Characterization of genome-reduced Bacillus subtilis strains and their application for the production of guanosine and thymidine

Microbial Cell Factories

Volumn 15, Issue 1, 2016, Pages

  Li, Yang ^a,d   Zhu, Xujun ^a   Zhang, Xueyu ^a,c   Fu, Jing ^a   Wang, Zhiwen ^a   Chen, Tao ^a,b   Zhao, Xueming ^a  

^a TIANJIN UNIVERSITY   (China)

^b HUBEI UNIVERSITY OF TECHNOLOGY   (China)

^c Tianjin Vocational College of Bioengineering   (China)

^d SHIHEZI UNIVERSITY   (China)

Author keywords

Bacillus subtilis; Chassis cell; Genome reduction; Guanosine; Nucleosides; Thymidine

Indexed keywords

AMIDOPHOSPHORIBOSYLTRANSFERASE; GUANOSINE; INOSINATE DEHYDROGENASE; NUCLEOSIDE DIPHOSPHATE KINASE; THYMIDINE; THYMIDINE KINASE; THYMIDYLATE SYNTHASE; ESCHERICHIA COLI PROTEIN; PHOSPHODIESTERASE; USHA PROTEIN, E COLI;

ARTICLE; BACILLUS SUBTILIS; BACTERIAL CHROMOSOME; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; CELL GROWTH; CONTROLLED STUDY; CYTOLYSIS; DUT GENE; ESCHERICHIA COLI; GENE DELETION; GENE INACTIVATION; GENE OVEREXPRESSION; GENETIC ENGINEERING; GENETIC MANIPULATION; GENETIC PROCEDURES; GENOME REDUCTION; GENOME SIZE; GROWTH RATE; GUAB GENE; MUTANT; NDK GENE; NONHUMAN; PRS GENE; PURA GENE; PURF GENE; SPORE GERMINATION; SPOROGENESIS; TDK GENE; THYA GENE; USHA GENE; WILD TYPE; GENETICS; GROWTH, DEVELOPMENT AND AGING; METABOLIC ENGINEERING; METABOLISM; PLASMID;

BACILLUS SUBTILIS; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; GENOME, BACTERIAL; GUANOSINE; METABOLIC ENGINEERING; PHOSPHORIC DIESTER HYDROLASES; PLASMIDS; THYMIDINE;

EID: 84973100850     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/s12934-016-0494-7     Document Type: Article

References (50)

