# Patent

## Title
Fusion proteins of superfolder green fluorescent protein and use thereof

## Abstract

The present disclosure pertains to methods of producing recombinant peptides that contain between 10 and 200 amino acid residues using novel carrier proteins derived from superfolder green fluorescent protein and its mutants.

## Background
RELATED APPLICATIONS
This application is a U.S. National Phase application of International Application No. PCT/US2013/033702, filed Mar. 25, 2013, which claims priority to, and the benefit of, U.S. provisional application No. 61/615,178, filed Mar. 23, 2012, the entire contents of each of which are incorporated herein by reference in their entireties.


INCORPORATION-BY-REFERENCE OF SEQUENCE LISTING
The contents of the text file named “45547-501001WO_ST25.txt,” which was created on Jul. 25, 2013 and is 36 KB in size, are hereby incorporated by reference in their entireties.
FIELD OF THE INVENTION
The present invention generally pertains to recombinant peptides that contain less than 200 amino acid residues and one or more novel carrier proteins derived from superfolder green fluorescent protein or mutants thereof as well as methods of producing the recombinant peptides using novel carrier proteins derived from superfolder green fluorescent protein or its mutants.
BACKGROUND OF THE INVENTION
Peptides are a group of biomolecules that have been broadly used as reagents in many biomedical research areas, therapeutic drugs in the treatment of diseases, and diagnostic agents in detecting pathogens and biomarkers. Two methods are generally used to synthesize peptides. One is chemical synthesis and the other is the recombinant expression. Chemical synthesis has been used for the preparation of a variety of therapeutic peptides including corticorelin, parathyroid hormone (PTH), glucagon-like peptide-1 (GLP-1) and its analogs exenatide and liragultide, enfuvirtide, calcitonin, bivalirudin, ziconotide, sermorelin, somatorelin, secretin, teduglutide, and insulin. This method needs multiple condensation reactions of amino acid fragments to generate peptides and requires tedious protection, deprotection, and purification processes. So far, most of commercial peptides with few than 50 amino acid residues are manufactured in this way. Given the increasing demand for peptides in pharmaceutical industry and biomedical research, the prices of amino acid fragments used for chemical synthesis of peptides have been continuously ascending. Therefore, for daily used therapeutic peptide drugs such as GLP-1 analogs, it will be difficult to maintain their affordable prices in the future. Although chemical synthesis of a peptide with more than 50 amino acid residues is technically achievable, the low yields and the exceeding amount of organic waste generated during the synthesis make it economically unfavourable. So far, most of peptides with more than 50 amino acid residues are recombinantly expressed in cell hosts such as bacterial, yeast, insect, and mammalian cells. For many years, it has been a common practice to use fusion proteins for the expression of peptides. The readily available carrier proteins include glutathione-S-transferase (WO94/04688 and Ray et al., BioTechnology, 11, 64, 1993), ribulokinase (U.S. Pat. No. 5,206,154 and Callaway et al., Antimicrob. Agents & Chemo., 37, 1614-1919, 1993), gp-55 protein (Gram H. et al., Biotechnology, 12, 1017-1023, 1994), ketosteroid isomerase (Kuliopulos A. et al., J. Am. Chem. Soc., 116, 4599-4607, 1994), ubiquitin (Pilon A. et al., Biotecnol. Prog. 13, 374-379, 1997), bovine prochymosin (Hauht et al., Biotechnolo. Bioengineer., 7, 55-61, 1998), GB1 domain (Darrinm et al., Biochemistry, 41, 7267-7274, 2003), RNA-binding protein (Sharon M. et al., Protein Exp. And Purif., 24, 374-383, 2002), SH2 domain (Fairlie W. et al., Protein Exp. And Purif. 26, 171-178, 2002), cellulose binding domain, small ubiquitin-like modifier, intein, bactericidal/permeability-increase protein, carbonic anhydrase (U.S. Pat. No. 5,962,270 and WO97/29127), alpha-lactalbumin (WO95/27782), beta-glactosidase (Shen S., PNAS, 281, 4627-4631, 1984), and chloramphenicol acetyltransferase (Dykes C. et al., European Journal of Biochemistry, 174, 411-416, 1988). These fusion carriers have been selected for their relatively high expression levels and fast folding processes in host cells. Although useful, the final yields of peptides recombinantly expressed using fusion carrier proteins typically do not exceed 100 mg/L. In addition, current available fusion protein methods for peptide expression also have many technical problems especially for the production of peptides smaller than 50 amino acid residues (Vileghe et al., Drug Discovery Today, 15, 40-56, 2010).
It would be highly desirable to provide with a new carrier protein overcoming the limitations of other existing carrier proteins for the production of recombinant peptides.
BRIEF SUMMARY OF THE INVENTION
The present invention is based at least in part on the unexpected discovery that superfolder green fluorescent protein or a mutant thereof, when used as carrier protein, leads to high expression levels of recombinant peptides in inclusion bodies or cytoplasm of bacterial cells. Accordingly, one aspect of the present invention relates to a novel carrier protein for constructing stable expression systems for the production of recombinant peptides as fusion proteins. In particular, the carrier protein includes superfolder green fluorescent protein or a mutant thereof.
In one embodiment, the fusion proteins as produced are expressed in intact and stable forms. In one embodiment, the novel carrier protein is easily removed by convenient methods and does not complicate subsequent steps of peptide purification. In one embodiment of the invention, the desired peptides are targeted to form inclusion bodies by engineering the carrier protein of the present invention for protection against in-cell proteolytic degradation. In accordance with the present invention there is provided a fusion carrier protein for expressing a target peptide, said fusion carrier protein being derived from superfolder green fluorescent protein, or a mutant thereof, and consisting of 237 or more amino acids in length. Preferably, the fusion carrier protein has an amino acid sequence as set forth in Formula I:

T1-A1-T2  (I)

wherein

    
    
        T1 is absent, a Met, a His-tag or at least one peptidic cleavage site,
        A1 is superfolder green fluorescent protein,
        T2 is absent, a His-tag or at least one peptidic cleavage site, provided that at most one of T1 and T2 is absent.
    
    


