Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology

Applied Microbiology and Biotechnology

Volumn 97, Issue 14, 2013, Pages 6113-6127

  Liu, Long ^a   Liu, Yanfeng ^a   Shin, Hyun Dong ^b   Chen, Rachel R ^b   Wang, Nam Sun ^c   Li, Jianghua ^a   Du, Guocheng ^a   Chen, Jian ^a  

^a JIANGNAN UNIVERSITY   (China)

^b Georgia Institute of Technology   (United States)

^c UNIVERSITY OF MARYLAND   (United States)

Author keywords

Bacillus species; Genome scale modeling; Microbial cell factory; Synthetic biology; Systems biology; Systems metabolic engineering

Indexed keywords

BACILLUS SPECIES; GENOME-SCALE MODELING; MICROBIAL CELL FACTORIES; SYNTHETIC BIOLOGY; SYSTEMS BIOLOGY; SYSTEMS METABOLIC ENGINEERINGS;

CELLS; CYTOLOGY; ENZYMES; GENES; INDUSTRIAL CHEMICALS; METABOLIC ENGINEERING; MODELS; PETROLEUM DEPOSITS;

BACTERIOLOGY;

AMYLASE; BIOSURFACTANT; MICROBIAL ENZYME; POLYGLUTAMIC ACID; PROTEOME; RIBOFLAVIN; SERINE PROTEINASE;

BACTERIUM; BIOCHEMICAL COMPOSITION; BIOENGINEERING; BIOMASS POWER; CELL ORGANELLE; ECONOMIC DEVELOPMENT; ENZYME ACTIVITY; INDUSTRIAL PRODUCTION; MICROBIAL ACTIVITY; PETROLEUM; PROTEIN; RENEWABLE RESOURCE; SUSTAINABLE DEVELOPMENT;

BACILLUS; BACILLUS SUBTILIS; ENZYME SYNTHESIS; GENE EXPRESSION SYSTEM; GENE SEQUENCE; GENETIC MANIPULATION; GENOTYPE; INDUSTRIAL PRODUCTION; METABOLIC ENGINEERING; MOLECULAR EVOLUTION; NONHUMAN; NUCLEOTIDE SEQUENCE; PHENOTYPE; PROTEIN EXPRESSION; PROTEIN SECRETION; REVIEW; SYNTHETIC BIOLOGY;

BACILLUS; BACTERIAL PROTEINS; BIOFUELS; INDUSTRIAL MICROBIOLOGY; SYNTHETIC BIOLOGY;

POSIBACTERIA;

EID: 84879840065     PISSN: 01757598     EISSN: 14320614     Source Type: Journal    
DOI: 10.1007/s00253-013-4960-4     Document Type: Review

References (129)

