Metabolic engineering of Thermoanaerobacterium saccharolyticum for n-butanol production

Metabolic Engineering

Volumn 21, Issue , 2014, Pages 17-25

  Bhandiwad, Ashwini ^a   Shaw, A Joe ^b,d   Guss, Adam ^a,e   Guseva, Anna ^a   Bahl, Hubert ^c   Lynd, Lee R ^a,b  

^a DARTMOUTH COLLEGE   (United States)

^b Mascoma Corporation   (United States)

^c UNIVERSITY OF ROSTOCK   (Germany)

^d Novogy Inc   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

Author keywords

Biofuels; Metabolic engineering; N Butanol; Thermophiles

Indexed keywords

BIOFUELS; GENE EXPRESSION;

ENZYMATIC ACTIVITIES; N-BUTANOL; THERMOANAEROBACTERIUM; THERMOPHILES; WILD-TYPE STRAIN;

METABOLIC ENGINEERING;

ACETIC ACID; ACETYL COENZYME A ACETYLTRANSFERASE; BUTANOL; BUTANOL DEHYDROGENASE; BUTYRALDEHYDE DEHYDROGENASE; BUTYRYL COENZYME A DEHYDROGENASE; ENOYL COENZYME A HYDRATASE; LACTIC ACID; OXIDOREDUCTASE; UNCLASSIFIED DRUG; XYLOSE;

ARTICLE; BACTERIAL GROWTH; BACTERIAL STRAIN; CARBON BALANCE; CONTROLLED STUDY; ENZYME ACTIVITY; GENE CLUSTER; GENE EXPRESSION; HIGH PERFORMANCE LIQUID CHROMATOGRAPHY; HUMAN; METABOLIC ENGINEERING; PRIORITY JOURNAL; PROMOTER REGION; THERMOANAEROBACTERIUM; THERMOANAEROBACTERIUM SACCHAROLYTICUM; WILD TYPE;

THERMOANAEROBACTERIUM SACCHAROLYTICUM;

BIOFUELS; METABOLIC ENGINEERING; N-BUTANOL; THERMOPHILES;

1-BUTANOL; METABOLIC ENGINEERING; THERMOANAEROBACTERIUM;

EID: 84888097068     PISSN: 10967176     EISSN: 10967184     Source Type: Journal    
DOI: 10.1016/j.ymben.2013.10.012     Document Type: Article

References (51)