In embodiments, A1 is superfolder green fluorescent protein having an amino acid sequence of Ser-Lys-Gly-Glu-Glu-Leu-Phe-Thr-Gly-Val-Val-Pro-Ile-Leu-Val-Glu-Leu-Asp-Gly-Asp-Val-Asn-Gly-His-Lys-Phe-Ser-Val-Arg-Gly-Glu-Gly-Glu-Gly-Asp-Ala-Thr-Asn-Gly-Lys-Leu-Thr-Leu-Lys-Phe-Ile-Cys-Thr- Thr-Gly-Lys-Leu-Pro-Val-Pro-Trp-Pro-Thr-Leu-Val-Thr-Thr-Leu-Thr-Tyr-Gly-Val-Gln-Cys-Phe-Ser-Arg-Tyr-Pro-Asp-His-Met-Lys-Arg-His-Asp-Phe-Phe-Lys-Ser-Ala-Met-Pro-Glu-Gly-Tyr-Val-Gln-Glu-Arg-Thr-Ile-Ser-Phe- Lys-Asp-Asp-Gly-Thr-Tyr-Lys-Thr-Arg-Ala-Glu-Val-Lys-Phe-Glu-Gly-Asp-Thr-Leu-Val-Asn-Arg-Ile-Glu-Leu-Lys-Gly-Ile-Asp-Phe-Lys-Glu-Asp-Gly-Asn-Ile-Leu-Gly-His-Lys-Leu-Glu-Tyr-Asn-Phe-Asn-Ser-His-Asn-Val-Tyr- Ile-Thr-Ala-Asp-Lys-Gln-Lys-Asn-Gly-Ile-Lys-Ala-Asn-Phe-Lys-Ile-Arg-His-Asn-Val-Glu-Asp-Gly-Ser-Val-Gln-Leu-Ala-Asp-His-Tyr-Gln-Gln-Asn-Thr-Pro-Ile-Gly-Asp-Gly-Pro-Val-Leu-Leu-Pro-Asp-Asn-His-Tyr-Leu-Ser- Thr-Gln-Ser-Val-Leu-Ser-Lys-Asp-Pro-Asn-Glu-Lys-Arg-Asp-His-Met-Val-Leu-Leu-Glu-Phe-Val-Thr-Ala-Ala-Gly-Ile-Thr-His-Gly-Met-Asp-Glu-Leu-Tyr-Lys (SEQ ID NO:1), or an amino acid sequence that is at least 80%, at least 90%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO:1.
The peptidic cleavage site can be selected for example from the group consisting of Met, Cys, Pro, Asn, Glu, Tyr, Trp, Lys, Arg, Asn-Gly, Asp-Met-Gln-Asp-Ile, Asp-Glu-Val-Asp-Ile, Leu-Glu-Val-Asp-Ile, Trp-Glu-His-Asp-Ile, Leu-Glu-His-Asp-Ile, Val-Glu-Ile-Asp-Ile, Val-Glu-His-Asp-Ile, Ile-Glu-Thr-Asp-Ile, Leu-Glu-Thr-Asp-Ile, Ile-Glu-Ala-Asp-Ile, Asp-Asp-Asp-Asp-Lys, Arg-Gly-Glu-Ile, Arg-Gly-Asp-Ile, Arg-Gly-Asp-Ile, Arg-Gly-Asp-Ala, Ile-Glu-Pro-Asp-Ile, Glu-Asn-Leu-Tyr-Phe-Gln-Gly (SEQ ID NO:3), Glu-Asn-Leu-Tyr-Phe-Gln-Ser (SEQ ID NO:5), and any other proteolytic sites known in this field.
The His-tag is preferably composed of three to eight histidine residues.
In one embodiment of the invention, a fusion protein comprises the fusion carrier protein as defined above, linked to at least one target peptide. The target peptide can be linked to the C-or N-terminus of the fusion carrier protein. Typically, the target peptide has a sequence between 10 and 200 amino acids in length.
In one embodiment of the invention, the DNA sequence of a fusion protein is codon-optimized for efficient translation in its cellular host.
In one embodiment of the invention, the target peptide is preferably selected from the group of peptide consisting of corticorelin, PTH, GLP-1 and its analogs exenatide and liragultide, enfuvirtide, calcitonin, bivalirudin, ziconotide, sermorelin, somatorelin, secretin, teduglutide, and proinsulin, hirudin, growth hormone, growth factors, growth hormone releasing factors, corticotropin, release factor, deslorelin, desmopressin, elcatonin, glucagons, leuprolide, leuteinizing hormone-releasing hormone, secretin, somatisation, thyrotropin-releasing hormone, triptorelin, vasoactive intestinal peptide, interferons, parathyroid hormone, BH3 peptides, beta-amyloidosis peptide or fragments thereof.
The fusion protein preferably further comprises a peptidic cleavage site between the fusion carrier protein and the target peptide.
In accordance with the present invention, there is further provided a nucleic acid sequence encoding the fusion protein described above. This nucleic acid sequence is codon-optimized for efficient translation in its cellular host.
Still in accordance with the present invention, there is provided an expression vector comprising the nucleic acid sequence described above, operably linked to a promoter for expression of said nucleic acid sequence coding for the fusion protein. The promoter can be for example the pL promoter, λ promoter, pBAD promoter, trc promoter, or T7 promoter.
Further in accordance with the present invention, there is provided a host cell, such as E. coli Top10, DH5α, DH10b, BL21, or JM101, transformed with the expression vector described above. Preferably, the host cell is from E. coli or B. subtilis. Alternatively, the host cell can be a yeast cell, an insect cell, or a mammalian cell.
In accordance with the present invention, there is provided a method for producing a fusion protein comprising the step of culturing the host cell as defined above under suitable conditions for expression of the expression vector, thereby producing a fusion protein. The suitable conditions can comprise an inducer for inducing the host cell to express the expression vector. Such inducer can be arabinose, IPTG or temperature. In one embodiment of the invention, the method further comprises a step of purification of the fusion protein produced.
The step of purification preferably comprises at least one of alcohol precipitation, ion exchange, and affinity purification using Ni-NTA agarose resin. In such method, the fusion protein is preferably further subjected to a proteolytic digestion to release the target peptide from the fusion protein. The proteolytic digestion can be for example achieved by CNBr, formic acid or HCl or by thrombin, or a protease, such as trypsin. The target peptide released can be further purified by HPLC.
In accordance with the present invention, there is provided the use of either a fusion carrier protein, or a nucleic acid, both as defined above, for expressing a target peptide. The nucleic acid can be used in an expression vector for expressing the target protein. A host cell as described above can also be used for expressing a target protein.
For the purpose of the present invention the following terms are defined below.
The term “sfGFP” or “superfolder green fluorescent protein” as used herein refers to a polypeptide derived from or based on the protein sequences of superfolder green fluorescent protein and its mutants (Pedelacq J. D. et al., Nature Biotechnology, 1; 79-88, 2006; and Tansila N. et al., Biotechnology Letters, 30; 1391-1396, 2008) and other permuted, truncated mutants, or hybrid forms in which certain amino acids have been deleted or replaced and modifications such as where one or more amino acids have been changed to a modified amino acid or unusual amino acid and modifications such as glycosylation so long as the hybrid or modified form retains the biological activity of sfGFP as a carrier protein. Preferred variants are those that have conservative amino acid substitutions made at one or more predicted non essential amino acid residues. A “conservative amino acid substitution” is one in which the amino acid residue is replaced with an amino acid residue having a similar side chain. Families of amino acid residues having similar side chains have been defined in the art. These families include amino acids with basic side chains (e.g., lysine, arginine, histidine), acidic side chains (e.g., aspartic acid, glutamic acid), uncharged polar side chains (e.g., glycine, asparagine, glutamine, serine, threonine, tyrosine, cysteine), nonpolar side chains (e.g., alanine, valine, leucine, isoleucine, proline, phenylalanine, methionine, tryptophan), beta branched side chains (e.g., threonine, valine, isoleucine) and aromatic side chains (e.g., tyrosine, phenylalanine, tryptophan, histidine). Thus, a predicted nonessential amino acid residue in a sfGFP is replaced with another amino acid residue from the same side chain family. Alternatively, in another embodiment, mutations can be introduced randomly along all or part of a sfGFP coding sequence, such as by saturation mutagenesis, and the resultant mutants can be screened to identify mutants that retain activity.
The amino acid sequence of the entire super folder green fluorescent protein without the first methionine and a code-optimized nucleic acid sequence of DNA encoding the protein are presented as SEQ ID NO:1 and SEQ ID NO:2 respectively.
The target peptide refers to any small protein or oligopeptide desired as a product. For practical applications of the invention, a peptide should contain at least ten amino acid residues linked by peptide bonds or at most two hundred amino acid residues linked by peptide bonds.
The “cleavage site” as used herein refers to the amino acid sequence, which contains an amino acid or a sequence of amino acids that provides a recognition site for a chemical agent or an enzyme such that the peptide chain is cleaved at that site by the chemical agent or enzyme.
A “transformed host cell” refers to a bacterial, yeast, insect, or mammalian cell that contains recombinant material or a bacterial, yeast, insect, or mammalian cell that contains genetic material required for the expression of a recombinant product. The genetic material many be introduced into the cell by any known method including transformation, transduction, electroporation and infection. Generally, throughout the present application, the term “transformed” or “transformation” will be used to refer to indistinctly to any of the known method referred above.
Unless otherwise defined, all technical and scientific terms used herein have the same meaning as commonly understood by one of ordinary skill in the art to which this invention belongs. Although methods and materials similar or equivalent to those described herein can be used in the practice or testing of the present invention, suitable methods and materials are described below. All publications, patent applications, patents, and other references mentioned herein are incorporated by reference in their entirety. In the case of conflict, the present specification, including definitions, will control. In addition, the materials, methods, and examples are illustrative only and are not intended to be limiting.
Other features and advantages of the invention will be apparent from the following detailed description and claims.



BRIEF DESCRIPTION OF THE FIGURES
FIG. 1A and FIG. 1B illustrate possible arrangement of the fusion protein of the present invention, wherein, a target peptide is linked to the C-terminus (FIG. 1A) or the N-terminus (FIG. 1B) or the carrier protein.
FIG. 2A and FIG. 2B illustrate various embodiments of the fusion protein of FIG. 1A and FIG. 1B, wherein a cleavage site (C-site) links the carrier protein and the target peptide.
FIG. 3A and FIG. 3B illustrate two other embodiments of the fusion protein of the present invention with single (FIG. 3A) and multiple (FIG. 3B) repeats of target peptides.
FIG. 4A and FIG. 4B illustrate respectively two plasmids pSFGFPN-NcoI and pSFGFPC-MCS expression vectors containing superfolder green fluorescent protein used as the carrier protein.
FIG. 5 illustrates a SDS-PAGE of the expressed prolispro-sfGFP fusion protein in the inclusion bodies 4 h and 21 h after induction with arabinose.
FIG. 6 illustrates a SDS-PAGE of the expressed sfGFP-proinsulin lispro fusion protein after digestion with trypsin and carboxypeptidase B.
FIG. 7 illustrates a MOLDI-TOF mass spectrometry analysis of the purified lispro.
FIG. 8 illustrates a SDS-PAGE of the expressed sfGFP-PTH fusion protein.
FIG. 9 illustrates a SDS-PAGE of the expressed sfGFP-Calcitonin fusion protein.
FIG. 10 illustrates a SDS-PAGE of the expressed sfGFP-GLP1 fusion protein.



