Clostridia: The importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications

Current Opinion in Biotechnology

Volumn 23, Issue 3, 2012, Pages 364-381

  Tracy, Bryan P ^b   Jones, Shawn W ^a   Fast, Alan G ^a   Indurthi, Dinesh C ^a   Papoutsakis, Eleftherios T ^a  

^a University of Delaware   (United States)

^b Elcriton Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOPROCESSING; BIOREFINERIES; BROAD SPECTRUM; COMPLEX CARBOHYDRATES; COMPLEX PHENOTYPE; FIRMICUTES; GENOMIC TOOLS; LARGE ARRAYS; MODULAR DESIGNS; TOXIC CHEMICALS;

CARBOHYDRATES; CARBON DIOXIDE; CELLULOSE; METABOLITES; REFINING;

BIOFUELS;

1,3 PROPANEDIOL; 2,3 BUTANEDIOL; ACETIC ACID; ACETOIN; ACETONE; ACRYLIC ACID; ALCOHOL; BIOFUEL; BUTANOL; BUTYRIC ACID; CARBON DIOXIDE; CARBON MONOXIDE; CELLULOSE; GLUCOSE; HEMICELLULOSE; HEXANOIC ACID; HEXANOL; HEXOSE; HYDROGEN; LACTIC ACID; OCTANOIC ACID; PROPANOL; PROPIONIC ACID; SUCCINIC ACID; XYLOSE;

BACTERIAL METABOLISM; BACTERIAL STRAIN; BIOFUEL PRODUCTION; CARBON FIXATION; CATABOLITE REPRESSION; CLOSTRIDIA; CLOSTRIDIUM; CLOSTRIDIUM ACETOBUTYLICUM; CLOSTRIDIUM BEIJERINCKII; CLOSTRIDIUM BUTYRICUM; CLOSTRIDIUM CELLULOLYTICUM; CLOSTRIDIUM KLUYVERI; CLOSTRIDIUM PROPIONICUM; CLOSTRIDIUM THERMOCELLUM; FERMENTATION; GENETIC ENGINEERING; GENETIC MANIPULATION; GLYCOLYSIS; METABOLIC ENGINEERING; METABOLITE; MOORELLA THERMOACETICA; MOORELLA THERMOAUTOTROPHICA; NONHUMAN; PENTOSE PHOSPHATE CYCLE; PRIORITY JOURNAL; REVIEW; SPOROGENESIS;

BIOFUELS; CELLULOSE; CLOSTRIDIUM; METABOLIC ENGINEERING; METABOLIC NETWORKS AND PATHWAYS;

BIODIVERSITY; CARBOHYDRATES; CARBON DIOXIDE; CELLULOSE; FUELS; METABOLISM; REFINING;

CLOSTRIDIA; FIRMICUTES;

EID: 84862010951     PISSN: 09581669     EISSN: 18790429     Source Type: Journal    
DOI: 10.1016/j.copbio.2011.10.008     Document Type: Review

References (160)

