portion of the fusion peptide remaining after acid cleavage of linker L.
Acid Cleavable Linkers and Fusion Peptides
A shown in FIG. 1, multimers of the single acid-cleavable DP pair provided enhanced rates of acid hydrolysis of an intact fusion peptide according to the order DP4>DP3>DP2>DP1 (see Table 2). Experiments in which individual amino acid substitutions were made at the position immediately following (i.e., on the carboxy side) the proline residue in the DP pair indicated that adding the aspartic acid had little if any effect (FIG. 4). The only amino acid substitution at this position that significantly enhanced the rate of acid hydrolysis was an additional proline (FIG. 4). Thus, the resultant sequence DPP reduced the half-time of acid hydrolysis by approximately two-fold over rate observed with the DP pair (FIG. 4).
Similar amino acid substitutions were made on the amino terminal side of the DP pair's aspartic acid residue (FIG. 3). While not as marked an effect as in the previous experiment, proline on the amino terminus side of the DP pair also had the shortest t1/2 of all amino acid substitutions. Of note is that the hydrophobic amino acids tryptophan and phenylalanine were actually significantly more inhibiting the acid hydrolysis than the other amino acids.
With this background, additional linkers were designed and prepared as indicated in Table 2. For illustration purposes only Table 2 provides a non-limiting number of embodiments of acid-cleavable peptide linkers that can be achieved given the empirical observations disclosed herein. Given this background and the technical guidance disclosed herein persons of ordinary skill in the art would be able to add to the list of acid-cleavable linkers that are encompassed by the inventive concept detailed in this specification and to the numerous uses for which cleavable peptide linkers are generally known in the art. For example the invention is useful for the expression and recovery of recombinantly produced peptides and proteins. Such proteins typically have high value in any number of applications including, but not limited to medical, biomedical, diagnostic, personal care, and affinity applications where the peptides of interest are used as linkers to various surfaces.
In one embodiment, the invention encompasses an acid-cleavable peptide linker, L, selected from the group consisting of:










A. DPDP,
(SEQ ID NO: 1)


 



B. DPDPDP,
(SEQ ID NO: 2)


 



C. DPDPDPDP,
(SEQ ID NO: 3)


 



D. DPDPDPP,
(SEQ ID NO: 4)


 



E. DPDPPDPP,
(SEQ ID NO: 5)


 



F. DPDPPDP,
(SEQ ID NO: 6)



and



 



G. DPPDPPDP,
(SEQ ID NO: 7)






wherein D is aspartic acid and P is proline;
In a preferred embodiment, the acid-cleavable peptide linker, L, is selected from the group consisting of DPDPDPP (SEQ ID NO:4), DPDPPDPP (SEQ ID NO:5), DPDPPDP (SEQ ID NO:6), and DPPDPPDP (SEQ ID NO:7).
The enhancement in the rate of acid hydrolysis demonstrated by the linkers of the invention is defined as the rate of acid hydrolysis of an intact fusion peptide comprising the acid-cleavable linker of the invention, as compared to the rate of acid hydrolysis of a fusion peptide when the linker comprises a single DP pair. In the context of this invention and throughout the specification, the acid-cleavable linkers may be referred to in a short-hand notation. Table 2 provides a nonlimiting illustrative list of specific embodiments of the acid-cleavable linkers showing their short-hand designations as well as their sequences and SEQ ID NO:.







TABLE 2







Embodiments of Linker L











Linker
Amino Acid
SEQ ID



Name
Sequence
NO:






DP2
DPDP
1


 



DP3
DPDPDP
2


 



DP4
DPDPDPDP
3


 



PP1
DPDPDPP
4


 



PP2
DPDPPDPP
5


 



PP3
DPDPPDP
6


 



PP4
DPPDPPDP
7









An additional embodiment of the invention encompasses a fusion peptide or fusion polypeptide comprising the acid-cleavable peptide linker wherein the fusion peptide has the structure,

PEP1-L-PEP2,

wherein PEP1 and PEP2 are functional peptides or polypeptides that are covalently linked to one another through the acid-cleavable peptide linker L.

In an additional embodiment of the invention, a fusion peptide or fusion polypeptide consisting essentially of one of the present acid-cleavable peptide linkers is provided wherein the fusion peptide has the structure,

PEP1-L-PEP2,

wherein PEP1 and PEP2 are functional peptides or polypeptides that are covalently linked to one another through the acid-cleavable peptide linker L.

Either PEP1 or PEP2, or both, may be a peptide of interest (“POI”). Such an embodiment of the fusion peptide may be soluble or insoluble in the cytoplasm of a recombinant cell. In the case wherein PEP1 and PEP2 are POIs that confer cytoplasmic solubility to the fusion peptide, the fusion peptide may be isolated from cellular components or even purified prior to acidic cleavage of linker L. Thus, the acid-cleavable linkers and fusion peptide of the present invention provide suitable means for the separation of a POI from a soluble fusion peptide.
As a nonlimiting illustrative example, the POI (e.g., PEP1) may be fused through L to an antigenic peptide (e.g., PEP2) to which specific antibodies are known. Conventional methodology thereby allows the fusion peptide to be isolated by immunological means, e.g., affinity chromatography on a column comprising an immobilized antibody directed to the antigenic peptide, as a first isolation step. Then after subsequent acid hydrolysis of the purified fusion peptide, the antigenic peptide may be separated from the POI by again submitting the acid-treated mixture to another round of affinity chromatography or immunoadsorption; e.g., on an affinity column or other affinity-substrate. Thus, the fusion peptide PEP1-L-PEP2 is suitably versatile to aid in the purification of POIs from soluble fusion peptides as well as from insoluble inclusion bodies.
As an additional nonlimiting illustrative example, the POI (e.g., PEP1) may be fused through L to a metal ion binding domain (e.g., PEP2) for which methods of adsorption to an ion-containing substrate are incorporated to purify the fusion peptide. Examples of such metal-binding domains include the 6×-His tag, or the metallothionein polypeptide or zinc-binding fragment thereof. Persons of ordinary skill in the art will recognize that these methods can be adapted to many situations wherein the newly synthesized fusion peptide remains soluble in the cell cytoplasm and PEP2, i.e. the non-POI portion of the fusion peptide is a known ligand or receptor that can be isolated by adsorption to an appropriate ligand-containing or receptor-containing substrate or support.
In an additional embodiment, one of PEP1 or PEP2 is a POI whereas the other of PEP1 or PEP2 is an inclusion body tag (“IBT”). In the context of this description an IBT functions to direct newly synthesized fusion peptide molecules into insoluble inclusion bodies within the recombinant cell, e.g., bacterial cell cytoplasm. In this embodiment, the acid-cleavable peptide linker provides a relatively simple means to release a POI from the insoluble portion of the fusion peptide comprising the IBT. For example, one could prepare an isolated preparation of inclusion bodies containing the desired fusion peptide wherein either of PEP1 or PEP2 is a POI with the remaining peptide being an IBT. Resuspending, contacting, or incubating the inclusion bodies in an acidic medium of sufficiently low pH and at the appropriate temperature for sufficient time would cleave the acid-cleavable peptide linker joining PEP1 to PEP2, thereby selectively cleaving the linker thereby yielding the POI in a soluble form while the IBT (or non-POI portion of the fusion peptide) remains insoluble. Therefore, the ease of separating the released soluble POI from the insoluble inclusion bodies provides a convenient and effective peptide purification step that can be combined with conventional biochemical peptide isolation methodology.
An additional type of fusion peptide may arise fortuitously, specifically wherein either of PEP1 or PEP2 unexpectedly acts to direct the newly synthesized fusion peptide into inclusion bodies. Stated another way, the situation may arise where a fusion peptide having a specific combination of PEP1 and PEP2, neither of which was known to have IBT-like properties, may unexpectedly accumulate in inclusion bodies. As long as at least one of either PEP1 or PEP2 becomes soluble after acid cleavage, isolation of a POI can be achieved according to the methods disclosed herein.
The acid-cleavable linkers within the fusion peptide cleave at an acidic pH of between about pH 1 and about pH 6, preferably between a pH of about pH 1 and about pH 4,more preferably between about pH 2 and about pH 4, even more preferably between about pH 3 and about pH 4, and most preferably about pH 4. Thus, it follows that the fusion peptide of the present invention would also be expected to be cleaved within the same pH ranges.
The enhanced rates of acid hydrolysis of the linkers and fusion peptides of the present invention are evidenced at a range of temperatures at the appropriate pH. Suitable temperature ranges are between about 40° C. to about 90° C., preferably from about 50° C. to about 80° C., more preferably between about 60° C. to about 70° C., and most preferably about 60° C.
In a further embodiment, the acid-cleavable linker is cleaved by incubating the fusion peptide at a pH of about pH 2 to about pH 4 and at a temperature of about 50° C. to about 80° C.
In view of this description, an even further embodiment of the invention encompassed herein comprises a method of preparing at least one peptide of interest (“POI”) from a fusion peptide comprising at least one POI, comprising:
a) providing a recombinant cell synthesizing a fusion peptide having the structure

PEP1-L-PEP2

    
    
        wherein,
        i) PEP1 and PEP2 are independently functional peptides wherein at least one is a peptide of interest (“POI”); and
        ii) L is an acid-cleavable linker comprising a peptide selected from the group consisting of:
    
    












A. DPDP,
(SEQ ID NO: 1)


 



B. DPDPDP,
(SEQ ID NO: 2)


 



C. DPDPDPDP,
(SEQ ID NO: 3)


 



D. DPDPDPP,
(SEQ ID NO: 4)


 



E. DPDPPDPP,
(SEQ ID NO: 5)


 



F. DPDPPDP,
(SEQ ID NO: 6)



and



 