DETAILED DESCRIPTION OF EXEMPLARY EMBODIMENTS
The expression of recombinant peptides by fusion proteins in either soluble form or in inclusion bodies is a well-known methodology. The present invention utilizes a novel carrier protein to provide an alternative approach for the production of recombinant peptides. The carrier protein is derived from superfolder green fluorescent protein. Recombinant peptides encoded by and released from fusion proteins are recovered according to these methods described herein. The invention provides fusion protein constructs to establish a new, low cost and highly efficient method for large-scale preparation of recombinant peptides.
In accordance with the present invention, there is thus provided a method for the production of recombinant peptides by use of a novel fusion protein. The carrier protein is superfolder green fluorescent protein or one of its mutants. The fusion protein led by superfolder green fluorescent protein is highly expressed in E. coli. The superfolder green florescent protein and the target peptide may be linked through a proteolytically sensitive (cleavage) site. The cleavage site is typically a specific amino acid or a specific sequence of amino acids to generate fusion proteins, which are selectively cleaved by a cleavage agent. The cleavage agent can be a chemical agent such as cyanogen bromide or acid. The cleavage agent can also be an endopeptidase such as trypsin, thrombin, enterokinase, or another specific protease.
One embodiment of the invention provides an improved method for obtaining a recombinant peptide from bacterial cells after expression inside the cells of a fusion protein in insoluble inclusion bodies. Expression of the fusion protein as inclusion bodies increases the production yield of the recombinant peptide and protects the integrity of the target peptide.
The second embodiment of the invention is directed to an improved method to simplify purification steps by the insertion of one or more His-tag into superfolder green fluorescent protein. After cleavage of the fusion protein is achieved by a chemical reagent or by an endopeptidase, the superfolder green fluorescent protein tag can be removed by repeating the His-tag affinity purification. Thus, the contaminations from digestion of other cellular proteins can be generally reduced.
The third embodiment is directed to a method to express the fusion proteins in which methionine residues link the target peptides and the carrier superfolder green florescent protein. The fusion protein is expressed in inclusion bodies and purified under a denaturing condition, e.g. with urea or guanidinium chloride. The fusion protein can be solubilized in formic acid and then cleaved with cyanogen bromide to release the target peptide. After the cleavage of the fusion protein, the fragment containing superfolder green fluorescent protein can be removed by chromatography.
The fourth embodiment is directed to a method to express the target peptides containing methionine residues. The fusion protein is expressed in inclusion bodies and purified under a denaturing condition, e.g. with urea or guanidinium chloride. The fusion protein can be refolded by dialysis against a physiological buffer. The fusion protein can be then cleaved with a proteolytic enzyme such as trypsin, TEV protease or thrombin to release the target peptide. After the cleavage of the fusion protein, the fragment containing superfolder green fluorescent protein can be removed by chromatography.
The fifth embodiment of this invention covers the fusion of the target peptide to the C-or N-terminus of the carrier protein that is superfolder green fluorescent protein as illustrated in FIG. 1A & FIG. 1B. The size of the target peptide can be from ten to two hundred amino acid residues. The carrier protein has the amino acid sequence listed in SEQ ID NO:1.
The size of the fusion protein will vary depending on the nature and number of copies of the target peptide. The fusion protein should be large enough to avoid degradation by endogenous proteases. The fusion protein can be arranged in two ways as illustrated in FIG. 1A and FIG. 1B. Alternatively, the target peptide is linked either to the N-terminus or to the C-terminus of the carrier protein (superfolder green fluorescent protein) via a cleavage site of a specific amino acid sequence (FIG. 2A and FIG. 2B). In FIG. 2A and FIG. 2B, C-site contains an amino acid or a sequence of amino acids that provides a recognition site for a chemical or enzymatic reaction such that the a chemical agent or an enzyme cleaves the peptide chain at that site.
The target peptide can be composed of one or more consecutive sequences of ten to two hundred amino acid residues. The large peptides are in particular those derived from protein sequences that do not have uniquely folded three dimensional structures. The various target peptides can have several forms as shown in FIG. 3A and FIG. 3B. In FIG. 3A, one includes a single copy of the target peptide. In FIG. 3B, a second is composed of multiple tandem repeats of a single target peptide. Each repeat may be the same or a different peptide. The repeats are linked by an “interconnecting” sequence, which may be Met, Lys, Arg, Glu-Asn-Leu-Tyr-Phe-Gln-Gly (SEQ ID NO:3), Glu-Asn-Leu-Tyr-Phe-Gln-Ser (SEQ ID NO:5), or other suitable amino acid sequences. The interconnecting sequence is not necessarily different the “connecting sequence” which links the carrier protein and the target peptide. The use of different connection linkers provide an advantage that two or more different cleavage agents (e.g. chemicals or enzymes) can individually release the target peptide from the fusion protein and separate the individual target peptides from each other.
Particular embodiments of the fused peptides which may appear as single or multiple-linked repeats include corticorelin, PTH, GLP-1 and its analogs exenatide and liragultide, enfuvirtide, calcitonin, bivalirudin, ziconotide, sermorelin, somatorelin, secretin, teduglutide, and proinsulin, hirudin, growth hormone, growth factors, growth hormone releasing factors, corticotropin, release factor, deslorelin, desmopressin, elcatonin, glucagons, leuprolide, leuteinizing hormone-releasing hormone, secretin, somatisation, thyrotropin-releasing hormone, triptorelin, vasoactive intestinal peptide, interferons, parathyroid hormone, BH3 peptides, beta-amyloidosis peptide. One common property of these peptides is than they all have flexible and fragile conformations that make them unstable and prone to proteolytic degradation.
The cleavage site and the target peptide are preferably selected so that the target peptide does not contain the same cleavage site. The cleavage sites include Met, Lys, Arg, Glu-Asn-Leu-Tyr-Phe-Gln-Gly (SEQ ID NO:3), Glu-Asn-Leu-Tyr-Phe-Gln-Ser (SEQ ID NO:5), or other suitable amino acid sequences. New cleavage sites may be designed in order to use a chemical cleavage reagent or an enzyme or the combination of the two. In some instances, it may be desirable to utilize a cleavage site to introduce a specific functional group to the C-terminus of the target peptide such as cleavage by cyanogen bromide.
The DNA sequence encoding the target peptide may be obtained from natural sources (e.g. genomic DNA) or via chemical synthesis utilizing the codon preference of bacterial cells or other host cells.
One embodiment of the invention provides a method to amplify the DNA sequence encoding a particular peptide contained in genomic DNA. Typically, two primers are designed to introduce two unique restriction sites at each end of the PCR product. The PCR reaction is performed in a PCR amplification device that provides control of the reaction temperature. A PCR DNA polymerase, e.g. the Taq, Pfu, Phusion DNA polymerase, is used in a PCR reaction and the reaction condition follows the protocol provided by the suppliers. PCR products are subjected to the direct digestion with at least one restriction enzyme or if necessary a cleanup procedure is conducted prior to restriction enzyme digestion. The digestion reaction mixture is cleaned up by DNA purification methods. DNA purification can be achieved by use of agarose gel electrophoresis or a PCR purification kit. The purified PCR products are used as inserts encoding target peptides. In some instances, the insert encoding the target peptide is not available from a natural source. In this latter case, the DNA fragment encoding the target peptide is prepared through chemical synthesis. Generally, at least two oligonucleotide primers are chemically synthesized with at least one restriction enzyme site at either end. The two oligonucleotides may be complementary or overlapped in the middle region with at lest ten base pairs. The PCR amplification may be employed to generate an intact insert from overlapped oligonucleotides.
The DNA sequence encoding a fusion protein contains at least four parts including a DNA sequence of the affinity tag, a DNA sequence of the carrier protein-superfolder green fluorescent protein, a DNA sequence of the cleavage site and a DNA sequence of the target peptide. Typically the arrangement of DNA sequence segments can be the same as those described in FIG. 2A and FIG. 2B. The DNA sequence of the affinity tag may be inserted in any place in the DNA sequence of the fusion protein. The DNA sequence of the fusion protein is ligated into any bacterial expression plasmid to construct an expression vector. The expression vector contains at least one promoter e.g. lac, T7, Tac, lamda, pL, or pBAD and one antibiotic marker, e.g. ampicillin, kanamycin, or tetracycline.
The constructed expression vector may be transformed into a bacterial host cell to replicate plasmid for small-scale DNA preparation (mini-prep) and sequencing. The identity of the construct is confirmed by DNA sequencing and the expression vector is transformed into a bacterial host cell to express the fusion protein. The cells harboring the fusion protein expression vector may be cultured in the LB medium or a minimal medium in the presence of at least one antibiotic. The expression of the fusion protein is induced with an inducer, eg. IPTG, galactoside, nalidixic acid, temperature, or arabinose.
The purification of fusion protein refers to the procedure by which the fusion protein is isolated from host cells. Cells are typically collected by centrifugation or filtration. The cell pellet is typically resuspended in the lysis buffer which contains 50 mM phosphate, 10 mM Tris, and 50 mM NaCl. The lysis buffer may contain a chaotropic agent, e.g. urea or guanidinium chloride. Suspended cells may be further subjected to French Press or ultra-sonication to thoroughly break the cells. The lysate is subjected to centrifugation to isolate the desired fusion protein from others. In some instances, the fusion protein is isolated from cells as pure inclusion bodies. The inclusion bodies may be isolated from a crude cell lysate by conventional techniques, e.g. by centrifugation. The crude inclusion bodies may be subjected to an initial purification step such as washing by a solution of 50 mM phosphate, 1 mM EDTA, pH 7.5 once and then washing with the same buffer containing low concentration of chaotropic reagent such as urea or guanidinium chloride at least twice. Pure inclusion bodies will be dissolved in a chaotropic buffer and then is subjected to refolding. The refolding process may be carried out by dialysis of the suspended sample against a physiological buffer or by removal of salts through a reverse-phase chromatographic column and followed by freeze-drying. In some instances, the fusion protein is produced in insoluble inclusion bodies inside cells but no affinity tag was engineered. In this case, the fusion protein in the lysate is roughly purified by solvent extraction and further purified by ion-exchange chromatography. If necessary, the fusion protein may be purified by reverse-phase HPLC. In other instances, the fusion protein may be purified through affinity chromatography such as His-tag binding Ni-NTA affinity beads under either native condition or denaturing conditions.
After cleavage, the mixture is used to isolate the target peptide from the carrier protein. In some instances, the mixture may be used directly for HPLC purification. The pH value of the mixture should be adjusted to below 3.0 and the sample is filtered to remove particles prior to HPLC purification. In some instances, the mixture is diluted with water (e.g. to  ̃10 fold) and lyophilized to dryness and then purified by reverse-phase HPLC column using an acetonitrile-water gradient containing 0.1% TFA. In other instances, the mixture is initially purified by His-tag affinity chromatography and reverse-phase chromatography to remove salts, the carrier protein, undigested fusion protein and non-specifically digested peptides. Finally, the pure peptide is lyophilized and the identity is confirmed by mass spectrometry.
Table 1 lists some recombinant peptides exemplified herein below, which has been expressed with the current invention. The data show that the present expression systems can efficiently produce pure peptides in high-yield.