1. Foley PL, Shuler ML. Considerations for the design and construction of a synthetic platform cell for biotechnological applications. Biotechnol Bioeng. 2010;105:26-36.
2. Leprince A, van Passel MW, dos Santos VA. Streamlining genomes: toward the generation of simplified and stabilized microbial systems. Curr Opin Biotechnol. 2012;23:651-8.
3. Ochman H. Genomes on the shrink. Proc Natl Acad Sci USA. 2005;102:11959-60.
4. Koonin EV. How many genes can make a cell: minimal gene set concept. Annu Rev Genomics Hum Genet. 2000;1(1):99-116.
5. Rocha EP. The organization of the bacterial genome. Annu Rev Genet. 2008;42:211-33.
6. Mira A, Klasson L, Andersson SG. Microbial genome evolution: sources of variability. Curr Opin Microbiol. 2002;5:506-12.
7. Gao H, Zhuo Y, Ashforth E, Zhang L. Engineering of a genome-reduced host: practical application of synthetic biology in the overproduction of desired secondary metabolites. Protein Cell. 2010;1:621-6.
8. Komatsu M, Uchiyama T, Omura S, Cane DE, Ikeda H. Genome-minimized Streptomyces host for the heterologous expression of secondary metabolism. Proc Natl Acad Sci USA. 2010;107:2646-51.
9. Sharma SS, Blattner FR, Harcum SW. Recombinant protein production in an Escherichia coli reduced genome strain. Metab Eng. 2007;9:133-41.
10. Lee JH, Sung BH, Kim MS, Blattner FR, Yoon BH, Kim JH, Kim SC. Metabolic engineering of a reduced-genome strain of Escherichia coli for l-threonine production. Microb Cell Fact. 2009;8:2.
11. Posfai G, Plunkett III G, Feher T, Frisch D, Keil GM, Umenhoffer K, Kolisnychenko V, Stahl B, Sharma SS, de Arruda M, et al. Emergent properties of reduced-genome Escherichia coli. Science. 2006;312:1044-6.
12. Mizoguchi H, Sawano Y, Kato J, Mori H. Superpositioning of deletions promotes growth of Escherichia coli with a reduced genome. DNA Res. 2008;15:277-84.
13. Hirokawa Y, Kawano H, Tanaka-Masuda K, Nakamura N, Nakagawa A, Ito M, Mori H, Oshima T, Ogasawara N. Genetic manipulations restored the growth fitness of reduced-genome Escherichia coli. J Biosci Bioeng. 2013;116:52-8.
14. Baumgart M, Unthan S, Ruckert C, Sivalingam J, Grunberger A, Kalinowski J, Bott M, Noack S, Frunzke J. Construction of a prophage-free variant of Corynebacterium glutamicum ATCC 13032 for use as a platform strain for basic research and industrial biotechnology. Appl Environ Microbiol. 2013;79:6006-15.
15. Lieder S, Nikel PI, de Lorenzo V, Takors R. Genome reduction boosts heterologous gene expression in Pseudomonas putida. Microb Cell Fact. 2015;14:23.
16. Ara K, Ozaki K, Nakamura K, Yamane K, Sekiguchi J, Ogasawara N. Bacillus minimum genome factory: effective utilization of microbial genome information. Biotechnol Appl Biochem. 2007;46:169-78.
17. Akeno Y, Ying BW, Tsuru S, Yomo T. A reduced genome decreases the host carrying capacity for foreign DNA. Microb Cell Fact. 2014;13:49.
18. Unthan S, Baumgart M, Radek A, Herbst M, Siebert D, Bruhl N, Bartsch A, Bott M, Wiechert W, Marin K, et al. Chassis organism from Corynebacterium glutamicum-a top-down approach to identify and delete irrelevant gene clusters. Biotechnol J. 2015;10:290-301.
19. Schallmey M, Singh A, Ward OP. Developments in the use of Bacillus species for industrial production. Can J Microbiol. 2004;50:1-17.
20. Westers H, Dorenbos R, van Dijl JM, Kabel J, Flanagan T, Devine KM, Jude F, Seror SJ, Beekman AC, Darmon E, et al. Genome engineering reveals large dispensable regions in Bacillus subtilis. Mol Biol Evol. 2003;20:2076-90.
21. Morimoto T, Kadoya R, Endo K, Tohata M, Sawada K, Liu S, Ozawa T, Kodama T, Kakeshita H, Kageyama Y, et al. Enhanced recombinant protein productivity by genome reduction in Bacillus subtilis. DNA Res. 2008;15:73-81.
22. Manabe K, Kageyama Y, Morimoto T, Ozawa T, Sawada K, Endo K, Tohata M, Ara K, Ozaki K, Ogasawara N. Combined effect of improved cell yield and increased specific productivity enhances recombinant enzyme production in genome-reduced Bacillus subtilis strain MGB874. Appl Environ Microbiol. 2011;77:8370-81.
23. Manabe K, Kageyama Y, Tohata M, Ara K, Ozaki K, Ogasawara N. High external pH enables more efficient secretion of alkaline alpha-amylase AmyK38 by Bacillus subtilis. Microb Cell Fact. 2012;11:74.
24. Toya Y, Hirasawa T, Morimoto T, Masuda K, Kageyama Y, Ozaki K, Ogasawara N, Shimizu H. 13 C-metabolic flux analysis in heterologous cellulase production by Bacillus subtilis genome-reduced strain. J Biotechnol. 2014;179:42-9.
25. Zhu H, Yang SM, Yuan ZM, Ban R. Metabolic and genetic factors affecting the productivity of pyrimidine nucleoside in Bacillus subtilis. Microb Cell Fact. 2015;14:54.
