WO2000018934A1 - Peptidyl prolyl cis-trans isomerases - Google Patents
Peptidyl prolyl cis-trans isomerases Download PDFInfo
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- WO2000018934A1 WO2000018934A1 PCT/IB1999/001669 IB9901669W WO0018934A1 WO 2000018934 A1 WO2000018934 A1 WO 2000018934A1 IB 9901669 W IB9901669 W IB 9901669W WO 0018934 A1 WO0018934 A1 WO 0018934A1
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- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/14—Hydrolases (3)
- C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
- C12N9/18—Carboxylic ester hydrolases (3.1.1)
- C12N9/20—Triglyceride splitting, e.g. by means of lipase
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- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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- C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
- C12N15/09—Recombinant DNA-technology
- C12N15/63—Introduction of foreign genetic material using vectors; Vectors; Use of hosts therefor; Regulation of expression
- C12N15/67—General methods for enhancing the expression
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- C—CHEMISTRY; METALLURGY
- C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
- C12N—MICROORGANISMS OR ENZYMES; COMPOSITIONS THEREOF; PROPAGATING, PRESERVING, OR MAINTAINING MICROORGANISMS; MUTATION OR GENETIC ENGINEERING; CULTURE MEDIA
- C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
- C12N9/90—Isomerases (5.)
Definitions
- the present invention relates to a novel enzyme.
- the invention relates to a novel cyclophilin-like peptidyl prolyl cis-trans isomerase.
- the folding of a protein is catalysed by an number of factors, including two isomerase families, namely protein disulphide isomerase, catalysing disulphide bond formation, and peptidyl prolyl cis-trans isomerase, catalysing the isomerisation of Xaa-Proline bonds.
- isomerases are inhibited by the immuno-suppressant drug cyclosporin A.
- the effects on secretion of heterologous peptides by overexpression of peptidyl prolyl cis-trans isomerases are however not known in the prior art.
- Proteins active in the E.R. are targeted to this compartment by a carboxy terminal extension of 4 amino acids.
- A. niger HDEL and KDEL have been reported to function as an E.R. retention signal (Jeenes D.J. , et al. , (1997) Gene 193:151-156).
- a method for producing a secretable polypeptide in an host cell comprising overexpressing a peptidyl prolyl cis- trans isomerase in the cell, thereby increasing the yield of the secreted polypeptide.
- the invention in a second aspect, relates to a polypeptide possessing foldase activity characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, having a signal sequence at the N-terminus and an endoplasmic reticulum retention signal at the C- terminus, and a molecular weight of 20.7 kDa and a deduced isoelectric point of 6.27.
- the invention relates to a polypeptide possessing foldase activity characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, encoded by a nucleic acid capable of hybridising under conditions of low, medium or high stringency with a 17 base oligonucleotide derived from SEQ ID No. 1.
- the invention relates to a polypeptide possessing foldase activity characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, encoded by a nucleic acid capable of hybridising under conditions of low, medium or high stringency with a 20 base oligonucleotide derived from SEQ ID No. 2.
- the invention relates to a polypeptide possessing foldase activity characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, which is at least 40% homologous to SEQ. LD. No. 2.
- Figure 1 is a restriction map of plasmid pPD23, which encodes A. niger cypB.
- Figure 2 shows an alignment of the cypB gene with peptidyl cis-trans isomerases from Orpinomyces, M. musculus and H. sapiens.
- Figure 3 shows an optimised alignment between the cypB gene and the Orpinimyces PPI gene.
- Figure 4 is a representation of pLIP4, which encodes the lip A gene.
- Figure 5 is a representation of ppd23dl3.
- Figure 6 is a representation of ppd23dl4.
- Figure 7 is a representation of ppd38d3
- the present invention relates to the overexpression of a peptidyl-prolyl cis-trans isomerase polypeptide (PPI) to increase the expression of secreted polypeptides from host cells.
- PPI peptidyl-prolyl cis-trans isomerase polypeptide
- PPI peptidyl-prolyl cis-trans isomerase polypeptide
- PPIs are ubiquitous, and several examples are known in the art. Examples include cyclophilin (see, for example, Bergsma et al. (1991) J. Biol. Chem. 266:23204-23214), parvulin, SurA (Rouviere and Gross, (1996) Genes Dev. 10:3170-3182) and FK506 binding proteins FKBP51 and FKBP52.
- PPI is responsible for the cis-trans isomerisation of peptidyl-prolyl bonds in polypeptides, thus promoting correct folding.
- the invention includes any polypeptide having PPI activity. This includes chaperone polypeptides, or fragments thereof, which may possess PPI activity (Wang & Tsou, (1998) FEBS lett. 425:382-384).
- the invention relates to PPI polypeptides of the cyclophilin family.
- the host cells are transformed host cells which express a heterologous gene product.
- the heterologous gene product is overexpressed, the tendency for the resulting polypeptides to be misfolded, and thus degraded in the ER as set forth above, is increased. Under these circumstances, therefore, overexpression of PPI in accordance with the invention is highly advantageous.
- the invention may also be used to increase the production of homologous polypeptides in host cells.
- the invention is useful where transcription of homologous polypeptides is increased, as a result of an increase in cell activity, caused by natural biological processes or by administration of agents capable of up regulating gene transcription.
- cells may be transformed with a expression systems capable of a causing upregulation of the endogenous genes, for example expression systems encoding transcription factors which are active on endogenous promoters.
- upregulation of PPI expression may be achieved by increasing the expression of endogenous PPI or by transforming the host cell with a coding sequence capable of producing PPI at elevated levels.
- host cells are transformed with a PPI-encoding sequence.
- the invention relates to a method for producing a secretable polypeptide in a host cell, comprising cotransfecting the cell with a first coding sequence encoding the polypeptide and a second coding sequence encoding a peptidyl prolyl cis-trans isomerase.