1. Abdel-Mawgoud AM, Aboulwafa MM, Hassouna NA-H (2008) Optimization of surfactin production by Bacillus subtilis isolate BS5. Appl Biochem Biotechnol 150:305-325
2. Anderson T, Miller J, Fierobe H, Clubb R (2013) Recombinant Bacillus subtilis that grows on untreated plant biomass. Appl Environ Microbiol 79:867-876
3. Ajikumar PK, Xiao WH, Tyo KEJ, Wang Y, Simeon F, Leonard E, Mucha O, Phon TH, Pfeifer B, Stephanopoulos G (2010) Isoprenoid pathway optimization for taxol precursor overproduction in Escherichia coli. Science 330:70-74
4. Alper H, Stephanopoulos G (2007) Global transcription machinery engineering: a new approach for improving cellular phenotype. Metab Eng 9:258-267
5. Amani H, Mehrnia MR, Sarrafzadeh MH, Haghighi M, Soudi MR (2010) Scale up and application of biosurfactant from Bacillus subtilis in enhanced oil recovery. Appl Biochem Biotechnol 162:510-523
6. Bajaj IB, Singhal RS (2009) Sequential optimization approach for enhanced production of poly(gamma-glutamic acid) from newly isolated Bacillus subtilis. Food Technol Biotechnol 47:313-322
7. Banik RM, Singh P, Pandey SK, Jagannadham MV (2010) Purification and characterization of highly thermostable alkaline phosphatase produced from B. licheniformis MTCC 1483. J Biotechnol 150:S350-S351
8. Barbe V, Cruveiller S, Kunst F, Lenoble P, Meurice G, Sekowska A, Vallenet D, Wang T, Moszer I, Médigue C (2009) From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later. Microbiology 155:1758-1775
9. Biswas R, Yamaoka M, Nakayama H, Kondo T, Yoshida K, Bisaria VS, Kondo A (2012) Enhanced production of 2,3-butanediol by engineered Bacillus subtilis. Appl Microbiol Biotechnol 94:651-658
10. Brans A, Filée P, Chevigné A, Claessens A, Joris B (2004) New integrative method to generate Bacillus subtilis recombinant strains free of selection markers. Appl Environ Microb 70:7241
11. Buescher JM, Liebermeister W, Jules M, Uhr M, Muntel J, Botella E, Hessling B, Kleijn RJ, Le Chat L, Lecointe F, Mäder U, Nicolas P, Piersma S, Ruegheimer F, Becher D, Bessieres P, Bidnenko E, Denham EL, Dervyn E, Devine KM, Doherty G, Drulhe S, Felicori L, Fogg MJ, Goelzer A, Hansen A, Harwood CR, Hecker M, Hubner S, Hultschig C, Jarmer H, Klipp E, Leduc A, Lewis P, Molina F, Noirot P, Peres S, Pigeonneau N, Pohl S, Rasmussen S, Rinn B, Schaffer M, Schnidder J, Schwikowski B, van Dijl JM, Veiga P, Walsh S, Wilkinson AJ, Stelling J, Aymerich S, Sauer U (2012) Global network reorganization during dynamic adaptations of Bacillus subtilis metabolism. Science 335:1099-1103
12. Cavalcante Barros FF, Ponezi AN, Pastore GM (2008) Production of biosurfactant by Bacillus subtilis LB5a on a pilot scale using cassava wastewater as substrate. J Ind Microbiol Biotechnol 35:1071-1078
13. Chang WT, Chen ML, Wang SL (2010) An antifungal chitinase produced by Bacillus subtilis using chitin waste as a carbon source. World J Microbiol Biotechnol 26:945-950
14. Chen J, Shi F, Zhang B, Zhu F, Cao W, Xu Z, Xu G, Cen P (2010a) Effects of cultivation conditions on the production of gamma-PGA with Bacillus subtilis ZJU-7. Appl Biochem Biotechnol 160:370-377
15. Chen N, Xing CG, Xie XX, Xu QY (2009) Optimization of technical conditions of producing ribavirin by Bacillus subtilis. Ann Microbiol 59:525-530
16. Chen PT, Chiang CJ, Chao YP (2007a) Strategy to approach stable production of recombinant nattokinase in Bacillus subtilis. Biotechnol Progr 23:808-813
17. Chen PT, Shaw JF, Chao YP, Ho THD, Yu SM (2010b) Construction of chromosomally located T7 expression system for production of heterologous secreted proteins in Bacillus subtilis. J Agr Food Chem 58:5392-5399
18. Chen XH, Koumoutsi A, Scholz R, Eisenreich A, Schneider K, Heinemeyer I, Morgenstern B, Voss B, Hess WR, Reva O (2007b) Comparative analysis of the complete genome sequence of the plant growth-promoting bacterium Bacillus amyloliquefaciens FZB42. Nat Biotechnol 25:1007-1014
