Bacillus subtilis as cell factory for pharmaceutical proteins: a biotechnological approach to optimize the host organism.

Bacillus subtilis is a rod-shaped, Gram-positive soil bacterium that secretes numerous enzymes to degrade a variety of substrates, enabling the bacterium to survive in a continuously changing environment. These enzymes are produced commercially and this production represents about 60% of the industrial-enzyme market. Unfortunately, the secretion of heterologous proteins, originating from Gram-negative bacteria or from eukaryotes, is often severely hampered. Several bottlenecks in the B. subtilis secretion pathway, such as poor targeting to the translocase, degradation of the secretory protein, and incorrect folding, have been revealed. Nevertheless, research into the mechanisms and control of the secretion pathways will lead to improved Bacillus protein secretion systems and broaden the applications as industrial production host. This review focuses on studies that aimed at optimizing B. subtilis as cell factory for commercially interesting heterologous proteins.

[1]  Guy Plunkett,et al.  Engineering a reduced Escherichia coli genome. , 2002, Genome research.

[2]  C. Colson,et al.  Purification and preliminary characterization of the extracellular lipase of Bacillus subtilis 168, an extremely basic pH-tolerant enzyme. , 1993, European journal of biochemistry.

[3]  A. Nakayama,et al.  SECRETION VECTOR OF BACILLUS SUBTILIS CONSTRUCTED FROM THE BACILLUS SUBTILIS α-AMYLASE PROMOTER AND SIGNAL PEPTIDE CODING REGION1 , 1984 .

[4]  B. Norman,et al.  Properties and Application of a Thermostable Maltogenic Amylase Produced by a Strain of Bacillus Modified by Recombinant‐DNA Techniques , 1984 .

[5]  S. Ng,et al.  Enhanced Secretory Production of a Single-Chain Antibody Fragment from Bacillus subtilis by Coproduction of Molecular Chaperones , 1998, Journal of bacteriology.

[6]  C. Harwood,et al.  D-Alanine substitution of teichoic acids as a modulator of protein folding and stability at the cytoplasmic membrane/cell wall interface of Bacillus subtilis. , 2000, The Journal of biological chemistry.

[7]  C. Harwood,et al.  Cell-associated degradation affects the yield of secreted engineered and heterologous proteins in the Bacillus subtilis expression system. , 2000, Microbiology.

[8]  B. Jürgen,et al.  Monitoring of Genes that Respond to Overproduction of Insoluble Recombinant Proteins in Escherichia Coli and Bacillus Subtilis , 2001 .

[9]  C. Harwood,et al.  Optimization of the Cell Wall Microenvironment Allows Increased Production of Recombinant Bacillus anthracis Protective Antigen from B. subtilis , 2002, Applied and Environmental Microbiology.

[10]  K. Yamane,et al.  Modification of length, hydrophobic properties and electric charge of Bacillus subtilis α-amylase signal peptide and their different effects on the production of secretory proteins in B. subtilis and Escherichia coli cells , 1989, Molecular and General Genetics MGG.

[11]  F. Kawamura,et al.  Construction of a Bacillus subtilis double mutant deficient in extracellular alkaline and neutral proteases , 1984, Journal of bacteriology.

[12]  S. Ebisu,et al.  Structural conversion from non-native to native form of recombinant human epidermal growth factor by Brevibacillus choshinensis. , 1999, Bioscience, biotechnology, and biochemistry.

[13]  S. Wong,et al.  Regulation of groE expression in Bacillus subtilis: the involvement of the sigma A-like promoter and the roles of the inverted repeat sequence (CIRCE) , 1995, Journal of bacteriology.

[14]  S. Bron,et al.  The effect of restriction on shotgun cloning and plasmid stability in Bacillus subtilis Marburg , 1987, Molecular and General Genetics MGG.

[15]  S. Udaka,et al.  Protein secretion inBacillus brevis , 2004, Antonie van Leeuwenhoek.

[16]  J. Olmos-Soto,et al.  Genetic system constructed to overproduce and secrete proinsulin in Bacillus subtilis , 2003, Applied Microbiology and Biotechnology.

[17]  T. Jahns,et al.  Regulation of leucine transport by intracellular pH in Bacillus pasteurii , 1996, Archives of Microbiology.

[18]  O. Merten Recombinant protein production with prokaryotic and eukaryotic cells : a comparative view on host physiology : selected articles from the meeting of the EFB Section on Microbial Physiology, Semmering, Austria, 5th-8th October 2000 , 2001 .