G. DPPDPPDP,
(SEQ ID NO: 7)






wherein D is aspartic acid and P is proline;
b) contacting the fusion peptide with a solution of sufficiently acidic pH so that linker L is cleaved, and
c) isolating the at least one POI.
It is contemplated that the recombinant cell be either prokaryotic or eukaryotic. Preferably, the recombinant cell is a microbial cell, and more preferably a recombinant bacterial cell. A preferred recombinant bacterial cell is a recombinant Escherichia coli cell.
The method of preparing the POI comprises an acid cleaving step that is performed at an acidic pH of between about 1 and about 6, preferably between a pH of about 1 and about 4, and more preferably between about 2 and about 3.
With respect to temperature, the acid cleaving step is performed at a suitable temperature range of between about 40° C. to about 90° C., preferably from about 50° C. to about 80° C., and more preferably between about 50° C. or 60° C. to about 70° C.
For the purpose of practicing the inventive method inclusion bodies may be isolated from recombinant cells using any known methods. The release of the POI from the insoluble IBT-containing complex can be affected in preparations of inclusion bodies of varied purity. Therefore the inventive method may be used in conjunction with various additional methods of isolating inclusion bodies based on the specific needs of persons of ordinary skill in the art. In another embodiment, the inclusion bodies in whole recombinant cell homogenates or whole recombinant cell extracts may be acid treated without further enrichment or purification and still provide acid hydrolytic release of the POI to a soluble form that is separable from the insoluble remnant of the fusion peptide and the remaining inclusion bodies. In an even further embodiment, the invention encompasses a recombinant cell, more specifically a recombinant yeast cell or recombinant bacterial cell, which expresses such a fusion peptide. In this context an especially desirable recombinant bacterial cell is Escherichia coli. 
A still further embodiment of the invention is the isolated or purified inclusion bodies comprising a fusion peptide of interest. The inclusion bodies comprising the fusion peptide PEP1-L-PEP2 function as a convenient means to store, freeze, transport POIs in a form from which they are easily separated from the unwanted portion by acid hydrolysis and isolated by conventional biochemical techniques.
Inclusion Body Tags
The fusion peptide comprising an IBT may further comprise an effective number of cross-linkable cysteine residues. As described in co-pending U.S. Provisional Patent Application No. 60/951,754 entitled “Recombinant Peptide Production Using a Cross-Linkable Solubility Tag”, the inclusion of an effective number of cross-linkable cysteine residues is useful to selectively precipitate and separate the IBT from the POI during processing. Upon acidic cleavage of the fusion peptide, the mixture of fragments (IBTs and POIs) is subjected to oxidizing conditions for a period of time sufficient to cross-link the effective number of cysteine residues incorporated into the IBT. The oxidative cross-linking selectively precipitates the IBTs from the soluble peptide of interest with the proviso that the peptide of interest is devoid of cross-linkable cysteine residues.
IBTs comprising cysteine residues may be effectively used as solubility tags in combination with a peptide of interest having cross-linkable cysteine residues. However, in such situations an oxidative-cross linking step will typically be omitted during subsequent POI isolation.
Peptides of Interest
The peptide of interest (“POI”) targeted for production using the present method is one that is appreciably soluble in the host cell and/or host cell liquid lysate under normal physiological conditions. In a preferred aspect, the peptides of interest are generally short (<300 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 of the present 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.
In general, the inventive acid-cleavable linkers can be used in a process to produce any peptide of interest that is (1) typically soluble in the cell and/or cell lysate under typical physiological conditions and/or (2) those that can be produced at significantly higher levels when expressed in the form of an inclusion body. In a preferred embodiment, the peptide of interest is appreciably soluble in the host cell and/or corresponding cell lysate under normal physiological and/or process conditions.
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 (i.e. expression in the form of a fusion protein protect the peptide of interest from proteolytic degradation). Typically the peptide of interest is less than 300 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 such as curative agents for diseases (e.g., insulin, interferon, interleukins, peptide hormones, anti-angiogenic peptides, and peptides (with the proviso that the peptide is not an antibody or an Fab portion of an antibody) 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 (e.g., biological tissues, biological molecules, hair-binding peptides (U.S. Patent Application Publication Nos. 2005-0226839, 2003-0152976, and 2002-0098524; International Patent Application Publication Nos. WO01/79479 and WO04/048399; and U.S. Pat. Nos. 7,736,633; 7,427,656; and 7,749,957), skin-binding peptides (U.S. Pat. Nos. 7,309,482; 7,427,656; 7,749,957; and 7,341,604), nail-binding peptides (U.S. Patent Application Publication No. 2005-0226839; U.S. Pat. No. 7,749,957), cellulose-binding peptides, polymer-binding peptides (U.S. Pat. Nos. 7,632,919; 7,928,076; 7,700,716; and 7,906,617), and clay-binding peptides (U.S. Pat. No. 7,749,957), for targeted delivery of at least one benefit agent (U.S. Pat. Nos. 7,220,405 and 7,749,957; and U.S. Patent Application Publication No. 2005-0226839).
In a preferred aspect, the peptide of interest is an affinity peptide identified from a combinatorially generated peptide library. In a further aspect, the peptide is selected from a combinatorially generated library wherein said library was prepared using a technique selected from the group consisting of phage display, yeast display, bacterial display, ribosomal display and mRNA display.
In a preferred aspect, the peptide of interest is selected from the group of hair binding peptides, skin binding peptides, nail binding peptides, tooth binding peptides, antimicrobial peptides, pigment binding peptides, clay-binding peptides, mineral binding peptides (e.g., calcium carbonate), and various polymer binding peptides.
Affinity peptides are particularly useful to target benefit agents imparting a desired functionality to a target material (e.g., hair, skin, etc.) for a defined application (U.S. Pat. Nos. 7,220,405; 7,736,633; and 7,749,957; and U.S. Patent Application Publication No. 2005-0226839 for a list of typical benefit agents such as conditioners, pigments/colorants, fragrances, etc.). The benefit agent may be 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. In another embodiment, the peptide of interest 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, antimicrobial agents, pigments, conditioners, dyes, fragrances, etc.). In another embodiment, the peptide of interest comprises 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. In yet another embodiment, the peptide of interest comprises 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 of different. 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), to name a few.
Cleavable Peptide Linkers
Fusion peptides comprising inclusion body tags will typically include at least one cleavable sequence separating the inclusion body tag from the polypeptide of interest. The cleavable sequence facilitates separation of the inclusion body tag(s) from the peptide(s) of interest. In one embodiment, 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). In a preferred embodiment, the cleavable sequence is provided by including (in the fusion peptide) at least one cleavable peptide linker between the inclusion body tag and the peptide of interest.
Generally, means to cleave peptide linkers include chemical hydrolysis, enzymatic agents, and combinations thereof. In one embodiment, 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 (cleaves methionine residues), N-chloro succinimide, iodobenzoic acid or BNPS-skatole [2-(2-nitrophenylsulfenyl)-3-methylindole] (cleaves tryptophan residues), dilute acids (cleaves at aspartic acid-proline bonds), and hydroxylamine (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.)).
In a preferred embodiment, one or more aspartic acid—proline acid-cleavable recognition sites (i.e., a cleavable peptide linker comprising one or more D-P dipeptide moieties) are included in the fusion protein construct to facilitate separation of the inclusion body tag(s) from the peptide of interest.
In another embodiment, the fusion peptide may include multiple regions encoding peptides of interest separated by one or more cleavable peptide linkers.
In another embodiment, one or more enzymatic cleavage sequences are included in the fusion protein construct to facilitate recovery of the peptide of interest. Examples of enzymes useful for cleaving the peptide linker may 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 the 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 (e.g. mechanical and/or chemical lysis). Methods to isolate the insoluble inclusion bodies/fusion peptides from the cell lysate are well known in the art (e.g., centrifugation, filtration, and combinations thereof). Once recovered from the cell lysate, the insoluble inclusion bodies and/or fusion peptides can be treated with a cleavage agent (chemical or enzymatic) to cleavage the inclusion body tag from the peptide of interest. In one embodiment, the fusion protein and/or inclusion body is diluted and/or dissolved in a suitable solvent prior to treatment with the cleavage agent. In a further embodiment, 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, and in a preferred embodiment, 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. In one embodiment, the peptide of interest is soluble while the inclusion body tag and/or fusion protein is insoluble in the defined process medium (typically an aqueous medium). In another embodiment, the peptide of interest is insoluble while the inclusion body tag is soluble in the defined process medium.
In a preferred embodiment, the inclusion body tag comprises an effective number of cross-linkable cysteine residues with the proviso that the peptide of interest is devoid of cysteine residues (U.S. Pat. No. 7,951,559). Upon cleavage, oxidative cross-linking is used to selectively cross-link the IBTs (typically insoluble). The conditions are controlled so that the cross-linked IBTs are insoluble while the peptide of interest remains soluble. The soluble peptide of interest is subsequently separated from the cross-linked IBTs using a conventional separation techniques such as centrifugation.
In an optional embodiment, the peptide of interest may be further purified using any number of purification techniques in the art such as ion exchange, gel purification techniques, and column chromatography (see U.S. Pat. No. 5,648,244), to name a few.
Fusion Peptides
Inclusion body tags are used to create chimeric polypeptides (“fusion peptides” or “fusion proteins”) that are insoluble within the host cell, forming inclusion bodies. Methods of synthesis and expression of genetic constructs encoding the present fusion peptides is well known to one of skill in the art.
The present fusion peptides will include at least one inclusion body tag (IBT) functionally linked to at least one peptide of interest (POI) via an acid-cleavable linker of the present invention. Typically, the fusion peptides will also include at least one cleavable peptide linker having a cleavage site between the inclusion body tag and the peptide of interest. In one embodiment, the inclusion body tag may include a cleavage site whereby inclusion of a separate cleavable peptide linker may not be necessary. In a preferred embodiment, the cleavage method is chosen to ensure that the peptide of interest is not adversely affected by the cleavage agent(s) employed. In a further embodiment, the peptide of interest may be modified to eliminate possible cleavage sites with the peptide so long as the desired activity of the peptide is not adversely affected.
One of skill in the art will recognize that the elements of the fusion protein can be structured in a variety of ways. Typically, the fusion protein will include at least one IBT (i.e., PEP1), at least one peptide of interest (POI) (i.e., PEP2), and at least one cleavable peptide linker (L) located between the IBT and the POI. Thus, such a fusion peptide conforms to the general structure PEP1-L-PEP2. The inclusion body tag may be organized as a leader sequence or a terminator sequence relative to the position of the peptide of interest within the fusion peptide. In another embodiment, a plurality of IBTs, POIs, and Ls are used when engineering the fusion peptide.