19. Cho YH, Song JY, Kim KM, Kim MK, Lee IY, Kim SB, Kim HS, Han NS, Lee BH, Kim BS (2010) Production of nattokinase by batch and fed-batch culture of Bacillus subtilis. New Biotechnol 27:341-346
20. Chtioui O, Dimitrov K, Gancel F, Nikov I (2010) Biosurfactants production by immobilized cells of Bacillus subtilis ATCC 21332 and their recovery by pertraction. Process Biochem 45:1795-1799
21. Coutte F, Leclere V, Bechet M, Guez JS, Lecouturier D, Chollet-Imbert M, Dhulster P, Jacques P (2010) Effect of pps disruption and constitutive expression of srfA on surfactin productivity, spreading and antagonistic properties of Bacillus subtilis 168 derivatives. J Appl Microbiol 109:480-491
22. Das K, Mukherjee AK (2007) Comparison of lipopeptide biosurfactants production by Bacillus subtilis strains in submerged and solid state fermentation systems using a cheap carbon source: some industrial applications of biosurfactants. Process Biochem 42:1191-1199
23. de Faria AF, Teodoro-Martinez DS, de Oliveira BGN, Vaz BG, Silva IS, Garcia JS, Totola MR, Eberlin MN, Grossman M, Alves OL, Durrant LR (2011) Production and structural characterization of surfactin (C-14/Leu(7)) produced by Bacillus subtilis isolate LSFM-05 grown on raw glycerol from the biodiesel industry. Process Biochem 46:1951-1957
24. de Jong B, Siewers V, Nielsen J (2011) Systems biology of yeast: enabling technology for development of cell factories for production of advanced biofuels. Curr Opion Biotechnol 23:1-7
25. Deepak V, Kalishwaralal K, Ramkumarpandian S, Babu SV, Senthilkumar SR, Sangiliyandi G (2008) Optimization of media composition for nattokinase production by Bacillus subtilis using response surface methodology. Bioresource Technol 99:8170-8174
26. Diao L, Dong Q, Xu Z, Yang S, Zhou J, Freudl R (2012) Functional implementation of the posttranslational SecB-SecA protein-targeting pathway in Bacillus subtilis. Appl Environ Microb 78:651-659
27. Duan YX, Chen T, Chen X, Zhao XM (2010) Overexpression of glucose-6-phosphate dehydrogenase enhances riboflavin production in Bacillus subtilis. Appl Microbiol Biotechnol 85:1907-1914
28. Dueber JE, Wu GC, Malmirchegini GR, Moon TS, Petzold CJ, Ullal AV, Prather KL, Keasling JD (2009) Synthetic protein scaffolds provide modular control over metabolic flux. Nat Biotechnol 27:753-759
29. Dunlop MJ, Dossani ZY, Szmidt HL, Chu HC, Lee TS, Keasling JD, Hadi MZ, Mukhopadhyay A (2011) Engineering microbial biofuel tolerance and export using efflux pumps. Mol Syst Biol 7:487
30. Fabret C, Dusko Ehrlich S, Noirot P (2002) A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol Microbiol 46:25-36
31. Fang T, Chen X, Li N, Song H, Bai J, Xiong J, Ying H (2010) Optimization of medium components for d-ribose production by transketolase-deficient Bacillus subtilis NJT-1507. Korean J Chem Eng 27:1725-1729
32. Fu LL, Xu ZR, Shuai JB, Hu CX, Dai W, Li WF (2008) High-level secretion of a chimeric thermostable lichenase from Bacillus subtilis by screening of site-mutated signal peptides with structural alterations. Curr Microbiol 56:287-292
33. Fu LL, Xu ZR, Li WF, Shuai JB, Lu P, Hu CX (2007) Protein secretion pathways in Bacillus subtilis: implication for optimization of heterologous protein secretion. Biotechnol Adv 25:1-12
34. Gerosa L, Sauer U (2011) Regulation and control of metabolic fluxes in microbes. Curr Opin Biotechnol 22:566-575
35. Goosens VJ, Otto A, Glasner C, Monteferrante CC, van der Ploeg R, Hecker M, Becher D, van Dijl JM (2013) Novel twin-arginine translocation pathway-dependent phenotypes of Bacillus subtilis unveiled by quantitative proteomics. J Proteome Res 12:796-807
36. Gong G, Zheng Z, Chen H, Yuan C, Wang P, Yao L, Yu Z (2009) Enhanced production of surfactin by Bacillus subtilis E8 mutant obtained by ion beam implantation. Food Technol Biotechnol 47:27-31
37. Hahne H, Mäder U, Otto A, Bonn F, Steil L, Bremer E, Hecker M, Becher D (2010) A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 192:870-882
38. Henry CS, Zinner JF, Cohoon MP, Stevens RL (2009) iBsu1103: a new genome-scale metabolic model of Bacillus subtilis based on SEED annotations. Genome Biol 10:R69