[19]  M. Sarvas,et al.  Secretion of Escherichia coli beta-lactamase from Bacillus subtilis by the aid of alpha-amylase signal sequence. , 1982, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Hideaki Tanaka,et al.  Length and structural effect of signal peptides derived from Bacillus subtilis alpha-amylase on secretion of Escherichia coli beta-lactamase in B. subtilis cells , 1984, Nucleic Acids Res..

[21]  J. Hoch,et al.  Genetics and biotechnology of Bacilli , 1984, Gene.

[22]  G Pohl,et al.  Expression of human insulin-like growth factor I in bacteria: use of optimized gene fusion vectors to facilitate protein purification. , 1987, Biochemistry.

[23]  J. Joly,et al.  Protein folding activities of Escherichia coli protein disulfide isomerase. , 1994, Biochemistry.

[24]  Ming Li,et al.  Cloning and characterization of the groESL operon from Bacillus subtilis , 1992, Journal of bacteriology.

[25]  S. Udaka,et al.  Production of human epidermal growth factor by Bacillus brevis increased with use of a stable plasmid from B. brevis 481. , 1992, Bioscience, biotechnology, and biochemistry.

[26]  L. Tran,et al.  Engineering a Bacillus subtilis expression-secretion system with a strain deficient in six extracellular proteases , 1991, Journal of bacteriology.

[27]  Jon Beckwith,et al.  Evolutionary domain fusion expanded the substrate specificity of the transmembrane electron transporter DsbD , 2002, The EMBO journal.

[28]  D. Henner,et al.  Cloning of the neutral protease gene of Bacillus subtilis and the use of the cloned gene to create an in vitro-derived deletion mutation , 1984, Journal of bacteriology.

[29]  D. Karamata,et al.  The wprA gene of Bacillus subtilis 168, expressed during exponential growth, encodes a cell-wall-associated protease. , 1996, Microbiology.

[30]  R. Doi,et al.  CONSTRUCTION OF A BACILLUS SUBTILIS MUTANT-DEFICIENT IN THREE EXTRACELLULAR PROTEASES , 1989 .

[31]  G. Dale,et al.  Increased solubility of trimethoprim-resistant type S1 DHFR from Staphylococcus aureus in Escherichia coli cells overproducing the chaperonins GroEL and GroES. , 1994, Protein engineering.

[32]  C. Harwood,et al.  Influence of a Cell-Wall-Associated Protease on Production of α-Amylase by Bacillus subtilis , 1998, Applied and Environmental Microbiology.

[33]  A. Sloma,et al.  Isolation and characterization of a novel extracellular metalloprotease from Bacillus subtilis , 1990, Journal of bacteriology.

[34]  D. Belin,et al.  A pathway for disulfide bond formation in vivo. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[35]  P. Çalık,et al.  Mass flux balance-based model and metabolic pathway engineering analysis for serine alkaline protease synthesis by , 1999 .

[36]  W. Quax,et al.  Alzheimer tau test and detergent cellulase made by genetic engineering (no 9 in a series of articles to promote a better understanding of the use of genetic engineering) , 1998 .

[37]  L. Hederstedt,et al.  Mutations in the Thiol-Disulfide Oxidoreductases BdbC and BdbD Can Suppress Cytochrome c Deficiency of CcdA-Defective Bacillus subtilis Cells , 2002, Journal of bacteriology.

[38]  T. Borchert,et al.  Effect of signal sequence alterations on export of levansucrase in Bacillus subtilis , 1991, Journal of bacteriology.

[39]  J E Bailey,et al.  Estimation of P-to-O ratio in Bacillus subtilis and its influence on maximum riboflavin yield. , 1999, Biotechnology and bioengineering.

[40]  Jacob Glenting,et al.  Development of a Heterologous Gene Expression System for Use in Lactococcus Lactis , 2001 .

[41]  P O Olins,et al.  Effect of overproduction of heat shock chaperones GroESL and DnaK on human procollagenase production in Escherichia coli. , 1992, The Journal of biological chemistry.

[42]  D. Missiakas,et al.  A new Escherichia coli gene, dsbG, encodes a periplasmic protein involved in disulphide bond formation, required for recycling DsbA/DsbB and DsbC redox proteins , 1997, Molecular microbiology.