- the invention relates to a method for expressing a secretable polypeptide in a host cell, comprising the steps of: a) transforming the cell with a coding sequence expressing a peptidyl prolyl cis- trans isomerase according to the invention; b) transforming the cell with a coding sequence expressing a desired polypeptide; and c) culturing the cell to produce the polypeptide.
- transfection and transformation are considered equivalent, and include any form of insertion of DNA into cells, including viral transduction, electroporation and conventional transfection techniques.
- the coding sequences encoding peptidyl prolyl cis-trans isomerase and the desired polypeptide may be inserted into the cells on vectors, or independently as naked DNA. The use of vectors is preferred. Where the peptidyl prolyl cis-trans isomerase and the desired polypeptide are present on separate vectors, either one of the separate vectors may be inserted into the host cell before the other. The order of insertion is not important, as long as increased levels of peptidyl prolyl cis-trans isomerase are obtained in the host cell during the expression of the desired polypeptide.
- the peptidyl prolyl cis-trans isomerase and the desired polypeptide may be present on the same vector.
- host cells may be constructed wherein a coding sequence expressing peptidyl prolyl cis-trans isomerase is integrated into the host cell and genome.
- This ⁇ can be achieved using an integrating expression vector to transform the cell with the said coding sequence.
- vector refers to discrete elements that are used to introduce heterologous DNA into cells for either expression or replication thereof. Selection and use of such vehicles are well within the skill of the artisan. Many vectors are available, and selection of appropriate vector will depend on the intended use of the vector and the host cell to be transformed with the vector. Each vector contains various components depending on its function and the host cell for which it is compatible.
- the vector components generally include, but are not limited to, one or more of the following: an origin of replication, one or more marker genes, an enhancer element, a promoter, a transcription termination sequence and a signal sequence.
- Most expression vectors are shuttle vectors, i.e. they are capable of replication in at least one class of organisms but can be transfected into another class of organisms for expression.
- a vector may be cloned in E. coli and then the same vector is transfected into yeast or other fungal cells even though it is not capable of replicating independently of the host cell chromosome.
- DNA can also be amplified, for example by PCR, and be directly transfected into the host cells without any replication component.
- an expression vector may contain a selection gene, also referred to as selectable marker.
- This gene encodes a protein necessary for the survival or growth of transformed host cells grown in a selective culture medium. Host cells not transformed with the vector containing the selection gene will not survive in the culture medium.
- Typical selection genes encode proteins that confer resistance to antibiotics and other toxins, e.g. ampicillin, neomycin, methotrexate or tetracycline, complement auxotrophic deficiencies, or supply critical nutrients not available from complex media.
- any marker gene can be used which facilitates the selection for transformants due to the phenotypic expression of the marker gene.
- Suitable markers for yeast are, for example, those conferring resistance to antibiotics G418, hygromycin or bleomycin, or provide for prototrophy in an auxotrophic yeast mutant, for example the URA3, LEU2, LYS2, TRPl, or HIS3 gene.
- E. coli genetic marker and an E. coli origin of replication are advantageously included. These can be obtained from E. coli plasmids, such as pBR322, Bluescript ® vector or a pUC plasmid, e.g. pUC18 or pUC19, which contain both E. coli replication origin and E. coli genetic marker conferring resistance to antibiotics, such as ampicillin.
- Expression and cloning vectors usually contain a promoter that is recognised by the host organism and is operably linked to nucleic acid encoding peptidyl prolyl cis-trans isomerase. Such a promoter may be inducible or constitutive.
- the promoters are operably linked to DNA encoding the peptidyl prolyl cis-trans isomerase by removing the promoter from the source DNA by restriction enzyme digestion and inserting the isolated promoter sequence into the vector. Both the native promoter sequence and many heterologous promoters may be used to direct amplification and/or expression of the peptidyl prolyl cis-trans isomerase coding sequence.
- operably linked refers to a juxtaposition wherein the components described are in a relationship permitting them to function in their intended manner.
- a control sequence "operably linked" to a coding sequence is ligated in such a way that expression of the coding sequence is achieved under conditions compatible with the control sequences.
- Suitable promoting sequences for use with yeast hosts may be regulated or constitutive and are preferably derived from a highly expressed fungal gene. Fungal promoters are known in the literature (for example, see Gurr, et al. , (1987) The structure and organisation of nuclear genes of filamentous fungi. In Kinghorn, J.R. (ed), Gene Structure in Eukaryotic Microbes, IRL Press, Oxford, pp. 93-139).
- Yeast promoters may also be used, such as the promoter of the yeast TRP1 gene, the ADHI or ADHII gene, the acid phosphatase (PH05) gene, a promoter of the yeast mating pheromone genes coding for the a- or ⁇ -factor or a promoter derived from a gene encoding a glycolytic enzyme such as the promoter of the enolase, glyceraldehyde-3-phosphate dehydrogenase (GAP), 3-phospho glycerate kinase (PGK), hexokinase, pyruvate decarboxylase, phosphofructokinase, glucose-6-phosphate isomerase, 3-phosphoglycerate mutase, pyruvate kinase, triose phosphate isomerase, phosphoglucose isomerase or glucokinase genes, the S.
- GAP glyceraldehyde-3-phosphate
- hybrid promoters comprising upstream activation sequences (UAS) of one yeast gene and downstream promoter elements including a functional TATA box of another yeast gene, for example a hybrid promoter including the UAS(s) of the yeast PH05 gene and downstream promoter elements including a functional TATA box of the yeast GAP gene (PH05- GAP hybrid promoter).
- a suitable constitutive PHO5 promoter is e.g.
- PH05 a shortened acid phosphatase PH05 promoter devoid of the upstream regulatory elements (UAS) such as the PH05 (-173) promoter element starting at nucleotide -173 and ending at nucleotide - 9 of the PH05 gene.
- UAS upstream regulatory elements
- fungal organisms such as a filamentous fungi, for example those used in the biotechnology industry; preferably Aspergillus, Trichoderma, Neurospora, Mucor or Penicillium, is preferred. More specifically, preferred host organisms include A. nidulans, A. tubigensis, A. sojae, A. awamori, A. oryzae, A. japonicus, A. aculeatus, N. crassa, T. reesei and T. viride.
