Promoter screening from Bacillus subtilis in various conditions hunting for synthetic biology and industrial applications

PLoS ONE

Volumn 11, Issue 7, 2016, Pages

  Song, Yafeng ^a,b   Nikoloff, Jonas M ^a   Fu, Gang ^a,b   Chen, Jingqi ^a,b   Li, Qinggang ^a,b   Xie, Nengzhong ^c,d   Zheng, Ping ^a,b   Sun, Jibin ^a,b   Zhang, Dawei ^a,b  

^a Tianjin Airport Economic Area   (China)

^b INSTITUTE OF GEOLOGY AND GEOPHYSICS   (China)

^c State Key Laboratory of Non food Biomass Energy and Enzyme Technology   (China)

^d NATIONAL ENGINEERING RESEARCH CENTER FOR NON FOOD BIOREFINERY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ALCOHOL; AMYLASE; BETA GALACTOSIDASE; ENVELOPE PROTEIN; GENOMIC DNA; GREEN FLUORESCENT PROTEIN; HEAT SHOCK PROTEIN; BACTERIAL PROTEIN; SODIUM CHLORIDE;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL METABOLISM; BACTERIAL STRAIN; CHROMOSOME; CONTROLLED STUDY; GENE AMPLIFICATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ANALYSIS; NONHUMAN; OSMOTIC PRESSURE; PROMOTER REGION; PROTEIN SECRETION; PROTEIN TARGETING; SEQUENCE ANALYSIS; SYNTHETIC BIOLOGY; THERMOSTABILITY; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; HEAT; METABOLISM; MICROBIOLOGY; NUCLEOTIDE SEQUENCE; PROCEDURES; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION;

ALPHA-AMYLASES; BACILLUS SUBTILIS; BACTERIAL PROTEINS; BASE SEQUENCE; BETA-GALACTOSIDASE; ETHANOL; GENE EXPRESSION REGULATION, BACTERIAL; GREEN FLUORESCENT PROTEINS; HEAT-SHOCK PROTEINS; HOT TEMPERATURE; INDUSTRIAL MICROBIOLOGY; OSMOTIC PRESSURE; PROMOTER REGIONS, GENETIC; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SODIUM CHLORIDE; SYNTHETIC BIOLOGY;

EID: 84978149927     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0158447     Document Type: Article

References (57)