39. Heravi KM, Wenzel M, Altenbuchner J (2011) Regulation of mtl operon promoter of Bacillus subtilis: requirements of its use in expression vectors. Microb Cell Fact 10:83
40. Hmidet N, Ali NEH, Zouari-Fakhfakh N, Haddar A, Nasri M, Sellemi-Kamoun A (2010) Chicken feathers: a complex substrate for the co-production of alpha-amylase and proteases by B. licheniformis NH1. J Ind Microbiol Biotechnol 37:983-990
41. Hong SW, Chu IH, Chung KS (2011) Purification and biochemical characterization of thermostable phytase from newly isolated Bacillus subtilis CF92. J Korean Soc Appl Bi 54:89-94
42. Huang J, Du Y, Xu G, Zhang H, Zhu F, Huang L, Xu Z (2011) High yield and cost-effective production of poly(gamma-glutamic acid) with Bacillus subtilis. Eng Life Sci 11:291-297
43. İleri N, Çalik P (2006) Effects of pH strategy on endo- and exo-metabolome profiles and sodium potassium hydrogen ports of β-lactamase-producing Bacillus licheniformis. Biotechnol Progr 22:411-419
44. Jeong JH, Kim JN, Wee YJ, Ryu HW (2010) The statistically optimized production of poly(gamma-glutamic acid) by batch fermentation of a newly isolated Bacillus subtilis RKY3. Bioresour Technol 101:4533-4539
45. Jung J, Yu KO, Ramzi AB, Choe SH, Kim SW, Han SO (2012) Improvement of surfactin production in Bacillus subtilis using synthetic wastewater by overexpression of specific extracellular signaling peptides, comX and phrC. Biotechnol Bioeng 109:2349-2356
46. Kakeshtia H, Kageyama Y, Ara K, Ozaki K, Nakamura K (2010) Enhanced extracellular production of heterologous proteins in Bacillus subtilis by deleting the C-terminal region of the SecA secretory machinery. Mol Biotechnol 46:250-257
47. Keasling JD (2010) Manufacturing molecules through metabolic engineering. Science 330:1355-1358
48. Kim IK, Roldão A, Siewers V, Nielsen J (2012) A systems-level approach for metabolic engineering of yeast cell factories. FEMS Yeast Res 12:228-248
49. Kimura K, Tran LSP, Do TH, Itoh Y (2009) Expression of the pgsB encoding the poly-gamma-dl-glutamate synthetase of Bacillus subtilis (natto). Biosci Biotechnol Biochem 73:1149-1155
50. Konsoula Z, Liakopoulou-Kyriakides M (2006) Thermostable alpha-amylase production by Bacillus subtilis entrapped in calcium alginate gel capsules. Enzyme Microb Technol 39:690-696
51. Kunst F, Ogasawara N, Moszer I, Albertini A, Alloni G, Azevedo V, Bertero M, Bessieres P, Bolotin A, Borchert S, Borriss R, Boursier L, Brans A, Braun M, Brignell SC, Bron S, Brouillet S, Bruschi CV, Caldwell B, Capuano V, Carter NM, Choi SK, Codani JJ, Connerton IF, Cummings NJ, Daniel RA, Denizot F, Devine KM, Dusterhoft A, Ehrlich SD, Emmerson PT, Entian KD, Errington J, Fabret C, Ferrari E, Foulger D, Fritz C, Fujita M, Fujita Y, Fuma S, Galizzi A, Galleron N, Ghim SY, Glaser P, Goffeau A, Golightly EJ, Grandi G, Guiseppi G, Guy BJ, Haga K, Haiech J, Harwood CR, Henaut A, Hilbert H, Holsappel S, Hosono S, Hullo MF, Itaya M, Jones L, Joris B, Karamata D, Kasahara Y, Klaerr-Blanchard M, Klein C, Kobayashi Y, Koetter P, Koningstein G, Krogh S, Kumano M, KuritaK LA, Lardinois S, Lauber J, Lazarevic V, Lee M, Levine A, Liu H, Masuda S, Mauel C, Medigue C, Medina N, Mellado RP, Mizuno M, Moestl D, Nakai S, Noback M, Noone D, O'Reilly M, Ogawa K, Ogiwara A, Oudega B, Park SH, ParroV PTM, Portetelle D, Porwollik S, Prescott AM, Presecan E, Pujic P, Purnelle B, Rapoport G, Rey M, Reynolds S, Rieger M, Rivolta C, Rocha E, Roche B, Rose M, Sadaie Y, Sato T, Scanlan E, Schleich S, Schroeter R, Scoffone F, Sekiguchi J, Sekowska A, Seror SJ, Serror P, Shin BS, Soldo B, Sorokin A, Tacconi E, Takagi T, Takahashi H, Takemaru K, Takeuchi M, Tamakoshi A, Tanaka T, Terpstra P, Tognoni A, Tosato V, Uchiyama S, Vandenbol M, Vannier F, Vassarotti A, Viari A, Wambutt R, Wedler E, Wedler H, Weitzenegger T, Winters P, Wipat A, Yamamoto H, Yamane K, Yasumoto K, Yata K, Yoshida K, Yoshikawa HF, Zumstein E, Yoshikawa H, Danchin A (1997) The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature 390:249-256
