Characterization and optimization of Bacillus subtilis ATCC 6051 as an expression host

Journal of Biotechnology

Volumn 163, Issue 2, 2013, Pages 97-104

  Kabisch, Johannes ^a   Thürmer, Andrea ^b   Hübel, Tanno ^c   Popper, Lutz ^d   Daniel, Rolf ^b   Schweder, Thomas ^a  

^a UNIVERSITY OF GREIFSWALD   (Germany)

^b UNIVERSITY OF GÖTTINGEN   (Germany)

^c MILTENYI BIOTEC GMBH   (Germany)

^d SternEnzym GmbH and Co KG   (Germany)

Author keywords

Bacillus; Genome sequencing; Heterologous expression; Production host

Indexed keywords

BACILLUS SUBTILIS; COMPLEX MEDIA; GENETICALLY MODIFIED; GENOME SEQUENCES; GENOME SEQUENCING; GENOMIC STABILITY; HETEROLOGOUS EXPRESSION; POINT MUTATIONS; POLYKETIDES; RECOMBINANT PROTEIN PRODUCTIONS; SUBTILIS; WILD TYPES;

BACILLI; BACTERIOLOGY; RECOMBINANT PROTEINS;

OPTIMIZATION;

ACETOIN; AMYLASE; POLYKETIDE; RECOMBINANT PROTEIN;

ARTICLE; AUXOTROPHY; BACILLUS SUBTILIS; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM TRANSFORMATION; CONTROLLED STUDY; CULTURE MEDIUM; CULTURE OPTIMIZATION; DNA MODIFICATION; GENE EXPRESSION SYSTEM; GENE INSERTION; GENE SEQUENCE; GENOMIC INSTABILITY; HETEROLOGOUS EXPRESSION; NONHUMAN; NUCLEOTIDE SEQUENCE; POINT MUTATION; PRIORITY JOURNAL; PROCESS OPTIMIZATION; PROMOTER REGION; PROTEIN EXPRESSION; SEQUENCE ALIGNMENT; STRAIN DIFFERENCE; WILD TYPE;

ALPHA-AMYLASES; BACILLUS SUBTILIS; BIOTECHNOLOGY; DNA, BACTERIAL; GENES, BACTERIAL; GENES, REPORTER; PHYLOGENY; POLYMORPHISM, GENETIC; RECOMBINANT PROTEINS;

BACILLUS SUBTILIS;

EID: 84872188636     PISSN: 01681656     EISSN: 18734863     Source Type: Journal    
DOI: 10.1016/j.jbiotec.2012.06.034     Document Type: Article

References (45)