1. Kang SY, Choi O, Lee JK, Ahn JO, Ahn JS, Hwang BY, et al. (2015) Artificial de novo biosynthesis of hydroxystyrene derivatives in a tyrosine overproducing Escherichia coli strain. Microb Cell Fact 14: 78. doi: 10.1186/s12934-015-0268-7 PMID: 26055892
2. Kang SY, Choi O, Lee JK, Hwang BY, Uhm TB, Hong YS. (2012) Artificial biosynthesis of phenylpropanoic acids in a tyrosine overproducing Escherichia coli strain. Microb Cell Fact 11: 153. doi: 10.1186/1475-2859-11-153 PMID: 23206756
3. Ng CY, Khodayari A, Chowdhury A, Maranas CD (2015) Advances in de novo strain design using integrated systems and synthetic biology tools. Curr Opin Chem Biol 28: 105-114. doi: 10.1016/j.cbpa.2015.06.026 PMID: 26177080
4. Qi H, Li BZ, Zhang WQ, Liu D, Yuan YJ (2015) Modularization of genetic elements promotes synthetic metabolic engineering. Biotechnol Adv.
5. Wang G, Bai L, Wang Z, Shi T, Chen T, Zhao X. (2014) Enhancement of riboflavin production by deregulating gluconeogenesis in Bacillus subtilis. World J Microbiol Biotechnol 30: 1893-1900. doi: 10.1007/s11274-014-1611-6 PMID: 24477882
6. 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. doi: 10.1007/s00253-009-2247-6 PMID: 19779711
7. 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. Bioresour Technol 102: 3934-3940. doi: 10.1016/j.biortech.2010.11.120 PMID: 21194928
8. Tojo S, Satomura T, Kumamoto K, Hirooka K, Fujita Y (2008) Molecular mechanisms underlying the positive stringent response of the Bacillus subtilis ilv-leu operon, involved in the biosynthesis of branched-chain amino acids. J Bacteriol 190: 6134-6147. doi: 10.1128/JB.00606-08 PMID: 18641142
9. Bienick MS, Young KW, Klesmith JR, Detwiler EE, Tomek KJ, Whitehead TA. (2014) The interrelationship between promoter strength, gene expression, and growth rate. PLoS One 9: e109105. doi: 10.1371/journal.pone.0109105 PMID: 25286161
10. Chen J, Zhu X, Tan Z, Xu H, Tang J, Xiao D, et al. (2014) Activating C4-dicarboxylate transporters DcuB and DcuC for improving succinate production. Appl Microbiol Biotechnol 98: 2197-2205. doi: 10.1007/s00253-013-5387-7 PMID: 24323285
11. Yamanishi M, Ito Y, Kintaka R, Imamura C, Katahira S, Ikeuchi A, et al. (2013) A genome-wide activity assessment of terminator regions in Saccharomyces cerevisiae provides a "terminatome" toolbox. ACS Synth Biol 2: 337-347. doi: 10.1021/sb300116y PMID: 23654277
12. Curran KA, Karim AS, Gupta A, Alper HS (2013) Use of expression-enhancing terminators in Saccharomyces cerevisiae to increase mRNA half-life and improve gene expression control for metabolic engineering applications. Metab Eng 19: 88-97. doi: 10.1016/j.ymben.2013.07.001 PMID: 23856240
13. Alper H, Fischer C, Nevoigt E, Stephanopoulos G (2005) Tuning genetic control through promoter engineering. Proc Natl Acad Sci U S A 102: 12678-12683. PMID: 16123130
14. Blazeck J, Liu L, Redden H, Alper H (2011) Tuning gene expression in Yarrowia lipolytica by a hybrid promoter approach. Appl Environ Microbiol 77: 7905-7914. doi: 10.1128/AEM.05763-11 PMID: 21926196
15. Davis JH, Rubin AJ, Sauer RT (2011) Design, construction and characterization of a set of insulated bacterial promoters. Nucleic Acids Res 39: 1131-1141. doi: 10.1093/nar/gkq810 PMID: 20843779
16. Lou C, Stanton B, Chen YJ, Munsky B, Voigt CA (2012) Ribozyme-based insulator parts buffer synthetic circuits from genetic context. Nat Biotechnol 30: 1137-1142. doi: 10.1038/nbt.2401 PMID: 23034349
17. Bai C, Zhang Y, Zhao X, Hu Y, Xiang S, Miao J, et al. (2015) Exploiting a precise design of universal synthetic modular regulatory elements to unlock the microbial natural products in Streptomyces. Proc Natl Acad Sci U S A.
18. Liu L, Liu Y, Shin HD, Chen RR, Wang NS, Li J, et al. (2013) Developing Bacillus spp. as a cell factory for production of microbial enzymes and industrially important biochemicals in the context of systems and synthetic biology. Appl Microbiol Biotechnol 97: 6113-6127. doi: 10.1007/s00253-013-4960-4 PMID: 23749118
