Rational improvement of the engineered isobutanol-producing Bacillus subtilis by elementary mode analysis

Microbial Cell Factories

Volumn 11, Issue , 2012, Pages

  Li, Shanshan ^a   Huang, Di ^a   Li, Yong ^a   Wen, Jianping ^a,b   Jia, Xiaoqiang ^a,b  

^a TIANJIN UNIVERSITY   (China)

^b BEIJING UNIVERSITY OF POSTS AND TELECOMMUNICATIONS   (China)

Author keywords

Bacillus subtilis; Elementary mode analysis; Isobutanol; Metabolic network; Rational strain improvement; Target prediction

Indexed keywords

ISOBUTANOL; LACTATE DEHYDROGENASE; PYRUVATE DEHYDROGENASE COMPLEX;

ANALYSIS; ARTICLE; BACILLUS SUBTILIS; BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOSYNTHESIS; ELEMENTARY MODE ANALYSIS; NONHUMAN; SIMULATION;

BACILLUS SUBTILIS; BACTERIAL PROTEINS; BUTANOLS; L-LACTATE DEHYDROGENASE; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS; PYRUVATE DEHYDROGENASE COMPLEX;

BACILLUS SUBTILIS;

EID: 84864516296     PISSN: None     EISSN: 14752859     Source Type: Journal    
DOI: 10.1186/1475-2859-11-101     Document Type: Article

References (50)