[43]  D. Missiakas,et al.  Identification and characterization of a new disulfide isomerase‐like protein (DsbD) in Escherichia coli. , 1995, The EMBO journal.

[44]  R. Ye,et al.  Engineering and production of streptokinase in a Bacillus subtilis expression-secretion system , 1994, Applied and environmental microbiology.

[45]  M. Sarvas,et al.  The class 1 outer membrane protein of Neisseria meningitidis produced in Bacillus subtilis can give rise to protective immunity , 1992, Molecular microbiology.

[46]  R. Ye,et al.  Functional Production and Characterization of a Fibrin-Specific Single-Chain Antibody Fragment from Bacillus subtilis: Effects of Molecular Chaperones and a Wall-Bound Protease on Antibody Fragment Production , 2002, Applied and Environmental Microbiology.

[47]  D. Jendrossek,et al.  Production of PHA depolymerase A (PhaZ5) from Paucimonas lemoignei in Bacillus subtilis. , 2002, FEMS microbiology letters.

[48]  K. Fisher,et al.  Expression of the staphylococcal protein A gene in Bacillus subtilis by gene fusions utilizing the promoter from a Bacillus amyloliquefaciens alpha-amylase gene , 1986, Journal of bacteriology.

[49]  M. Dwyer,et al.  Cloning and characterization of the gene for an additional extracellular serine protease of Bacillus subtilis , 1991, Journal of bacteriology.

[50]  E. Ferrari,et al.  Replacement of the Bacillus subtilis subtilisin structural gene with an In vitro-derived deletion mutation , 1984, Journal of bacteriology.

[51]  M. Hecker,et al.  ClpXP Protease Regulates the Signal Peptide Cleavage of Secretory Preproteins in Bacillus subtilis with a Mechanism Distinct from That of the Ecs ABC Transporter , 2002, Journal of bacteriology.

[52]  G. Homuth,et al.  The dnaK operon of Bacillus subtilis is heptacistronic , 1997, Journal of bacteriology.

[53]  R. Ye,et al.  High-level secretory production of intact, biologically active staphylokinase from Bacillus subtilis. , 1999, Biotechnology and bioengineering.

[54]  S. Ng,et al.  Efficient Production of a Functional Single-Chain Antidigoxin Antibody via an Engineered Bacillus subtilis Expression-Secretion System , 1993, Bio/Technology.

[55]  C. Georgopoulos,et al.  Identification and characterization of the Escherichia coli gene dsbB, whose product is involved in the formation of disulfide bonds in vivo. , 1993, Proceedings of the National Academy of Sciences of the United States of America.

[56]  R. Gupta,et al.  An overview on fermentation, downstream processing and properties of microbial alkaline proteases , 2002, Applied Microbiology and Biotechnology.

[57]  S. Karlin,et al.  Characterizations of Highly Expressed Genes of Four Fast-Growing Bacteria , 2001, Journal of bacteriology.

[58]  F. Hartl,et al.  Successive action of DnaK, DnaJ and GroEL along the pathway of chaperone-mediated protein folding , 1992, Nature.

[59]  K. Chow,et al.  Construction of an efficient Bacillus subtilis system for extracellular production of heterologous proteins. , 1998, Journal of biotechnology.

[60]  W. Schumann,et al.  CIRCE, a novel heat shock element involved in regulation of heat shock operon dnaK of Bacillus subtilis , 1994, Journal of bacteriology.

[61]  K. Cantell,et al.  Secretion of interferon by Bacillus subtilis. , 1983, Gene.

[62]  P Neubauer,et al.  Monitoring of genes that respond to overproduction of an insoluble recombinant protein in Escherichia coli glucose-limited fed-batch fermentations. , 2000, Biotechnology and bioengineering.

[63]  S. Bron,et al.  Thiol-Disulfide Oxidoreductases Are Essential for the Production of the Lantibiotic Sublancin 168* , 2002, The Journal of Biological Chemistry.

[64]  J. Beckwith,et al.  Identification of a protein required for disulfide bond formation in vivo , 1991, Cell.

[65]  Sau-Ching Wu,et al.  Engineering of a Bacillus subtilis Strain with Adjustable Levels of Intracellular Biotin for Secretory Production of Functional Streptavidin , 2002, Applied and Environmental Microbiology.