19. Westers L, Westers H, Quax WJ (2004) Bacillus subtilis as cell factory for pharmaceutical proteins: a biotechnological approach to optimize the host organism. Biochim Biophys Acta 1694: 299-310. PMID: 15546673
20. Ferreira LC, Ferreira RC, Schumann W (2005) Bacillus subtilis as a tool for vaccine development: from antigen factories to delivery vectors. An Acad Bras Cienc 77: 113-124. PMID: 15692682
21. Jones KL, Kim SW, Keasling JD (2000) Low-copy plasmids can perform as well as or better than high-copy plasmids for metabolic engineering of bacteria. Metab Eng 2: 328-338. PMID: 11120644
22. Chen J, Gai Y, Fu G, Zhou W, Zhang D, Wen J. (2015) Enhanced extracellular production of alpha-amylase in Bacillus subtilis by optimization of regulatory elements and over-expression of PrsA lipoprotein. Biotechnol Lett 37: 899-906. doi: 10.1007/s10529-014-1755-3 PMID: 25515799
23. Chen J, Fu G, Gai Y, Zheng P, Zhang D, Wen J. (2015) Combinatorial Sec pathway analysis for improved heterologous protein secretion in Bacillus subtilis: identification of bottlenecks by systematic gene overexpression. Microb Cell Fact 14: 92. doi: 10.1186/s12934-015-0282-9 PMID: 26112883
24. Overkamp W, Ercan O, Herber M, van Maris AJ, Kleerebezem M, Kuipers UP. (2015) Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis. Environ Microbiol 17: 346-363. doi: 10.1111/1462-2920.12676 PMID: 25367190
25. Bernhardt J, Weibezahn J, Scharf C, Hecker M (2003) Bacillus subtilis during feast and famine: visualization of the overall regulation of protein synthesis during glucose starvation by proteome analysis. Genome Res 13: 224-237. PMID: 12566400
26. Kohlstedt M, Sappa PK, Meyer H, Maass S, Zaprasis A, Hoffmann T, et al. (2014) Adaptation of Bacillus subtilis carbon core metabolism to simultaneous nutrient limitation and osmotic challenge: a multiomics perspective. Environ Microbiol 16: 1898-1917. doi: 10.1111/1462-2920.12438 PMID: 24571712
27. Trang TPP, Nguyen D, Schumann W (2012) Development of a strong intracellular expression system for Bacillus subtilis by optimizing promoter elements. Journal Of Biotechnology 157: 167-172. doi: 10.1016/j.jbiotec.2011.10.006 PMID: 22100269
28. Wang J, Ai X, Mei H, Fu Y, Chen B, Yu Z, et al. (2013) High-throughput identification of promoters and screening of highly active promoter-5′-UTR DNA region with different characteristics from Bacillus thuringiensis. PLoS One 8: e62960. doi: 10.1371/journal.pone.0062960 PMID: 23675447
29. Smolke CD, Silver PA (2011) Informing biological design by integration of systems and synthetic biology. Cell 144: 855-859. doi: 10.1016/j.cell.2011.02.020 PMID: 21414477
30. Nicolas P, Mader U, Dervyn E, Rochat T, Leduc A, Pigeonneau N, et al. (2012) Condition-dependent transcriptome reveals high-level regulatory architecture in Bacillus subtilis. Science 335: 1103-1106. doi: 10.1126/science.1206848 PMID: 22383849
31. Wang PZ, Doi RH (1984) Overlapping promoters transcribed by Bacillus subtilis sigma 55 and sigma 37 RNA polymerase holoenzymes during growth and stationary phases. J Biol Chem 259: 8619-8625. PMID: 6330116
32. You C, Zhang XZ, Zhang YH (2012) Simple cloning via direct transformation of PCR product (DNA Multimer) to Escherichia coli and Bacillus subtilis. Appl Environ Microbiol 78: 1593-1595. doi: 10.1128/AEM.07105-11 PMID: 22194286
33. Koga K, Ikegami A, Nakasone K, Murayama R, Akanuma G, Natori Y, et al. (2006) Construction of Bacillus subtilis strains carrying the transcriptional bgaB fusion with the promoter region of each rrn operon and their differential transcription during spore development. J Gen Appl Microbiol 52: 119-124. PMID: 16778356
34. Wong Ng J, Chatenay D, Robert J, Poirier MG (2010) Plasmid copy number noise in monoclonal populations of bacteria. Phys Rev E Stat Nonlin Soft Matter Phys 81: 011909. PMID: 20365401
35. Yuan G, Wong SL (1995) Regulation of groE expression in Bacillus subtilis: the involvement of the sigma A-like promoter and the roles of the inverted repeat sequence (CIRCE). J Bacteriol 177: 5427-5433. PMID: 7559325
36. Cormack BP, Valdivia RH, Falkow S (1996) FACS-optimized mutants of the green fluorescent protein (GFP). Gene 173: 33-38. PMID: 8707053