1. National Academy of Sciences (U.S.), National Academy of Engineering, National Academies Press (U.S.), National Research Council (U.S.). Panel on Alternative Liquid Transportation Fuels: Liquid Transportation Fuels from Coal and Biomass: Technological Status, Costs, and Environmental Impacts. National Academies Press; 2009.
2. Berezina O.V., Brandt A., Yarotsky S., Schwarz W.H., Zverlov V.V. Isolation of a new butanol-producing Clostridium strain: high level of hemicellulosic activity and structure of solventogenesis genes of a new Clostridium saccharobutylicum isolate. Syst Appl Microbiol 2009, 32:449-459.
3. Bramono S.E., Lam Y.S., Ong S.L., He J. A mesophilic Clostridium species that produces butanol from monosaccharides and hydrogen from polysaccharides. Bioresour Technol 2011, 102:9558-9563.
4. Jiang L., Wang J., Liang S., Wang X., Cen P., Xu Z. Butyric acid fermentation in a fibrous bed bioreactor with immobilized Clostridium tyrobutyricum from cane molasses. Bioresour Technol 2009, 100:3403-3409.
5. Jones D.T., Woods D.R. Acetone-butanol fermentation revisited. Microbiol Rev 1986, 50:484-524.
6. Leschine S. Degradation of polymers: cellulose, xylan, pectin, starch. Handbook on Clostridia 2005, 101-131. CRC Press. P. Dürre (Ed.).
7. Wang X., Jin B. Process optimization of biological hydrogen production from molasses by a newly isolated Clostridium butyricum W5. J Biosci Bioeng 2009, 107:138-144.
8. Baba S.I., Tashiro Y., Shinto H., Sonomoto K. Development of high-speed and highly efficient butanol production systems from butyric acid with high density of living cells of Clostridium saccharoperbutylacetonicum. J Biotechnol 2011, 10/1016/j/jbiotec.2011.06.004.
9. Kim J., Shin S.G., Han G., O'Flaherty V., Lee C., Hwang S. Common key acidogen populations in anaerobic reactors treating different wastewaters: molecular identification and quantitative monitoring. Water Res 2011, 45:2539-2549.
10. Oshiro M., Hanada K., Tashiro Y., Sonomoto K. Efficient conversion of lactic acid to butanol with pH-stat continuous lactic acid and glucose feeding method by Clostridium saccharoperbutylacetonicum. Appl Microbiol Biotechnol 2010, 87:1177-1185.
11. Shin S.G., Lee S., Lee C., Hwang K., Hwang S. Qualitative and quantitative assessment of microbial community in batch anaerobic digestion of secondary sludge. Bioresour Technol 2010, 101:9461-9470.
12. Tang Y.Q., Ji P., Hayashi J., Koike Y., Wu X.L., Kida K. Characteristic microbial community of a dry thermophilic methanogenic digester: its long-term stability and change with feeding. Appl Microbiol Biotechnol 2011, 91:1447-1461.
13. Tashiro Y., Takeda K., Kobayashi G., Sonomoto K., Ishizaki A., Yoshino S. High butanol production by Clostridium saccharoperbutylacetonicum N1-4 in fed-batch culture with pH-stat continuous butyric acid and glucose feeding method. J Biosci Bioeng 2004, 98:263-268.
14. Tirado-Acevedo O., Chinn M.S., Grunden A.M. Production of biofuels from synthesis gas using microbial catalysts. Adv Appl Microbiol 2010, 70:57-92.
15. Bahl H., Gottwald M., Kuhn A., Rale V., Andersch W., Gottschalk G. Nutritional factors affecting the ratio of solvents produced by Clostridium acetobutylicum. Appl Environ Microbiol 1986, 52:169-172.
16. Ferchichi M., Crabbe E., Gil G.H., Hintz W., Almadidy A. Influence of initial pH on hydrogen production from cheese whey. J Biotechnol 2005, 120:402-409.
17. Chatzifragkou A., Papanikolaou S., Dietz D., Doulgeraki A.I., Nychas G.J., Zeng A.P. Production of 1,3-propanediol by Clostridium butyricum growing on biodiesel-derived crude glycerol through a non-sterilized fermentation process. Appl Microbiol Biotechnol 2011, 91:101-112.
18. Gungormusler M., Gonen C., Azbar N. Continuous production of 1,3-propanediol using raw glycerol with immobilized Clostridium beijerinckii NRRL B-593 in comparison to suspended culture. Bioprocess Biosyst Eng 2011, 34:727-733.
19. Gungormusler M., Gonen C., Ozdemir G., Azbar N. 1,3-Propanediol production potential of Clostridium saccharobutylicum NRRL B-643. New Biotechnol 2010, 27:782-788.