In a further embodiment, the fusion peptide may include a plurality of IBTs (as defined herein), POIs, and Ls that are the same or different.
In another embodiment of the fusion peptide, neither of PEP1 or PEP2 comprises an IBT, but rather the fusion peptide remains soluble. As a nonlimiting illustrative, example, the POI (e.g., PEP1) may be fused through L to an antigenic peptide (e.g., PEP2) to which specific antibodies are known. Conventional methodology thereby allows the fusion peptide to be isolated by immunological means, e.g., affinity chromatography on a column comprising an immobilized antibody directed to the antigenic peptide, as a first isolation step. Then after subsequent acid hydrolysis of the purified fusion peptide, the antigenic peptide may be separated from the POI by again submitting the acid-treated mixture to another round of affinity chromatography or immunoadsorption on; e.g., an affinity column or other affinity-substrate. Thus, the fusion peptide PEP1-L-PEP2 is suitably versatile to aid in the purification of POIs from soluble fusion peptides as well as from insoluble inclusion bodies.
The fusion peptide should be insoluble in an aqueous medium at a temperature of about 10° C. to about 50° C., preferably about 10° C. to about 40° C. The aqueous medium typically comprises a pH range of about pH 5 to about pH 12, preferably about pH 6 to about pH 10, and most preferably about pH 6 to about pH 8. The temperature, pH, and/or ionic strength of the aqueous medium can be adjusted to obtain the desired solubility characteristics of the fusion peptide/inclusion body.
Method of Making a Peptides of Interest Using Insoluble Fusion Peptides
The inclusion body tags are used to make fusion peptides that form inclusion bodies within the production host. This method is particularly attractive for producing significant amounts of soluble peptide of interest that (1) are difficult to isolation from other soluble components of the cell lysate and/or (2) are difficult to product in significant amounts within the target production host.
In the present methods, a POI is fused to one end of an inventive acid-cleavable linker while an IBT is fused at the other end thereby forming an insoluble fusion protein. Expression of the genetic construct encoding the fusion protein produces an insoluble form of the peptide of interest that accumulates in the form of inclusion bodies within the host cell. The host cell is grown for a period of time sufficient for the insoluble fusion peptide to accumulate within the cell.
The host cell is subsequently lysed using any number of techniques well known in the art. The insoluble fusion peptide/inclusion bodies are then separated from the soluble components of the cell lysate using a simple and economical technique such as centrifugation and/or membrane filtration. The insoluble fusion peptide/inclusion body can then be further processed in order to isolate the peptide of interest. Typically, this will include resuspension of the fusion peptide/inclusion body in a liquid medium suitable for cleaving the fusion peptide, separating the inclusion body tag from the peptide of interest. The fusion protein is typically designed to include a cleavable peptide linker separating the inclusion body tag from the peptide of interest. The cleavage step can be conducted using any number of techniques well known in the art (chemical cleavage, enzymatic cleavage, and combinations thereof). The peptide of interest can then be separated from the inclusion body tag(s) and/or fusion peptides using any number of techniques well known in the art (centrifugation, filtration, precipitation, column chromatography, etc.). Preferably, the peptide of interest (once cleaved from fusion peptide) has a solubility that is significantly different than that of the inclusion body tag and/or remaining fusion peptide. In a further preferred embodiment, oxidative cross-linking is used to selectively precipitate the IBT (comprising an effective number of cross-linkable cysteine residues) from the peptide of interest (when devoid of cross-linkable cysteine residues). For example, IBT139.CCPGCC, IBT-139(5C), and IBT186, were designed to include an effective number of cross-linkable cysteine residues.
Transformation and Expression
Once the inclusion body tag has been identified and paired with the appropriate peptide of interest, construction of cassettes and vectors that may be transformed in to an appropriate expression host is common and well known in the art. 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. Suitable vectors comprise a region 5′ of the gene which harbors transcriptional initiation controls and a region 3′ of the DNA fragment which controls transcriptional termination. It is most preferred when both control regions are derived from genes homologous to the transformed host cell, although it is to be understood that such control regions need not be derived from the genes native to the specific species chosen as a production host.
Transcription initiation control regions or promoters, which are useful to drive expression of the genetic constructs encoding the fusion peptides in the desired host cell, are numerous and familiar to those skilled in the art. Virtually any promoter capable of driving these constructs is suitable for the present invention including but not limited to CYC1, HIS3, GAL1, GAL10, ADH1, PGK, PHO5, GAPDH, ADC1, TRP1, URA3, LEU2, ENO, TPI (useful for expression in Saccharomyces); AOX1 (useful for expression in Pichia); and lac, ara (pBAD), tet, trp, IPL, IPR, T7, tac, and trc (useful for expression in Escherichia coli) as well as the amy, apr, npr promoters and various phage promoters useful for expression in Bacillus. 
Termination control regions may also be derived from various genes native to the preferred hosts. Optionally, a termination site may be unnecessary; however, it is most preferred if included.
Preferred host cells for expression of the present fusion peptides 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. For example, it is contemplated that any of bacteria, yeast, and filamentous fungi will be suitable hosts for expression of the present nucleic acid molecules encoding the fusion peptides. Because of transcription, translation, and the protein biosynthetic apparatus is the same irrespective of the cellular feedstock, genes are expressed irrespective of the carbon feedstock used to generate the cellular biomass. 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 that are added to the culture and are 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 fungal or yeast species such as Aspergillus, Trichoderma, Saccharomyces, Pichia, Yarrowia, Candida, Hansenula, or 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. Preferred bacterial host strains include Escherichia, Pseudomonas, and Bacillus. In a highly preferred aspect, the bacterial host strain is Escherichia coli. 
Fermentation Media
Fermentation media in the present invention 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. Additionally the carbon substrate may also be one-carbon substrates such as carbon dioxide, or methanol for which metabolic conversion into key biochemical intermediates has been demonstrated. In addition to one and two carbon substrates methylotrophic organisms are also known to utilize a number of other carbon containing compounds such as methylamine, glucosamine and a variety of amino acids for metabolic activity. For example, methylotrophic yeast are known to utilize the carbon from methylamine to form trehalose or glycerol (Bellion et al., Microb. Growth C1 Compd., [Int. Symp.], 7th (1993), 415-32. Editor(s): Murrell, J. Collin; Kelly, Don P. Publisher: Intercept, Andover, UK). Similarly, various species of Candida will metabolize alanine or oleic acid (Sulter et al., Arch. Microbiol. 153:485-489 (1990)). Hence 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.
Although it is contemplated that all of the above mentioned carbon substrates and mixtures thereof are suitable in the present invention, preferred carbon substrates are glucose, fructose, and sucrose.
In addition to an appropriate carbon source, fermentation media must contain suitable minerals, salts, cofactors, buffers and other components, known to those skilled in the art, suitable for the growth of the cultures and promotion of the expression of the present fusion peptides.
Culture Conditions
Suitable culture conditions can be selected dependent upon the chosen production host. 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 may include 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.
Fermentations may be performed under aerobic or anaerobic conditions where aerobic conditions are generally preferred.
Industrial Batch and Continuous Fermentations
A 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 CO2. 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., 36:227 (1992).
Although the present invention is typically 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.
EXAMPLES
The present invention is further defined in the following Examples. It should be understood that these Examples, while indicating preferred embodiments of the invention, are given by way of illustration only. From the above discussion and the guidance provided by the Examples, one skilled in the art can ascertain the essential characteristics of this invention, and without departing from the 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, and “cat#” means catalog number.
General Methods
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); 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., Short Protocols in Molecular Biology, 5th Ed. Current Protocols and John Wiley and Sons, Inc., N.Y., 2002.
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, D.C., 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.
Expression Vector pLD001
Plasmid pLD001 (SEQ ID NO: 254) has been previous reported as a suitable expression vector for E. coli (see U.S. Patent Application Publication No. 2010-0158823 A1 to Wang et al.; incorporated herein by reference).
The vector pLD001 was derived from the commercially available vector pDEST17 (Invitrogen, Carlsbad, Calif.). It includes sequences derived from the commercially available vector pET31b (Novagen, Madison, Wis.) that encode a fragment of the enzyme ketosteroid isomerase (KSI). The KSI fragment was included as a fusion partner to promote partition of the peptides into insoluble inclusion bodies in E. coli. The KSI-encoding sequence from pET31b was modified using standard mutagenesis procedures (QuickChange II, Stratagene, La Jolla, Calif.) to include three additional Cys codons, in addition to the one Cys codon found in the wild type KSI sequence. In addition, all Asp codons in the coding sequence were replaced by Glu codons. Plasmid pLD001, given by SEQ ID NO: 254, was constructed using standard recombinant DNA methods, which are well known to those skilled in the art.
Coding sequences bounded by BamHI and AscI sites may be ligated between BamHI and AscI sites in pLD001 using standard recombinant DNA methods. The resulting gene fusions resulted in a peptide of interest was fused downstream from a modified fragment of ketosteroid isomerase (KSI(C4)E) that served to drive the peptide into insoluble inclusion bodies in E. coli (See U.S. Patent Application Publication No. 2009-0029420A1; herein incorporated by reference)
Example 1
Preparation of Plasmid pLX121
A genetic construct was prepared for evaluating the performance of the inventive acid-cleavable linker by fusing the linker to an inclusion body tag on one end, and a soluble peptide of interest at the linker's opposite end. The peptide of interest used in the present examples was prepared from a previously reported peptide-based triblock dispersant (U.S. Patent Application Publication No. 2005-0054752).
Cloning of the TBP1 Gene
The TBP1 gene, encoding the TBP1 peptide, was selected for evaluation of the inventive acid-cleavable linkers. The synthetic TBP1 peptide is peptide-based triblock dispersant comprising a carbon-black binding domain, a hydrophilic peptide linker, and a cellulose binding domain (see Example 15 of U.S. patent application Ser. No. 10/935,254, herein incorporated by reference).
The TBP1 gene (SEQ ID NO: 17) encoding the 68 amino acid peptide TBP101 (SEQ ID NO: 19) was assembled from synthetic oligonucleotides (Sigma-Genosys, Woodlands, Tex.; Table 3).