TABLE 1







Examples of the expressed recombinant peptides











Peptide
Size (AA)
Yield (mg/L)















Proinlusin lispro
82
>300



proinsulin
82
>300



Proinsulin glargine
82
>300



PTH
34
>50



calcitonin
33
>50



GLP-1
39
>50










The term “isolated” or “purified” material refers to material that is substantially or essentially free from components that normally accompany it as found in its native state. For instance, this refers to the DNA segment as originally isolated, and does not exclude other isolated proteins, genes, or coding regions later added to the composition by the hand of man. Purity and homogeneity are typically determined using analytical chemistry techniques such as polyacrylamide gel electrophoresis or high performance liquid chromatography. A protein that is the predominant species present in a preparation is substantially purified. An isolated nucleic acid is separated from other open reading frames that flank the gene and encode proteins other than the gene.
As used herein, an “isolated” or “purified” protein or biologically active portion thereof is substantially free of cellular material or other contaminating proteins from the cell or tissue source from which the fusion protein or target protein is derived, or substantially free from chemical precursors or other chemicals when chemically synthesized. The language “substantially free of cellular material” includes preparations of fusion protein or target protein in which the protein is separated from cellular components of the cells from which it is isolated or recombinantly produced. In one embodiment, the language “substantially free of cellular material” includes preparations of target protein having less than about 30% (by dry weight) of non-target protein (also referred to herein as a “contaminating protein”), more preferably less than about 20% of non-target protein, still more preferably less than about 10% of non-target protein, and most preferably less than about 5% non-target protein. When the target protein or biologically active portion thereof is recombinantly produced, it is also preferably substantially free of culture medium, i.e., culture medium represents less than about 20%, more preferably less than about 10%, and most preferably less than about 5% of the volume of the protein preparation. In embodiments, the purity of target protein is at least 80%, at least 90%, at least 95%, or at least 98%.
The present invention additionally relates to nucleic acids that encode the fusion protein of the invention. Nucleic acids encoding the fusion proteins may be obtained by any method known in the art (e.g., by PCR amplification using synthetic primers hybridizable to the 3′ and 5′ termini of the sequence and/or by cloning from a cDNA or genomic library using an oligonucleotide sequence specific for the given gene sequence).
For recombinant expression of the target protein, the nucleic acid containing all or a portion of the nucleotide sequence encoding the protein may be inserted into an appropriate expression vector (i.e., a vector that contains the necessary elements for the transcription and translation of the inserted peptide coding sequence). In some embodiments, the regulatory elements are heterologous (i.e., not the native gene promoter). Alternately, the necessary transcriptional and translational signals may also be supplied by the native promoter for the genes and/or their flanking regions.
A variety of host vector systems may be utilized to express the peptide coding sequence(s). These include, but are not limited to: (i) mammalian cell systems that are infected with vaccinia virus, adenovirus, and the like; (ii) insect cell systems infected with baculovirus and the like; (iii) yeast containing yeast vectors or (iv) bacteria transformed with bacteriophage, DNA, plasmid DNA, or cosmid DNA. Depending upon the host vector system utilized, any one of a number of suitable transcription and translation elements may be used.
Promoter/enhancer sequences within expression vectors may utilize plant, animal, insect, or fungus regulatory sequences, as provided in the invention. For example, promoter/enhancer elements can be used from yeast and other fungi (e.g., the GAL4 promoter, the alcohol dehydrogenase promoter, the phosphoglycerol kinase promoter, the alkaline phosphatase promoter). Alternatively, or in addition, they may include animal transcriptional control regions, e.g., (i) the insulin gene control region active within pancreatic β cells (see, e.g., Hanahan, et al., 1985. Nature 315: 115 122); (ii) the immunoglobulin gene control region active within lymphoid cells (see, e.g., Grosschedl, et al., 1984. Cell 38: 647 658); (iii) the albumin gene control region active within liver (see, e.g., Pinckert, et al., 1987. Genes and Dev 1: 268 276; (iv) the myelin basic protein gene control region active within brain oligodendrocyte cells (see, e.g., Readhead, et al., 1987. Cell 48: 703 712); and (v) the gonadotropin releasing hormone gene control region active within the hypothalamus (see, e.g., Mason, et al., 1986. Science 234: 1372 1378), and the like.
Expression vectors or their derivatives include, e.g. human or animal viruses (e.g., vaccinia virus or adenovirus); insect viruses (e.g., baculovirus); yeast vectors; bacteriophage vectors (e.g., lambda phage); plasmid vectors and cosmid vectors.
A host cell strain may be selected that modulates the expression of inserted sequences of interest, or modifies or processes expressed peptides encoded by the sequences in the specific manner desired. In addition, expression from certain promoters may be enhanced in the presence of certain inducers in a selected host strain; thus facilitating control of the expression of a genetically engineered peptides. Moreover, different host cells possess characteristic and specific mechanisms for the translational and post translational processing and modification (e.g., glycosylation, phosphorylation, and the like) of expressed peptides. Appropriate cell lines or host systems may thus be chosen to ensure the desired modification and processing of the foreign peptide is achieved. For example, peptide expression within a bacterial system can be used to produce an unglycosylated core peptide; whereas expression within mammalian cells ensures “native” glycosylation of a heterologous peptide.
As described above, also included in the invention are derivatives, fragments, homologs, analogs and variants of sfGFP for use as a carrier protein and nucleic acids encoding these proteins or polypeptides. For nucleic acids, derivatives, fragments, and analogs provided herein are defined as sequences of at least 6 (contiguous) nucleic acids, and which have a length sufficient to allow for specific hybridization. For amino acids, derivatives, fragments, and analogs provided herein are defined as sequences of at least 4 (contiguous) amino acids, a length sufficient to allow for specific recognition of an epitope.
The length of the fragments is less than the length of the corresponding full-length nucleic acid or polypeptide from which sfGFP, or nucleic acid encoding same, is derived. Derivatives and analogs may be full length or other than full length, if the derivative or analog contains a modified nucleic acid or amino acid. Derivatives or analogs of sfGFP include, e.g., molecules including regions that are substantially homologous to the protein, in various embodiments, by at least about 30%, 50%, 70%, 80%, or 95%, 98%, or even 99%, identity over an amino acid sequence of identical size or when compared to an aligned sequence in which the alignment is done by a computer homology program known in the art. For example sequence identity can be measured using sequence analysis software (Sequence Analysis Software Package of the Genetics Computer Group, University of Wisconsin Biotechnology Center, 1710 University Avenue, Madison, Wis. 53705), with the default parameters therein.
In the case of polypeptide sequences, which are less than 100% identical to a reference sequence, the non-identical positions are preferably, but not necessarily, conservative substitutions for the reference sequence. Conservative substitutions typically include substitutions within the following groups: glycine and alanine; valine, isoleucine, and leucine; aspartic acid and glutamic acid; asparagine and glutamine; serine and threonine; lysine and arginine; and phenylalanine and tyrosine. Thus, included in the invention are peptides having mutated sequences such that they remain homologous, e.g. in sequence, in function, and in antigenic character or other function, with a protein having the corresponding parent sequence. Such mutations can, for example, be mutations involving conservative amino acid changes, e.g., changes between amino acids of broadly similar molecular properties. For example, interchanges within the aliphatic group alanine, valine, leucine and isoleucine can be considered as conservative. Sometimes substitution of glycine for one of these can also be considered conservative. Other conservative interchanges include those within the aliphatic group aspartate and glutamate; within the amide group asparagine and glutamine; within the hydroxyl group serine and threonine; within the aromatic group phenylalanine, tyrosine and tryptophan; within the basic group lysine, arginine and histidine; and within the sulfur-containing group methionine and cysteine. Sometimes substitution within the group methionine and leucine can also be considered conservative. Preferred conservative substitution groups are aspartate-glutamate; asparagine-glutamine; valine-leucine-isoleucine; alanine-valine; phenylalanine-tyrosine; and lysine-arginine.
