# Patent

## Title
Signal peptide for the production of recombinant proteins

## Abstract

The present invention comprises a signal peptide with a cleavage site to a recombinant protein, wherein the last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA).

## Background
SEQUENCE LISTING
The text file Sequence 904ST25.txt, created Sep. 21, 2007, and of size 13 kilobytes, filed herewith, is hereby incorporated by reference.
BACKGROUND OF THE INVENTION
1. Field of the Invention
The invention relates to a signal peptide for the production of recombinant proteins.
2. Background Art
The large-scale industrial production of recombinant proteins is of increasing importance to the biotechnology and pharmaceutical industry. In general, recombinant proteins are produced either in mammalian cell culture or in microbial systems. Compared to mammalian cell culture, microbial systems have the advantage that in this manner recombinant proteins can be produced in a shorter time and with lower costs. Hence bacteria, preferably those of the genus Escherichia, more preferably E. coli, are most suitable for the production of recombinant proteins. In E. coli, recombinant proteins can in principle be produced in various ways:

    1. Intracellular production as soluble protein;
    2. Intracellular production as inclusion bodies;
    3. Secretion into the periplasm or into the nutrient medium.


The production process for the recombinant protein always consists of two parts. The first part is the fermentation, which leads to the crude product. In this case, the fermentation result, which contains the recombinant protein and also contaminating host proteins, is described as the crude product. The second part of the production process comprises the purification of the recombinant protein starting from the crude product.
In addition to the production costs of the crude product which is present directly after the fermentation as a mixture containing the recombinant protein and host proteins, the labor and costs for the production of the recombinant protein are also to a considerable extent determined by the costs of purification of the crude product to the desired recombinant protein. The purification is in most cases performed over several stages by means of chromatographic procedures. Purification from contaminating host proteins, some of which are immunogenic or toxic, is an important aspect.
The secretion of proteins in E. coli in most cases takes place via the so-called sec pathway (Driessen et al., 1998). This system is responsible for the export of certain bacterial proteins. The genes for these proteins each have a so-called signal sequence at the 5′ end. During protein synthesis, this is translated into a signal peptide and effects the secretion of the protein through the cytoplasmic membrane. After secretion, the signal peptide is removed by the enzyme signal peptidase and the mature protein is released.
The sec system can also be used for the secretion of recombinant, for example heterologous, proteins (Lee et al., Methods in Molecular Biology 308, 2005). For this, the recombinant gene for the recombinant protein to be produced is linked with a signal sequence (“in-frame fusion”), which results in the production of a signal peptide-protein fusion product. The signal peptide encoded by the signal sequence mediates the secretion of the recombinant protein across the cytoplasmic membrane into the periplasm by means of the bacterial sec system. In this, the signal peptide is cleaved off at the cleavage site between signal peptide and the recombinant protein, and the desired recombinant protein is obtained in the periplasm. The recombinant protein can then be purified from the periplasm.
Compared to the other production processes, secretion offers the advantage that the recombinant protein is obtained directly as native, soluble, correctly folded protein, which in contrast to the “inclusion body” process does not have to be denatured and again renatured, a step which is attended by major losses in yield. Moreover, in this case the crude product is contaminated with fewer host proteins compared to intracellular soluble production, since the periplasm of bacteria contains far fewer host proteins than the cytoplasm.
Under certain conditions or in certain bacterial strains, the recombinant protein is released from the periplasm into the nutrient medium (e.g. Ray et al., 2002; EP0338410B1; Nagahari et al., 1985; Yang et al., 1998; EP0677109B1) and can be purified from this.
Compared to secretion into the periplasm, secretion of the proteins into the nutrient medium offers an advantage that the protein is then present in still purer form. Moreover as the first purification step, laborious preparation of the periplasm or disintegration of the cells is unnecessary, but rather the much simpler and more reproducible removal of the whole cells.
As aforesaid, for the secretion of a protein to be produced, the gene coding for it is linked with a signal sequence, which has the effect that the protein to be produced is initially produced as a fusion product with the signal peptide encoded by the signal sequence. This signal peptide effects the secretion of the protein produced.
Signal peptides are made up of three regions: the N-terminal N region (1-5 amino acids) as a rule contains one or more amino acids, which bear a positive charge. The H region lying in the middle mostly consists of 7-15 amino acids, many of which are hydrophobic. The C region as a rule comprising 3-7 amino acids mostly contains neutral, short-chain amino acids (A, G, S, T or C) at position −1 and −3 before the cleavage site.
Various signal sequences and the corresponding signal peptides are described in the state of the art, e.g. phoA, ompA, pelB, ompF, ompT, lamB, malE, staphylococcal protein A and stII (Choi & Lee, 2004; EP0396612B1). The signal peptide of the cyclodextrin glycosyltransferase (CGTase) from various strains, such as for example Klebsiella oxytoca (Klebsiella pneumoniae M5a1), and the use thereof for the secretion of CGTase in E. coli strains is described in U.S. Pat. No. 5,395,927. Also described (EP0448093B1) is the fact that a recombinant protein, such as for example a hirudin derivative, can be produced and secreted in E. coli strains through fusion of the gene for the recombinant protein with the signal sequence of the CGTase. In the case of a specific hirudin derivative, this leads to a yield of 250 mg/l in a shaker flask culture and 2.63 g/l in a fermentation. EP0448093B1 however also describes the fact that with another recombinant protein yields of only up to 25 mg/l were obtained. The signal peptide of CGTase is like all other known signal peptides—not capable of mediating secretion of any recombinant protein in equally high yields. Since every recombinant protein is encoded by its own DNA sequence and in particular the DNA sequence at the transition point between signal sequence and the sequence coding for the recombinant protein is therefore different, as a rule an optimal signal peptide must be found for each recombinant protein.
SUMMARY OF THE INVENTION
One objective of the present invention is to provide novel signal peptides. The problem is solved by means of a signal peptide, which is characterized in that its last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA).