- a preferred host organism for the expression of the nucleic acid constructs of the present invention and/or for the preparation of the heterologous polypeptides according to the present invention is an organism of the genus Aspergillus, advantageously Aspergillus niger.
- a transgenic Aspergillus according to the present invention can be prepared by following the teachings of Rambosek, J. and Leach, J. 1987 (Recombinant DNA in filamentous fungi: Progress and Prospects. CRC Crit. Rev. Biotech ol. 6:357- 393), Davis R.W. 1994 (Heterologous gene expression and protein secretion in Aspergillus. In: Martinelli S.D. , Kinghorn J.R.
- expression constructs are prepared by inserting a heterologous nucleotide sequence (such as a nucleotide sequence coding for an amylase enzyme) into a construct designed for expression in filamentous fungi.
- a heterologous nucleotide sequence such as a nucleotide sequence coding for an amylase enzyme
- the constructs contain the promoter according to the present invention which is active in fungi.
- the heterologous nucleotide sequence can be fused to a signal sequence which directs the protein encoded by the heterologous nucleotide sequence to be secreted.
- a signal sequence of fungal origin is used.
- a terminator active in fungi may also be employed.
- heterologous nucleotide sequence is fused to a fungal gene encoding a stable protein.
- This can stabilise the protein encoded by the heterologous nucleotide sequence which encodes a desired polypeptide.
- a cleavage site recognised by a specific protease, can be introduced between the fungal protein and the protein encoded by the heterologous nucleotide sequence, so the produced fusion protein can be cleaved at this position by the specific protease thus liberating the protein encoded by the heterologous nucleotide sequence.
- a site which is recognised by a KEX-2 like peptidase found in at least some Aspergilli (Broekhuijsen et al 1993 J Biotechnol 31 135-145).
- a fusion leads to cleavage in vivo resulting in protection of the expressed product and not a larger fusion protein.
- Heterologous expression in Aspergillus has been reported for several genes coding for bacterial, fungal, vertebrate and plant proteins. With regard to product stability and host strain modifications, some heterologous proteins are not very stable when they are secreted into the culture fluid of fungi. Most fungi produce several extracellular proteases which degrade heterologous proteins. To avoid this problem special fungal strains with reduced protease production have been used as host for heterologous production.
- filamentous fungi For the transformation of filamentous fungi, several transformation protocols have been developed for many filamentous fungi (Ballance 1991, ibid). Many of them are based on preparation of protoplasts and introduction of DNA into the protoplasts using PEG and Ca ions. The transformed protoplasts then regenerate and the transformed fungi are selected using various selective markers. Among the markers used for transformation are a number of auxotrophic markers such as argB, trpC, niaD and pyrG, antibiotic resistance markers such as benomyl resistance, hygromycin resistance and phleomycin resistance. A commonly used transformation marker is the amdS gene of A. nidulans which in high copy number allows the fungus to grow with acrylamide as the sole nitrogen source.
- auxotrophic markers such as argB, trpC, niaD and pyrG
- antibiotic resistance markers such as benomyl resistance, hygromycin resistance and phleomycin resistance.
- Enhancers are relatively orientation and position independent.
- An expression vector includes any vector capable of expressing peptidyl prolyl cis-trans isomerase encoding nucleic acids that are operatively linked with regulatory sequences, such as promoter regions, that are capable of expression of such DNAs.
- an expression vector refers to a recombinant DNA or RNA construct, such as a plasmid, a phage, recombinant virus or other vector, that upon introduction into an appropriate host cell, results in expression of the cloned DNA.
- Appropriate expression vectors are well known to those with ordinary skill in the art and include those that are replicable in eukaryotic and/or prokaryotic cells and those that remain episomal or those which integrate into the host cell genome.
- Plasmids according to the invention employs conventional ligation techniques. Isolated plasmids or DNA fragments are cleaved, tailored, and religated in the form desired to generate the plasmids required. If desired, analysis to confirm correct sequences in the constructed plasmids is performed in a known fashion. Suitable methods for constructing expression vectors, preparing in vitro transcripts, introducing
- DNA into host cells and performing analyses for assessing peptidyl prolyl cis-trans isomerase expression and function are known to those skilled in the art.
- Gene presence, amplification and/or expression may be measured in a sample directly, for example, by conventional Southern blotting, Northern blotting to quantitate the transcription of mRNA, dot blotting (DNA or RNA analysis), or in situ hybridisation, using an appropriately labelled probe which may be based on a sequence provided herein.
- Those skilled in the art will readily envisage how these methods may be modified, if desired.
- the same or similar considerations will apply to the design of a vector encoding the desired polypeptide.
- the PPI and the desired polypeptide may be encoded on the same vector, whether episomal or integrating, and be expressed therefrom.
- the desired polypeptide is a polypeptide encoded by a heterologous nucleotide sequence not derived from the host organism.
- Typical examples of a nucleotide sequence encoding a desired polypeptide include sequences coding for proteins and enzymes that modify metabolic and catabolic processes.
- the heterologous nucleotide sequence may code for an agent for introducing or increasing pathogen resistance.
- the heterologous nucleotide sequence may code for a non-native protein of a filamentous fungus, preferably of the genus Aspergillus, or a compound that is of benefit to animals or humans.
- nucleotide sequences according to the invention include pectinases, pectin depolymerases, polygalacturonases, pectate lyases, pectin lyases, hexose oxidase, oxidoreductases, lipases, glucan lyase, rhamno- galacturonases, hemicellulases, endo- ⁇ -glucanases, arabinases, or acetyl esterases, or combinations thereof, as well as antisense sequences thereof.
- the desired polypeptide may be a protein giving nutritional value to a food or crop. Typical examples include plant proteins that can inhibit the formation of anti-nutritive factors and plant proteins that have a more desirable amino acid composition (e.g. a higher lysine content than a non- transgenic plant) .