Where a particular polypeptide is said to have a specific percent identity to a reference polypeptide of a defined length, the percent identity is relative to the reference peptide. Thus, a peptide that is 50% identical to a reference polypeptide that is 100 amino acids long can be a 50 amino acid polypeptide that is completely identical to a 50 amino acid long portion of the reference polypeptide. It might also be a 100 amino acid long polypeptide, which is 50% identical to the reference polypeptide over its entire length. Of course, other polypeptides will meet the same criteria.
In embodiments, the carrier protein of the invention has a sequence at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 97%) identical to SEQ ID NO: 1. In embodiments, the fusion protein of the invention includes a target protein and a carrier protein that has a sequence at least 80% (e.g., at least 85%, at least 90%, at least 95%, or at least 97%) identical to SEQ ID NO: 1. In embodiments, the nucleic acid encoding the fusion protein includes a
The invention also encompasses allelic variants of the disclosed polynucleotides or peptides; that is, naturally occurring alternative forms of the isolated polynucleotide that also encode peptides that are identical, homologous or related to that encoded by the polynucleotides. Alternatively, non naturally occurring variants may be produced by mutagenesis techniques or by direct synthesis.
Species homologs of the disclosed polynucleotides and peptides are also provided by the present invention. “Variant” refers to a polynucleotide or polypeptide differing from the polynucleotide or polypeptide of the present invention, but retaining essential properties thereof. Generally, variants are overall closely similar, and in many regions, identical to the polynucleotide or polypeptide of the present invention. The variants may contain alterations in the coding regions, non coding regions, or both.
In some embodiments, altered sequences include insertions such that the overall amino acid sequence is lengthened while the protein retains trafficking properties. Additionally, altered sequences may include random or designed internal deletions that shorten the overall amino acid sequence while the protein retains transport properties.
All publications and patent documents cited herein are incorporated herein by reference as if each such publication or document was specifically and individually indicated to be incorporated herein by reference. Citation of publications and patent documents is not intended as an admission that any is pertinent prior art, nor does it constitute any admission as to the contents or date of the same. The invention having now been described by way of written description, those of skill in the art will recognize that the invention can be practiced in a variety of embodiments and that the foregoing description and examples below are for purposes of illustration and not limitation of the claims that follow.
EXAMPLES
Example 1
Construction of Expression Vector pSFGFPN-NcoI
The construction of all plasmids in this invention followed standard cloning and QuikChange site-directed mutagenesis procedures using Phusion high-fidelity DNA polymerase from New England Biolabs Inc. Sequences of all plasmids constructed were verified by DNA sequencing. All oligonucleotide primers were purchased from Integrated DNA Technologies, Inc.
The plasmid pSFGFPN-NcoI contained a codon-optimized gene coding superfolder green fluorescent protein with a C-terminal 6× His-tag. There was also a NcoI restriction site that overlaped the first two amino acid coding nucleotides of the superfolder green fluorescent protein gene. This site was generated for the future cloning of a target peptide gene into the plasmid to form a fusion gene with superfolder green fluorescent protein at its C-terminus. To construct pSFGFPN-NcoI, two oligonucleotide primers 5′-AATTAACCATGGTTAGCAAAGGTG-3′ and 5′-GATCTCGAGCTTTAATGGTGATGATGATGGTGGCTGCCTTTATACAG-3′ were used to amplify a synthetic superfolder green fluorescent protein DNA using polymerase chain reactions (PCRs). The first primer contains a NcoI restriction site; the second primer contains a XhoI restriction site. The superfolder green fluorescent protein DNA shown as SEQ ID NO:2 was synthesized in Epoch biolabs Inc and codon optimized for efficient translation of the coded superfolder green fluorescent protein in E. coli. The PCR-amplified DNA was digested with NcoI and XhoI restriction enzymes for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut pBAD/Myc-His A vector from Invitrogen Inc using T4 DNA ligase. The precut pBAD/Myc-His A vector was obtained by digesting pBAD/Myc-His A with NcoI and XhoI restriction enzymes and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top10 cells. The transformed cells were grown on a lysogeny broth (LB) plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using two sequencing oligonucleotide primers 5′-CCTACCTGACGCTTTTTATCGCAACTC-3′ and 5′-GGCTGAAAATCTTCTCTCATCCGCC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPN-NcoI.
Example 2
Construction of Expression Vector pSFGFPC-MCS
The plasmid pSFGFPC-MCS contained a codon-optimized gene coding superfolder green fluorescent protein with a N-terminal 6× His-tag. There was also a multiple cloning site (MCS) containing restriction sites for XhoI, BglII, PstI, KpnI, EcoRI and HindIII at the C-terminal end of the superfolder green fluorescent protein gene. This multiple cloning site was generated for the future cloning of a target peptide gene into the plasmid to form a fusion gene with superfolder green fluorescent protein at its N-terminus. To obtain pSFGFPC-MCS, two primers 5′-AACCATGGTTCACCATCATCATCACCATGCGGCGAGCAA-3′ and 5′-ATCTCGAGCTTTATACAGTTCATCCATA-3′ were used to amplify the same synthetic superfolder green fluorescent protein DNA using PCR. The first primer contains a NcoI restriction site; the second primer contains a XhoI restriction site. The PCR-amplified DNA was digested with NcoI and XhoI restriction enzymes for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut pBAD/Myc-His A vector from Invitrogen Inc using T4 DNA ligase. The precut pBAD/Myc-His A vector was obtained by digesting pBAD/Myc-His A with NcoI and XhoI restriction enzymes and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using two sequencing oligonucleotide primers 5′-CCTACCTGACGCTTTTTATCGCAACTC-3′ and 5′-GGCTGAAAATCTTCTCTCATCCGCC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPC-MCS.
Example 3
Construction of Expression Vector pSFGFPN-prolispro
The expression vector pSFGFPN-prolispro contained a gene coding the precursor protein (prolispro; its amino acid sequence is shown as SEQ ID NO:7) of human insulin analog lispro fused at the N-terminus of superfolder green fluorescent protein that also has a C-terminal 6× His tag. In front of the prolispro gene, a tripeptide Met-Ala-Arg coding sequence was inserted for the following easy cleavage of this tripeptitide with trypsin. The linker peptide between prolispro and superfolder green fluorescent protein was an octapeptide Arg-Glu-Asn-Leu-Tyr-Phe-Gln-Gly. This octapeptide can be hydrolyzed by both trypsin after Arg and TEV protease between Gln and Gly. The DNA sequence for this octapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPN-prolispro, two primers 5′-GAATTAACCATGGCGCGTTTCGTTAACCAACACCTG-3′ and 5′-AACCCATGGCTCCCTGAAAATACAGGTTTTCACGATTACAGTAATTTTC-3′ were used to amplify a synthetic prolispro DNA using PCR. Both primers contain a NcoI restriction site. The synthetic prolispro DNA was provided by Epoch Biolab Inc. and its sequence shown as SEQ ID NO: 8 was optimized for efficient translation in E. coli. The PCR-amplified DNA was digested with NcoI restriction enzyme for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut psfGFPN-NcoI vector using T4 DNA ligase. The precut psfGFPN-NcoI vector was obtained by digesting psfGFPN-NcoI with NcoI and DpnI restriction enzymes for three hours and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-CCTACCTGACGCTTTTTATCGCAACTC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPN-prolispro. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:9 and has a DNA sequence as SEQ ID NO:10.
Example 4
Construction of Expression Vector pSFGFPN-proinsulin
The expression vector pSFGFPN-proinsulin contained a gene coding the precursor protein (proinsulin; its amino acid sequence is shown as SEQ ID NO:11 and its nucleotide sequence is shown as SEQ ID NO:12) of human insulin fused at the N-terminus of superfolder green fluorescent protein that also has a C-terminal 6× His tag. In front of the proinsulin gene, a tripeptide Met-Ala-Arg coding sequence was inserted for the following easy cleavage of this tripeptitide with trypsin. The linker peptide between proinsulin and superfolder green fluorescent protein was an octapeptide Arg-Glu-Asn-Leu-Tyr-Phe-Gln-Gly. This octapeptide can be hydrolyzed by both trypsin after Arg and TEV protease between Gln and Gly. The DNA sequence for this octapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPN-proinsulin, two primers 5′-CCGAAAACTCGTCGCGAAGCAGAGG-3′ and 5′-AGTATAGAAGAAGCCACGTTCACC-3′ were used to amplify the expression vector pSFGFPN-prolispro using PCR. The PCR-amplified DNA was phosphorylated using T4 polynucleotide kinase and then digested by DpnI restriction enzyme to remove the original pSFGFPN-prolispro. The finally digested DNA was separated by agarose electrophoresis. The desired band was cut and extracted using Qiagen gel extraction kits. The extracted DNA was then ligated to itself using T4 DNA ligase. The ligated product was then chemically transformed into Top10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-CCTACCTGACGCTTTTTATCGCAACTC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPN-proinsulin. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:13 and has a DNA sequence as SEQ ID NO:14.