BRIEF DESCRIPTION OF THE DRAWINGS
FIG. 1 shows an overview of amino acids.
FIG. 2 shows the plasmid map of plasmid pJF118ut.
FIG. 3 shows the plasmid map of plasmid pCGT.
FIG. 4 shows the plasmid map of plasmid pKP651.
FIG. 5 shows the plasmid map of plasmid pKP652.
FIG. 6 shows the plasmid map of plasmid pKPIFN.
FIG. 7 shows the plasmid map of plasmid pBaBIFN1.
FIG. 8 shows the plasmid map of plasmid pFab-anti-lysozyme.
FIG. 9 shows an immunoblot wherein culture supernatants from interferon•2b-producing cells (see Example 2) are analyzed.

    Track 1: Size standard;
    Tracks 2 and 3: 20 and 40 ng interferon•2b;
    Tracks 4-6: Supernatant from cultures with plasmid pBaBIFN1 after 24, 48 and 72 hrs;
    Tracks 7-9: Supernatant from cultures with plasmid pKPIFN after 24, 48 and 72 hrs;
    Tracks 10-12: Supernatant from cultures with plasmid pKP651 after 24, 48 and 72 hrs;
    Tracks 13-15: Supernatant from cultures with plasmid pKP652 after 24, 48 and 72 hrs.
    In each case, 5 μl were applied at 24 hrs, and 1 μl at 48 hrs and 72 hrs.





DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENT(S)
In an embodiment of the present invention, a signal peptide in which the last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA) is provided. Preferably, the signal peptide has the amino acid sequence: MKRNRFFNTSAAIAISIALQIFFPSASAFA (SEQ ID NO: 1) or an amino acid sequence wherein compared to SEQ ID NO: 1 one to ten preferably one to five and more preferably one to three amino acids, with the exception of the last three amino acids before the cleavage site, are altered.
As set forth above, a signal peptide consists of different regions, which contain amino acids from a certain group (e.g. charged or hydrophobic or short-chain). The person skilled in the art can therefore create a novel signal peptide with unchanged properties by replacement of an amino acid by another with comparable properties. For this reason, signal peptides wherein, compared to SEQ ID NO: 2, 1-10, more preferably 1-5, most preferably 1-3 amino acids, are altered, should also be regarded as signal peptides according to the invention. Preferably these are exchanges of amino acids that have similar biochemical properties, for example basic amino acids (lysine, arginine, histidine) for basic ones, and acidic amino acids (aspartate, glutamate, asparagine, glutamine) for acidic ones, hydrophobic for hydrophobic, etc. An overview of the biochemical properties of amino acids is shown in FIG. 1.
The invention further relates to the signal sequence coding for the signal peptide according to the invention. This is characterized in that it codes for a signal peptide with a cleavage site whereof the last three amino acids before the cleavage site are alanine-phenylalanine-alanine. Preferably this is a signal sequence with the DNA sequence ATGAAAAGAAACCGTTTTTTTAATACCTCGGCTGCTATTGCCATTTCGATTGCATTACAGAT CTTTTTTCCGTCCGCTTCCGCTTTCGCT (SEQ ID NO: 2) and all DNA sequences, which, on the basis of the degenerate genetic code, code for the amino acid sequence SEQ ID NO: 1.
During a screening operation, the properties of various signal sequences, which had been obtained by modification of the CGTase signal sequence (MKRNRFFNTSAAIAISIALNTFFCSMQTIA, SEQ ID NO: 3) were compared. Surprisingly, it was found that the signal sequence according to the invention is suitable for the production and secretion of a larger spectrum of recombinant proteins in higher yield in host cells than the CGTase signal sequence or also other signal sequences.
A DNA sequence according to the invention can be obtained by gene synthesis or ligation of appropriate oligonucleotides by methods known to the person skilled in the art. The DNA sequence according to the invention is linked in-frame to the gene of the recombinant protein to be produced by methods known to the person skilled in the art (e.g. after Lee et al., 2005) and can be introduced into a vector.
This combination of signal sequence and recombinant gene is preferably equipped with expression signals (promoter, transcription and translation start, ribosome binding site) functional in E. coli. All promoters known to the person skilled in the art, on the one hand for example inducible promoters, such as the lac, tac, trc, lambda PL, ara or tet promoter or sequences derived therefrom are suitable as promoters. On the other hand, constitutive expression can also be effected through the use of a constitutive promoter, such as for example the GAPDH promoter. However, the promoter normally linked with the gene of the recombinant protein to be produced can also be used.
Accordingly, the invention also relates to an expression construct comprising an expression signal, a signal sequence according to the invention and an in-frame linked recombinant gene coding for a recombinant protein which is to be produced.
The expression construct according to the invention is introduced into a host cell by the use of methods known to the person skilled in the art. This is effected for example in a vector, such as a plasmid, that is a derivative of a known expression vector such as pUC18, pBR322, pACYC184, pASK-IBA3 or pET. For example, genes that code for resistance to ampicillin, tetracycline, chloramphenicol, kanamycin or other antibiotics are suitable as selection markers for plasmids.
Plasmids that contain the signal sequence according to the invention or an expression construct according to the invention are also an object of the invention. The recombinant protein is preferably a heterologous protein. Preferably the recombinant protein is a protein, which is used in technical preparations, or a protein, which is used as a pharmaceutical active substance (biologics or biopharmaceutical). Examples of such proteins are hirudin, insulin, interferons, such as alpha or beta interferon (e.g. interferon α2b), antibodies or antibody fragments (such as for example Fab fragments, scFv) or other binding proteins or enzymes, such as CGTase.
The expression construct according to the invention is introduced into a microorganism cell (host cell) by methods known to the person skilled in the art. Subsequently, the expression construct according to the invention can be present in the host cell as a plasmid or be integrated into the chromosome of the host cell.
Another object includes microbes that contain the signal sequence according to the invention or an expression construct according to the invention or a plasmid according to the invention.
The host cells are cells of a bacterial strain from the family Enterobacteriaceae, preferably a strain of the species Escherichia coli. More preferable is an Escherichia (E.) coli strain, which is characterized in that after transformation with the expression construct according to the invention it has a higher concentration of the recombinant protein in the periplasm or in the nutrient medium than the strain E. coli W3110 (ATCC 27325) after transformation with the expression construct according to the invention.
The following E. coli strains are most preferable:

    
    
        BLR: Ray et al., 2002, commercially available from Novagen
        K802=CGSC* 5610: Yang et al., 1998
        WCM105: preparable according to EP0338410B1
        MM28=CGSC* #5892: Nagahari et al., 1985
        RV308=ATCC** 31608; EP0677109B1
        RR1: ATCC** 31434: Nagahari et al., 1985
    
    
    * commercially available via the E. coli Genetic Stock Center CGSC (830 Kline Biology Tower, MCD Biology Department, 266 Whitney Ave., PO box 208103, Yale University, New Haven,
    ** commercially available via LGC Promochem, Mercatorstr. 51, 46485 Wesel, Germany.


The secretion of the protein produced takes place via the sec system of the host cell. After secretion into the periplasm, the signal peptide according to the invention is removed by a signal peptidase (e.g. LepB in E. coli) and the desired recombinant protein is formed.
The invention thus also relates to a process for the fermentative production of a recombinant protein by means of a host cell containing the expression construct according to the invention in a fermentation medium. This process is characterized in that a host strain according to the invention is cultured in a fermentation medium, the host strain produces the recombinant protein in the form of in-frame signal peptide-protein fusion product, wherein the signal peptide is a signal peptide according to the invention and on secretion of signal peptide-protein fusion product through the cytoplasmic membrane into the periplasm, the signal peptide is cleaved off at the cleavage site between signal peptide and the recombinant protein and the desired recombinant protein is obtained in the periplasm or the fermentation medium and the recombinant protein is purified after the fermentation.
The recombinant protein is secreted into the periplasm or preferably into the fermentation medium in fermentation. Moreover, the recombinant protein can be purified either from the periplasm of the host cells or preferably from the fermentation medium after removal of the cells.
The fermentation of the bacterial strain for the production of the recombinant protein according to the invention is preferably effected in a whole medium or minimal salt medium. These media are known from the literature.
As the carbon source, in principle all utilizable sugars, sugar alcohols, organic acids or salts thereof, starch hydrolyzates, molasses or other substances can be used. However, glucose or glycerin is preferably used. Combined feeding with several different carbon sources is also possible. As nitrogen sources, urea, ammonia and salts thereof, nitrate sources and other N sources can be used. The possible nitrogen sources also include complex amino acid mixtures, such as yeast extract, peptone, malt extract, soya peptone, casamino acids, corn steep liquor, and NZ amines (e.g. Kerry Bio-Science, Chicago, USA).
Furthermore, other components, such as vitamins, salts, yeast extract, amino acids and trace elements, through which cell growth is improved, can be added to the medium.
The strain is preferably incubated under aerobic culturing conditions for a period of 16-150 hrs and in the region of the optimal growth temperature for the strain in question.
As the optimal temperature region, 15-55° C. is preferred. A temperature between 28 and 37° C. is more preferable.
The strain can be grown in a shaker flask or fermenter, there being no restrictions as regards volume. It can be grown in a batch process, a fed batch or a continuous process.
Expression of the recombinant protein takes place either constitutively, i.e. non-induced, or by induction by physical or physiological stimuli. Expression can for example be induced by addition of a substance inducing the promoter, for example lactose or IPTG in the case of lac or tac promoter.
The purification of proteins from the periplasm or the culture medium can be effected by methods known to the person skilled in the art, such as disintegration or removal of the cells, chromatographic purification, complexation, filtration or precipitation of the protein.
The cells contain interferon•2b expression plasmids, which differ in their signal sequences. The interferon•2b formed was detected with antibodies (arrow). The use of the signal sequence according to the invention results in increased interferon•2b production.
The following examples serve for further illustration of the invention.
Example 1: Creation of a Signal Sequence According to the Invention and a Vector According to the Invention
As the starting plasmid, the plasmid pCGT was created as follows:
A DNA fragment with the SEQ ID NO: 4, which contains a cyclodextrin glycosyltransferase (CGTase) gene from Klebsiella pneumoniae M5a1 (Gene bank No. M15264), was prepared by gene synthesis. This DNA fragment was cloned into the expression vector pJF118ut (FIG. 2), which has been deposited at the DSMZ —Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH [German Collection of Microorganisms and Cell Cultures](Braunschweig) under the number DSM 18596. pJF118ut is a derivative of the known expression vector pKK223-3 (Amersham Pharmacia Biotech) and in addition to the β-lactamase gene and the tetracycline resistance gene also contains the tac promoter, which is repressed by the LacIq gene product, the gene whereof is also present on the plasmid, and which can be switched on by an inducer, such as for example D-lactose or isopropyl-β-D-thiogalactopyranoside (IPTG).
The plasmid pJF118ut was completely cleaved with the restriction enzyme EcoRI and the bases remaining at each of the 5′ ends of the linear DNA fragment were removed with S1 nuclease. The vector DNA molecule prepared in this manner was ligated with the CGTase-containing DNA fragment (SEQ ID NO: 4) using T4 ligase. The strain DH5α was transformed with the ligation preparation by the CaCl2 method, selection for plasmid-containing cells being performed using ampicillin (100 mg/l). The plasmid was isolated again from ampicillin -resistant transformants and examined by restriction analysis. The plasmid created in this manner, wherein the expression of the CGTase gene is under the control of the tac promoter, was designated pCGT (FIG. 3).
The gene for a CGTase fused to the signal sequence for the CGTase was removed: for this, the 8448 bp plasmid was cleaved with the restriction enzymes SspI and PacI in a partial digestion by methods known to the person skilled in the art. The 6390 bp fragment was isolated and treated with Klenow enzyme, whereby the ends were smoothed. The 2058 bp fragment was removed.
Subsequently, the following four DNA fragments were prepared by gene synthesis:








phoA-IFN·2b









SEQ ID NO: 5









ATTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGG



 


AATTGTGAGCGGATAACAATTTCACACAGGAAACAGAATTCTAAGGAGGA


 


AATTATATGAAACAAAGCACTATTGCACTGGCACTCTTACCGTTACTGTT


 


TACCCCTGTGACAAAAGCTTGTGACTTACCTCAGACCCATTCACTGGGCT


 


CACGCCGTACGCTGATGCTGTTAGCACAGATGCGTCGCATTTCTCTGTTT


 


AGTTGTTTGAAAGACCGTCATGATTTTGGGTTCCCGCAAGAAGAGTTTGG


 


TAATCAGTTTCAGAAAGCCGAAACTATTCCGGTTCTGCACGAAATGATTC


 


AACAGATTTTTAACCTGTTTTCGACAAAGGATAGCTCTGCCGCGTGGGAT


 


GAAACCTTACTGGATAAGTTCTACACCGAACTGTACCAGCAACTGAATGA


 


TCTGGAAGCATGCGTTATCCAGGGCGTGGGTGTCACAGAAACTCCGCTGA


 


TGAAGGAGGACAGCATTCTGGCGGTGCGCAAATATTTCCAGCGTATCACG


 


CTGTATCTGAAAGAGAAAAAATATTCGCCATGCGCGTGGGAGGTCGTGCG


 


CGCGGAGATCATGCGCAGTTTCTCTTTGAGCACCAACCTGCAAGAATCCT


 


TGCGTTCCAAAGAATAATAGTCTAGAAGCTTGGCTGTTTTGGCGGATGAG


 


ompA-IFN·2b








SEQ ID NO: 6









ATTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGG



 


AATTGTGAGCGGATAACAATTTCACACAGGAAACAGAATTCTAAGGAGGA


 


AATTATATGAAAAAGACAGCTATCGCGATTGCAGTGGCACTGGCTGGTTT


 


CGCTACCGTAGCGCAGGCTTGTGACTTACCTCAGACCCATTCACTGGGCT


 


CACGCCGTACGCTGATGCTGTTAGCACAGATGCGTCGCATTTCTCTGTTT


 


AGTTGTTTGAAAGACCGTCATGATTTTGGGTTCCCGCAAGAAGAGTTTGG


 


TAATCAGTTTCAGAAAGCCGAAACTATTCCGGTTCTGCACGAAATGATTC


 


AACAGATTTTTAACCTGTTTTCGACAAAGGATAGCTCTGCCGCGTGGGAT


 


GAAACCTTACTGGATAAGTTCTACACCGAACTGTACCAGCAACTGAATGA


 


TCTGGAAGCATGCGTTATCCAGGGCGTGGGTGTCACAGAAACTCCGCTGA


 


TGAAGGAGGACAGCATTCTGGCGGTGCGCAAATATTTCCAGCGTATCACG


 


CTGTATCTGAAAGAGAAAAAATATTCGCCATGCGCGTGGGAGGTCGTGCG


 


CGCGGAGATCATGCGCAGTTTCTCTTTGAGCACCAACCTGCAAGAATCCT


 


TGCGTTCCAAAGAATAATAGTCTAGAAGCTTGGCTGTTTTGGCGGATGAG


 


cgt-IFN·2b








SEQ ID NO: 7









ATTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGG



 


AATTGTGAGCGGATAACAATTTCACACAGGAAACAGAATTCTAAGGAGGA


 


AATTATATGAAAAGAAACCGTTTTTTTAATACCTCGGCTGCTATTGCCAT


 


TTCGATTGCATTAAATACTTTTTTTTGTAGCATGCAGACGATTGCTTGTG


 


ACTTACCTCAGACCCATTCACTGGGCTCACGCCGTACGCTGATGCTGTTA


 


GCACAGATGCGTCGCATTTCTCTGTTTAGTTGTTTGAAAGACCGTCATGA


 


TTTTGGGTTCCCGCAAGAAGAGTTTGGTAATCAGTTTCAGAAAGCCGAAA


 