- the desired polypeptide may be an enzyme that can be used in food processing such as chymosin, thaumatin and ⁇ -galactosidase.
- the desired polypeptide may moreover be any one of a pest toxin, ADP-glucose pyrophosphorylase (e.g. see EP-A-0455316), a glucanase or genomic ⁇ -l,4-endoglucanase.
- the heterologous nucleotide sequence may code for an intron of a particular nucleotide sequence, wherein the intron can be in sense or antisense orientation.
- the heterologous nucleotide sequence can be the nucleotide sequence coding for the arabinofuranosidase enzyme which is the subject of PCT patent application PCT/EP96/01009 (incorporated herein by reference).
- the heterologous nucleotide sequence can be any of the nucleotide sequences coding for the ADP-glucose pyrophosphorylase enzymes which are the subject of PCT patent application PCT/EP94/01082 (incorporated herein by reference).
- the heterologous nucleotide sequence can be any of the nucleotide sequences coding for the ⁇ -glucan lyase enzyme which are described in PCT patent application PCT/EP94/03397 (incorporated herein by reference).
- the heterologous nucleotide sequence can be any of the sequences coding for T. languinosus amylase, as described in PCT patent application PCT/EP95/02607, incorporated herein by reference.
- the heterologous nucleotide sequence can be any of the nucleotide sequences coding for the glucanase enzyme which are described in PCT patent application PCT/EP96/01008 (incorporated herein by reference).
- the nucleic acid encoding PPI will also include, operatively linked thereto, an ER retention signal.
- the ER retention signal is a tetrapeptide, which is advantageously HDEL, HEEL or KDEL.
- the ER retention signal targets the polypeptide to the ER and causes it to be retained therein.
- a polypeptide which possesses a foldase activity and is characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, having a signal sequence at the N terminus and an endoplasmic reticulum retention signal at the C terminus, and a molecular weight of 20.7 kilodaltons and a deduced isoelectric point of 6.27.
- the novel PPI according to this aspect of the invention is obtainable from a fungal organism, such as a filamentous fungus, for example those used in the biotechnology industry; preferably Aspergillus, Trichoderma or Penicillium; preferably A. niger.
- a fungal organism such as a filamentous fungus, for example those used in the biotechnology industry; preferably Aspergillus, Trichoderma or Penicillium; preferably A. niger.
- PPI PPI
- SEQ ID No. 2 An example of a PPI according to the invention is set forth in SEQ ID No. 2.
- the molecule identified in this sequence is obtainable from Aspergillus niger and is referred to herein as CYPB.
- PPI enzymes which satisfy the criteria set forth above are referred to herein in general as "CYPB" enzymes.
- the invention provides CYPB as set forth in SEQ ID No. 2, or a bioisostere thereof.
- bioisostere is used in accordance with its common usage in the art, to refer to namely a compound having a similar (but not the same) or a different structure and having the same biological functional effect.
- the bioisostere of the invention is obtainable from a fungal organism, such as a filamentous fungus, for example those used in the biotechnology industry; preferably Aspergillus, Trichoderma or Penicillium; preferably A. niger.
- a nucleic acid encoding an enzyme according to the invention In addition to being useful for the production of recombinant PPI protein, these nucleic acids are also useful as probes, thus readily enabling those skilled in the art to identify and/or isolate nucleic acid encoding PPIs or homologues thereof.
- the nucleic acid may be unlabelled or labelled with a detectable moiety.
- nucleic acid according to the invention is useful e.g. in a method determining the presence of PPI-specific nucleic acid, said method comprising hybridising the DNA (or RNA) encoding (or complementary to) PPI to a test sample nucleic acid and determining the presence of the PPI.
- the invention provides nucleic acid sequence that is complementary to, or hybridises under stringent conditions to, a nucleic acid sequence encoding a PPI of a fragment thereof.
- fragments of PPI-encoding nucleic acids are between 10 and 200 nucleotides in length, preferably between 15 and 50 nucleotides in length, and most preferably about 20 nucleotides in length.
- the invention also provides a method for amplifying a nucleic acid test sample comprising priming a nucleic acid polymerase (chain) reaction with nucleic acid (DNA or RNA) encoding (or complementary to) the PPI.
- the nucleic acid is DNA and further comprises a replicable vector comprising the nucleic acid encoding the PPI operably linked to control sequences recognised by a host transformed by the vector.
- the invention provides host cells transformed with such a vector and a method of using a nucleic acid encoding a PPI to effect the production of PPI, comprising expressing PPI- encoding nucleic acid in a culture of the transformed host cells and, if desired, recovering PPI from the host cell culture.
- Isolated PPI nucleic acid includes nucleic acid that is free from at least one contaminant nucleic acid with which it is ordinarily associated in the natural source of PPI nucleic acid or in crude nucleic acid preparations, such as DNA libraries and the like. Isolated nucleic acid thus is present in other than in the form or setting in which it is found in nature.
- isolated PPI encoding nucleic acid includes PPI nucleic acid in ordinarily PPI-expressing cells where the nucleic acid is in a chromosomal location different from that of natural cells or is otherwise flanked by a different DNA sequence than that found in nature.
- isolated nucleic acids e.g. DNAs or RNAs, encoding CYPB having the sequence set forth in SEQ. ID. No. 2, or fragments thereof.
- the invention provides a DNA molecule encoding CYPB as set forth in SEQ. LD. No. 2, or a fragment thereof.
- a DNA comprises a coding single stranded DNA, a double stranded DNA of said coding DNA and complementary DNA thereto, or this complementary (single stranded) DNA itself.
- the preferred sequence encoding CYPB is that having substantially the same nucleotide sequence as the coding sequences in SEQ ID No. 2, with the nucleic acid having the same sequence as the coding sequence in SEQ ID No. 2 being most preferred.
- nucleotide sequences which are substantially the same share at least about 90 % identity.
- nucleic acids of the invention are preferably substantially homologous to the sequence of CYPB as shown in SEQ ID No. 2.