Example 5
Construction of Expression Vector pSFGFP-proglargine
The expression vector pSFGFPN-proglargine contained a gene coding the precursor protein (proglargine; its amino acid sequence is shown as SEQ ID NO:15 and its nucleotide sequence is shown as SEQ ID NO:16) of human insulin analog glargine fused at the N-terminus of superfolder green fluorescent protein that also has a C-terminal 6× His tag. In front of the proinsulin gene, a tripeptide Met-Ala-Arg coding sequence was inserted for the following easy cleavage of this tripeptitide with trypsin. The linker peptide between proglargine and superfolder green fluorescent protein was an octapeptide Arg-Glu-Asn-Leu-Tyr-Phe-Gln-Gly. This octapeptide can be hydrolyzed by both trypsin after Arg and TEV protease between Gln and Gly. The DNA sequence for this octapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPN-proglargine, two primers 5′-CGTGAAAACCTGTATTTTCAGG-3′ and 5′-GCCACAGTAATTTTCCAGCTTATAC-3′ were used to amplify the expression vector pSFGFPN-proinsulin using PCR. The PCR-amplified DNA was phosphorylated using T4 polynucleotide kinase and then digested by DpnI restriction enzyme to remove the original pSFGFPN-proinsulin. The finally digested DNA was separated by agarose electrophoresis. The desired band was cut and extracted using Qiagen gel extraction kits. The extracted DNA was then ligated to itself using T4 DNA ligase. The ligated product was then chemically transformed into Top10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-CCTACCTGACGCTTTTTATCGCAACTC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPN-proglargine. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:17 and has a DNA sequence as SEQ ID NO:18.
Example 6
Construction of Expression Vector pSFGFPC-PTH
The expression vector pSFGFPC-PTH contained a gene coding PTH (its amino acid sequence is shown as SEQ ID NO:19 and its nucleotide sequence is shown as SEQ ID NO:20) fused at the C-terminus of superfolder green fluorescent protein that also has a N-terminal 6× His tag. The linker peptide between superfolder green fluorescent protein and PTH was a hexapeptide Glu-Asn-Leu-Tyr-Phe-Gln. This hexapeptide can be recognized and hydrolyzed TEV protease after Gln. The DNA sequence for this hexapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPC-PTH, two primers 5′-ACCTCGAGATGAAAACCTGTATTTTCAGTCTGTTTCTGAAA-3′ and 5′-TCTAATTCCCTTAGAAGTTGTTAAGCTCCTG-3′ were used to amplify a synthetic PTH gene using PCR. The first primer contains a XhoI restriction site; the second contains a EcoRI restriction site. The synthetic PTH DNA was provided by Epoch Biolabs Inc. and sequence optimized for efficient translation in E. coli. The PCR-amplified DNA was digested with XhoI and EcoRI restriction enzymes for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut psfGFPC-MCS vector using T4 DNA ligase. The precut psfGFPC-MCS vector was obtained by digesting psfGFPC-MCS with XhoI and EcoRI restriction enzymes for three hours and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-GGCTGAAAATCTTCTCTCATCCGCC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPC-PTH. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:21 and has a DNA sequence as SEQ ID NO:22.
Example 7
Construction of Expression Vector pSFGFPC-calcitonin
The expression vector pSFGFPC-PTH contained a gene coding salmon calcitonin (its amino acid sequence is shown as SEQ ID NO:23 and its nucleotide sequence is shown as SEQ ID NO:24) fused at the C-terminus of superfolder green fluorescent protein that also has a N-terminal 6× His tag. The linker peptide between superfolder green fluorescent protein and calcitonin was a hexapeptide Glu-Asn-Leu-Tyr-Phe-Gln. This hexapeptide can be recognized and hydrolyzed TEV protease after Gln. The DNA sequence for this hexapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPC-calcitonin, two primers 5′-AGCTCGAGATGAAAACCTGTATTTTCAGTGCTCTGCGCTGTC-3′ and 5′-TCGAATTCCCTTACGGGGTACCAGA-3′ were used to amplify a synthetic calcitonin gene using PCR. The first primer contains a XhoI restriction site; the second contains a EcoRI restriction site. The synthetic calcitonin DNA was provided by Epoch Biolabs Inc. and sequence optimized for efficient translation in E. coli. The PCR-amplified DNA was digested with XhoI and EcoRI restriction enzymes for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut psfGFPC-MCS vector using T4 DNA ligase. The precut psfGFPC-MCS vector was obtained by digesting psfGFPC-MCS with XhoI and EcoRI restriction enzymes for three hours and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-GGCTGAAAATCTTCTCTCATCCGCC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPC-calcitonin. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:25 and has a DNA sequence as SEQ ID NO:26.
Example 8
Construction of Expression Vector pSFGFPC-GLP1
The expression vector pSFGFPC-GLP1 contained a gene coding GLP-1 (its amino acid sequence is shown as SEQ ID NO:27 and its nucleotide sequence is shown as SEQ ID NO:28) fused at the C-terminus of superfolder green fluorescent protein that also has a N-terminal 6× His tag. The linker peptide between superfolder green fluorescent protein and GLP-1 was a hexapeptide Glu-Asn-Leu-Tyr-Phe-Gln. This hexapeptide can be recognized and hydrolyzed TEV protease after Gln. The DNA sequence for this hexapeptide is also codon optimized for efficient translation in E. coli. To construct pSFGFPC-GLP1, two primers 5′-AGCTCGAGATGAAAACCTGTATTTTCAGCACGGTGGTGGTAC-3′ and 5′-TCGAATTCCCTTAAGACGGCGGCGGCGCACC-3′ were used to amplify a synthetic GLP-1 gene using PCR. The first primer contains a XhoI restriction site; the second contains a EcoRI restriction site. The synthetic GLP-1 DNA was provided by Epoch Biolabs Inc. and sequence optimized for efficient translation in E. coli. The PCR-amplified DNA was digested with XhoI and EcoRI restriction enzymes for three hours. The finally digested DNA was separated by agarose electrophoresis. The desired band for the digested DNA was cut and extracted using Qiagen gel extraction kits. The extracted digested DNA was then ligated with a precut psfGFPC-MCS vector using T4 DNA ligase. The precut psfGFPC-MCS vector was obtained by digesting psfGFPC-MCS with XhoI and EcoRI restriction enzymes for three hours and cleaned using Qiagen PCR clean kits. The ligated product was then chemically transformed into Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. Five survived colonies were selected to grow in 5 mL liquid LB media for plasmid extraction using Qiagen gel extraction kits. The extracted plasmids were then sequenced using a sequencing oligonucleotide primer 5′-GGCTGAAAATCTTCTCTCATCCGCC-3′ to confirm the correct insert. The finally obtained plasmid is named as pSFGFPC-GLP-1. In this plasmid, the fusion gene codes a fusion protein with a sequence shown as SEQ ID NO:29 and has a DNA sequence as SEQ ID NO:30.
Example 9
Expression of Prolispro
To express the prolispro-sfGFP protein, a sequence confirmed psfGFPN-prolispro plasmid was used to chemically transform E. coli Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The cells were grown for an additional 22 hours and then collected by centrifugation (4500 r.p.m., 20 min, 4° C.). The whole cell culture turned green three hours after induction. The final collected cell pellet showed strong fluorescence even under daylight indicating a very high expression level of the prolispro-sfGFP fusion protein.
The collected cells were re-suspended in 20 mL of lysis buffer (50 mM HEPES, pH 7.4, 500 mM NaCl, 10 mM DTT, 10% glycerol, 0.1% Triton X-100, 5 mM imidazole, and 1 μg/mL lysozyme). The resuspended cells were sonicated and the lysate was clarified by centrifugation (10200 r.p.m., 60 min, 4° C.). The following SDS-PAGE analysis of the supernatant and the cell debris indicating most of the fusion protein was expressed in inclusion bodies as an insoluble form. Therefore, we followed an inclusion body purification protocol to purify the expressed prolispro-sfGFP fusion protein. The supernatant was discarded and the pellet was resuspended in a 40 mL washing buffer containing 50 mM Tris-HCl (pH 8.0), 100 mM NaCl, 0.1% NaN3, and 0.5% Triton-X100 and centrifuged again (10200 r.p.m., 20 min, 4° C.). After that, the supernatant was discarded and the pellet was then resuspended in the same 40 mL washing buffer without Triton-X100 and centrifuged (10200 r.p.m., 20 min, 4° C.). The process was repeated two more times. A SDS-PAGE analysis showed fairly pure inclusion bodies. The final pellet was resuspended in 8 M urea and then purified using Ni-NTA resins in a denaturing condition. The finally determined expression level of the prolispro-sfGFP fusion protein was 1.5 g/L which corresponded to 350 mg/L of prolispro. A time dependence of the prolispro-sfGFP fusion protein expression was also tested. Cells induced at 4 h and 21 h were collected and their inclusion bodies were then purified. FIG. 5 shows the relative expression levels at two conditions. It is obvious that 21 h induction gave a much higher expression level of the prolispro-sfGFP fusion protein.
Example 10
Processing the Prolispro-sfGFP Fusion Protein to Obtain Mature Lispro