TABLE 3







Oligonucleotides Used to Prepare the TBP1











SEQ


Oligonucleotide

ID


Name
Nucleotide Sequence (5′-3′)
NO:












TBP1(+)1
GGATCCATCGAAGGTCGTTTCCACGAA
8



AACTGGCCGTCTGGTGGCGGTACCTC




TACTTCCAAAGCTTCCACCACTACGAC




TTCTAGCAAAACCACCACTACAT



 


TBP1(+)2
CCTCTAAGACTACCACGACTACCTCCAA
9



AACCTCTACTACCTCTAGCTCCTCTACG




GGCGGTGGCACTCACAAGACCTCTACTC




AGCGTCTGCTGGCTGCATAA



 


TBP1(−)1
TTATGCAGCCAGCAGACGCTGAGTAGAG
10



GTCTTGTGAGTGCCACCGCCCGTAGAG




GAGCTAGAGGTAGT



 


TBP1(−)2
AGAGGTTTTGGAGGTAGTCGTGGTAGTC
11



TTAGAGGATGTAGTGGTGGTTTTGCTAG




AAGTCGTAGTGGT



 


TBP1(−)3
GGAAGCTTTGGAAGTAGAGGTACCGC
12



CACCAGACGGCCAGTTTTCGTGGAAAC




GACCTTCGATGGATCC









Each oligonucleotide was phosphorylated with ATP using T4 polynucleotide kinase. The resulting oligonucleotides were mixed, boiled for 5 min, and then cooled to room temperature slowly. Finally, the annealed oligonucleotides were ligated with T4 DNA ligase to give synthetic DNA fragment TBP1, given as SEQ ID NO: 17, which encodes the TBP101 peptide (SEQ ID NO: 19).
Construction of pINK101 Expression Plasmid:
Lambda phage site-specific recombination was used for preparation and expression of the present fusion proteins (GatewayTM System; Invitrogen, Carlsbad, Calif.). TBP1 was integrated into the GatewayTM system for protein over-expression. In the first step, 2 μL of the TBP1 ligation mixture was used in a 50-μL PCR reaction. Reactions were catalyzed by Pfu DNA polymerase (Stratagene, La Jolla, Calif.), following the standard PCR protocol. Primer 5′TBP1 (5′-CACCGGATCCATCGAAGGTCGT-3′; SEQ ID NO: 21) and 3′TBP1 (5′-TCATTATGCAGCCAGCAGCGC-3′; SEQ ID NO: 20) were used for amplification of the TBP1 fragment. The design of these primers adds an additional sequence of CACC and another stop codon TGA were added to the 5′ and 3′ ends of the amplified fragments.
The amplified TBP1 was directly cloned into pENTRTM/D-TOPO® vector (SEQ ID NO: 22) using Invitrogen's pENTRTM directional TOPO® cloning kit (Invitrogen; Catalog K2400-20), resulting in the GatewayTM entry plasmid pENTR-TBP1. This entry plasmid was propagated in One Shot® TOP10 E. coli cells (Invitrogen). The accuracy of the PCR amplification and cloning procedures were confirmed by DNA sequencing analysis. The entry plasmid was mixed with pDEST17 (Invitrogen, SEQ ID NO: 23). LR recombination reactions were catalyzed by LR CLONASETM (Invitrogen). The destination plasmid, pINK101 was constructed and propagated in the DH5a E. coli strain. The accuracy of the recombination reaction was determined by DNA sequencing. All reagents for LR recombination reactions (i.e., lambda phage site-specific recombination) were provided in Invitrogen's E. coli expression system with the GATEWAYTM Technology kit. The site-specific recombination process followed the manufacturer's instructions (Invitrogen).
The resulting plasmid, named pINK101, contains the coding region for recombinant protein 6H-TBP1, named INK101 (SEQ ID NO 18), which is an 11.6 kDa protein. The protein sequence includes a 6×His tag and a 24 amino acid linker that includes Factor Xa protease recognition site before the sequence of the TBP101 peptide.
The amino acid coding region for the 6×His tag and the following linker comprising the Factor Xa protease recognition site were excised from pINK101 by digestion with the NdeI and BamHI restriction enzymes.
The TBP1 gene (SEQ ID NO:17) encodes a polypeptide (SEQ ID NO:19) having a ST linker flanked by Gly-Gly-Gly amino acids. The system was made more modular by further mutagenesis to change the upstream amino acid sequence from Gly-Gly-Gly to Ala-Gly-Gly (codon GGT changed to GCC) and the downstream Gly-Gly-Gly to Gly-Gly-Ala (codon GGT GGC changed to GGC GCC). These changes provided a NgoMI restriction site and a Kasl restriction site flanking the ST linker, thus facilitating replacement of any element in TBP1.
Further modifications were made to TBP101 including the addition of an acid cleavable site to facilitate the removal of any tag sequence encoded by the region between the NdeI and BamHI sites of the expression plasmid. The resulting plasmid was called pLX121 (also referred to as “pINK101DP”; SEQ ID NO: 250). These modifications changed the amino acids E-G to D-P (acid cleavable aspartic acid—proline linkage) using the Stratagene QUIKCHANGE® II Site-Directed Mutagenesis Kit Cat#200523 (La Jolla, Calif.) as per the manufacturer's protocol using the primers INK101+(5′-CCCCTTCACCGGATCCATCGATCCACGTTTCCACGAAAACTGGCC-3′; SEQ ID NO: 24) and INK101-(5′-GGCCAGTTTTCGTGGAAACGTGGATCGATGGATCCGGTGAAGGGG-3′; SEQ ID NO: 25). The sequences were confirmed by DNA sequence analysis. The coding region (SEQ ID NO: 251) and the corresponding amino acid sequence of the modified protein (SEQ ID NO: 26), INK101DP, are provided.







INK101DP Peptide (SEQ ID NO: 26):


MSYYHHHHHHLESTSLYKKAGSAAAPFTGSIDPRFHENWPSAGGTSTSKA


 


STTTTSSKTTTTSSKTTTTTSKTSTTSSSSTGGATHKTSTQRLLAA






The aspartic acid—proline acid cleavable linker is in bold type. The DP pair replaces the EG pair found in the unmodified TBP101 peptide. The modified TBP101 peptide (i.e., a model peptide of interest) is underlined.
The INK101DP peptide conforms to the general structure PEP1-L-PEP2, wherein PEP1 containing the 6×His tag and Factor Xa cleavage site was found to function as an IBT, whereas PEP2 functions as a POI (i.e., a carbon black binding peptide). In this instance, the 6×His tag was found to be necessary for directing the accumulation of the newly synthesized fusion peptide in insoluble inclusion bodies within the recombinant bacterial cell cytoplasm.
Example 2
Acid Hydrolysis of Peptide Linkers Containing Multiple DP Residues
This example demonstrates the enhanced rate of acid hydrolysis of a fusion peptide having a linker comprising more than one consecutively arranged aspartic acid-proline (i.e., DP) pair. Specifically, the rate of acid hydrolysis of fusion peptides having peptide linkers comprising one, two, three or four consecutive DP pairs were measured and compared.
Strain and Media
Escherichia coli BL21-A1 was obtained from Invitrogen Corp. (Cat. #607003, Carlsbad, Calif.). Expression plasmid pINK101DP (Example 1) was previously described in U.S. Patent Application Publication No. 2005-0054752) Cells were grown at 37° C. in Miller's LB broth (Cat. #46-050-CM, Mediatech, Inc., Herndon, Va.) with 0.2% L-(+)-arabinose (Cat. #A3256, Sigma-Aldrich, Inc., St. Louis, Mo.) and 100 μg/mL ampicillin (Cat. #A1066, Sigma-Aldrich, Inc., St. Louis, Mo.). Cells were plated on LB agar plates with 100 μg/mL ampicillin (Cat. #L1004, Teknova, Inc., Hollister, Calif.).
Construction of pINK101DP Variants Containing Additional DPs
One to three additional DP residues were added to pINK101DP by site-directed mutagenesis using a QUIKCHANGETM II Kit (Cat. #200524, Stratagene, La Jolla, Calif.). Primers pairs used to add additional DP residues are provided in Table 4. Reactions were thermocycled in a Gene Amp 9700 using the thermocycling parameters provided in Table 5 (Perkin Elmer Applied Biosystems, Norwalk, Conn.). Escherichia coli BL21-A1 was transformed with 1 μL of QUIKCHANGETM reaction product according to manufacturer's directions and transformants were selected on LB agar plates with 100 μg/mL ampicillin. DNA sequences were obtained for six isolates from each transformation in order to identify those with the desired mutations.