1. Dellomonaco C, Fava F, Gonzalez R. The path to next generation biofuels: successes and challenges in the era of synthetic biology. Microb Cell Fact 2010, 9:3. 10.1186/1475-2859-9-3, 2817670, 20089184.
2. Atsumi S, Hanai T, Liao JC. Non-fermentative pathways for synthesis of branched-chain higher alcohols as biofuels. Nature 2008, 451:86-U13. 10.1038/nature06450, 18172501.
3. Fava F, Ohtake H, Pesaresi P. Biotechnology for a more sustainable environment decontamination and energy production. J Biotechnol 2012, 157:443-445. 10.1016/j.jbiotec.2012.01.029, 22370451.
4. Blombach B, Riester T, Wieschalka S, Ziert C, Youn JW, Wendisch VF, Eikmanns BJ. Corynebacterium glutamicum tailored for efficient isobutanol production. Appl Environ Microbiol 2011, 77:3300-3310. 10.1128/AEM.02972-10, 3126470, 21441331.
5. Smith KM, Cho KM, Liao JC. Engineering Corynebacterium glutamicum for isobutanol production. Appl Microbiol Biotechnol 2010, 87:1045-1055. 10.1007/s00253-010-2522-6, 2886118, 20376637.
6. Li SS, Wen JP, Jia XQ. Engineering Bacillus subtilis for isobutanol production by heterologous Ehrlich pathway construction and the biosynthetic 2-ketoisovalerate precursor pathway overexpression. Appl Microbiol Biotechnol 2011, 91:577-589. 10.1007/s00253-011-3280-9, 21533914.
7. Higashide W, Li YC, Yang YF, Liao JC. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl Environ Microbiol 2011, 77:2727-2733. 10.1128/AEM.02454-10, 3126361, 21378054.
8. Chen X, Nielsen KF, Borodina I, Kielland-Brandt MC, Karhumaa K. Increased isobutanol production in Saccharomyces cerevisiae by overexpression of genes in valine metabolism. Biotechnol Biofuels 2011, 4:21. 10.1186/1754-6834-4-21, 3162486, 21798060.
9. Stülke J, Hillen W. Regulation of carbon catabolism in Bacillus species. Annu Rev Microbiol 2000, 54:849-880. 10.1146/annurev.micro.54.1.849, 11018147.
10. Atsumi S, Wu TY, Eckl EM, Hawkins SD, Buelter T, Liao JC. Engineering the isobutanol biosynthetic pathway in Escherichia coli by comparison of three aldehyde reductase/alcohol dehydrogenase genes. Appl Microbiol Biotechnol 2010, 85:651-657. 10.1007/s00253-009-2085-6, 2802489, 19609521.
11. Bastian S, Liu X, Meyerowitz JT, Snow CD, Chen MMY, Arnold FH. Engineered ketol-acid reductoisomerase and alcohol dehydrogenase enable anaerobic 2-methylpropan-1-ol production at theoretical yield in Escherichia coli. Metab Eng 2011, 13:345-352. 10.1016/j.ymben.2011.02.004, 21515217.
12. Cassman M, Arkin A, Doyle F, Katagiri F, Lauffenburger D, Stokes C. Systems Biology 2007, Springer Verlag: International Research and Development.
13. Becker J, Zelder O, Häfner S, Schröder H, Wittmann C. From zero to hero-Design-based systems metabolic engineering of Corynebacterium glutamicum for L-lysine production. Metab Eng 2011, 13:159-168. 10.1016/j.ymben.2011.01.003, 21241816.
14. Park JH, Lee KH, Kim TY, Lee SY. Metabolic engineering of Escherichia coli for the production of L-valine based on transcriptome analysis and in silico gene knockout simulation. P Natl Acad Sci USA 2007, 104:7797-7802.
15. Unrean P. Trinh CT. Srienc F: Rational design and construction of an efficient E. coli for production of diapolycopendioic acid. Metab Eng 2010, 12:112-122.
16. Brochado AR, Matos C, Møller BL, Hansen J, Mortensen UH, Patil KR. Improved vanillin production in baker's yeast through in silico design. Microb Cell Fact 2010, 9:84. 10.1186/1475-2859-9-84, 2992047, 21059201.
17. Asadollahi MA, Maury J, Patil KR, Schalk M, Clark A, Nielsen J. Enhancing sesquiterpene production in Saccharomyces cerevisiae through in silico driven metabolic engineering. Metab Eng 2009, 11:328-334. 10.1016/j.ymben.2009.07.001, 19619667.
18. Ruppin E, Papin JA, de Figueiredo LF, Schuster S. Metabolic reconstruction, constraint-based analysis and game theory to probe genome-scale metabolic networks. Curr Opin Biotechnol 2010, 21:502-510. 10.1016/j.copbio.2010.07.002, 20692823.
19. Schuster S, Fell DA, Dandekar T. A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 2000, 18:326-332. 10.1038/73786, 10700151.
20. Trinh CT, Wlaschin A, Srienc F. Elementary mode analysis: a useful metabolic pathway analysis tool for characterizing cellular metabolism. Appl Microbiol Biotechnol 2009, 81:813-826. 10.1007/s00253-008-1770-1, 2909134, 19015845.
21. Driouch H, Melzer G, Wittmann C. Integration of in vivo and in silico metabolic fluxes for improvement of recombinant protein production. Metab Eng 2012, 14:47-58. 10.1016/j.ymben.2011.11.002, 22115737.
22. Melzer G, Esfandabadi ME, Franco-Lara E, Wittmann C. Flux Design: In silico design of cell factories based on correlation of pathway fluxes to desired properties. BMC Syst Biol 2009, 3:120. 10.1186/1752-0509-3-120, 2808316, 20035624.
23. Trinh CT, Li J, Blanch HW, Clark DS. Redesigning Escherichia coli metabolism for anaerobic production of isobutanol. Appl Environ Microbiol 2011, 77:4894-4904. 10.1128/AEM.00382-11, 3147371, 21642415.
24. Matsuda F, Furusawa C, Kondo T, Ishii J, Shimizu H, Kondo A. Engineering strategy of yeast metabolism for higher alcohol production. Microb Cell Fact 2011, 10:70. 10.1186/1475-2859-10-70, 3184262, 21902829.