To obtain mature lispro, the prolispro-sfGFP fusion protein was refolded using a quick refolding process. The Ni-NTA purified prolispro-sfGFP was stored in 8 M urea and 10 mM Tris-HCl (pH 9.2). A refolding buffer containing 10 mM Tris-HCl (pH 9.2), 10 mM glycine, 1 mM EDTA, and 4.5 mM cystine was then slowly added to the prolispro-sfGFP solution in a 1:1 ratio finally by volume. Next, cysteine was added to the above solution to a final concentration of 0.5 mM and mixed gently by inverting the tubes 2-3 times and the tube was placed in an incubator without agitation for 45 min at 30° C. The presence of cystine and cysteine enables the formation of disulfide bonds for the correct folding of prolispro. Overnight dialysis was then performed to change the buffer of the folded prolispro-sfGFP protein to a digestion buffer (50 mM Tris-HCl, pH 9.0).
After dialysis, the prolispro-sfGFP solution was collected and concentrated to 1 mg/mL and then digested by trypsin (E/S: 1:600, w/w) and carboxypeptidase B (E/S: 1:600, w/w) at 4° C. for 5 h. 0.5 μg/mL leupeptin was then added to terminate the digestion reactions. FIG. 6 is a SDS-PAGE gel that showed the prolispro-sfGFP protein before and after digestion with trypsin and carboxypeptidase B. The gel clearly indicates the desired processing of the prolispro-sfGFP fusion protein to lispro. The lispro band in the gel clearly matched the band of the commercially available insulin. The gel also indicates the correct folding process. Otherwise, trypsin would have recognized the arginine residue in the B chain and gave a much smaller digestion product band.
The trypsin and carboxypeptidase B digested products of the prolispro-sfGFP fusion protein was then dialyzed against a buffer containing 50 mM sodium phosphate (pH 8) and then loaded on a Sephedex G-25 gel filtration column from GE Healthcare. Different digested products were eluted from the column using the same buffer. The fractions containing lispro were collected and concentrated to 1 mg/mL. The finally obtained yield of pure lispro was around 200 mg/L. The purified lispro was also subjected to the MALDI-TOF mass spectrometry analysis. The detected molecular weight shown in FIG. 7 was 5733.6 Da that agreed well with the theoretical molecular weight (5733 Da).
Example 11
Expression of the Proinsulin-sfGFP Fusion Protein
To express the proinsulin-sfGFP fusion protein, a sequence confirmed psfGFPN-proinsulin plasmid was used to chemically transform E. coli Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The following purification procedures of the expressed fusion protein from the inclusion bodies were as same as those for the prolispro-sfGFP fusion protein. The finally determined expression level of the proinsulin-sfGFP fusion protein was 145 mg/L that corresponded to around 350 mg/L expression level of proinsulin.
Example 12
Expression of the Proglargine-sfGFP Fusion Protein
To express the proglargine-sfGFP fusion protein, a sequence confirmed psfGFPN-proglargine plasmid was used to chemically transform E. coli Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The following purification procedures of the expressed fusion protein from the inclusion bodies were as same as those for the prolispro-sfGFP fusion protein. The finally determined expression level of the proglargine-sfGFP fusion protein was 140 mg/L that corresponded to around 345 mg/L expression level of proinsulin.
Example 13
Expression of the sfGFP-PTH Fusion Protein
To express the sfGFP-PTH fusion protein, a sequence confirmed psfGFPC-PTH plasmid was used to chemically transform E. coli Top 10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The cells were grown for an additional 16 hours and then collected by centrifugation (4500 r.p.m., 20 min, 4° C.).
The collected cells were re-suspended in 20 mL of lysis buffer (50 mM HEPES, pH 7.4, 500 mM NaCl, 10 mM DTT, 10% glycerol, 0.1% Triton X-100, 5 mM imidazole, and 1 μg/mL lysozyme). The resuspended cells were sonicated and the lysate was clarified by centrifugation (10200 r.p.m., 60 min, 4° C.). The following SDS-PAGE analysis of the supernatant and the cell debris indicating part of the fusion protein was expressed in the cytoplasm in a soluble form and part of the fusion protein was expressed in inclusion bodies in an insoluble form. Because of the easy processing of the soluble protein, we let the supernatant mix with Ni-NTA resins and purified the soluble fusion protein by eluting the resins with the lysis buffer with 250 mM imidazole. FIG. 8 shows the different fractions of the sfGFP-PTH fusion protein eluted from Ni-NTA resins indicating high purity. The determined expression yield of the finally obtained sfGFP-PTH fusion was 600 mg/L that corresponded to 60 mg/L expression level for PTH itself. Given that part of the fusion protein was in the inclusion bodies, the real expression levels of the sfGFP-PTH fusion protein and PTH were higher. The purified sfGFP-PTH fusion was also digested by TEV protease to release PTH. The digested products were further separated using reverse phase HPLC on a C18 column using an acetonitrile-water gradient containing 0.1% TFA to obtain pure PTH.
Example 14
Expression of the sfGFP-calcitonin Fusion Protein
To express the sfGFP-calcitonin fusion protein, a sequence confirmed psfGFPC-calcitonin plasmid was used to chemically transform E. coli Top10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The cells were grown for an additional 16 hours and then collected by centrifugation (4500 r.p.m., 20 min, 4° C.).
The collected cells were re-suspended in 20 mL of lysis buffer (50 mM HEPES, pH 7.4, 500 mM NaCl, 10 mM DTT, 10% glycerol, 0.1% Triton X-100, 5 mM imidazole, and 1 μg/mL lysozyme). The resuspended cells were sonicated and the lysate was clarified by centrifugation (10200 r.p.m., 60 min, 4° C.). Similarly as PTH, the following SDS-PAGE analysis of the supernatant and the cell debris indicating part of the fusion protein was expressed in the cytoplasm in a soluble form and part of the fusion protein was expressed in inclusion bodies in an insoluble form. We processed the purification of the fusion protein from the supernatant. The supernatant was mix with Ni-NTA resins and purified the soluble fusion protein by eluting the resins with the lysis buffer with 250 mM imidazole. The determined expression yield of the finally obtained sfGFP-PTH fusion was 500 mg/L that corresponded to 50 mg/L expression level for calcitonin itself. The induction time dependence of the fusion protein expression was also analyzed by collecting cells at different times and analyzing the purified fusion protein from the cytoplasm. FIG. 9 shows the expression level peaked around 8-10 h induction. The purified sfGFP-calcitonin fusion was also digested by TEV protease to release calcitonin. The digested products were further separated using reverse phase HPLC on a C18 column using an acetonitrile-water gradient containing 0.1% TFA to obtain pure calcitonin.
Example 15
Expression of GLP-1
To express the sfGFP-GLP-1 fusion protein, a sequence confirmed psfGFPC-GLP1 plasmid was used to chemically transform E. coli Top10 cells. The transformed cells were grown on a LB plate containing 100 μg/mL ampicillin overnight. A single colony was selected to grow in a 5 mL LB culture containing 100 μg/mL ampicillin overnight. This overnight culture was then used to inoculate a 1 L 2YT medium containing μg/mL ampicillin and grown at 37° C. until the OD600 was 0.7. A 20% arabinose solution was then added to the medium to final concentration of 0.2% to induce the expression of the fusion protein. The cells were grown for an additional 16 hours and then collected by centrifugation (4500 r.p.m., 20 min, 4° C.).
The collected cells were re-suspended in 20 mL of lysis buffer (50 mM HEPES, pH 7.4, 500 mM NaCl, 10 mM DTT, 10% glycerol, 0.1% Triton X-100, 5 mM imidazole, and 1 μg/mL lysozyme). The resuspended cells were sonicated and the lysate was clarified by centrifugation (10200 r.p.m., 60 min, 4° C.). Similarly as PTH and calcitonin, the following SDS-PAGE analysis of the supernatant and the cell debris indicating part of the sfGFP-GLP-1 fusion protein was expressed in the cytoplasm in a soluble form and part of the fusion protein was expressed in inclusion bodies in an insoluble form. We processed the purification of the fusion protein from the supernatant. The supernatant was mix with Ni-NTA resins and purified the soluble fusion protein by eluting the resins with the lysis buffer with 250 mM imidazole. A SDS-PAGE analysis of the purified fusion protein shown in FIG. 10 indicated high purity. The determined expression yield of the finally obtained sfGFP-GLP-1 fusion was 500 mg/L that corresponded to 65 mg/L expression level for GLP-1 itself. The purified sfGFP-GLP-1 fusion was also digested by TEV protease to release calcitonin. The digested products were further separated using reverse phase HPLC on a C18 column using an acetonitrile-water gradient containing 0.1% TFA to obtain pure calcitonin.
INCORPORATION BY REFERENCE
The entire disclosure of each of the patent documents and scientific articles referred to herein is incorporated by reference for all purposes.
EQUIVALENTS
The invention can be embodied in other specific forms without departing from the spirit or essential characteristics thereof. The foregoing embodiments are therefore to be considered in all respects illustrative rather than limiting on the invention described herein. Scope of the invention is thus indicated by the appended claims rather than by the foregoing description, and all changes that come within the meaning and range of equivalency of the claims are intended to be embraced therein.