- “Substantial homology” where homology indicates sequence identity, means more than 40% sequence identity, preferably more than 45% sequence identity and most preferably a sequence identity of 50% or more, as judged by direct sequence alignment and comparison.
- Substantially homologous amino acid sequences and nucleotide sequences can have
- homology e.g., at least 80% homology, or at least 85% homology, such
- Nucleotide sequence homology can be determined using the "Align” program of Myers and Miller, ("Optimal Alignments in Linear Space", C-ABIOS 4, 11-17,
- amino acid sequence can indicate a quantitative measure of homology between two sequences.
- the percent sequence homology can be calculated as (N re - - N ⁇ )*100/N re y , wherein
- N di f is the total number of non-identical residues in the two sequences when aligned
- N ref is the number of residues in one of the sequences.
- sequence AGTCAGTC will have a sequence similarity of 75% with the sequence
- amino acids divided by the number of nucleotides or amino acids in the shorter of the
- RNA sequences are said to be similar, or have a degree
- RNA sequence is considered equal to uracil (U) in the RNA sequence.
- RNA sequences within the scope of the invention can be derived from DNA sequences,
- thymidine (T) in the DNA sequence being considered equal to uracil (U) in RNA
- amino acid sequence similarity or identity or homology can be determined using the BlastP program (Altschul et al., Nucl. Acids Res. 25, 3389-3402, incorporated herein by reference) and available at NCBI, advantageously using default
- nucleic acids according to the invention are fragments of the CYPB- encoding sequence. Fragments of the nucleic acid sequence of a few nucleotides in length, preferably 5 to 150 nucleotides in length, are especially useful as probes.
- nucleic acids can alternatively be characterised as those nucleotide sequences which encode a CYPB protein and hybridise to the DNA sequences set forth SEQ ID No. 2, or a selected fragment of said DNA sequence. Preferred are such sequences encoding CYPB which hybridise under high stringency conditions to the sequence of SEQ ID No. 2 or a fragment thereof as defined above.
- Stringency of hybridisation refers to conditions under which polynucleic acids hybrids are stable. Such conditions are evident to those of ordinary skill in the field. As known to those of skill in the art, the stability of hybrids is reflected in the melting temperature (Tm) of the hybrid which decreases approximately 1 to 1.5°C with every 1 % decrease in sequence homology. In general, the stability of a hybrid is a function of sodium ion concentration and temperature. Typically, the hybridisation reaction is performed under conditions of higher stringency, followed by washes of varying stringency.
- high stringency refers to conditions that permit hybridisation of only those nucleic acid sequences that form stable hybrids in 1 M Na + or an equivalent salt concentration, at 65-68 °C.
- High stringency conditions can be provided, for example, by hybridisation in an aqueous solution containing 6x SSC, 5x Denhardt's, 1 % SDS (sodium dodecyl sulphate), 0.1 Na + pyrophosphate and 0.1 mg/ml denatured salmon sperm DNA as non specific competitor.
- high stringency washing may be done in several steps, with a final wash (about 30 min) at the hybridisation temperature in 0.2 - 0. lx SSC, 0.1 % SDS.
- Moderate stringency refers to conditions equivalent to_ hybridisation in the above described solution but at about 60-62°C. In that case the final wash is performed at the hybridisation temperature in lx SSC, 0.1 % SDS.
- Low stringency refers to conditions equivalent to hybridisation in the above described solution at about 52-56°C. In that case, the final wash is performed at the hybridisation temperature in 4x SSC, 0.1 % SDS.
- the CYPB protein of the present invention comprises an ER retention signal.
- a polypeptide possessing foldase activity characterised by having a capability to catalyse the cis-trans isomerisation of a peptide bond on the N terminal side of proline residues in polypeptides, encoded by a nucleic acid capable of hybridising under conditions of low, medium or high stringency with a 17 base oligonucleotide derived from SEQ ID No. 1.
- low stringency conditions are used.
- SEQ. ID. No. 1 represents a degenerated sequence encoding an ER retention signal. Since this signal is likely to be located on any CYPB protein which is located in the ER, the presence of this sequence may advantageously be used to characterise and isolate CYPB polypeptides in accordance with the present invention.
- the nucleic acids of _ the invention are obtainable according to methods well known in the art. For example, a DNA of the invention is obtainable by chemical synthesis, using polymerase chain reaction (PCR) or by screening a genomic library or a suitable cDNA library prepared from a source believed to possess CYPB and to express it at a detectable level.
- Chemical methods for synthesis of a nucleic acid of interest include triester, phosphite, phosphoramidite and H-phosphonate methods, PCR and other autoprimer methods as well as oligonucleotide synthesis on solid supports. These methods may be used if the entire nucleic acid sequence of the nucleic acid is known, or the sequence of the nucleic acid complementary to the coding strand is available. Alternatively, if the target amino acid sequence is known, one may infer potential nucleic acid sequences using known and preferred coding residues for each amino acid residue.
- An alternative means to isolate a gene encoding a PPI according to the invention is to use PCR technology as described e.g. in section 14 of Sambrook et al., 1989. This method requires the use of oligonucleotide probes that will hybridise to PPI nucleic acid. Strategies for selection of oligonucleotides are described below.
- cDNA expression libraries are screened with probes or analytical tools designed to identify the gene of interest or the protein encoded by it.
- suitable means include monoclonal or polyclonal antibodies that recognise and specifically bind to CYPB; oligonucleotides of about 20 to 80 bases in length that encode known or suspected CYPB cDNA from the same or different species; and/or complementary or homologous cDNAs or fragments thereof that encode the same or a hybridising gene.
- Appropriate probes for screening genomic DNA libraries include, but are not limited to oligonucleotides, cDNAs or fragments thereof that encode the same or hybridising DNA; and/or homologous genomic DNAs or fragments thereof.
- a nucleic acid encoding CYPB may be isolated by screening suitable cDNA or genomic libraries under suitable hybridisation conditions with a probe, i.e. a nucleic acid disclosed herein including oligonucleotides derivable from the sequences set forth in SEQ ID NO. 2.