52. Kurosawa K, Hosaka T, Tamehiro N, Inaoka T, Ochi K (2006) Improvement of alpha-amylase production by modulation of ribosomal component protein S12 in Bacillus subtilis 168. Appl Environ Microb 72:71-77
53. Kwon EY, Kim KM, Kim MK, Lee IY, Kim BS (2011) Production of nattokinase by high cell density fed-batch culture of Bacillus subtilis. Bioproc Biosyst Eng 34:789-793
54. Lammers CR, Flórez LA, Schmeisky AG, Roppel SF, Mäder U, Hamoen L, Stülke J (2010) Connecting parts with processes: SubtiWiki and SubtiPathways integrate gene and pathway annotation for Bacillus subtilis. Microbiology 156:849-859
55. Lee BH, Kim BK, Lee YJ, Chung CH, Lee JW (2010a) Industrial scale of optimization for the production of carboxymethylcellulase from rice bran by a marine bacterium, Bacillus subtilis subsp subtilis A-53. Enzyme Microb Technol 46:38-42
56. Lee DG, Jang MK, Lee OH, Kim NY, Ju SA, Lee SH (2008) Over-production of a glycoside hydrolase family 50 beta-agarase from Agarivorans sp JA-1 in Bacillus subtilis and the whitening effect of its product. Biotechnol Lett 30:911-918
57. Lee SJ, Pan JG, Park SH, Choi SK (2010b) Development of a stationary phase-specific autoinducible expression system in Bacillus subtilis. J Biotechnol 149:16-20
58. Li H, Zhang G, Deng A, Chen N, Wen T (2011a) De novo engineering and metabolic flux analysis of inosine biosynthesis in Bacillus subtilis. Biotechnol Lett 33:1575-1580
59. Li S, Wen J, Jia X (2011b) Engineering Bacillus subtilis for isobutanol production by heterologous Ehrlich pathway construction and the biosynthetic 2-ketoisovalerate precursor pathway overexpression. Appl Microbiol Biotechnol 91:577-589
60. Liu JF, Yang J, Yang SZ, Ye RQ, Mu BZ (2012) Effects of different amino acids in culture media on surfactin variants produced by Bacillus subtilis TD7. Appl Biochem Biotechnol 166:2091-2100
61. Liu S, Endo K, Ara K, Ozaki K, Ogasawara N (2008a) Introduction of marker-free deletions in Bacillus subtilis using the AraR repressor and the ara promoter. Microbiology 154:2562-2570
62. Liu YH, Lu FP, Li Y, Yin XB, Wang Y, Gao C (2008b) Characterisation of mutagenised acid-resistant alpha-amylase expressed in Bacillus subtilis WB600. Appl Microbiol Biotechnol 78:85-94
63. Lu Y, Lin Q, Wang J, Wu Y, Bao W, Lv F, Lu Z (2010) Overexpression and characterization in Bacillus subtilis of a positionally nonspecific lipase from Proteus vulgaris. J Ind Microbiol Biotechnol 37:919-925
64. Mäder U, Schmeisky AG, Florez LA, Stülke J (2012) SubtiWiki - a comprehensive community resource for the model organism Bacillus subtilis. Nucleic Acids Res 40:D1278-D1287
65. Manabe K, Kageyama Y, Morimoto T, Ozawa T, Sawada K, Endo K, Tohata M, Ara K, Ozaki K, Ogasawara N (2011) Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874. Appl Environ Microbiol 77:8370-8381
66. Manabe K, Kageyama Y, Tohata M, Ara K, Ozaki K, Ogasawara N (2012) High external pH enables more efficient secretion of alkaline alpha-amylase AmyK38 by Bacillus subtilis. Microb Cell Fact 11:74
67. glv promoter. Microb Cell Fact 9:55
68. Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, Manabe K, Kanaya S, Ara K, Ozaki K, Ogasawara N (2008) Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res 15:73-81
69. Moszer I, Glaser P, Danchin A (1995) SubtiList: a relational database for the Bacillus subtilis genome. Microbiology 141:261-268
70. Mulder KCL, Bandola J, Schumann W (2013) Construction of an artificial secYEG operon allowing high level secretion of alpha-amylase, Protein Expr Purif http://dx.doi.org/10.1016/j.pep.2013.02.008
71. Na D, Yoo SM, ChungH PH, Park JH, Lee SY (2013) Metabolic engineering of Escherichia coli using synthetic small regulatory RNAs. Nat Biotechnol 30:170-174