1. Atsumi S., Cann A.F., Connor M.R., Shen C.R., Smith K.M., Brynildsen M.P., Chou K.J., Hanai T., Liao J.C. Metabolic engineering of Escherichia coli for 1-butanol production. Metab. Eng. 2008, 10:305-311.
2. Barnard D., Casanueva A., Tuffin M., Cowan D. Extremophiles in biofuel synthesis. Environ. Technol. 2010, 31:871-888.
3. Berezina O.V., Zakharova N.V., Brandt A., Yarotsky S.V., Schwarz W.H., Zverlov V.V. Reconstructing the clostridial n-butanol metabolic pathway in Lactobacillus brevis. Appl. Microbiol. Biotechnol. 2010, 87:635-646.
4. Bond-Watts B.B., Bellerose R.J., Chang M.C. Enzyme mechanism as a kinetic control element for designing synthetic biofuel pathways. Nat. Chem. Biol. 2011, 7:222-227.
5. Boynton Z.L., Bennet G.N., Rudolph F.B. Cloning, sequencing, and expression of clustered genes encoding beta-hydroxybutyryl-coenzyme A (CoA) dehydrogenase, crotonase, and butyryl-CoA dehydrogenase from Clostridium acetobutylicum ATCC 824. J. Bacteriol. 1996, 178:3015-3024.
6. Buckel, W., Thauer, R. K., 2012. Energy conservation via electron bifurcating ferredoxin reduction and proton/Na(+) translocating ferredoxin oxidation. Biochim. Biophys. Acta.
7. Currie D.H., Herring C.D., Guss A.M., Olson D.G., Hogsett D.A., Lynd L.R. Functional heterologous expression of an engineered full length CipA from Clostridium thermocellum in Thermoanaerobacterium saccharolyticum. Biotechnol. Biofuels 2013, 6:32.
8. Demain A.L., Newcomb M., Wu J.H. Cellulase, clostridia, and ethanol. Microbiol. Mol. Biol. Rev.: MMBR 2005, 69:124-154.
9. Dong H., Tao W., Dai Z., Yang L., Gong F., Zhang Y., Li Y. Biobutanol. Adv. Biochem. Eng./Biotechnol. 2012, 128:85-100.
10. Dürre P. Fermentative butanol production: bulk chemical and biofuel. Ann. N.Y. Acad. Sci. 2008, 1125:353-362.
11. Dürre P., Kuhn A., Gottwald M., Gottschalk G. Enzymatic investigations on butanol dehydrogenase and butyraldehyde dehydrogenase in extracts of Clostridium acetobutylicum. Appl. Microbiol. Biotechnol. 1987, 26:268-272.
12. Fischer R.J., Helms J., Durre P. Cloning, sequencing, and molecular analysis of the sol operon of Clostridium acetobutylicum, a chromosomal locus involved in solventogenesis. J. Bacteriol. 1993, 175:6959-6969.
13. Freierschroder D., Wiegel J., Gottschalk G. Butanol formation by Clostridium thermosaccharolyticum at neutral Ph. Biotechnol. Lett. 1989, 11:831-836.
14. Gheshlaghi R., Scharer J.M., Moo-Young M., Chou C.P. Metabolic pathways of clostridia for producing butanol. Biotechnol. Adv. 2009, 27:764-781.
15. Gibson D.G., Young L., Chuang R.Y., Venter J.C., Hutchison C.A., Smith H.O. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 2009, 6:343-345.
16. Grayson M. Biofuels. Nature 2011, 474:S1.
17. Hartmanis M.G., Gatenbeck S. Intermediary metabolism in Clostridium acetobutylicum: levels of enzymes involved in the formation of acetate and butyrate. Appl. Environ. Microbiol. 1984, 47:1277-1283.
18. Hemme C.L., Mouttaki H., Lee Y.J., Zhang G., Goodwin L., Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., Saunders E., Brettin T., Detter J.C., Han C.S., Pitluck S., Land M.L., Hauser L.J., Kyrpides N., Mikhailova N., He Z., Wu L., Van Nostrand J.D., Henrissat B., He Q., Lawson P.A., Tanner R.S., Lynd L.R., Wiegel J., Fields M.W., Arkin A.P., Schadt C.W., Stevenson B.S., McInerney M.J., Yang Y., Dong H., Xing D., Ren N., Wang A., Huhnke R.L., Mielenz J.R., Ding S.Y., Himmel M.E., Taghavi S., van der Lelie D., Rubin E.M., Zhou J. Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J. Bacteriol. 2010, 192:6494-6496.
19. Hill P.W., Klapatch T.R., Lynd L.R. Bioenergetics and end-product regulation of Clostridium thermosaccharolyticum in response to nutrient limitation. Biotechnol. Bioeng. 1993, 42:873-883.
20. Hino T., Miyazaki K., Kuroda S. Role of extracellular acetate in the fermentation of glucose by a ruminal bacterium, Megasphaera elsdenii. J. Gen. Appl. Microbiol. 1991, 37:121-129.
21. Inui M., Suda M., Kimura S., Yasuda K., Suzuki H., Toda H., Yamamoto S., Okino S., Suzuki N., Yukawa H. Expression of Clostridium acetobutylicum butanol synthetic genes in Escherichia coli. Appl. Microbiol. Biotechnol. 2008, 77:1305-1316.
22. Jones D.T., Woods D.R. Acetone-butanol fermentation revisited. Microbiol. Rev. 1986, 50:484-524.
23. Lehmann D., Honicke D., Ehrenreich A., Schmidt M., Weuster-Botz D., Bahl H., Lutke-Eversloh T. Modifying the product pattern of Clostridium acetobutylicum: physiological effects of disrupting the acetate and acetone formation pathways. Appl. Microbiol. Biotechnol. 2012, 94:743-754.
24. Li F., Hinderberger J., Seedorf H., Zhang J., Buckel W., Thauer R.K. Coupled ferredoxin and crotonyl coenzyme A (CoA) reduction with NADH catalyzed by the butyryl-CoA dehydrogenase/Etf complex from Clostridium kluyveri. J. Bacteriol. 2008, 190:843-850.
25. Lynd L.R., Laser M.S., Bransby D., Dale B.E., Davison B., Hamilton R., Himmel M., Keller M., McMillan J.D., Sheehan J., Wyman C.E. How biotech can transform biofuels. Nat. Biotechnol. 2008, 26:169-172.
26. Lynd L.R., van Zyl W.H., McBride J.E., Laser M. Consolidated bioprocessing of cellulosic biomass: an update. Curr. Opin. Biotechnol. 2005, 16:577-583.