CTATTCCGGTTCTGCACGAAATGATTCAACAGATTTTTAACCTGTTTTCG


 


ACAAAGGATAGCTCTGCCGCGTGGGATGAAACCTTACTGGATAAGTTCTA


 


CACCGAACTGTACCAGCAACTGAATGATCTGGAAGCATGCGTTATCCAGG


 


GCGTGGGTGTCACAGAAACTCCGCTGATGAAGGAGGACAGCATTCTGGCG


 


GTGCGCAAATATTTCCAGCGTATCACGCTGTATCTGAAAGAGAAAAAATA


 


TTCGCCATGCGCGTGGGAGGTCGTGCGCGCGGAGATCATGCGCAGTTTCT


 


CTTTGAGCACCAACCTGCAAGAATCCTTGCGTTCCAAAGAATAATAGTCT


 


AGAAGCTTGGCTGTTTTGGCGGATGAG


 


AFA-IFN·2b








SEQ ID NO: 8









ATTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGG



 


AATTGTGAGCGGATAACAATTTCACACAGGAAACAGAATTCTAAGGAGGA


 


AATTATATGAAAAGAAACCGTTTTTTTAATACCTCGGCTGCTATTGCCAT


 


TTCGATTGCATTACAGATCTTTTTTCCGTCCGCTTCCGCTTTCGCTTGTG


 


ACTTACCTCAGACCCATTCACTGGGCTCACGCCGTACGCTGATGCTGTTA


 


GCACAGATGCGTCGCATTTCTCTGTTTAGTTGTTTGAAAGACCGTCATGA


 


TTTTGGGTTCCCGCAAGAAGAGTTTGGTAATCAGTTTCAGAAAGCCGAAA


 


CTATTCCGGTTCTGCACGAAATGATTCAACAGATTTTTAACCTGTTTTCG


 


ACAAAGGATAGCTCTGCCGCGTGGGATGAAACCTTACTGGATACGTTCTA


 


CACCGAACTGTACCAGCAACTGAATGATCTGGAAGCATGCGTTATCCAGG


 


GCGTGGGTGTCACAGAAACTCCGCTGATGAAGGAGGACAGCATTCTGGCG


 


GTGCGCAAATATTTCCAGCGTATCACGCTGTATCTGAAAGAGAAAAAATA


 


TTCGCCATGCGCGTGGGAGGTCGTGCGCGCGGAGATCATGCGCAGTTTCT


 


CTTTGAGCACCAACCTGCAAGAATCCTTGCGTTCCAAAGAATAATAGTCT


 


AGAAGCTTGGCTGTTTTGGCGGATGAG






All the DNA fragments contain the tac promoter region and the gene for interferon•2b and four different signal sequences (shown bold). These four different signal sequences code for the following four different signal peptides, the first three signal peptides (SEQ ID NO: 9, 10, 3) being known from the state of the art, and the fourth signal peptide (SEQ ID NO: 2) being according to the invention:









phoA:




MKQSTIALALLPLLFTPVTKA
SEQ ID NO: 9


 


ompA:


MKKTAIAIAVALAGFATVAQA
SEQ ID NO: 10


 


cgt:


MKRNRFFNTSAAIAISIALNTFFCSMQTIA
SEQ ID NO: 3


 


AFA:


MKRNRFFNTSAAIAISIALQIFFPSASAFA
SEQ ID NO: 2






Through these cloning operations, the following four plasmids were formed:

    
    
        pKP651 (phoA signal sequence) FIG. 4
        pKP652 (ompA signal sequence) FIG. 5
        pKPIFN (cgt signal sequence) FIG. 6
        pBaBIFN1 (AFA: signal sequence according to invention) FIG. 7
    
    


These plasmids were introduced by known methods into the E. coli strain DH5α. The strain according to the invention DH5/pBaBIFN1 has been deposited at the DSMZ (Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, D-38142 Braunschweig [German Collection of Microorganisms and Cell Cultures]) under the number DSM 18343 in accordance with the Budapest Treaty.
Example 2: Increasing Interferon Production by Use of the Signal Sequence According to the Invention
Plasmid pKP651 (phoA signal sequence), pKP652 (ompA signal sequence), pKPIFN (cgt signal sequence) and pBaBIFN1 (AFA signal sequence according to the invention)(see Example 1) were introduced into strain WCM105 (preparable according to EP0338410B1) by transformation by standard methods (by CaCl2 transformation). Plasmid-containing strains were selected using ampicillin (100 mg/L).
The following strains were obtained:


    
    
        WCM105/pKP651 (phoA signal sequence)
        WCM105/pKP652 (ompA signal sequence)
        WCM105/pKPIFN (cgt signal sequence)
        WCM105/pBaBIFN1 (AFA signal sequence)
    
    