[66]  M. Uhlén,et al.  Expression of the staphylococcal protein A gene in Bacillus subtilis by integration of the intact gene into the B. subtilis chromosome , 1986, Journal of bacteriology.

[67]  S. Bron,et al.  Functional analysis of the secretory precursor processing machinery of Bacillus subtilis: identification of a eubacterial homolog of archaeal and eukaryotic signal peptidases. , 1998, Genes & development.

[68]  John M. McCoy,et al.  Production of Recombinant Bovine Enterokinase Catalytic Subunit in Escherichia coli Using the Novel Secretory Fusion Partner DsbA , 1995, Bio/Technology.

[69]  J. Mccoy,et al.  A Thioredoxin Gene Fusion Expression System That Circumvents Inclusion Body Formation in the E. coli Cytoplasm , 1993, Bio/Technology.

[70]  S. Udaka,et al.  Genetic Transformation of Bacillus brevis with Plasmid DNA by Electroporation , 1989 .

[71]  M. Sarvas,et al.  A gene (prsA) of Bacillus subtilis involved in a novel, late stage of protein export , 1991, Molecular microbiology.

[72]  C. Georgopoulos,et al.  The Escherichia coli dsbC (xprA) gene encodes a periplasmic protein involved in disulfide bond formation. , 1994, The EMBO journal.

[73]  A. Sloma,et al.  Gene encoding a minor extracellular protease in Bacillus subtilis , 1988, Journal of bacteriology.

[74]  J. Reichert,et al.  Clinical development of therapeutic recombinant proteins. , 2003, BioTechniques.

[75]  N. Vasantha,et al.  Secretion of a heterologous protein from Bacillus subtilis with the aid of protease signal sequences , 1986, Journal of bacteriology.

[76]  S. Bron,et al.  Evaluation of Bottlenecks in the Late Stages of Protein Secretion in Bacillus subtilis , 1999, Applied and Environmental Microbiology.

[77]  Gunnar von Heijne,et al.  Protein transport: Life and death of a signal peptide , 1998, Nature.

[78]  R. H. Baltz,et al.  Industrial Microorganisms: Basic and Applied Molecular Genetics , 1993 .

[79]  O. Ramírez,et al.  Improvement of culture conditions to overproduce β-galactosidase from Escherichia coli in Bacillus subtilis , 1997, Applied Microbiology and Biotechnology.

[80]  F B Anspach,et al.  Endotoxin removal from protein solutions. , 2000, Journal of biotechnology.

[81]  P. Çalık,et al.  Metabolic flux analysis for human therapeutic protein productions and hypothesis for new therapeutical strategies in medicine , 2002 .

[82]  Nicola Zamboni,et al.  Genome engineering reveals large dispensable regions in Bacillus subtilis. , 2003, Molecular biology and evolution.

[83]  K. Fisher,et al.  Protease-deficient Bacillus subtilis host strains for production of Staphylococcal protein A , 1987, Applied and environmental microbiology.

[84]  F. Castellino,et al.  A Fast-acting, Modular-structured Staphylokinase Fusion with Kringle-1 from Human Plasminogen as the Fibrin-targeting Domain Offers Improved Clot Lysis Efficacy* , 2003, The Journal of Biological Chemistry.

[85]  H. Hennecke,et al.  Escherichia coli genes required for cytochrome c maturation , 1995, Journal of bacteriology.

[86]  K. Bae,et al.  Enhancement of Secretion and Extracellular Stability of Staphylokinase in Bacillus subtilis bywprA Gene Disruption , 2000, Applied and Environmental Microbiology.

[87]  R. Doi,et al.  Determination of the signal peptidase cleavage site in the preprosubtilisin of Bacillus subtilis. , 1986, The Journal of biological chemistry.

[88]  S. Ehrlich,et al.  Essential Bacillus subtilis genes , 2003, Proceedings of the National Academy of Sciences of the United States of America.

[89]  S. Udaka Extracellular production of proteins by microorganisms. I. Screening for protein-producing bacteria. , 1976 .

[90]  Koreaki Ito,et al.  Identification and characterization of an Escherichia coli gene required for the formation of correctly folded alkaline phosphatase, a periplasmic enzyme. , 1992, The EMBO journal.

[91]  M. Simonen,et al.  Protein secretion in Bacillus species , 1993, Microbiological reviews.

[92]  M. Hecker,et al.  The Clp Proteases of Bacillus subtilisAre Directly Involved in Degradation of Misfolded Proteins , 2000, Journal of bacteriology.