## Claims

1. A method for enhancing expression of a fusion protein that comprises a target peptide, the method comprising culturing a host cell transformed with an expression vector comprising a nucleic acid encoding a fusion protein that comprises a fusion carrier protein linked to at least one target peptide, wherein the fusion carrier protein has an amino add sequence as set forth in Formula


T1-A1-T2  (I),


wherein
T1is absent, a Met, a His-tag or at least one peptidic cleavage site,
A1 is superfolder green fluorescent protein, which has the amino acid sequence Ser-Lys-Gly-Glu-Glu-Leu-Phe-Thr-Gly-Val-Val-Pro-lle-Leu-Val-Glu-Leu-Asp-Gly-Asp-Val-Asn-Gly-His-Lys-Phe-Ser-Val-Arg-Gly-Glu-Gly-Glu-Gly-Asp-Ala-Thr-Asn-Gly-Lys-Leu-Thr-Leu-Lys-Phe-lle-Cys-Thr-Thr-Gly-Lys- Leu-Pro-Val-Pro-Trp-Pro-Thr-Leu-Val-Thr-Thr-Leu-Thr-Tyr-Gly-Val-Gln-Cys-Phe-Ser-Arg-Tyr-Pro-Asp-His-Met-Lys-Arg-His-Asp-Phe-Phe-Lys-Ser-Ala-Met-Pro-Glu-Gly-Tyr-Val-Gln-Glu-Arg-Thr-lle-Ser-Phe-Lys-Asp-Asp- Gly-Thr-Tyr-Lys-Thr-Arg-Ala-Glu-Val-Lys-Phe-Glu-Gly-Asp-Thr-Leu-Val-Asn-Arg-lle-Glu-Leu-Lys-Gly-lle-Asp-Phe-Lys-Glu-Asp-Gly-Asn-lle-Leu-Gly-His-Lys-Leu-Glu-Tyr-Asn-Phe-Asn-Ser-His-Asn-Val-Tyr-lle-Thr-Ala- Asp-Lys-Gln-Lys-Asn-Gly-lle-Lys-Ala-Asn-Phe-Lys-lle-Arg-His-Asn-Val-Glu-Asp-Gly-Ser-Val-Gln-Leu-Ala-Asp-His-Tyr-Gln-Gln-Asn-Thr-Pro-lle-Gly-Asp-Gly-Pro-Val-Leu-Leu-Pro-Asp-Asn-His-Tyr-Leu-Ser-Thr-Gln-Ser- Val-Leu-Ser-Lys-Asp-Pro-Asn-Glu-Lys-Arg-Asp-His-Met-Val-Leu-Leu-Glu-Phe-Val-Thr-Ala-Ala-Gly-lle-Thr-His-Gly-Met-Asp-Glu-Leu-Tyr-Lys (SEQ ID NO: 1), or an amino acid sequence that is at least 90%, at least 95%, at least 97%, or at least 99% identical to SEQ ID NO: 1,
T2 is absent, a His-tag or at least one peptidic cleavage site, provided that at most one of T1 and T2 is absent, and
wherein the target peptide is selected from the group consisting of PTH, GLP-1, exenatide, liraglutide, calcitonin, and proinsulin,

under suitable conditions for expression of the expression vector, thereby producing the fusion protein encoded by the nucleic acid in bacterial inclusion bodies, wherein the suitable conditions comprist an inducer for inducing the host cell to express the expression vector.

2. The method of claim 1, wherein the fusion protein comprises a target peptide that is proinsulin.

3. The method of claim 1, wherein the fusion protein has an amino acid sequence that is at least 90%, at least 95%, at least 97%, or at least 99% identical to the sequence selected from SEQ ID Nos: 9, 13, 17, 21, 25, and 29.

4. The method of claim 1, wherein the nucleic acid has the sequence selected from SEQ ID Nos: 10, 14, 18, 22, 26, and 30.

5. The method of claim 1, wherein the fusion protein comprises a target peptide that is PTH.

6. The method of claim 1, wherein the fusion protein comprises a target peptide that is exenatide.

7. The method of claim 1, wherein the fusion protein comprises a target peptide that is liraglutide.

8. The method of claim 1, wherein the fusion protein comprises a target peptide that is calcitonin.

9. The method of claim 1, wherein the fusion protein comprises a target peptide that is GLP-1.