37. Zhang XZ, You C, Zhang YH (2014) Transformation of Bacillus subtilis. Methods Mol Biol 1151: 95-101. doi: 10.1007/978-1-4939-0554-6-7 PMID: 24838881
38. Schneider TD, Stephens RM (1990) Sequence logos: a new way to display consensus sequences. Nucleic Acids Res 18: 6097-6100. PMID: 2172928
39. Crooks GE, Hon G, Chandonia JM, Brenner SE (2004) WebLogo: a sequence logo generator. Genome Res 14: 1188-1190. PMID: 15173120
40. Haldenwang WG (1995) The sigma factors of Bacillus subtilis. Microbiol Rev 59: 1-30. PMID: 7708009
41. Rollenhagen C, Antelmann H, Kirstein J, Delumeau O, Hecker M, Yudkin MD. (2003) Binding of sigma (A) and sigma(B) to core RNA polymerase after environmental stress in Bacillus subtilis. J Bacteriol 185: 35-40. PMID: 12486038
42. Higgins D, Dworkin J (2012) Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev 36: 131-148. doi: 10.1111/j.1574-6976.2011.00310.x PMID: 22091839
43. Kingston AW, Liao X, Helmann JD (2013) Contributions of the sigma(W), sigma(M) and sigma(X) regulons to the lantibiotic resistome of Bacillus subtilis. Mol Microbiol 90: 502-518. doi: 10.1111/mmi.12380 PMID: 23980836
44. Schumann W (2003) The Bacillus subtilis heat shock stimulon. Cell Stress Chaperones 8: 207-217. PMID: 14984053
45. Asai K, Ootsuji T, Obata K, Matsumoto T, Fujita Y, Sadaie Y. (2007) Regulatory role of RsgI in sigI expression in Bacillus subtilis. Microbiology 153: 92-101. PMID: 17185538
46. Eiamphungporn W, Helmann JD (2008) The Bacillus subtilis sigma(M) regulon and its contribution to cell envelope stress responses. Mol Microbiol 67: 830-848. doi: 10.1111/j.1365-2958.2007.06090.x PMID: 18179421
47. Jervis AJ, Thackray PD, Houston CW, Horsburgh MJ, Moir A (2007) SigM-responsive genes of Bacillus subtilis and their promoters. J Bacteriol 189: 4534-4538. PMID: 17434969
48. Tamehiro N, Okamoto-Hosoya Y, Okamoto S, Ubukata M, Hamada M, Naganama H, et al. (2002) Bacilysocin, a novel phospholipid antibiotic produced by Bacillus subtilis 168. Antimicrob Agents Chemother 46: 315-320. PMID: 11796336
49. Guo X, Li Y, Peng K, Hu Y, Li C, Xia B, et al. (2005) Solution structures and backbone dynamics of arsenate reductase from Bacillus subtilis: reversible conformational switch associated with arsenate reduction. J Biol Chem 280: 39601-39608. PMID: 16192272
50. Haynes KA, Silver PA (2009) Eukaryotic systems broaden the scope of synthetic biology. J Cell Biol 187: 589-596. doi: 10.1083/jcb.200908138 PMID: 19948487
51. Quan J, Saaem I, Tang N, Ma S, Negre N, Gong H, et al. (2011) Parallel on-chip gene synthesis and application to optimization of protein expression. Nat Biotechnol 29: 449-452. doi: 10.1038/nbt.1847 PMID: 21516083
52. Zhang F, Carothers JM, Keasling JD (2012) Design of a dynamic sensor-regulator system for production of chemicals and fuels derived from fatty acids. Nat Biotechnol 30: 354-359. doi: 10.1038/nbt.2149 PMID: 22446695
53. Brewster RC, Jones DL, Phillips R (2012) Tuning promoter strength through RNA polymerase binding site design in Escherichia coli. PLoS Comput Biol 8: e1002811. doi: 10.1371/journal.pcbi.1002811 PMID: 23271961
54. Hahne H, Mader U, Otto A, Bonn F, Steil L, Bremer E, et al. (2010) A comprehensive proteomics and transcriptomics analysis of Bacillus subtilis salt stress adaptation. J Bacteriol 192: 870-882. doi: 10.1128/JB.01106-09 PMID: 19948795
55. Dempwolff F, Moller HM, Graumann PL (2012) Synthetic motility and cell shape defects associated with deletions of flotillin/reggie paralogs in Bacillus subtilis and interplay of these proteins with NfeD proteins. J Bacteriol 194: 4652-4661. doi: 10.1128/JB.00910-12 PMID: 22753055
56. Keren L, Zackay O, Lotan-Pompan M, Barenholz U, Dekel E, Sasson V, et al. (2013) Promoters maintain their relative activity levels under different growth conditions. Mol Syst Biol 9: 701. doi: 10.1038/msb.2013.59 PMID: 24169404
57. Gerosa L, Kochanowski K, Heinemann M, Sauer U (2013) Dissecting specific and global transcriptional regulation of bacterial gene expression. Mol Syst Biol 9: 658. doi: 10.1038/msb.2013.14 PMID: 23591774