TABLE 4







Mutagenesis Primers











Primer

SEQ ID



ID
Nucleotide Sequence
NO:






for DP2
CCCCTTCACCGGATCCATCGATCCAG
13




ATCCACGTTTCCACGAAAACTGGCC



 



for DP3
CCCCTTCACCGGATCCATCGATCCAG
14




ATCCAGATCCACGTTTCCACGAAAACT





GGCC



 



for DP4
CCCCTTCACCGGATCCATCGATCCAG
15




ATCCAGATCCAGATCCACGTTTCCAC





GAAAACTGGCC



 



Remote
GTAATACGGTTATCCACAGAATCAG
16



Rev









Reaction Components—

















10X QUIKCHANGE TM reaction buffer
 5 μL



QUIKCHANGE TM dNTP mix
 1 μL



Pfu polymerase
 1 μL



10 μM forward primer
 1 μL



10 μM reverse primer
 1 μL



Water
40 mL

















TABLE 5







Thermocycling program










Segment
Cycles
Temperature
Time













1
1
95° C.
 2 minutes


2
18
95° C.
50 seconds




55° C.
 1 minute




68° C.
10 minutes


3
1
68° C.
10 minutes


4
1
 4° C.
hold









Preparation of Peptide-Containing Inclusion Bodies

Strains containing each mutant plasmid were grown for 18 hrs at 37° C. in LB with 0.2% arabinose and 100 μg/mL ampicillin. Cells were lysed by adding 75 mg/mL CELYTICTM Express reagent (Cat. #C1990, Sigma Aldrich, St. Louis, Mo.) and incubating at 37° C. for 20 minutes. Inclusion body pellets were separated from lysed cell cultures by centrifugation at 9,000×g for 1 minute. Pellets were washed three times with 1⁄3rd the original culture volume of 20 mM Tris-Cl, pH 8.0, and then resuspended in 1/10th the original culture volume of 20 mM Tris-Cl, pH8.0.
Acid Hydrolysis of Peptide in Inclusion Body Pellets
Pellets were washed once and then resuspended in 1/10th the original culture volume of sterile, filtered water. One mL of inclusion body suspension was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 500 μL of 20 mM H2PO4, pH 2.2 (Cat. #0260-1, J. T. Baker, Phillipsburg, N.J.). A 100 μL time-zero sample was removed and neutralized by adding 50 μL of 100 mM MES, pH 8.9 (Cat. #475893, Calbiochem, La Jolla, Calif.). The remaining inclusion body sample was incubated at 65° C. Additional samples were taken at 2, 6 and 24 hours and neutralized in the same manner as the time-zero sample.
Separation of Hydrolyzed Peptide/Tag Fragments
25 μL of each neutralized sample was mixed with 75 μL 8 M guanidine-HCl (Cat. #5502UA, Life Technologies, Inc., Gaithersburg, Md.) and 25 μL of that mixture was injected onto a GraceVydacC18 HPLC column (Cat. #218TP54, Resolution Systems, Holland Mich.) run on an Agilent 1100 HPLC system (Agilent, Foster City, Calif.). Run conditions were 0.1% TFA in water and acetonitrile, gradient from 10-90% acetonitrile in 28 minutes, 0.35 mL/min, 40° C. Peak identities were confirmed by running fractions on denaturing acrylamide gels.
Analysis of HPLC Data
HPLC data was analyzed using ChemStation software (Hewlett Packard GmbH, Waldbrunn, Germany). Hydrolysis rates were determined by measuring the reduction in peak area for the unhydrolyzed peptide at each time point (FIG. 1).
Results and Conclusion
The rate of acid hydrolysis of the acid-labile linkers was based on the rate of disappearance of the corresponding parent fusion peptide (FIG. 1). Generally, each fusion peptide comprising more than one DP pair per linker was acid cleaved at a higher rate than the fusion peptide with one DP pair thereby indicating the relative rates of acid-cleavage demonstrated by the linkers of the present invention. In general, the rates of acid hydrolysis of the fusion peptides having the corresponding linkers follows the order DP4>DP3>DP2>DP.
The rate of acid-cleavage of the fusion peptide can be modeled under this set of conditions as a simple linear combination of first order rate constants (FIG. 2). Decreasing the t1/2 for hydrolysis can be accomplished by increasing the DP number.
In the experiments described in Example 4, linkers comprising three consecutive DP pairs, i.e. DP3, formed the core linker into which additional proline residues were introduced at various locations within the DP3 sequence. The introduction of one or more additional proline residues immediately after the proline of DP pair was predicated on the results of saturation mutagenesis experiments described in Example 3, and summarized in FIGS. 3 and 4. These experiments show that an additional proline added immediately after the proline of a single DP pair, provided enhanced fusion peptide hydrolysis rates.
Example 3
Effect of Saturation Mutagenesis at Amino Acid Positions Immediately Preceding or Following a Single DP Linker
This Example demonstrates the effects of amino acid changes in the positions immediately upstream of the D residue in a single DP pair (i.e., the IBT side of the test fusion peptide) and downstream of the P residue in the single DP pair (i.e., the POI side of the test fusion peptide).
Construction of pINK101DP Variants Containing Amino Acid Changes on Either Side of DP Linker
The strains and media follow those described in Example 2. Multiple changes were made to residues on either side of the DP linker in pINK101DP by site-directed mutagenesis using a QUIKCHANGETM II Kit (Cat. #200524, Stratagene, La Jolla, Calif.). Reactions were thermocycled in a Gene Amp 9700 (Perkin Elmer Applied Biosystems, Norwalk, Conn.). The primers used to introduce changes are provided in Table 6 and the thermocycling program parameters are provided in Table 7. Escherichia coli BL21-A1 was transformed with 1 μL of QUIKCHANGETM reaction product according to manufacturer's directions and transformants were selected on LB agar plates with 100 μg/mL ampicillin. In cases where no transformants were obtained (DP-Asp, DP-Glu, DP-Gly, DP-His, DP-Ile, DP-Leu, DP-Lys, DP-Met, DP-Pro, DP-Thr, DP-Trp), 2 μL of QUIKCHANGETM reaction product was used to transform E. coli 10G Elite Electrocompetent Cells (Lucigen Corp., Middleton, Wis.) according to manufacturer's directions, for the purpose of generating super-coiled plasmid DNA. Transformants were selected on LB agar plates with 100 μg/mL ampicillin. DNA sequences were obtained for six isolates from each transformation in order to identify those with the desired mutations. Plasmid was prepared from the identified isolates using QIAprep Spin Miniprep Kit (QIAGEN Inc., Valencia, Calif.). Escherichia coli BL21-A1 was then transformed with 10 ng of plasmid DNA according to manufacturer's directions and transformants were selected on LB agar plates with 100 μg/mL ampicillin.







TABLE 6







Primers used to introduce modifications to


residues flanking DP residues













SEQ ID



Primer ID
Nucleotide Sequence
NO:














DP1Alafor
CACCGGATCCATCGATCCAGCATT
27




CCACGAAAACTGGCCGTC



 



DP1Alarev
GACGGCCAGTTTTCGTGGAATGCT
28




GGATCGATGGATCCGGTG



 



DP1Asnfor
CACCGGATCCATCGATCCAAACTT
29




CCACGAAAACTGGCCGTC



 



DP1Asnrev
GACGGCCAGTTTTCGTGGAAGTTT
30




GGATCGATGGATCCGGTG



 



DP1Aspfor
CACCGGATCCATCGATCCAGATTT
31




CCACGAAAACTGGCCGTC



 



DP1Asprev
GACGGCCAGTTTTCGTGGAAATCT
32




GGATCGATGGATCCGGTG



 



DP1Cysfor
CACCGGATCCATCGATCCATTGTT
33




CCACGAAAACTGGCCGTC



 



DP1Cysrev
GACGGCCAGTTTTCGTGGAACAAT
34




GGATCGATGGATCCGGTG



 



DP1Glnfor
CACCGGATCCATCGATCCACAGTT
35




CCACGAAAACTGGCCGTC



 



DP1Glnrev
GACGGCCAGTTTTCGTGGAACTGT
36




GGATCGATGGATCCGGTG



 



DP1Glufor
CACCGGATCCATCGATCCAGAATT
37




CCACGAAAACTGGCCGTC



 



DP1Glurev
GACGGCCAGTTTTCGTGGAATTCT
38




GGATCGATGGATCCGGTG



 



DP1Glyfor
CACCGGATCCATCGATCCAGGATT
39




CCACGAAAACTGGCCGTC



 



DP1Glyrev
GACGGCCAGTTTTCGTGGAATCCT
40




GGATCGATGGATCCGGTG



 



DP1Hisfor
CACCGGATCCATCGATCCACACTT
41




CCACGAAAACTGGCCGTC



 



DP1Hisrev
GACGGCCAGTTTTCGTGGAAGTGT
42




GGATCGATGGATCCGGTG



 



DP1Ilefor
CACCGGATCCATCGATCCAATCTT
43




CCACGAAAACTGGCCGTC



 



DP1Ilerev
GACGGCCAGTTTTCGTGGAAGATT
44




GGATCGATGGATCCGGTG



 



DP1Leufor
CACCGGATCCATCGATCCACTCTT
45




CCACGAAAACTGGCCGTC



 



DP1Leurev
GACGGCCAGTTTTCGTGGAAGAGT
46




GGATCGATGGATCCGGTG



 



DP1Lysfor
CACCGGATCCATCGATCCAAAATT
47




CCACGAAAACTGGCCGTC



 



DP1Lysrev
GACGGCCAGTTTTCGTGGAATTTT
48




GGATCGATGGATCCGGTG



 



DP1Metfor
CACCGGATCCATCGATCCAATGTT
49




CCACGAAAACTGGCCGTC



 



DP1Metrev
GACGGCCAGTTTTCGTGGAACATT
50




GGATCGATGGATCCGGTG



 



DP1Phefor
CACCGGATCCATCGATCCATTCTT
51




CCACGAAAACTGGCCGTC



 



DP1Pherev
GACGGCCAGTTTTCGTGGAAGAAT
52




GGATCGATGGATCCGGTG



 