- a probe i.e. a nucleic acid disclosed herein including oligonucleotides derivable from the sequences set forth in SEQ ID NO. 2.
- Suitable libraries are commercially available or can be prepared e.g. from cell lines, tissue samples, and the like.
- a probe is e.g. a single-stranded DNA or RNA that has a sequence of nucleotides that includes between 10 and 50, preferably between 15 and 30 and most preferably at least about 20 contiguous bases that are the same as (or the complement of) an equivalent or greater number of contiguous bases set forth in SEQ ID No. 2.
- the nucleic acid sequences selected as probes should be of sufficient length and sufficiently unambiguous so that false positive results are minimised.
- the nucleotide sequences are usually based on conserved or highly homologous nucleotide sequences or regions of CYPB.
- the nucleic acids used as probes may be degenerate at one or more positions. The use of degenerate oligonucleotides may be of particular importance where a library is screened from a species in which preferential codon usage in that species is not known.
- nucleic acid probes of the invention are labelled with suitable label means for ready detection upon hybridisation.
- suitable label means is a radiolabel.
- the preferred method of labelling a DNA fragment is by incorporating ⁇ P dATP with the Klenow fragment of DNA polymerase in a random priming reaction, as is well known in the art. Oligonucleotides are usually end-labelled with ⁇ 32 P-labelled ATP and polynucleotide kinase.
- non- radioactive may also be used to label the fragment or oligonucleotide, including e.g. enzyme labelling, fluorescent labelling with suitable fluorophores and biotinylation.
- the selected clones may be used to rescreen the same or a different library to obtain overlapping clones. If the library is genomic, then the overlapping clones may include exons and introns. If the library is a cDNA library, then the overlapping clones will include an open reading frame. In both instances, complete clones may be identified by comparison with the DNAs and deduced amino acid sequences provided herein.
- nucleotide sequences of the invention may be designed.
- antisense-type agents to reduce expression of CYPB if desired, may be designed.
- nucleic acid of the invention can be readily modified by nucleotide substitution, nucleotide deletion, nucleotide insertion or inversion of a nucleotide stretch, and any combination thereof.
- Such mutants can be used e.g. to produce a CYPB mutant that has an amino acid sequence differing from the CYPB sequences as found in nature. Mutagenesis may be predetermined (site-specific) or random. A mutation which is not a silent mutation must not place sequences out of reading frames and preferably will not create complementary regions that could hybridise to produce secondary mRNA structure such as loops or hairpins.
- ⁇ ZAP-- . gerN402 cDNA library is constructed from A. niger cDNA by use of ZAP- cDNA synthesis kit from Stratagene, using the instructions provided by the manufacturer.
- NZY plates containing the following medium (per litre): 5g NaCl, 2g MgSO 4 »7H 2 O, 5g yeast extract, lOg casein hydrolysate, 15g agar, pH adjusted to 7.5 with NaOH.
- the medium is autoclaved, cooled to about 65°C and poured into the plates. 240 ml of medium is used per plate.
- the inoculated NZY plates are incubated overnight at 37°C and plaque lifts of the plates are made. Two lifts are made for each plate on Hybond N (Amersham) filters.
- the DNA is fixed using UV radiation for 4 min. and the filters are hybridised as described in the following using, as the probe, a degenerate oligonucleotide that is labelled with 32 P-dCTP using Terminal Transferase (Boehringer Mannheim) according the following procedure.
- the filters are prehybridised for 4 hours at 56°C in 50 ml prehybridisation buffer containing 12.5 ml 20x SSC (0.3 M Na 3 citrate, 3 M NaCl), 2.5 ml lOOx Denhardt's solution, 2.5 ml 10% SDS and 32.5ml water. 300 ⁇ l 10 mg/ml denatured salmon sperm DNA is added to the prehybridisation buffer immediately before use. Following prehybridisation, the radiolabelled oligonucleotide is added and filters are hybridised overnight at 56°C. Next day the filters are washed twice with 4x SSC + 0.1 % SDS for 30 min at 56°C.
- the filters are autoradiographed for 16 hours and positive clones are isolated. A clone is counted as positive only if there is a hybridisation signal on both plaque lifts of the NZY plate.
- the plasmid containing the cypB gene encoding a cyclophilin like peptidyl prolyl cis-trans isomerase B is designated pPD23.
- a restriction map of the clone is made.
- the fragment is cloned in the Ec ⁇ RI and Xhol site of pBluescript SK+ .
- the restriction map showing the structure op pPD23 is shown in fig. 1.
- the gene is sequenced using the cycle sequencing method.
- the complete sequence is shown in SEQ. ID. No. 2.
- the sequence is determined on both strands for the whole construct.
- the deduced amino acid sequence is aligned using the ClustalW program with three cyclophilin like peptidyl prolyl cis-trans isomerases B.
- the alignment is shown in fig 2.
- the above alignment shows that CYPB is homologous _ to the other known CYPB sequences.
- a search in the SWISS-PROT database is performed and does not show any sequences with a higher homology than those shown in the alignment (fig. 2).
- the sequence with the highest homology is a precursor for the cyclophilin like peptidyl prolyl cis-trans isomerase from Orpinomyces sp. where the identity is found to be 63 % (fig. 3).
- Residues 1 - 23 are recognised as a signal sequence, leaving a mature protein of 186 amino acids with a deduced molecular weight of 20,7 kDa and a deduced iso-electric point (pi) of 6.27.
- the CYPB protein contains a putative E.R. retention signal at its extreme C-terminus (position 209-212).
- One putative N-glycosylation site is found in CYPB at position 139-142.
- a conserved motif for cyclophilin-type peptidyl-prolyl cis- trans isomerase is present at position 79 - 96.
- a fragment, containing the part of the gene encoding for the mature CYPB protein, is generated by PCR with the following primers:
- PCR is performed at 52°C using pfu polymerase.
- the E.R. target sequence is excluded from this construct.