26. Shi S, Chen T, Zhang Z, Chen X, Zhao X. Transcriptome analysis guided metabolic engineering of Bacillus subtilis for riboflavin production. Metab Eng. 2009;11:243-52.
27. De Wulf P, Soetaert W, Schwengers D, Vandamme EJ. Optimization of d-ribose production with a transketolase-affected Bacillus subtilis mutant strain in glucose and gluconic acid-based media. J Appl Microbiol. 1997;83:25-30.
28. Fu J, Wang Z, Chen T, Liu W, Shi T, Wang G, Tang YJ, Zhao X. NADH plays the vital role for chiral pure d-(-)-2,3-butanediol production in Bacillus subtilis under limited oxygen conditions. Biotechnol Bioeng. 2014;111:2126-31.
29. Zhang X, Zhang R, Bao T, Rao Z, Yang T, Xu M, Xu Z, Li H, Yang S. The rebalanced pathway significantly enhances acetoin production by disruption of acetoin reductase gene and moderate-expression of a new water-forming NADH oxidase in Bacillus subtilis. Metab Eng. 2014;23:34-41.
30. Kunst F, Ogasawara N, Moszer I, Albertini AM, Alloni G, Azevedo V, Bertero MG, Bessieres P, Bolotin A, Borchert S, et al. The complete genome sequence of the gram-positive bacterium Bacillus subtilis. Nature. 1997;390:249-56.
31. Smith TJ, Blackman SA, Foster SJ. Autolysins of Bacillus subtilis: multiple enzymes with multiple functions. Microbiology. 2000;146(Pt 2):249-62.
32. Smith TJ, Foster SJ. Autolysins during sporulation of Bacillus subtilis 168. FEMS Microbiol Lett. 1997;157(1):141-7.
33. Wang Y, Chen Z, Zhao R, Jin T, Zhang X, Chen X. Deleting multiple lytic genes enhances biomass yield and production of recombinant proteins by Bacillus subtilis. Microb Cell Fact. 2014;13:129.
34. Higgins D, Dworkin J. Recent progress in Bacillus subtilis sporulation. FEMS Microbiol Rev. 2012;36:131-48.
35. Naclerio G, Baccigalupi L, Zilhao R, Felice MD, Ricca E. Bacillus subtilis spore coat assembly requires cotH gene expression. J Bacteriol. 1996;178:4375-80.
36. Chen Y, Ray WK, Helm RF, Melville SB, Popham DL. Levels of germination proteins in Bacillus subtilis dormant, superdormant, and germinating spores. PLoS One. 2014;9:e95781.
37. Bott KF, Wilson GA. Metabolic and nutritional factors influencing the development of competence for transfection of Bacillus subtilis. Bacteriol Rev. 1968;32:370-8.
38. Vojcic L, Despotovic D, Martinez R, Maurer KH, Schwaneberg U. An efficient transformation method for Bacillus subtilis DB104. Appl Microbiol Biotechnol. 2012;94:487-93.
39. Hamoen LW. Controlling competence in Bacillus subtilis: shared use of regulators. Microbiology. 2003;149:9-17.
40. Sauer U, Hatzimanikatis V, Hohmann HP, Manneberg M, van Loon AP, Bailey JE. Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis. Appl Environ Microbiol. 1996;62:3687-96.
41. Vickers CE, Blank LM, Kromer JO. Chassis cells for industrial biochemical production. Nat Chem Biol. 2010;6:875-7.
42. Tannler S, Decasper S, Sauer U. Maintenance metabolism and carbon fluxes in Bacillus species. Microb Cell Fact. 2008;7:19.
43. Mitsuya H, Weinhold KJ, Furman PA. St Clair MH, Lehrman SN, Gallo RC, Bolognesi D, Barry DW, Broder S: 3'-Azido-3'-deoxythymidine (BW A509U): an antiviral agent that inhibits the infectivity and cytopathic effect of human T-lymphotropic virus type III/lymphadenopathy-associated virus in vitro. Proc Natl Acad Sci U S A. 1985;82:7096-100.
44. Lee HC, Kim JH, Kim JS, Jang W, Kim SY. Fermentative production of thymidine by a metabolically engineered Escherichia coli strain. Appl Environ Microbiol. 2009;75:2423-32.
45. Shi T, Wang G, Wang Z, Fu J, Chen T, Zhao X. Establishment of a markerless mutation delivery system in Bacillus subtilis stimulated by a double-strand break in the chromosome. PLoS One. 2013;8:e81370.
46. Harwood CR, Cutting SM. Molecular biological methods for Bacillus. England: Wiley; 1990.
47. Shi T, Wang Y, Wang Z, Wang G, Liu D, Fu J, Chen T, Zhao X. Deregulation of purine pathway in Bacillus subtilis and its use in riboflavin biosynthesis. Microb Cell Fact. 2014;13:101.
48. Fabret C, Ehrlich SD, Noirot P. A new mutation delivery system for genome-scale approaches in Bacillus subtilis. Mol Microbiol. 2002;46:25-36.
49. Feng D, Li M, Zhu S, Zhou W, Huang J, Feng D. Study on sucrose-glucose bifunction assay of biosensor analyzer. Food Science. 2002;23:117-21.
50. Magaña AA, Wrobel K, Caudillo YA, Zaina S, Lund G, Wrobel K. High-performance liquid chromatography determination of 5-methyl-2'-deoxycytidine, 2'-deoxycytidine, and other deoxynucleosides and nucleosides in DNA digests. Anal Biochem. 2008;374:378-85.