DP1Profor
CACCGGATCCATCGATCCACCATT
53




CCACGAAAACTGGCCGTC



 



DP1Prorev
GACGGCCAGTTTTCGTGGAATGGT
54




GGATCGATGGATCCGGTG



 



DP1Serfor
CACCGGATCCATCGATCCATCCTT
55




CCACGAAAACTGGCCGTC



 



DP1Serrev
GACGGCCAGTTTTCGTGGAAGGAT
56




GGATCGATGGATCCGGTG



 



DP1Thrfor
CACCGGATCCATCGATCCAACCTT
57




CCACGAAAACTGGCCGTC



 



DP1Thrrev
GACGGCCAGTTTTCGTGGAAGGTT
58




GGATCGATGGATCCGGTG



 



DP1Trpfor
CACCGGATCCATCGATCCATGGTT
59




CCACGAAAACTGGCCGTC



 



DP1Trprev
GACGGCCAGTTTTCGTGGAACCAT
60




GGATCGATGGATCCGGTG



 



DP1Tyrfor
CACCGGATCCATCGATCCATACTT
61




CCACGAAAACTGGCCGTC



 



DP1Tyrrev
GACGGCCAGTTTTCGTGGAAGTAT
62




GGATCGATGGATCCGGTG



 



DP1Valfor
CACCGGATCCATCGATCCAGTTTT
63




CCACGAAAACTGGCCGTC



 



DP1Valrev
GACGGCCAGTTTTCGTGGAAAACT
64




GGATCGATGGATCCGGTG



 



AlaDP1for
CCCCTTCACCGGATCCGCCGATCC
65




ACGTTTCCACGAAAAC



 



ArgDP1for
CCCCTTCACCGGATCCCGTGATCC
66




ACGTTTCCACGAAAAC



 



AsnDP1for
CCCCTTCACCGGATCCAACGATCC
67




ACGTTTCCACGAAAAC



 



AspDP1for
CCCCTTCACCGGATCCGATGATCC
68




ACGTTTCCACGAAAAC



 



CysDP1for
CCCCTTCACCGGATCCTTGGATCC
69




ACGTTTCCACGAAAAC



 



GlnDP1for
CCCCTTCACCGGATCCCAGGATCC
70




ACGTTTCCACGAAAAC



 



GluDP1for
CCCCTTCACCGGATCCGAAGATCC
71




ACGTTTCCACGAAAAC



 



GlyDP1for
CCCCTTCACCGGATCCGGAGATCC
72




ACGTTTCCACGAAAAC



 



HisDP1for
CCCCTTCACCGGATCCCACGATCC
73




ACGTTTCCACGAAAAC



 



LeuDP1for
CCCCTTCACCGGATCCCTCGATCC
74




ACGTTTCCACGAAAAC



 



LysDP1for
CCCCTTCACCGGATCCAAAGATCC
75




ACGTTTCCACGAAAAC



 



MetDP1for
CCCCTTCACCGGATCCATGGATCC
76




ACGTTTCCACGAAAAC



 



PheDP1for
CCCCTTCACCGGATCCTTCGATCC
77




ACGTTTCCACGAAAAC



 



ProDP1for
CCCCTTCACCGGATCCCCAGATCC
78




ACGTTTCCACGAAAAC



 



SerDP1for
CCCCTTCACCGGATCCTCCGATCC
79




ACGTTTCCACGAAAAC



 



ThrDP1for
CCCCTTCACCGGATCCACCGATCC
80




ACGTTTCCACGAAAAC



 



TrpDP1for
CCCCTTCACCGGATCCTGGGATCC
81




ACGTTTCCACGAAAAC



 



TyrDP1for
CCCCTTCACCGGATCCTACGATCC
82




ACGTTTCCACGAAAAC



 



ValDP1for
CCCCTTCACCGGATCCGTTGATCC
83




ACGTTTCCACGAAAAC



 



AlaDP1rev
GTTTTCGTGGAAACGTGGATCGGC
84




GGATCCGGTGAAGGGG



 



ArgDP1rev
GTTTTCGTGGAAACGTGGATCACG
85




GGATCCGGTGAAGGGG



 



AsnDP1rev
GTTTTCGTGGAAACGTGGATCGTT
86




GGATCCGGTGAAGGGG



 



AspDP1rev
GTTTTCGTGGAAACGTGGATCATC
87




GGATCCGGTGAAGGGG



 



CysDP1rev
GTTTTCGTGGAAACGTGGATCCAA
88




GGATCCGGTGAAGGGG



 



GlnDP1rev
GTTTTCGTGGAAACGTGGATCCTG
89




GGATCCGGTGAAGGGG



 



GluDP1rev
GTTTTCGTGGAAACGTGGATCTTC
90




GGATCCGGTGAAGGGG



 



GlyDP1rev
GTTTTCGTGGAAACGTGGATCTCC
91




GGATCCGGTGAAGGGG



 



HisDP1rev
GTTTTCGTGGAAACGTGGATCGTG
92




GGATCCGGTGAAGGGG



 



LeuDP1rev
GTTTTCGTGGAAACGTGGATCGAG
93




GGATCCGGTGAAGGGG



 



LysDP1rev
GTTTTCGTGGAAACGTGGATCTTT
94




GGATCCGGTGAAGGGG



 



MetDP1rev
GTTTTCGTGGAAACGTGGATCCAT
95




GGATCCGGTGAAGGGG



 



PheDP1rev
GTTTTCGTGGAAACGTGGATCGAA
96




GGATCCGGTGAAGGGG



 



ProDP1rev
GTTTTCGTGGAAACGTGGATCTGG
97




GGATCCGGTGAAGGGG



 



SerDP1rev
GTTTTCGTGGAAACGTGGATCGGA
98




GGATCCGGTGAAGGGG



 



ThrDP1rev
GTTTTCGTGGAAACGTGGATCGGT
99




GGATCCGGTGAAGGGG



 



TrpDP1rev
GTTTTCGTGGAAACGTGGATCCCA
100




GGATCCGGTGAAGGGG



 



TyrDP1rev
GTTTTCGTGGAAACGTGGATCGTA
101




GGATCCGGTGAAGGGG



 



ValDP1rev
GTTTTCGTGGAAACGTGGATCAAC
102




GGATCCGGTGAAGGGG









PCR Reaction components
















10X QUIKCHANGE ® reaction buffer
5 μL



QUIKCHANGE TM dNTP mix
1 μL



Pfu polymerase
1 μL



10 μM forward primer
1 μL



10 μM reverse primer
1 μL



Water
40 μL 

















TABLE 7







Thermocycling program parameters










Segment
Cycles
Temperature
Time













1
1
95° C.
30 seconds


2
25
95° C.
30 seconds




55° C.
 1 minute




68° C.
 6 minutes


3
1
68° C.
 8 minutes


4
1
 4° C.
hold









Preparation of Peptide-Containing Inclusion Bodies

The preparation of peptide-containing inclusion bodies followed the procedures described in Example 2.
Acid Hydrolysis of Peptide in Inclusion Body Pellets
Pellets were washed once and then resuspended in 1/10th the original culture volume of sterile, filtered water. 300 μL of inclusion body suspension was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 130 μL of 20 mM H2PO4, pH 2.2 (Cat. #0260-1, J. T. Baker, Phillipsburg, N.J.). A 40-μL time-zero sample was removed and neutralized by adding 20 μL of 100 mM MES, pH 8.9 (Cat. #475893, Calbiochem, La Jolla, Calif.). The remaining inclusion body sample was incubated at 70° C. Additional samples were taken at 2 and 6 hours and neutralized in the same manner as the time-zero sample.
Separation of Hydrolyzed Peptide/Tag Fragments and HPLC Analysis
The hydrolyzed peptide/solubility tag fragments were separated using the process described in Example 2. HPLC analysis was conducted as described in Example 2.
Results and Conclusion
The rate of hydrolysis was minimally affected by the majority of amino acid changes immediately preceding the D residue of the DP pair in the linker although proline in this position marginally enhanced the hydrolysis rate (FIG. 3). Substitution of tryptophan or phenylalanine for isoleucine on the amino-terminal side of the DP linker significantly slows the rate of acid hydrolysis (FIG. 3). As such, substituting tryptophan or phenylalanine on the amino-terminal side of the DP linker may be useful to increase the stability of the DP linker in applications where acid cleavage of a DP pair is not desired (e.g., a DP linker is present in a protein or peptide of interest where acid cleavage is not desired).
An unexpected result was that only the substitution of proline for arginine at the position immediately following the proline residue of the DP linker substantially increases the rate of acid hydrolysis (FIG. 4). Therefore, the effect on acid hydrolysis rates of additional proline residues inserted upon a DP3 background was assessed.
Example 4
Effect of Introducing Additional Proline Residues to the DPDPDP Linker
Based on the conclusion from Example 3, that an additional proline on the C-terminal side of the single DP linker further accelerates the rate of hydrolysis, one or two prolines were added to an analogous position within the DP3 linker. Example 4 demonstrates the effect on acid hydrolysis rate of the test fusion peptide of adding proline residues to the DPDPDP linker (SEQ ID NO:2). These derivatives of DP3 are referred to as PP1, PP2, PP3 and PP4 (see Table 2 for sequences).
The strain, growth media, and construction of expression plasmid pDP3 is described in Example 2.
Construction of pDP3 Variants Containing Additional Proline Residues in the DP3 Linker
Additional proline residues were introduces at various positions in the DP3 linker by site-directed mutagenesis using a QUIKCHANGETM II Kit (Cat. #200524, Stratagene, La Jolla, Calif.). The primers used to prepare the corresponding variants are shown in Table 8. Reactions were thermocycled in a Gene Amp 9700 (Perkin Elmer Cetus, Norwalk, Conn.). The PCR reaction components and the thermocycling program parameters follow those described in Example 3. Escherichia coli BL21-A1 was transformed with 1 μL of QUIKCHANGETM reaction product according to manufacturer's directions and transformants were selected on LB agar plates with 100 μg/mL ampicillin. Transformants with the desired mutations were identified by DNA sequencing. In the case of PP4, no transformants were obtained and the transformation was repeated using E. coli 10G Elite Electrocompetent Cells as described in Example 3.