[93]  K. Ng,et al.  Engineering of a Staphylokinase-based Fibrinolytic Agent with Antithrombotic Activity and Targeting Capability toward Thrombin-rich Fibrin and Plasma Clots* , 2003, Journal of Biological Chemistry.

[94]  A. Kosugi,et al.  Heterologous Production of Clostridium cellulovorans engB, Using Protease-Deficient Bacillus subtilis, and Preparation of Active Recombinant Cellulosomes , 2002, Journal of bacteriology.

[95]  M. Hecker,et al.  Proteome and transcriptome based analysis of Bacillus subtilis cells overproducing an insoluble heterologous protein , 2001, Applied Microbiology and Biotechnology.

[96]  W. Baumeister,et al.  Chaperonin‐mediated protein folding: GroES binds to one end of the GroEL cylinder, which accommodates the protein substrate within its central cavity. , 1992, The EMBO journal.

[97]  S. Wong,et al.  Isolation and characterization of Bacillus subtilis groE regulatory mutants: evidence for orf39 in the dnaK operon as a repressor gene in regulating the expression of both groE and dnaK , 1995, Journal of bacteriology.

[98]  S. Udaka,et al.  Cloning and characterization of the gene for a protein thiol-disulfide oxidoreductase in Bacillus brevis , 1995, Journal of bacteriology.

[99]  I. Palva Molecular cloning of alpha-amylase gene from Bacillus amyloliquefaciens and its expression in B. subtilis. , 1982, Gene.

[100]  F. Baneyx,et al.  Protein folding in the cytoplasm of Escherichia coli: requirements for the DnaK‐DnaJ‐GrpE and GroEL‐GroES molecular chaperone machines , 1996, Molecular microbiology.

[101]  T. Kajino,et al.  A Protein Disulfide Isomerase Gene Fusion Expression System That Increases the Extracellular Productivity ofBacillus brevis , 2000, Applied and Environmental Microbiology.

[102]  G von Heijne,et al.  Species‐specific variation in signal peptide design Implications for protein secretion in foreign hosts , 1989, FEBS letters.

[103]  M. Sarvas,et al.  Bacillus subtilis PrsA is required in vivo as an extracytoplasmic chaperone for secretion of active enzymes synthesized either with or without pro‐sequences , 1993, Molecular microbiology.

[104]  P. Çalık,et al.  Carbon sources affect metabolic capacities of Bacillus species for the production of industrial enzymes: theoretical analyses for serine and neutral proteases and alpha-amylase. , 2001, Biochemical engineering journal.

[105]  C. Robertson,et al.  Physiological and Genetic Strategies for Enhanced Subtilisin Production by Bacillus subtilis , 1992, Biotechnology progress.

[106]  M. Sarvas,et al.  The PrsA lipoprotein is essential for protein secretion in Bacillus subtilis and sets a limit for high‐level secretion , 1993, Molecular microbiology.

[107]  Folker Meyer,et al.  Comparing expression level‐dependent features in codon usage with protein abundance: An analysis of ‘predictive proteomics’ , 2004, Proteomics.

[108]  E. Nudler,et al.  Cooperation of GroEL/GroES and DnaK/DnaJ heat shock proteins in preventing protein misfolding in Escherichia coli. , 1992, Proceedings of the National Academy of Sciences of the United States of America.

[109]  S. Udaka,et al.  The Efficient Production of Human Epidermal Growth Factor by Bacillus brevis , 1996, Annals of the New York Academy of Sciences.

[110]  S. Udaka Screening for Protein-producing Bacteria , 1976 .

[111]  S. Bron,et al.  Cellular lysis in Bacillus subtilis; the affect of multiple extracellular protease deficiencies , 1999 .

[112]  E. Ferrari,et al.  Commercial Production of Extracellular Enzymes , 1993 .

[113]  S. Bron,et al.  Functional Analysis of Paralogous Thiol-disulfide Oxidoreductases in Bacillus subtilis * , 1999, The Journal of Biological Chemistry.

[114]  R. Doi,et al.  Biology of Bacilli. Applications to industry. , 1992, Biotechnology.

[115]  A. Horwich,et al.  GroEL‐Mediated protein folding , 1997, Protein science : a publication of the Protein Society.

[116]  R. Liddington,et al.  Crystal structure of the anthrax toxin protective antigen , 1997, Nature.