The production of interferon•2b in the resulting strains was studied. For this, the strains were cultured in 10 ml of LB medium containing 100 mg/L of ampicillin and with 1% glucose at 30° C. At an optical density of 0.5 at 600 nm (OD600), the production of interferon•2b was induced by addition of IPTG (isopropylthiogalactoside) to 0.5 mM. After 24 hrs, 48 hrs and 72 hrs, the interferon formed and secreted was quantified in the culture supernatant by separation of the proteins in the SDS gel and detection in the immunoblot with anti-interferon specific antibodies as follows:
1 μl (48 and 72 h) or 5 μl (24 h) of supernatant respectively were treated with sample buffer (2×Tris SDS -sample buffer (Invitrogen Cat. No. LC2676): 0.125 M Tris.HCl, pH 6.8, 4% w/v SDS, 20% v/v glycerin, 0.005% v/v bromophenol blue, 5% beta-mercaptoethanol). In addition, defined quantities of interferon•2b were applied as the standard. Denaturing of the proteins was effected by heating at 100° C. for 5 mins, cooling for 2 mins on ice and centrifuging down. The proteins were separated by electrophoresis in a 12% NuPAGE® Bis-Tris gel (Invitrogen Cat. No. NP0341) with 1×MES-containing running buffer (Invitrogen Cat. No. NP0002) (Electrophoresis parameters: 40 mins at 200 V).
Detection and quantification by immunoblot was carried out according to the following procedure:
Transfer in the wet blot procedure:


    Module: Amersham: Hoefer TE 22 Mini Tank Transfer Unit, Code Number: 80-6204-26
    Membrane: nitrocellulose membrane (Schleicher & Schuell, BA 85, cellulose nitrate (E), 0.45 μm pore size)
    Cut Whatman filters and nitrocellulose membrane to suitable size and soak in transfer buffer (Invitrogen Cat. No. LC3675) in the absence of air bubbles using foamed material pieces (sponges).
    Structure of sandwich: black grating, connection with the cathode, 2 sponges, each 3 mm thick, Whatman paper, SDS-polyacrylamide gel, NC membrane, Whatman, 1 sponge, 6 mm thick, white grating, connection with the anode.
    Transfer conditions: I=200 mA constant current, U=unlimited, run time 60 mins.

Prehybridization

    Incubation of the membrane in 25 ml of prehybridization buffer. Rock for 30 mins at RT.

Hybridization—1st antibody

    Incubation of the membrane in 25 ml of prehybridization buffer+0.15 μg/ml (->3.75 μg) anti-human-IFN alpha antibody (Pepro Tech EC, via Biozol Cat. No.: 500-P32A)
    Rock for 90 mins or overnight at RT.

Washing

    Rock for 10 seconds with 1×PBS, RT, pour off buffer
    Rock for 2×15 mins with 1×PBS, RT, pour off buffer

Hybridization—2nd antibody

    Incubation of the membrane in 25 ml of prehybridization buffer+25 μl (1:1000) goat anti-rabbit IgG horseradish peroxidase conjugate (HRP) (Southern Biotech, via Biozol Cat. No.: 4050-05)
    Rock for 60 mins at RT.

Washing

    Rock for 10 seconds with 1×PBS, RT, pour off buffer
    Rock for 2×15 mins with 1×PBS, RT, pour off buffer

Detection by chemiluminescence

    Prepare Lumi-Light Western blotting substrate (Roche, Cat. No.: 2015200): mix Lumi-Light luminol/enhancer solution and Lumi-Light stable peroxide solution in the ratio 1:1:3 ml/NC membrane.


Incubate blot for 5 mins at RT with Lumi-Light Western blotting substrate, allow excess to run off, cover membrane with clingfilm and immediately cover with an X-ray film (Kodak, X-OMAT), expose for 2 mins, develop and fix. For weak signals, the exposure is repeated over a longer time period.
Buffers


    Prehybridization buffer: 5% skim milk powder in 1×PBS 10×PBS: 100 mM NaH2PO4, 1.5 M NaCl, pH 7.5 with NaOH, 0.5% Triton 100
    1×PBS: dilute 10×PBS 1:10 with completely desalinated water

Quantification

    A quantitative assessment was made after scanning in the immunoblots with a Biorad GS-800 calibrated densitometer using the Quantity One 1-D-Analysis Software (Biorad) by comparison with the standard applied.
    FIG. 9 shows an immunoblot from this example. In Table 1, the quantified yields of interferon•2b are summarized:









TABLE 1







Yields of interferon•2b obtained after 24, 48 or


72 hrs with different plasmids, which each differ by the


signal sequence used.















Yield of




Signal
Culture
interferon•2b



Plasmid
sequence
(hrs)
(mg/l)
















pBaBIFN1
AFA
24
4



pBaBIFN1
AFA
48
25



pBaBIFN1
AFA
72
156



pKPIFN
cgt
24
4



pKPIFN
cgt
48
21



pKPIFN
cgt
72
95



pKP651
phoA
24
0



pKP651
phoA
48
0



pKP651
phoA
72
22



pKP652
ompA
24
4



pKP652
ompA
48
18



pKP652
ompA
72
41










This result shows unambiguously that the signal sequence according to the invention SEQ ID NO: 2 is superior to the other signal sequences as regards the yield and secretion of the protein to be produced.
Example 3: Creation of an Improved CGTAse Production Plasmid by the Insertion of the Signal Sequence According to the Invention
The plasmid pCGT (see Example 1) bears the gene for a CGTase in-frame fused to the signal sequence for the CGTase. This signal sequence was now replaced by the signal sequence according to the invention.
For this, the 8448 bp plasmid was cleaved with the restriction enzymes SspI and BglII in a partial digestion by methods known to the person skilled in the art. The 8119 bp fragment was isolated and treated with Klenow enzyme, whereby the ends were smoothed. The 329 bp fragment, which contains the CGTase signal sequence and about 150 bp of the 5′ end of the CGTase gene, was removed.
The following 329 bp DNA fragment, which is identical to the aforesaid fragment as regards sequence, except that the CGTase signal sequence has been replaced by the signal sequence according to the invention, was prepared by gene synthesis:








SEQ ID NO: 11









ATTCTGAAATGAGCTGTTGACAATTAATCATCGGCTCGTATAATGTGTGG



 


AATTGTGAGCGGATAACAATTTCACACAGGAAACAGATAATGAAAAGAAA


 


CCGTTTTTTTAATACCTCGGCTGCTATTGCCATTTCGATTGCATTACAGA


 


TCTTTTTTCCGTCCGCTTCCGCTTTCGCTGCTGAACCAGAAGAAACTTAT


 


CTTGATTTTCGTAAGGAGACAGATATATTTTCTATTCCTTGATCGTTTCA


 


GCGATGGAGATCCAAGTAATAATGCAGGGTTTAATTCTGCAACCTACGAT


 


CCTAATAATTTAAAAAAATATACTGGAGGA






This DNA fragment was ligated with the 8119 bp fragment isolated, by a method known to the person skilled in the art. The plasmid pCM703AFA formed in this manner was checked by sequencing.
Example 4: Improvement of CGTase Production by Use of the Signal Sequence According to the Invention
Plasmid pCM703AFA and plasmid pCGT (see Example 3) were introduced into the following strains by transformation by standard methods (e.g. by CaCl2 transformation):

    
    
        K802=CGSC* 5610: Yang et al., 1998
        WCM105: preparable according to EP0338410B1
    
    
    Selection for plasmid-containing strains was effected using ampicillin (100 mg/L).
    As a result, the following strains according to the invention were obtained:
    
        WCM105/pCM703AFA
        K802/pCM703AFA
    
    
    And the following control strains:
    
        WCM105/pCGT
        K802/pCGT
    
    
    These strains were used for the production of a cyclodextrin-glycosyltransferase and are grown in 10 ml in LB medium with 1% glucose and 100 mg/L ampicillin at 30° C. At OD 0.5, the production of the cyclodextrin glycosyltransferase is induced by addition of IPTG (isopropylthiogalactoside) to 0.5 mM. In the supernatant of the cultures of the strains, the yield of cyclodextrin glycosyltransferase was determined by the following activity test:
    Test buffer: 5 mM Tris-HCl buffer>pH 6.5, 5 mM CaSO4.2H2O
    Substrate: 10% Noredux solution in test buffer (pH 6.5)
    Test preparation: 1 ml substrate solution+1 ml centrifuged culture supernatant (5 mins, 12,000 rpm)+3 ml methanol Reaction temperature: 40° C.

Enzyme Test:
    
        Preconditioning of the solutions (ca. 5 mins at 40° C.)
        Addition of the enzyme solution to the substrate solution; rapid mixing (Whirl mixer)
        Incubation for 3 mins at 40° C.
        Stopping of the enzyme reaction by addition of methanol; rapid mixing (Whirl mixer)
        Cooling of the mixture on ice (ca. 5 mins)
        Centrifuging down (5 mins, 12,000 rpm) and pipetting off the clear supernatant
        HPLC analysis of the CD produced

Enzyme activity: A=G*V1*V2/(t*MG) (units/ml)

    
    
    A=activity
    G=Content of CD in mg/l =test mixture: area units×104/ Standard solution (10 mg/ml)/area units
    V1=dilution factor/test mixture (→5)
    V2=dilution factor/enzyme solution
    t=reaction time in mins (→3)
    MG=molecular weight in g/mol (CD→973)
    1 Unit=1•Mol product/min.









TABLE 2







Yield of cyclodextrin glycosyltransferase in various


strains.











cyclodextrin glycosyltransferase



Strain
produced (U/ml)














WCM105/pCGT
99



WCM105/pCM703AFA
158



K802/pCGT
67



K802/pCM703AFA
81










Example 5: Improvement of Hirudin Production by Use of the Signal Sequence According to the Invention

The plasmid pCMT203 described in patent EP0448093B1 was altered by replacement of the signal sequence used by the signal sequence according to the invention AFA. This replacement was effected analogously to Examples 1 and 3. The plasmid formed was named pCMT203AFA.

    pCMT203 and pCMT203AFA were introduced into strain WCM105 (preparable according to EP0338410B1) by transformation by standard methods (e.g. by CaCl2 transformation).


Selection for plasmid-containing strains was effected using ampicillin (100 mg/L).

    The following strains were obtained:
    
        WCM105/pCMT203
        WCM105/pCMT203AFA
    
    


Both strains were cultured in a 10 l fermenter, as described in EP0448093B1, and the hirudin formed was quantified, as described in EP0448093B1, 45 hrs after addition of IPTG. The results in Table 3 show that the use of the signal sequence according to the invention leads to increased yields of hirudin.







TABLE 3







Yield of hirudin (in AT-U/ml and g/L) in 10 l


fermentations 45 hrs after induction with IPTG in various


strains.