TABLE 8







Primers used in the construction of DP3 variants











SEQ




ID


Primer ID
Nucleotide Sequence
NO:





DPDPDPPfor
CATCGATCCAGATCCAGATCCACCACGTTT
104


“PP1”
CCACGAAAACTGGCC



 


DPDPDPPrev
GGCCAGTTTTCGTGGAAACGTGGTGGATC
105


“PP1”
TGGATCTGGATCGATG



 


DPDPPDPPfor
CATCGATCCAGATCCACCAGATCCACCAC
106


“PP2”
GTTTCCACGAAAACTGGC



 


DPDPPDPPrev
GCCAGTTTTCGTGGAAACGTGGTGGATCT
107


“PP2”
GGTGGATCTGGATCGATG



 


DPDPPDPfor
GATCCATCGATCCAGATCCACCAGATCCAC
108


“PP3”
GTTTCCACGAAAAC



 


DPDPPDPrev
GTTTTCGTGGAAACGTGGATCTGGTGGAT
109


“PP3”
CTGGATCGATGGATC



 


DPPDPPDPfor
CACCGGATCCATCGATCCACCAGATCCAC
110


“PP4”
CAGATCCACGTTTCCACGAAAAC



 


DPPDPPDPrev
GTTTTCGTGGAAACGTGGATCTGGTGGAT
111


“PP4”
CTGGTGGATCGATGGATCCGGTG









Preparation of Peptide-Containing Inclusion Bodies

The preparation of the peptide-containing inclusion bodies follows the procedures described in Example 2.
Acid Hydrolysis of Peptide in Inclusion Body Pellets
Pellets were washed once and then resuspended in 1/10th the original culture volume of sterile, filtered water. For PP1, 250 μL of inclusion body suspension was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 120 μL of 20 mM H2PO4. For PP2, PP3, and PP4, 500 μL of inclusion body suspension was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 120 μL of 20 mM H2PO4, pH 2.2 (Cat. #0260-1, J. T. Baker, Phillipsburg, N.J.). A 20 μL time-zero sample was removed and neutralized by adding 10 μL of 100 mM MES, pH 8.9 (Cat. #475893, Calbiochem, La Jolla, Calif.). The remaining inclusion body sample was incubated at 70° C. Additional samples were taken at 0.5, 1, 2 4 hours and neutralized in the same manner as the time-zero sample.
Separation of Hydrolyzed Peptide/Tag Fragments and HPLC Analysis
The hydrolyzed peptide/solubility tag fragments were separated using the process described in Example 2. HPLC analysis was conducted as described in Example 2.
Results and Conclusion
The rate of hydrolysis is increased by the addition of proline residues to the DP3 linker, with PP2 and PP4 showing the highest rate of acid-cleavage (FIGS. 5 and 6).
Example 5
Effect of pH and Temperature on Acid Hydrolysis
The following example was conducted to demonstrate the effect of changes in pH and temperature on the rate of acid hydrolysis on various DP linkers.
Strains and Media
Strains are described in Examples 2 and 4, media and growth conditions in Example 2.
Preparation of Peptide-Containing Inclusion Bodies
The preparation of the peptide-containing inclusion bodies follows the procedures described in Example 2.
Acid Hydrolysis of Peptide in Inclusion Body Pellets (Varying pH)
Pellets were washed once and then resuspended in 1/10th the original culture volume of sterile, filtered water. For DP1, DP3, and PP2; 580 μL, 290 μL, and 720 μL of inclusion body suspension, respectively, was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 360 μL of sterile, filtered water. Each sample was divided into three 120 μL aliquots and then re-pelleted by centrifugation at 9,000×g for 1 minute. For each sample, one of the three aliquots was resuspended in 0.25% phosphoric acid, pH 2.10 (Cat. #0260-1, J. T. Baker, Phillipsburg, N.J.), 0.25% formic acid, pH 2.44 (Cat. #FX0440-7, E. M. Science, Gibbstown, N.J.) or 0.25% acetic acid, pH 2.88 (Cat. #AX0073-6, EMD Chemicals, Gibbstown, N.J.). A 20 μL time-zero sample was removed from each and neutralized by adding 10 μL of 100 mM MES, pH 8.9 (Cat. #475893, Calbiochem, La Jolla, Calif.). The remaining inclusion body sample was incubated at 70° C. Additional samples were taken at 1, 2, 4 and 6 hours and neutralized in the same manner as the time-zero sample. The results are provided in FIG. 7.
Acid Hydrolysis of Peptide in Inclusion Body Pellets (Reduced Temperature)
Pellets were washed once and then resuspended in 1/10th the original culture volume of sterile, filtered water. For DP3 and PP2, 240 μL and 450 μL of inclusion body suspension, respectively, was pelleted by centrifugation at 9,000×g for 1 minute and then resuspended in 240 μL of sterile, filtered water. Each sample was divided into two 120 μL aliquots and then re-pelleted by centrifugation at 9,000×g for 1 minute. For each sample, one of the two aliquots was resuspended in 0.25% phosphoric acid, pH 2.10 (Cat. #0260-1, J. T. Baker, Phillipsburg, N.J.) or 0.25% formic acid, pH 2.44 (Cat. #FX0440-7, E. M. Science, Gibbstown, N.J.). A 20 μL time-zero sample was removed from each and neutralized by adding 10 μL of 100 mM MES, pH 8.9 (Cat. #475893, Calbiochem, La Jolla, Calif.). The remaining inclusion body sample was incubated at 50° C. Additional samples were taken at 1, 2, 6 and 24 hours and neutralized in the same manner as the time-zero sample. The results are provided in FIG. 8.
Separation of Hydrolyzed Peptide/Tag Fragments and HPLC Analysis
The hydrolyzed peptide/solubility tag fragments were separated using the process described in Example 2. HPLC analysis was conducted as described in Example 2.
Results and Conclusion
The results of hydrolysis in 0.25% w/v acid solutions at 70° C. (FIG. 7) and 50° C. are illustrated (FIG. 8).
The relative hydrolysis rate in formic acid, pH 2.44, was not substantially different from phosphoric acid, pH 2.10 for either DP3 or PP2 at either 70° C. (FIG. 7) or 50° C. However, the hydrolysis rate at 50° C. was reduced approximately 2-fold for PP2 and 3-fold for DP3 as compared to the rate at 70° C.
Example 6
Preparation of Constructs Incorporating Different Acid Labile Sequences
This example describes the assembly of four constructs that contain different acid-labile sequences that separate the two domains of the protein. The fusion peptides were designed to have an inclusion body tag (KSI(C4E); SEQ ID NO: 252) linked to a peptide of interest (HC353; SEQ ID NO: 253) where the two components are separated by an acid-cleavable peptide linker. The following four acid-cleavable linkers were engineered between KSI(C4E) and HC353:










DP



 



DPDPDP
(SEQ ID NO: 2)


 



DPDPPDPP
(SEQ ID NO: 5)


 



DPPDPPDP
(SEQ ID NO: 7)






Construction of KSI(C4E).DP.HC353:

The gene for HC353 was synthesized by DNA2.0 (Menlo Park, Calif.) with BamHI and Ascl flanking the 5′ and 3′ ends of the gene, respectively. The gene incorporated nucleotides that code for the amino acid sequence DP just downstream of the BamHI site. The HC353 gene was cloned into the BamHI-AscI sites of the plasmid pLD001 (SEQ ID NO: 254), yielding plasmid pJZ353.
The resulting DNA construct (SEQ ID NO: 255) encoded the fusion peptide KSI(C4E).DP.HC353 (SEQ ID NO: 256).
Construction of KSI(C4E).DPDPDP.HC353:
In order to modify the acid-cleavable linker between KSI(C4E) and HC353, two additional DP sequences were incorporated into the sequence encoding KSI(C4E).DP.HC353. This was accomplished by the QuikChange Site-Directed Mutagenesis kit by Stratagene (La Jolla, Calif.). The following two primers were used to introduce the additional sequences:







353.DP3 UP:


(SEQ ID NO: 257)


gcttgtcagggatccgatcctgaccctgatccatctgctcaatctcaa


ctgcc


 


353.DP3 DOWN:


(SEQ ID NO: 258)


ggcagttgagattgagcagatggatcagggtcaggatcggatccctga


caagc






The resulting plasmid pLR688 expressed a DNA construct (SEQ ID NO: 259) encoding fusion peptide KSI(C4E).DPDPDP.HC353 (SEQ ID NO: 260).

Construction of KSI(C4E).DPDPPDPP.HC353:

In order to modify the acid-cleavable linker between KSI(C4E) and HC353, two additional P residues were incorporated into the sequence encoding KSI(C4E).DPDPDP.HC353 (pLR688). This was accomplished by the QuikChange Site-Directed Mutagenesis kit by Stratagene (La Jolla, Calif.). The following two primers were used to introduce the additional sequences:







PP2 HC353 UP:


(SEQ ID NO: 261)


gatccgatcctgaccctccagatccaccgtctgctcaatctcaactgc


 


PP2 HC353 DOWN:


(SEQ ID NO: 262)


gcagttgagattgagcagacggtggatctggagggtcaggatcggatc






The resulting plasmid pLR726 expressed a DNA construct (SEQ ID NO: 263) encoding fusion peptide KSI(C4E).DPDPPDPP.HC353 (SEQ ID NO: 264).