72. Nicolas P, Mäder U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, Bidnenko E, Marchadier E, Hoebeke M, Aymerich S, Becher D, Bisicchia P, Botella E, Delumeau O, Doherty G, Denham EL, Fogg MJ, Fromion V, Goelzer A, Hansen A, Härtig E, Harwood CR, Homuth G, Jarmer H, Jules M, Klipp E, Le Chat L, Lecointe F, Lewis P, Liebermeister W, March A, Mars RAT, Priyanka N, Noone D, Pohl S, Rinn B, Rügheimer F, Sappa PK, Samson F, Schaffer M, Schwikowski B, Steil L, Stülke J, Wiegert T, Devine KM, Wilkinson AJ, van Dijl JM, Hecker M, Völker U, Bessières P, Noirot P (2012) Condition dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335:1103-1106
73. Ochi K (2007) From microbial differentiation to ribosome engineering. Biosci Biotechnol Biochem 71:1373-1386
74. Oh C, De Zoysa M, Kang DH, Lee Y, Whang I, Nikapitiya C, Heo SJ, Yoon KT, Affan A, Lee J (2011) Isolation, purification, and enzymatic characterization of extracellular chitosanase from marine bacterium Bacillus subtilis CH2. J Microbiol Biotechnol 21:1021-1025
75. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R (2007) Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 282:28791-28799
76. Ozcan BD, Ozcan N (2008) Expression of thermostable alpha-amylase gene from Bacillus stearothermophilus in various Bacillus subtilis strains. Ann Microbiol 58:265-268
77. Perkins J, Wyss M, Sauer U, Hohmann HP (2009) Metabolic engineering of B. subtilis. In: CD Smolke, J Nielsen (eds) Metabolic pathway engineering handbook. CRC, Boca Raton.
78. Phan TTP, Nguyen HD, Schumann W (2012) Development of a strong intracellular expression system for Bacillus subtilis by optimizing promoter elements. J Biotechnol 157:167-172
79. Ponte Rocha MV, Gomes Barreto RV, Melo VMM, Barros Goncalves LR (2009) Evaluation of cashew apple juice for surfactin production by Bacillus subtilis LAMI008. Appl Biochem Biotechnol 155:366-378
80. Rajagopalan G, Krishnan C (2008a) Alpha-amylase production from catabolite derepressed Bacillus subtilis KCC103 utilizing sugarcane bagasse hydrolysate. Bioresource Technol 99:3044-3050
81. Rajagopalan G, Krishnan C (2008b) Optimization of agro-residual medium for alpha-amylase production from a hyper-producing Bacillus subtilis KCC103 in submerged fermentation. J Chem Technol Biotechnol 84:618-625
82. Romero-Garcia S, Hernández-Bustos C, Merino E, Gosset G, Martinez A (2009) Homolactic fermentation from glucose and cellobiose using Bacillus subtilis. Microb Cell Fact 8:23
83. Romero S, Merino E, Bolívar F, Gosset G, Martinez A (2007) Metabolic engineering of Bacillus subtilis for ethanol production: lactate dehydrogenase plays a key role in fermentative metabolism. Appl Environ Microb 73:5190-5198
84. Rückert C, Blom J, Chen X, Reva O, Borriss R (2011) Genome sequence of B. amyloliquefaciens type strain DSM7(T) reveals differences to plant-associated B. amyloliquefaciens FZB42. J Biotechnol 155:78-85
85. Saimmai A, Rukadee O, Sobhon V, Maneerat S (2012) Biosurfactant production by Bacillus subtilis TD4 and Pseudomonas aeruginosa SU7 grown on crude glycerol obtained from biodiesel production plant as sole carbon source. J Sci Ind Res 71:396-406
86. Sanghi A, Garg N, Sharma J, Kuhar K, Kuhad RC, Gupta VK (2008) Optimization of xylanase production using inexpensive agro-residues by alkalophilic Bacillus subtilis ASH in solid-state fermentation. World J Microbi Biotechnol 24:633-640
87. Sathish T, Prakasham RS (2010) Enrichment of glutaminase production by Bacillus subtilis RSP-GLU in submerged cultivation based on neural network-genetic algorithm approach. J Chem Technol Biotechnol 85:50-58
88. Schallmey M, Singh A, Ward OP (2004) Developments in the use of Bacillus species for industrial production. Can J Microbiol 50:1-17
89. Schumann W (2007) Production of recombinant proteins in Bacillus subtilis. Adv Appl Microbiol 62:137-189
90. Shi F, Xu ZN, Cen PL (2006) Efficient production of poly-gamma-glutamic acid by Bacillus subtilis ZJU-7. Appl Biochem Biotechnol 133:271-281
91. Shi S, Chen T, Zhang Z, Chen X, Zhao X (2009a) Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metab Eng 11:243-252