27. Mai V., Lorenz W.W., Wiegel J. Transformation of Thermoanaerobacterium sp. strain JW/SL-YS485 with plasmid pIKM1 conferring kanamycin resistance. FEMS Microbiol. Lett. 1997, 148:163-167.
28. Mistry F.R., Cooney C.L. Production of ethanol by Clostridium thermosaccharolyticum: II. A quantitative model describing product distributions. Biotechnol. Bioeng. 1989, 34:1305-1320.
29. Moat A.G., Foster J.W., Spector M.P. Microbial Physiology 2002, Wiley InterScience (Online Service), Wiley-Liss, New York, (pp. xx, 714 p. ill. 26cm).
30. Müller V., Imkamp F., Biegel E., Schmidt S., Dilling S. Discovery of a ferredoxin:NAD+-oxidoreductase (Rnf) in Acetobacterium woodii: a novel potential coupling site in acetogens. Ann. N.Y. Acad. Sci. 2008, 1125:137-146.
31. Nielsen D.R., Leonard E., Yoon S.H., Tseng H.C., Yuan C., Prather K.L. Engineering alternative butanol production platforms in heterologous bacteria. Metab. Eng. 2009, 11:262-273.
32. Nölling J., Breton G., Omelchenko M.V., Makarova K.S., Zeng Q., Gibson R., Lee H.M., Dubois J., Qiu D., Hitti J., Wolf Y.I., Tatusov R.L., Sabathe F., Doucette-Stamm L., Soucaille P., Daly M.J., Bennett G.N., Koonin E.V., Smith D.R. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J. Bacteriol. 2001, 183:4823-4838.
33. Olson D.G., McBride J.E., Shaw A.J., Lynd L.R. Recent progress in consolidated bioprocessing. Curr. Opin. Biotechnol. 2012, 23:396-405.
34. Papoutsakis, E.T., 2000. Equations and calculations for fermentations of butyric acid bacteria. Reprinted from Biotechnol. Bioeng. XXVI, 174-187 (1984). Biotechnol. Bioeng. 67, 813-826.
35. Petersen D.J., Bennett G.N. Cloning of the Clostridium acetobutylicum ATCC 824 acetyl coenzyme A acetyltransferase (thiolase; EC 2.3.1.9) gene. Appl. Environ. Microbiol. 1991, 57:2735-2741.
36. Shanks R.M., Caiazza N.C., Hinsa S.M., Toutain C.M., O'Toole G.A. Saccharomyces cerevisiae-based molecular tool kit for manipulation of genes from gram-negative bacteria. Appl. Environ. Microbiol. 2006, 72:5027-5036.
37. Shao W., Deblois S., Wiegel J. A high-molecular-weight, cell-associated xylanase isolated from exponentially growing Thermoanaerobacterium sp. strain JW/SL-YS485. Appl. Environ. Microbiol. 1995, 61:937-940.
38. Shaw A., Covalla S.F., Miller B.B., Firliet B.T., Hogsett D.A., Herring C.D. Urease expression in a Thermoanaerobacterium saccharolyticum ethanologen allows high titer ethanol production. Metab. Eng. 2012, 14:528-532.
39. Shaw A.J., Covalla S.F., Hogsett D.A., Herring C.D. Marker removal system for Thermoanaerobacterium saccharolyticum and development of a markerless ethanologen. Appl. Environ. Microbiol. 2011, 77:2534-2536.
40. Shaw A.J., Hogsett D.A., Lynd L.R. Identification of the [FeFe]-hydrogenase responsible for hydrogen generation in Thermoanaerobacterium saccharolyticum and demonstration of increased ethanol yield via hydrogenase knockout. J. Bacteriol. 2009, 191:6457-6464.
41. Shaw A.J., Hogsett D.A., Lynd L.R. Natural competence in Thermoanaerobacter and Thermoanaerobacterium species. Appl. Environ. Microbiol. 2010, 76:4713-4719.
42. Shaw A.J., Jenney F.E., Adams M.W.W., Lynd L.R. End-product pathways in the xylose fermenting bacterium, Thermoanaerobacterium saccharolyticum. Enzyme Microb. Tech. 2008, 42:453-458.
43. Shaw A.J., Podkaminer K.K., Desai S.G., Bardsley J.S., Rogers S.R., Thorne P.G., Hogsett D.A., Lynd L.R. Metabolic engineering of a thermophilic bacterium to produce ethanol at high yield. Proc. Natl. Acad. Sci. USA 2008, 105:13769-13774.
44. Shen C.R., Lan E.I., Dekishima Y., Baez A., Cho K.M., Liao J.C. Driving forces enable high-titer anaerobic 1-butanol synthesis in Escherichia coli. Appl. Environ. Microbiol. 2011, 77:2905-2915.
45. Sillers R., Al-Hinai M.A., Papoutsakis E.T. Aldehyde-alcohol dehydrogenase and/or thiolase overexpression coupled with CoA transferase downregulation lead to higher alcohol titers and selectivity in Clostridium acetobutylicum fermentations. Biotechnol. Bioeng. 2009, 102:38-49.
46. Smith W.K., Cleveland C.C., Reed S.C., Miller N.L., Running S.W Bioenergy potential of the United States constrained by satellite observations of existing productivity. Environ. Sci. Technol. 2012, 46:3536-3544.
47. Steen E.J., Chan R., Prasad N., Myers S., Petzold C.J., Redding A., Ouellet M., Keasling J.D. Metabolic engineering of Saccharomyces cerevisiae for the production of n-butanol. Microb. Cell Fact. 2008, 7:36.
48. Stim-Herndon K.P., Petersen D.J., Bennett G.N. Characterization of an acetyl-CoA C-acetyltransferase (thiolase) gene from Clostridium acetobutylicum ATCC 824. Gene 1995, 154:81-85.
49. Thauer R.K., Jungermann K., Decker K. Energy conservation in chemotrophic anaerobic bacteria. Bacteriol. Rev. 1977, 41:100-180.
50. Wang S., Huang H., Moll J., Thauer R.K. NADP+ reduction with reduced ferredoxin and NADP+ reduction with NADH are coupled via an electron-bifurcating enzyme complex in Clostridium kluyveri. J. Bacteriol. 2010, 192:5115-5123.
51. Zeikus J.G. Thermophilic bacteria - ecology, physiology and technology. Enzyme Microb. Tech. 1979, 1:243-252.