1. Anagnostopoulos C., Spizizen J. Requirements for transformation in Bacillus subtilis. Journal of Bacteriology 1961, 81:741-746.
2. Belitsky B.R., Sonenshein A.L. Role and regulation of Bacillus subtilis glutamate dehydrogenase genes. Journal of Bacteriology 1998, 180:6298-6305.
3. Blackman S.A., Smith T.J., Foster S.J. The role of autolysins during vegetative growth of Bacillus subtilis 168. Microbiology 1998, 144(Pt 1):73-82.
4. Chen R., Guttenplan S.B., Blair K.M., Kearns D.B. Role of the sigmaD-dependent autolysins in Bacillus subtilis population heterogeneity. Journal of Bacteriology 2009, 191:5775-5784.
5. Chipman D.M., Shaanan B. The ACT domain family. Current Opinion in Structural Biology 2001, 11:694-700.
6. Florez L.A., Roppel S.F., Schmeisky A.G., Lammers C.R., Stulke J. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database (Oxford) 2009, bap012.
7. Grant S.G., Jessee J., Bloom F.R., Hanahan D. Differential plasmid rescue from transgenic mouse DNAs into Escherichia coli methylation-restriction mutants. Proceedings of the National Academy of Sciences of the United States of America 1990, 87:4645-4649.
8. Grant W.D. Cell wall teichoic acid as a reserve phosphate source in Bacillus subtilis. Journal of Bacteriology 1979, 137:35-43.
9. Grundy F.J., Henkin T.M. The S box regulon: a new global transcription termination control system for methionine and cysteine biosynthesis genes in gram-positive bacteria. Molecular Microbiology 1998, 30:737-749.
10. Henner D.J., Band L., Shimotsu H. Nucleotide sequence of the Bacillus subtilis tryptophan operon. Gene 1985, 34:169-177.
11. Holme T., Arvidson S., Lindholm B., Pavlu B. Enzymes: laboratory-scale production. Process Biochemistry 1970, 5:62-66.
12. Imamura D., Kuwana R., Kroos L., Feig M., Takamatsu H., Watabe K. Substrate specificity of SpoIIGA, a signal-transducing aspartic protease in Bacilli. Journal of Biochemistry 2011, 149:665-671.
13. Junne S., Klingner A., Kabisch J., Schweder T., Neubauer P. A two-compartment bioreactor system made of commercial parts for bioprocess scale-down studies: impact of oscillations on Bacillus subtilis fed-batch cultivations. Biotechnology Journal 2011, 6:1009-1017.
14. Kazuo K., Shigehiko K., Naotake O. Genome-wide analysis of transcriptional regulators in Bacillus subtilis. Functional Genomics of Gram-Positive Microorganisms 2003.
15. Kobayashi K., Ehrlich S.D., Albertini A., Amati G., Andersen K.K., Arnaud M., Asai K., Ashikaga S., Aymerich S., Bessieres P., Boland F., Brignell S.C., Bron S., Bunai K., Chapuis J., Christiansen L.C., Danchin A., Debarbouille M., Dervyn E., Deuerling E., Devine K., Devine S.K., Dreesen O., Errington J., Fillinger S., Foster S.J., Fujita Y., Galizzi A., Gardan R., Eschevins C., Fukushima T., Haga K., Harwood C.R., Hecker M., Hosoya D., Hullo M.F., Kakeshita H., Karamata D., Kasahara Y., Kawamura F., Koga K., Koski P., Kuwana R., Imamura D., Ishimaru M., Ishikawa S., Ishio I., Le Coq D., Masson A., Mauel C., Meima R., Mellado R.P., Moir A., Moriya S., Nagakawa E., Nanamiya H., Nakai S., Nygaard P., Ogura M., Ohanan T., O'Reilly M., O'Rourke M., Pragai Z., Pooley H.M., Rapoport G., Rawlins J.P., Rivas L.A., Rivolta C., Sadaie A., Sadaie Y., Sarvas M., Sato T., Saxild H.H., Scanlan E., Schumann W., Seegers J.F., Sekiguchi J., Sekowska A., Seror S.J., Simon M., Stragier P., Studer R., Takamatsu H., Tanaka T., Takeuchi M., Thomaides H.B., Vagner V., van Dijl J.M., Watabe K., Wipat A., Yamamoto H., Yamamoto M., Yamamoto Y., Yamane K., Yata K., Yoshida K., Yoshikawa H., Zuber U., Ogasawara N. Essential Bacillus subtilis genes. Proceedings of the National Academy of Sciences of the United States of America 2003, 100:4678-4683.
16. Kobayashi K., Kuwana R., Takamatsu H. kinA mRNA is missing a stop codon in the undomesticated Bacillus subtilis strain ATCC 6051. Microbiology 2008, 154:54-63.
17. Kodama T., Endo K., Ara K., Ozaki K., Kakeshita H., Yamane K., Sekiguchi J. Effect of Bacillus subtilis spo0A mutation on cell wall lytic enzymes and extracellular proteases, and prevention of cell lysis. Journal of Bioscience and Bioengineering 2007, 103:13-21.
18. Lahooti M., Harwood C.R. Transcriptional analysis of the Bacillus subtilis teichuronic acid operon. Microbiology 1999, 145(Pt 12):3409-3417.
19. LeDeaux J.R., Grossman A.D. Isolation and characterization of kinC, a gene that encodes a sensor kinase homologous to the sporulation sensor kinases KinA and KinB in Bacillus subtilis. Journal of Bacteriology 1995, 177:166-175.
20. Li M.Z., Elledge S.J. Harnessing homologous recombination in vitro to generate recombinant DNA via SLIC. Nature Methods 2007, 4:251-256.