92. Shi S, Shen Z, Chen X, Chen T, Zhao X (2009b) Increased production of riboflavin by metabolic engineering of the purine pathway in Bacillus subtilis. Biochem Eng J 46:28-33
93. Shi X, Feng M, Zhao Y, Guo X, Zhou P (2008) Overexpression, purification and characterization of a recombinant secretary catalase from Bacillus subtilis. Biotechnol Lett 30:181-186
94. Sierro N, Makita Y, de Hoon M, Nakai K (2008) DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res 36:D93-D96
95. Soni SK, Goyal N, Gupta JK, Soni R (2012) Enhanced production of alpha-amylase from Bacillus subtilis subsp. spizizenii in solid state fermentation by response surface methodology and its evaluation in the hydrolysis of raw potato starch. Starch-Starke 64:64-77
96. Su Y, Li X, Liu Q, Hou Z, Zhu X, Guo X, Ling P (2010) Improved poly-gamma-glutamic acid production by chromosomal integration of the Vitreoscilla hemoglobin gene (vgb) in Bacillus subtilis. Bioresource Technol 101:4733-4736
97. Tanaka K, Henry CS, Zinner JF, Jolivet E, Cohoon MP, Xia F, Bidnenko V, Ehrlich SD, Stevens RL, Noirot P (2013) Building the repertoire of dispensable chromosome regions in Bacillus subtilis entails major refinement of cognate large-scale metabolic model. Nucleic Acids Res 41:687-699
98. Tanyildizi MS, Oezer D, Elibol M (2007) Production of bacterial alpha-amylase by B. amyloliquefaciens under solid substrate fermentation. Biochem Eng J 37:294-297
99. Tjalsma H, Antelmann H, Jongbloed JDH, Braun PG, Darmon E, Dorenbos R, Dubois JYF, Westers H, Zanen G, Quax WJ, Kuipers OP, Bron S, Hecker M, van Dijl JM (2004) Proteomics of protein secretion by Bacillus subtilis: separating the "secrets" of the secretome. Microbiol Mol Biol R 68:207-233
100. Tyo KEJ, Ajikumar PK, Stephanopoulos G (2009) Stabilized gene duplication enables long-term selection-free heterologous pathway expression. Nat Biotechnol 27:760-765
101. van Dijl JM, Hecker M (2013) Bacillus subtilis: from soil bacterium to super-secreting cell factory. Microb Cell Fact 12:3
102. Veith B, Herzberg C, Steckel S, Feesche J, Maurer KH, Ehrenreich P, Bäumer S, Henne A, Liesegang H, Merkl R (2004) The complete genome sequence of Bacillus licheniformis DSM13, an organism with great industrial potential. J Mol Microb Biotechnol 7:204-211
103. Voigt B, Schweder T, Sibbald M, Albrecht D, Ehrenreich A, Bernhardt J, Feesche J, Maurer KH, Gottschalk G, van Dijl JM, Hecker M (2006) The extracellular proteome of Bacillus licheniformis grown in different media and under different nutrient starvation conditions. Proteomics 6:268-281
104. Wang Y, Weng J, Waseem R, Yin X, Zhang R, Shen Q (2012) Bacillus subtilis genome editing using ssDNA with short homology regions. Nucleic Acids Res 40:e91
105. Wang Z, Chen T, Ma X, Shen Z, Zhao X (2011) Enhancement of riboflavin production with Bacillus subtilis by expression and site-directed mutagenesis of zwf and gnd gene from Corynebacterium glutamicum. Bioresource Technol 102:3934-3940
106. Wenzel M, Mueller A, Siemann-Herzberg M, Altenbuchner J (2011) Self-inducible Bacillus subtilis expression system for reliable and inexpensive protein production by high-cell-density fermentation. Appl Environ Microb 77:6419-6425
107. Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Séror SJ, Beekman AC, Darmon E, Eschevins C, de Jong A, Bron S, Kuipers OP, Albertini AM, Antelmann H, Hecker M, Zamboni N, Sauer U, Bruand C, Ehrlich DS, Alonso JC, Salas M, Quax WJ (2003) Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol 20:2076-2090
108. Widner B, Thomas M, Sternberg D, Lammon D, Behr R, Sloma A (2000) Development of marker-free strains of Bacillus subtilis capable of secreting high levels of industrial enzymes. J Ind Microbiol Biotechnol 25:204-212
109. Wolff S, Antelmann H, Albrecht D, Becher D, Bernhardt J, Bron S, Buettner K, van Dijl JM, Eymann C, Otto A, Tam LT, Hecker M (2007) Towards the entire proteome of the model bacterium Bacillus subtilis by gel-based and gel-free approaches. J Chromatogr B 849:129-140