Strain
Hirudin (AT-U/ml)
Hirudin (g/L)





WCM105/pCMT203
42000
2.63


WCM105/pCMT203AFA
55400
3.47









Example 6: Improvement of the Production of a Functional Fab Antibody Fragment by Use of the Signal Sequence According to the Invention

The present example describes the improved production of a Fab fragment of the well-characterized anti-lysozyme antibody D1.3.
As the starting vector for the cloning and expression of the genes of the anti-lysozyme Fab fragment, the plasmid pJF118ut (see Example 1) was used. The two reading frames for the heavy chain (VH-CH1 domains) and for the light chain (VL-CL domains) of the anti-lysozyme Fab fragment each including a signal sequence were cloned into this plasmid in two consecutive steps.
For this, the following procedure was used: The DNA fragment with the SEQ ID NO: 12 (heavy chain) was prepared by gene synthesis and contains a gene fusion product consisting of the signal sequence of the ompA gene of E. coli and the reading frame for the heavy chain (VH-CH1) of the Fab fragment. Six histidine codons directly follow this reading frame and thus form the C terminus of the fusion protein. By means of this His tag, a simple purification of the fully assembled Fab fragment is subsequently possible by affinity chromatography. This DNA fragment was cleaved with the restriction enzymes EcoRI and PstI and ligated with the expression vector pJF118ut, which had been cleaved with the same restriction enzymes. The plasmid resulting from this cloning, wherein the expression of the gene for the heavy chain is under the control of the tac promoter, was described as pHC-anti-lysozyme.
The DNA fragment with the SEQ ID NO: 13 (light chain) was also prepared by gene synthesis and contains a gene fusion product consisting of a DNA sequence coding for the signal peptide of a CGTase described in SEQ ID NO: 3 (shown bold in SEQ ID NO: 7) and the reading frame for the light chain (VL-CL) of the Fab fragment. This DNA fragment was first cleaved with the restriction enzyme PstI and then ligated with the vector pHC-anti-lysozyme, which had been cleaved with the same restriction enzyme. The plasmid resulting from this was described as pFab-anti-lysozyme (FIG. 9). In this manner, an artificial operon consisting of the respective reading frames for the heavy and the light chain, which is under the control of the tac promoter, was created. With this, synchronous expression of both genes is possible by addition of an inducer (e.g. IPTG).
For the preparation of the plasmids according to the invention pFab-anti-lysozymeVLAFA and pFab-anti-lysozymeVHAFA, either the signal sequence for the light chain (pFab-anti-lysozymeVLAFA) or the signal sequence for the heavy chain (pFab-anti-lysozymeVHAFA) was replaced with the signal sequence according to the invention SEQ ID NO: 2 in a manner analogous to that described in Example 1.
For the preparation of the anti-lysozyme-Fab fragment, the strain WCM105 (see Example 4) was transformed by the CaCl2 method with the plasmids pFab-anti-lysozyme and pFab-anti-lysozymeVLAFA or pFab-anti-lysozymeVHAFA. The selection for plasmid-containing cells was effected using ampicillin (100 mg/l).
The production of the anti-lysozyme-Fab fragment was carried out on the 10 l scale. The production process was carried out in 10 l stirred tank fermenters.
The fermenter filled with 6 l of the medium FM4 (1.5 g/l KH2PO4, 5 g/l (NH4)2SO4, 0.3 g/l MgSO4×7H2O, 0.05 g/l CaCl2×2H2O, 0.075 g/l FeSO4×7H2O, 1 g/l Na3citrate×2H2O, 0.5 g/l NaCl), 1 ml/l trace element solution (0.15 g/l Na2MoO4×2H2O, 2.5 g/l Na3BO3, 0.7 g/l CoCl2×6H2O, 0.25 g/l CuSO4×5H2O, 1.6 g/l MnCl2×4H2O, 0.3 g/l ZnSO4×7H2O), 5 mg/l vitamin B1, 3 g/l phytone, 1.5 g/l yeast extract, 10 g/l glucose, 100 mg/l ampicillin was inoculated in the ratio 1:10 with a preculture which had been cultured overnight in the same medium. During the fermentation, a temperature of 30° C. was set and the pH value was kept constant at a value of 7.0 by metering in NH4OH or H3PO4. Glucose was metered in throughout the fermentation so that the maximal glucose concentration in the medium was <10 g/l. Expression was induced by addition of isopropyl-β-D-thiogalactopyranoside (IPTG) to 0.1 mM at the end of the logarithmic growth phase.
After 72 hrs fermentation, samples were taken, and the cells removed from the culture medium by centrifugation. The anti-lysozyme-Fab fragment was purified from the culture supernatants by affinity chromatography, as described in Skerra (1994, Gene 141, 79-84).
The quantification and determination of the activity of the purified anti-lysozyme-Fab fragment were performed by means of an ELISA test with lysozyme as the antigen (Skerra, 1994, Gene 141, 79-84).
In Table 4, the yields of functional anti-lysozyme-Fab fragment that could be isolated in each case from 20 ml of culture supernatant after 72 hrs fermentation are listed.







TABLE 4







Anti-lysozyme-Fab fragment yields in the culture


supernatant after 72 hrs fermentation













anti-lysozyme-Fab




Anti-lysozyme-Fab
fragment yield




fragment [mg]
[g/l] in the




purified from 20 ml
culture supernatant



Strain
of supernatant
(extrapolated)















WCM105/
25
1.25



pFab-anti-



lysozyme



WCM105/
30
1.5



pFab-anti-



lysozymeVLAFA



WCM105/
33
1.65



pFab-anti-



lysozymeVHAFA

## Claims

1. An isolated signal peptide with a cleavage site to a recombinant protein, wherein the last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA), the signal peptide comprising SEQ ID NO: 1.

2. An isolated signal peptide with a cleavage site to a recombinant protein the amino acid sequence of which comprises SEQ ID NO: 1 but with 1 to 3 conservative amino acid substitutions, wherein the last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA).

3. An isolated signal peptide with a cleavage site to a recombinant protein the amino acid sequence of which comprises SEQ ID NO: 1 but with 1 conservative amino acid substitution, wherein the last three amino acids before the cleavage site are alanine-phenylalanine-alanine (AFA).