Construction of KSI(C4E).DPPDPPDP.HC353:

In order to modify the acid-cleavable linker between KSI(C4E) and HC353, two additional P residues were incorporated into the sequence encoding KSI(C4E).DPDPDP.HC353 (pLR688). This was accomplished by the QuikChange Site-Directed Mutagenesis kit by Stratagene (La Jolla, Calif.). The following two primers were used to introduce the additional sequences:







353 PP4 UP:


(SEQ ID NO: 265)


gtcagggatccgatcctccagaccctccagatccatctgctcaatc


 


353 PP4 DOWN:


(SEQ ID NO: 266)


gattgagcagatggatctggagggtctggaggatcggatccctgac






The resulting plasmid pLR816 expressed a DNA construct (SEQ ID NO: 267) encoding fusion peptide KSI(C4E).DPPDPPDP.HC353 (SEQ ID NO: 268).

Example 7
Production of IBT Fusions to Peptides HC353
Strains expressing the fusions of KSI(C4E) to peptide HC353 with variants of the DP acid cleavage described in Example 6 were grown in one liter of autoinduction medium (10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L NaCl, 50 mM Na2HPO4, 50 mM KH2PO4, 25 mM (NH4)2SO4, 3 mM MgSO4, 0.75% glycerol, 0.075% glucose and 0.05% arabinose, 50 mg/mL Spectinomycin) at 37° C., and 200 rpm incubator shaker for 20 hours. The cells were harvested by centrifugation, resuspended in 200 mL of lysis buffer (50 mM Tris pH 7.5, 5 mM EDTA, 100 mM NaCl) using a tissue homogenizer (Brinkman Homogenizer model PCU11 at setting 3-4) and collected again by centrifugation at 8000 rpm for 5 min. The washed cells were resuspended with a homogenizer in 200 mL of lysis buffer to the pellet containing 50 mg of lysozyme and allowed to sit on ice for three hours before being frozen at −20° C. The cell suspension was thawed at 37° C., homogenized and subject to sonication using a Branson Sonifier model 450 sonicator equipped with a 5 mm probe (Branson Ultrasonics Corporation, Danbury, Conn.) at 20% maximum output, 2 pulses per second for 1 min, repeat once.
The disrupted cells were transferred to 50-mL conical tubes and the insoluble fraction containing the inclusion bodies was harvested by centrifugation for 10 min at 10,000 rpm. The inclusion bodies were resuspended in 200 mL of BENZONASE® buffer (20 mM Tris-HCl pH 7.5 5 mM MgCl2, 100 mM NaCl) containing 1250 U of BENZONASE® endonuclease (Sigma Aldrich, St. Louis Mo.). The slurry was stirred for 1 hr at 37° C. and centrifuged. The inclusion bodies were washed by resuspension in deionized water with a homogenizer and harvested by centrifugation for 10 min at 10,000 rpm.
Example 8
Improved Acid Cleavage for the Production of Peptide HC353
The purpose of this experiment is to show that the new acid cleavage sequences identified in Example 4 with peptide TBP1 allow for improved acid cleavage when another peptide is fused to the insolubility tag and therefore are of general use. Improved acid cleavage means faster at equal pH and temperature, at a lower temperature for equal pH and incubation time or at a higher pH for equal temperature and incubation time.
Each inclusion body paste was resuspended to 10% w/v in water containing 50 mM NaCl. Each slurry (70 mL) was acidified by addition of HCl to pH 6, pH 5, pH 4, pH 3, or pH 2. The acidified slurries were incubated at 60° C., 70° C. or 80° C. with periodic manual agitation. Aliquots of the acidified slurries were collected at 15, 30, 60, 90, 120, 180 and 240 min and placed on ice. Once all the aliquots were collected, the samples were neutralized by addition of 1 M NaOH.
The efficiency of the acid cleavage was assessed by SDS polyacrylamide gel electrophoresis and the gels were stained with Coomassie blue. The bands corresponding to HC353 and KSI which have similar MW, could be resolved easily because of the abnormally slow gel mobility of HC353. The summary data is provided in Table 9 and is shown in FIGS. 9, 10, 11, and 12 where in each of the figures arrows are used to indicate the full length fusion construct (“F”), the peptide of interest HC353 (“H”) and the inclusion body tag KSI(C4E) (“K”). The data confirms the results obtained with another peptide fusion in Example 4 and indicates that the improved acid cleavage sites can be used broadly for the production of different peptides.







TABLE 9







Data summary of the variant acid cleavage sites showing


fusion proteins more labile to acid pH (faster kinetics,


less acidic pH or lower temperature).













Fastest time
Lowest temp.
Highest pH for




for complete
for complete
complete



Cleavage
digest
digest @
digest



Sequence
@ pH 2, 80° C.
pH 2, 4 hrs
@ 80° C., 4 hrs


Strain ID
(SEQ ID NO:)
(min)
(° C.)
(pH)














LD1474
DP
240
80
2


 


LR2050
DPDPPDPP
60
60
4



(SEQ ID NO: 5)





 


LR2321
DPPDPPDP
90
70
3



(SEQ ID NO: 7)





 


LR1755
DPDPDP
120
70
3



(SEQ ID NO: 2)

## Claims

1. A fusion peptide comprising two peptides separated by an acid-cleavable linker according to the following general formula:


PEP1-L-PEP2


wherein,
a) PEP1 and PEP2 are independently functional peptides wherein at least one is a peptide of interest (“POI”); and
b) L is an acid-cleavable linker comprising a peptide DPPDPPDP (SEQ ID N0:7), wherein D is aspartic acid and P is proline.

2. The fusion peptide of claim 1 wherein PEP1 and PEP2 are nonidentical.

3. The fusion peptide of claim 2, wherein the fusion peptide is soluble in a recombinant cell.

4. The fusion peptide of claim 3 wherein the recombinant cell is a recombinant microbial cell.

5. The fusion peptide of claim 4 wherein the recombinant microbial cell is a recombinant bacterial cell.

6. The fusion peptide of claim 4 wherein the recombinant microbial cell is a recombinant yeast cell.

7. The fusion peptide of claim 2, wherein the fusion peptide is insoluble in a recombinant cell.

8. The fusion peptide of claim 7 wherein the recombinant cell is a recombinant microbial cell.

9. The fusion peptide of claim 8 wherein the recombinant microbial cell is a recombinant yeast cell.

10. The fusion peptide of claim 9 wherein the recombinant microbial cell is a recombinant bacterial cell.

11. The fusion peptide of claim 2 wherein either of PEP1 or PEP2 comprises an inclusion body tag (“IBT”).

12. The fusion peptide of claim 11 wherein the fusion peptide is present in inclusion bodies.

13. The fusion peptide of claim 2 wherein the acid-cleavable linker is cleaved by incubation at a pH in the range from about pH 1 to about pH 4.

14. The fusion peptide of claim 2 wherein the acid-cleavable linker is cleaved by incubating at a temperature of about 40° C. to about 90° C.

15. The fusion peptide of claim 14 wherein the acid-cleavable linker is cleaved by incubating at a temperature of about 50° C. to about 80° C.

16. The fusion peptide of claim 15 wherein the acid-cleavable linker is cleaved by incubating at a temperature of about 60° C. to about 70° C.

17. The fusion peptide of claim 2 wherein the acid-cleavable linker is cleaved by incubating at a pH of about pH 2 to about pH 4 and at a temperature of about 50° C. to about 80° C.

18. A recombinant cell expressing a fusion protein having the structure


PEP1-L-PEP2

wherein,
i) PEP1 and PEP2 are independently functional peptides, one of which is a POI; and
ii) L is an acid-cleavable linker comprising a peptide DPPDPPDP (SEQ ID N0:7),
wherein D is aspartic acid and P is proline; and
wherein the expressed fusion peptide is present in the recombinant cell.

19. The recombinant cell of claim 18 wherein the recombinant cell is a recombinant microbial cell.

20. The recombinant cell of claim 19 wherein the recombinant cell is a recombinant bacterial cell.

21. The recombinant cell of claim 19 wherein the recombinant cell is a recombinant microbial cell is a recombinant yeast cell.

22. An acid-cleavable peptide linker comprising a peptide DPPDPPDP (SEQ ID NO:7), wherein D is aspartic acid and P is proline.

23. A method of preparing at least one peptide of interest (“POI”) from a fusion peptide comprising at least one POI, comprising:
a) providing a recombinant cell synthesizing the fusion peptide of claim 1;
b) contacting the fusion peptide with a solution of sufficiently acidic pH so that linker L is cleaved, and
c) isolating the at least one POI.

24. The method of claim 23 wherein the recombinant cell is a recombinant microbial cell.

25. The method of claim 24 wherein the recombinant microbial cell is a recombinant yeast cell.

26. The method of claim 24 wherein the recombinant microbial cell is a recombinant bacterial cell.

27. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a pH in the range from about pH 1 to about pH 4.

28. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a pH in the range from about pH 2 to about pH 4.

29. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a pH in the range from about pH 3 to about pH 4.

30. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a pH of about 4.

31. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a temperature of about 40° C. to about 90° C.

32. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a temperature of about 50° C. to about 80° C.

33. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a temperature of about 60° C. to about 70° C.

34. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a temperature of about 60° C.

35. The method of claim 23 wherein the acid-cleavable linker is cleaved by incubating the fusion peptides at a pH of about pH 2 to about pH 4 using a temperature of about 50° C. to about 80° C.

36. The method of claim 23, wherein PEP1 and PEP2 are both POIs.

37. The method of claim 36, wherein the fusion peptide is soluble in the recombinant cell.

38. The method of claim 36, wherein the fusion peptide is insoluble in the recombinant cell.

39. The method of claim 38, wherein cleaving the fusion peptide under acidic conditions renders the at least one POI soluble.

40. The method of claim 23, wherein either PEP1 or PEP2 of the fusion peptide comprises an inclusion body tag, thereby comprising a non-POI portion of the fusion peptide.

41. The method of claim 40, wherein the non-POI portion remains insoluble after cleaving the fusion peptide.