110. Wu QL, Chen T, Gan Y, Chen X, Zhao XM (2007) Optimization of riboflavin production by recombinant Bacillus subtilis RH44 using statistical designs. Appl Microbiol Biotechnol 76:783-794
111. Wu Q, Xu H, Shi N, Yao J, Li S, Ouyang P (2008) Improvement of poly(gamma-glutamic acid) biosynthesis and redistribution of metabolic flux with the presence of different additives in Bacillus subtilis CGMCC 0833. Appl Microbiol Biotechnol 79:527-535
112. Xu C, Liu L, Zhang Z, Jin D, Qiu J, Chen M (2013) Genome-scale metabolic model in guiding metabolic engineering of microbial improvement. Appl Microbiol Biotechnol 97:519-539
113. Xue J, Ahring BK (2011) Enhancing isoprene production by genetic modification of the 1-deoxy-d-xylulose-5-phosphate pathway in Bacillus subtilis. Appl Environ Microb 77:2399-2405
114. Yan X, Yu HJ, Hong Q, Li SP (2008) Cre/lox system and PCR-based genome engineering in Bacillus subtilis. Appl Environ Microb 74:5556-5562
115. Yang M, Zhang W, Ji S, Cao P, Chen Y, Zhao X (2013) Generation of an artificial double promoter for protein expression in Bacillus subtilis through a promoter trap system. PloS One 8:e56321
116. You C, Zhang XZ, Zhang YHP (2012) Simple cloning via direct transformation of PCR Product (DNA multimer) to Escherichia coli and Bacillus subtilis. Appl Environ Microb 78:1593-1595
117. Yue Y, Lian J, Tian P, Tan T (2009) Cloning of amidase gene from Rhodococcus erythropolis and expression by distinct promoters in Bacillus subtilis. J Mol Catal B-Enzym 56:89-95
118. Zakataeva NP, Nikitina OV, Gronskiy SV, Romanenkov DV, Livshits VA (2010) A simple method to introduce marker-free genetic modifications into the chromosome of naturally nontransformable Bacillus amyloliquefaciens strains. Appl Microbiol Biotechnol 85:1201-1209
119. Zamboni N, Fendt SM, Rühl M, Sauer U (2009) 13C-based metabolic flux analysis. Nat Protoc 4:878-892
120. Zhang C, Zhang X, Yao Z, Lu Y, Lu F, Lu Z (2011a) A new method for multiple gene inactivations in Bacillus subtilis 168, producing a strain free of selectable markers. Can J Microbiol 57:427-436
121. Zhang D, Feng X, Zhou Z, Zhang Y, Xu H (2012a) Economical production of poly(gamma-glutamic acid) using untreated cane molasses and monosodium glutamate waste liquor by Bacillus subtilis NX-2. Bioresource Technol 114:583-588
122. Zhang H, Zhu J, Zhu X, Cai J, Zhang A, Hong Y, Huang J, Huang L, Xu Z (2012b) High-level exogenous glutamic acid-independent production of poly-(gamma-glutamic acid) with organic acid addition in a new isolated Bacillus subtilis C10. Bioresource Technol 116:241-246
123. Zhang XZ, Sathitsuksanoh N, Zhu Z, Zhang YHP (2011b) One-step production of lactate from cellulose as the sole carbon source without any other organic nutrient by recombinant cellulolytic Bacillus subtilis. Metab Eng 13:364-372
124. Zhang XZ, Yan X, Cui ZL, Hong Q, Li SP (2006) mazF, a novel counter-selectable marker for unmarked chromosomal manipulation in Bacillus subtilis. Nucleic Acids Res 34:e71-e71
125. Zhang XZ, Zhang YHP (2010) One-step production of biocommodities from lignocellulosic biomass by recombinant cellulolytic Bacillus subtilis: opportunities and challenges. Eng Life Sci 10:398-406
126. Zhang XZ, Zhang YHP (2011) Simple, fast and high-efficiency transformation system for directed evolution of cellulase in Bacillus subtilis. Microb Biotechnol 4:98-105
127. Zhao Q, Ding R, Kang Y, Chen J (2008) Expression of pectate lyase A from Aspergillus nidulans in Bacillus subtilis. World J Microb Biotechol 24:2607-2612
128. Zhou K, Zou R, Zhang C, Stephanopoulos G, Too HP (2013) Optimization of amorphadiene synthesis in Bacillus subtilis via transcriptional, translational and media modulation. Biotechnol Bioeng. doi: 10.1002/bit.24900
129. Zhu FM, Ji SY, Zhang WW, Li W, Cao BY, Yang MM (2008) Development and application of a novel signal peptide probe vector with PGA as reporter in Bacillus subtilis WB700: twenty-four tat pathway signal peptides from Bacillus subtilis were monitored. Mol Biotechnol 39:225-230