- the C-terminal part of the protein is extended with a
- E.coli expressed protein is purified by means of Immobilised Metal Affinity Chromatography (Ni-NTA resin, Qiagen) and gel filtration (Superdex 75, Pharmacia).
- the apparent molecular weight of the purified CYPB is determined on a SDS-PAGE ⁇ gel to be approximately 21 kDa.
- the exact molecular mass is determined by MALDI-TOF analysis, revealing a molecular weight of 21100.6 Da.
- N-terminal sequencing revealed the first 10 amino acids of the mature sequence (EDAQPRGPK - residues 24 to 32 in SEQ. ID. No. 2).
- a assay based on the stereospecific degradation of the substrate suc-Ala-Ala-Pro-Phe- pNA (Sigma) by ⁇ -chemotrypsin (Boehringer Mannheim) is set up to determine the activity of CYPB.
- the traHS-isomer of this substrate is rapidly degraded by ⁇ - chemotrypsin.
- 88% of the substrate is present as trans and 12% as ris-isomer.
- the conversion of the cw-isomer to the tr ⁇ ns-isomer is rate limiting and is catalysed by peptidyl prolyl cis-trans isomerases.
- CYPB is assayed at 25 °C in 50mM HEPES buffer pH 7.8 containing 50 ⁇ M substrate and 25 ⁇ M ⁇ -chemotrypsin.
- 0.5 nM CYPB protein is added to the mixture and the absorbance at 380nm is measured every 0.5 sec. Addition of CYPB protein clearly leads to a quicker degradation of the substrate, proving the foldase activity thereof.
- the plasmid pLIP4 ( Figure 4) comprises the entire genomic sequence of the UpA gene. This sequence is set forth in SEQ. ID. No.4. CYPB is expressed from either ppd23dl4 or ppd23dl3, as shown in Figures 5 and 6 respectively.
- ppd23dl4 comprises the CypB sequence under the control of the glaA promoter (generally available; see, for example, Ward et al. , (1995) Biotechnology 13:498r503), which is inducible.
- ppd23dl3 comprises the CypB sequence under the control of the A. nidulans gpdA promoter (Punt et al , (1991) J. Biotechnol. 17: 19-34), which is constitutively active. In both cases, the CypB gene is followed by the A. nidulans trpC terminator.
- Antibiotic resistance is incorporated into the plasmids by insertion of a hygromycin resistance gene (isolated from Streptomyces hygroscopicus and E. coli) under the control of the gpdA promoter.
- the protoplasts produced are mixed with pLIP4, together with ppd23dl4 or ppd23dl3, by cotransformation, using pyrG and antibiotic resistance markers to select for the desired recombinants.
- a screening procedure used to visualise fungal lipase after ultrathin layer isoelectric focusing is adapted to screen Aspergillus transformants grown on agar plates. This procedure is very convenient for the initial analysis of expressing and non- expressing transformed Aspergillus strains. Screening of lipase producers on agar plates is done using 2% olive oil as the substrate of the enzyme (lipase) as well as the inducer of the lipase promoter. In addition, the plate contains a fluorescent dye Rhodamine B (N-9-(2-carboxyphenyl)-6-(diethylamino)-3H-xanthen-3-ylidene-N-ethylethanaminium chloride).
- the transformants are induced to secrete lipase.
- the lipase secreted into the agar plate hydrolyses the olive oil causing the formation of orange fluorescent colonies that are visible upon UV irradiation (350nm).
- the detection of fluorescent colonies is observed after about 24 hours of growth, depending on the transformant.
- the lipase producing strains can be identified as orange fluorescent strains that are visible by eye. Under these plate screening conditions, the untrans formed strain give no background fluorescence and appear as opaque pink colonies.
- the 16 transformants that show orange fluorescent halos are cultivated in shake flasks containing 100 ml of minimal medium plus 1 % olive oil, 0.5% yeast extract, 0.2% casamino acids and grown for 8 days.
- the amount of lipase secreted is quantitated by applying 10 ⁇ l of cell-free culture supernatant into holes punched in the olive oil - rhodamine B agar plates and incubating the plates overnight at 37 C.
- the cell free culture supernatant from the 5 transformants that give the most intense fluorescence are further analysed by chromatography.
- Culture supernatant from the five different lipase secreting transformants found positive by the plate screening method are desalted using NAP 5 columns (Pharmacia: contain Sephadex G-25 medium) and equilibrated in 1M (NH 4 ) 2 SO 4 50mM sodium acetate pH 5.5.
- the desalted culture supernatant is fractionated by hydrophobic interaction chromatography on a Biogel Phenyl-5 PW Column (Biorad). Elution is done by a descending salt gradient of 1M to zero Molar (NH 4 ) 2 SO 4 20mM sodium acetate, pH 5.5.
- a single discrete protein peak is observed after fractionation. The area of the protein peaks is calculated among the different transformants and compared with the untransformed strains.
- the table below summarises the levels of Lipase secreted by the 5 transformants.
- the best transformant shows a 62 fold increased in the amount of lipase purified after HIC fractionation.
- the table also shows the varying amounts of lipase produced by the different transformants after 6 days of growth under unoptimised small scale shake flask condition.
- the discrete protein peak after fractionation by HIC is freeze dried and resuspended in water.
- the amino acid composition and the protein concentration of the purified lipase protein are determined to obtain a correlation coefficient between UV absorbance at 280 nm and protein concentration. This allows the estimation of Lipase concentration in homogenous preparations.
- the Lipase protein is carboxymethylated and the sequence of the first 15 amino acids is determined by N-terminal amino acid sequencing.
- the 15 amino acid sequence of the recombinant lipase is exactly the same as the native lipase indicating correct signal sequence cleavage.
- the different protein fractions collected after HIC are separated on a 12% Tris- Glycine SDS gel. Silver staining reveals one protein band, confirming the homogeneity of the protein peaks.
- the crude extract shows a major lipase band as the only protein band that accumulated in the culture supernatant in very high amounts when the fungus is cultured in medium containing oil.