21. Lulko A.T., Veening J.-W., Buist G., Smits W.K., Blom E.J., Beekman A.C., Bron S., Kuipers O.P. Production and secretion stress caused by overexpression of heterologous alpha-amylase leads to inhibition of sporulation and a prolonged motile phase in Bacillus subtilis. Applied and Environment Microbiology 2007, 73:5354-5362.
22. Mogk A., Hayward R., Schumann W. Integrative vectors for constructing single-copy transcriptional fusions between Bacillus subtilis promoters and various reporter genes encoding heat-stable enzymes. Gene 1996, 182:33-36.
23. Neubauer P., Haggstrom L., Enfors S.O. Influence of substrate oscillations on acetate formation and growth yield in Escherichia coli glucose limited fed-batch cultivations. Biotechnology and Bioengineering 1995, 47:139-146.
24. Noguchi H., Park J., Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Research 2006, 34:5623-5630.
25. Petersen T.N., Brunak S., von Heijne G., Nielsen H. SignalP 4.0: discriminating signal peptides from transmembrane regions. Nature Methods 2011, 8:785-786.
26. Rice P., Longden I., Bleasby A. EMBOSS: the European Molecular Biology Open Software Suite. Trends in Genetics 2000, 16:276-277.
27. Richter M., Lombardot T., Kostadinov I., Kottmann R., Duhaime M.B., Peplies J., Glockner F.O. JCoast-a biologist-centric software tool for data mining and comparison of prokaryotic (meta)genomes. BMC Bioinformatics 2008, 9:177.
28. Richter M., Rossello-Mora R. Shifting the genomic gold standard for the prokaryotic species definition. Proceedings of the National Academy of Sciences of the United States of America 2009, 106:19126-19131.
29. Rudner D.Z., LeDeaux J.R., Ireton K., Grossman A.D. The spo0K locus of Bacillus subtilis is homologous to the oligopeptide permease locus and is required for sporulation and competence. Journal of Bacteriology 1991, 173:1388-1398.
30. Salzberg L.I., Helmann J.D. Phenotypic and transcriptomic characterization of Bacillus subtilis mutants with grossly altered membrane composition. Journal of Bacteriology 2008, 190:7797-7807.
31. Sambrook J., Russell D.W. Transformation of E. coli by Electroporation 2006, Cold Spring Harbor Protocols, (pdb.prot3933).
32. Sanchez H., Cozar M.C., Martinez-Jimenez M.I. Targeting the Bacillus subtilis genome: an efficient and clean method for gene disruption. Journal of Microbiological Methods 2007, 70:389-394.
33. Sierro N., Makita Y., de Hoon M., Nakai K. DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Research 2008, 36:D93-D96.
34. Silbersack J., Jürgen B., Hecker M., Schneidinger B., Schmuck R., Schweder T. An acetoin-regulated expression system of Bacillus subtilis. Applied Microbiology and Biotechnology 2006, 73:895-903.
35. Soldo B., Lazarevic V., Pagni M., Karamata D. Teichuronic acid operon of Bacillus subtilis 168. Molecular Microbiology 1999, 31:795-805.
36. 2 treatment. Innovative Food Science & Emerging Technologies 2003, 4:161-165.
37. Srivatsan A., Han Y., Peng J., Tehranchi A.K., Gibbs R., Wang J.D., Chen R. High-precision, whole-genome sequencing of laboratory strains facilitates genetic studies. PLoS Genetics 2008, 4:e1000139.
38. Stülke J., Hanschke R., Hecker M. Temporal activation of beta-glucanase synthesis in Bacillus subtilis is mediated by the GTP pool. Journal of General Microbiology 1993, 139:2041-2045.
39. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 1994, 22:4673-4680.
40. UniProt-Consortium T. Reorganizing the protein space at the Universal Protein Resource (UniProt). Nucleic Acids Research 2012, 40:D71-D75.
41. Weinrauch Y., Penchev R., Dubnau E., Smith I., Dubnau D. A Bacillus subtilis regulatory gene product for genetic competence and sporulation resembles sensor protein members of the bacterial two-component signal-transduction systems. Genes and Development 1990, 4:860-872.
42. Wu S.-C., Yeung J.C., Duan Y., Ye R., Szarka S.J., Habibi H.R., Wong S.-L. 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. Applied and Environment Microbiology 2002, 68:3261-3269.
43. Wu W.T., Hsu Y.L., Ko Y.F., Yao L.L. Effect of shear stress on cultivation of Bacillus thuringiensis for thuringiensin production. Applied Microbiology and Biotechnology 2002, 58:175-177.
44. Zeigler D.R. The genome sequence of Bacillus subtilis subsp. spizizenii W23: insights into speciation within the B. subtilis complex and into the history of B. subtilis genetics. Microbiology 2011, 157:2033-2041.
45. Zeigler D.R., Prágai Z., Rodriguez S., Chevreux B., Muffler A., Albert T., Bai R., Wyss M., Perkins J.B. The origins of 168, W23, and other Bacillus subtilis legacy strains. Journal of Bacteriology 2008, 190:6983-6995.