25. Sauer U, Hatzimanikatis V, Hohmann HPGM, Manneberg M, van Loon AP, Bailey JE. Physiology and metabolic fluxes of wild-type and riboflavin-producing Bacillus subtilis. Appl Environ Microbiol 1996, 62:3687-3696. 168177, 8837424.
26. Gao HC, Jiang X, Pogliano K, Aronson AI. The E1 beta and E2 subunits of the Bacillus subtilis pyruvate dehydrogenase complex are involved in regulation of sporulation. J Bacteriol 2002, 184:2780-2788. 10.1128/JB.184.10.2780-2788.2002, 135025, 11976308.
27. Segrè D, Vitkup D, Church GM. Analysis of optimality in natural and perturbed metabolic networks. P Natl Acad Sci USA 2002, 99:15112-15117.
28. Patil KR, Rocha I, Förster J, Nielsen J. Evolutionary programming as a platform for in silico metabolic engineering. BMC Bioinformatics 2005, 6:308. 10.1186/1471-2105-6-308, 1327682, 16375763.
29. Nakano MM, Zuber P. Anaerobic growth of a "strict aerobe" (Bacillus subtilis). Annu Rev Microbiol 1998, 52:165-190. 10.1146/annurev.micro.52.1.165, 9891797.
30. Choi HS, Lee SY, Kim TY, Woo HM. In Silico Identification of Gene Amplification Targets for Improvement of Lycopene Production. Appl Environ Microbiol 2010, 76:3097-3105. 10.1128/AEM.00115-10, 2869140, 20348305.
31. Garvie EI. Bacterial lactate dehydrogenases. Microbiol Mol Biol Rev 1980, 44:106-139.
32. Hodgson JA, Lowe PN, Perham RN. Wild-type and mutant forms of the pyruvate dehydrogenase multienzyme complex from Bacillus subtilis. Biochem J 1983, 211:463-472. 1154380, 6409095.
33. Atsumi S, Li Z, Liao JC. Acetolactate synthase from Bacillus subtilis serves as a 2-ketoisovalerate decarboxylase for isobutanol biosynthesis in Escherichia coli. Appl Environ Microbiol 2009, 75:6306-6311. 10.1128/AEM.01160-09, 2753059, 19684168.
34. Romero S, Merino E, Bolívar F, Gosset G, Martinez A. Metabolic engineering of Bacillus subtilis for ethanol production: lactate dehydrogenase plays a key role in fermentative metabolism. Appl Environ Microbiol 2007, 73:5190-5198. 10.1128/AEM.00625-07, 1950962, 17586670.
35. Jian J, Zhang SQ, Shi ZY, Wang W, Chen GQ, Wu QO. Production of polyhydroxyalkanoates by Escherichia coli mutants with defected mixed acid fermentation pathways. Appl Microbiol Biotechnol 2010, 87:2247-2256. 10.1007/s00253-010-2706-0, 20535465.
36. Petersohn A, Antelmann H, Gerth U, Hecker M. Identification and transcriptional analysis of new members of the σB regulon in Bacillus subtilis. Microbiology 1999, 145:869-880. 10.1099/13500872-145-4-869, 10220166.
37. Medema MH, Breitling R, Bovenberg R, Takano E. Exploiting plug-and-play synthetic biology for drug discovery and production in microorganisms. Nat Rev Microbiol 2011, 9:131-137. 10.1038/nrmicro2478, 21189477.
38. Liu S, Zhang DX, Wang M, Cui WJ, Chen KK, Du GC, Chen J, Zhou ZM. The order of expression is a key factor in the production of active transglutaminase in Escherichia coli by co-expression with its pro-peptide. Microb Cell Fact 2011, 10:112. 10.1186/1475-2859-10-112, 3286405, 22196373.
39. Oh YK, Palsson BO, Park SM, Schilling CH, Mahadevan R. Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data. J Biol Chem 2007, 282:28791-28799. 10.1074/jbc.M703759200, 17573341.
40. Sauer U, Bailey JE. Estimation of P-to-O ratio in Bacillus subtilis and its influence on maximum riboflavin yield. Biotechnol Bioeng 1999, 64:750-754. 10.1002/(SICI)1097-0290(19990920)64:6<750::AID-BIT15>3.0.CO;2-S, 10417225.
41. Dauner M, Sauer U. Stoichiometric growth model for riboflavin-producing Bacillus subtilis. Biotechnol Bioeng 2001, 76:132-143. 10.1002/bit.1153, 11505383.
42. Pfeiffer T, Sánchez-Valdenebro I, Nuño JC, Montero F, Schuster S. METATOOL: for studying metabolic networks. Bioinformatics 1999, 15:251-257. 10.1093/bioinformatics/15.3.251, 10222413.
43. Sambrook J. Russel DW: Molecular cloning: a laboratory manual 2001, Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press, 3.
44. Anagnostopoulos C, Spizizen J. Requirements for transformation in Bacillus subtilis. J Bacteriol 1961, 81:741-746. 279084, 16561900.
45. Savijoki K, Palva A. Molecular genetic characterization of the L-lactate dehydrogenase gene (ldhL) of Lactobacillus helveticus and biochemical characterization of the enzyme. Appl Environ Microbiol 1997, 63:2850-2856. 168581, 9212432.
46. Murarka A, Clomburg JM, Moran S, Shanks JV, Gonzalez R. Metabolic analysis of wild-type Escherichia coli and a pyruvate dehydrogenase complex (PDHC)-deficient derivative reveals the role of PDHC in the fermentative metabolism of glucose. J Biol Chem 2010, 285:31548-31558. 10.1074/jbc.M110.121095, 2951229, 20667837.
47. Bradford MM. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal Chem 1976, 72:248-254.
48. Bolten CJ, Kiefer P, Letisse F, Portais JC, Wittmann C. Sampling for metabolome analysis of microorganisms. Anal Chem 2007, 79:3843-3849. 10.1021/ac0623888, 17411014.
49. Wang ZW, Chen T, Ma XH, Shen Z, Zhao XM. Enhancement of riboflavin production with Bacillus subtilis by expression and site-directed mutagenesis of zwf and gnd gene from Corynebacterium glutamicum. Bioresour Technol 2011, 102:3934-3940. 10.1016/j.biortech.2010.11.120, 21194928.
50. Yuan G, Wong SL. Regulation of groE expression in Bacillus subtilis the involvement of the σA-like promoter and the roles of the inverted repeat sequence (CIRCE). J Bacteriol 1995, 177:5427-5433. 177347, 7559325.