- N-linked oligosaccharides is achieved by digestion of the lipase with Endo- -N-acetyl-glucosamidase H from Streptomyces (Sigma). Endo H treatment of recombinant lipase secreted into the growth medium alters the mobility of the band seen on SDS-PAGE and runs as a single species with a molecular mass of approximately 30 kDa. This indicates the extent of N-linked glycosylation.
- MALDI-TOF mass spectrometry is performed using purified lipase mixed with a matrix solution consisting of sinapinic acid (3,5-Dimethoxy-4-hydroxy cinnamic acid) in 70% acetonitrile, 0.1 % TFA.
- the molecular mass determined from the desalted recombinant lipase is 32,237 Daltons.
- N-linked oligosaccharides account for approximately 10% of the molecular weight of recombinant lipase.
- Aspergillus strain N592 (cspAl, pyrA5) has been transformed with a plasmid allowing expression of cypB under the strong constitutive gpdA promoter. Putative transformants are screened by PCR to confirm the presence of this plasmid. The number of integrated copies and the level of cypB expression in this strain (N592: :pPD23dl3) is determined by Southern and Northern analysis respectively.
- Glucoamylase is regarded as a well secreted protein and it is commonly used as a fusion protein to aid the secretion of difficult target proteins.
- ER endoplasmic reticulum
- PDI protein disulphide isomerase
- PPI peptidyl prolyl cis-trans isomerase
- foldases In order to remain in the ER, and therefor to be diverted from the bulk flow of secreted proteins, foldases have specific retention and retrieval signal.
- a common carboxy terminal tetrapeptide, HDEL has been identified as a signal capable of retaining a protein within the lumen of the ER. Removal of this tetrapeptide leads to secretion of the protein (Pelham (1990) Trends Biochem. Sci. 15, 483-486)
- the CYPB protein contains a signal sequence and a putative ER retention signal, indicating that the protein is targeted and retained in the ER. However the retention signal in this protein is slightly divergent from the known retention signals. At position -3 (counting from the last amino acid residue) the CYPB protein contains a glutamic acid residue. This HEEL sequence has not been identified as an ER retention signal. To evaluate if this sequence is capable of retaining CYPB within the lumen of the ER, a GFP construct is made containing both the CYPB signal sequence and the CYPB ER retention signal. Expression of this gene is driven by the strong, constitutive gpdA promoter (plasmid pPD38d3; figure 7).
- Transformants of the Aspergillus niger strain D15 are screened by PCR for insertion of the GFP expression plasmid. Strains containing the expression constructs are analysed for the expression of GFP. Strain D15::pPD38d3#5 is grown overnight in liquid cultures and showed that GFP is directed to a tubular network within the cell. Equivalent constructs in A. nidulans have been demonstrated to target GFP to the ER, illuminating a network similar to our findings (Fernandez-Abalos, et al. (1998) Mol. Microbiol. 27, 121-130). Staining of hyphae with ER-Tracker DPX (Molecular Probes) illuminates the same type of tubular network.
- DIOC 6 a stain for mitochondria at low concentration, but also effective for ER staining when applied at higher concentrations, reveals the same tubular network as seen for DPX and GFP. DIOC 6 staining is however hampered by a diffusion of the stain out of the ER, resulting only in a staining of the mitochondria.
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EP99969744A EP1117806A1 (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
JP2000572381A JP2002525120A (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerase |
CA002340789A CA2340789A1 (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
NZ510037A NZ510037A (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
GB0103639A GB2357769B (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
KR1020017003743A KR20010082208A (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
US09/806,399 US6638737B1 (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
BR9914146-9A BR9914146A (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
AU59932/99A AU764169B2 (en) | 1998-09-30 | 1999-09-30 | Peptidyl prolyl cis-trans isomerases |
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US10/043,142 Division US6607904B2 (en) | 1998-09-30 | 2002-01-14 | Peptidyl prolyl cis-trans isomerases |
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US8940519B2 (en) | 2009-04-24 | 2015-01-27 | Dupont Nutrition Biosciences Aps | Method of producing a lipolytic enzyme |
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TWI752110B (en) * | 2016-11-11 | 2022-01-11 | 日商斯德武利姆股份有限公司 | Therapeutic agent for cerebral infarction |
BR112019025784A2 (en) * | 2017-06-06 | 2020-07-07 | Danisco Us Inc. | yeast with improved alcohol production |
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US5459051A (en) | 1993-03-26 | 1995-10-17 | Celtrix Pharmaceuticals, Inc. | Methods and vectors for over-expression of ubiquitin fusion proteins in host cells |
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US5482850A (en) * | 1993-10-29 | 1996-01-09 | New England Biolabs, Inc. | Method for identifying anti-parasitic compounds |
GB9413419D0 (en) | 1994-07-04 | 1994-08-24 | Danisco | Amylase enzyme |
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US20010034045A1 (en) * | 2000-03-24 | 2001-10-25 | Genencor International, Inc. | Increased production of secreted proteins by recombinant eukaryotic cells |
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Non-Patent Citations (3)
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CHEN H ET AL: "A cyclophilin from the polycentric anaerobic rumen fungus Orpinomyces sp. strain PC-2 is highly homologous to vertebrate cyclophilin B", PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF USA., vol. 92, no. 7, 28 March 1995 (1995-03-28), NATIONAL ACADEMY OF SCIENCE. WASHINGTON., US, pages 2587 - 2591, XP002129590, ISSN: 0027-8424 * |
HORNBOGEN T ET AL: "Two new cyclophilins from Fusarium sambucinum and Aspergillus niger", BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS, vol. 187, no. 2, 16 September 1992 (1992-09-16), ORLANDO, FL US, pages 791 - 796, XP002129591 * |
XU M ET AL.: "PDI-, PPI- and chaperone-catalyzed refolding of recombinant human IL-2 and GM-CSF", SCIENCE IN CHINA (SERIES B), vol. 38, no. 4, April 1995 (1995-04-01), Beijing,CN, pages 429 - 437, XP000867824 * |
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