20. Nicolaou S.A., Gaida S.M., Papoutsakis E.T. A comparative view of metabolite and substrate stress and tolerance in microbial bioprocessing: from biofuels and chemicals, to biocatalysis and bioremediation. Metab Eng 2010, 12:307-331.
21. Kim J.H., Block D.E., Mills D.A. Simultaneous consumption of pentose and hexose sugars: an optimal microbial phenotype for efficient fermentation of lignocellulosic biomass. Appl Microbiol Biotechnol 2010, 88:1077-1085.
22. Paredes C.J., Alsaker K.V., Papoutsakis E.T. A comparative genomic view of clostridial sporulation and physiology. Nat Rev Microbiol 2005, 3:969-978.
23. Köpke M., Held C., Hujer S., Liesegang H., Wiezer A., Wollherr A., Ehrenreich A., Liebl W., Gottschalk G., Dürre P. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci USA 2010, 107:13087-13092.
24. Seedorf H., Fricke W.F., Veith B., Bruggemann H., Liesegang H., Strittimatter A., Miethke M., Buckel W., Hinderberger J., Li F.L., et al. The genome of Clostridium kluyveri, a strict anaerobe with unique metabolic features. Proc Natl Acad Sci USA 2008, 105:2128-2133.
25. Dorn M., Andreesen J.R., Gottschalk G. Fermentation of fumarate and L-malate by Clostridium formicoaceticum. J Bacteriol 1978, 133:26-32.
26. Köpke M., Mihalcea C., Liew F., Tizard J.H., Ali M.S., Conolly J.J., Al-Sinawi B., Simpson S.D. 2,3-butanediol production by acetogenic bacteria, an alternative route to chemical synthesis, using industrial waste gas. Appl Environ Microbiol 2011, 77:5467-5475.
27. Kridelbaugh D., Doerner K.C. Development of a defined medium for Clostridium scatologenes ATCC 25775. Lett Appl Microbiol 2009, 48:426-432.
28. Akedo M., Cooney C.L., Sinskey A.J. Direct demonstration of lactate-acrylate interconversion in Clostridium propionicum. Bio-Technology 1983, 1:791-794.
29. Dabrock B., Bahl H., Gottschalk G. Parameters affecting solvent production by Clostridium pasteurianum. Appl Environ Microbiol 1992, 58:1233-1239.
30. Forsberg C.W. Production of 1,3-propanediol from glycerol by Clostridium acetobutylicum and other Clostridium species. Appl Environ Microbiol 1987, 53:639-643.
31. George H.A., Johnson J.L., Moore W.E., Holdeman L.V., Chen J.S. Acetone, isopropanol, and butanol production by Clostridium beijerinckii (syn. Clostridium butylicum) and Clostridium aurantibutyricum. Appl Environ Microbiol 1983, 45:1160-1163.
32. Johns A.T. The mechanism of propionic acid formation by Clostridium propionicum. J Gen Microbiol 1952, 6:123-127.
33. Butel M.J., Rimbault A., Khelifa N., Campion G., Szylit O., Rocchiccioli F. Formation of 2-hydroxy-4-methylpentanoic acid from L-leucine by Clostridium butyricum. FEMS Microbiol Lett 1995, 132:171-176.
34. Elsden S.R., Hilton M.G., Waller J.M. End products of metabolism of aromatic amino-acids by clostridia. Arch Microbiol 1976, 107:283-288.
35. Anaerobe Laboratory Manual 1977, L.V. Holdeman, E.P. Cato, W.E.C. Moore (Eds.).
36. Wagner E., Meyer K.F., Dozier C.C. Studies on the metabolism of B. botulinus in various media. J Bacteriol 1925, 10:321-412.
37. Lincke T., Behnken S., Ishida K., Roth M., Hertweck C. Closthioamide: an unprecedented polythioamide antibiotic from the strictly anaerobic bacterium Clostridium cellulolyticum. Angew Chem Int Ed 2010, 49:2011-2013.
38. Drake H.L., Daniel S.L., Kusel K., Matthies C., Kuhner C., Braus-Stromeyer S. Acetogenic bacteria: what are the in situ consequences of their diverse metabolic versatilities?. Biofactors 1997, 6:13-24.
39. Drake H.L., Gossner A.S., Daniel S.L. Old acetogens, new light. Ann N Y Acad Sci 2008, 1125:100-128.
40. Esteve-Nunez A., Caballero A., Ramos J.L. Biological degradation of 2,4,6-trinitrotoluene. Microbiol Mol Biol Rev 2001, 65:335-352.
41. Kulkarni M., Chaudhari A. Microbial remediation of nitro-aromatic compounds: an overview. J Environ Manage 2007, 85:496-512.
42. Carmona M., Zamarro M.T., Blazquez B., Durante-Rodriguez G., Juarez J.F., Valderrama J.A., Barragan M.J., Garcia J.L., Diaz E. Anaerobic catabolism of aromatic compounds: a genetic and genomic view. Microbiol Mol Biol Rev 2009, 73:71-133.
43. Bhowmik A., Asahino A., Shiraki T., Nakamura K., Takamizawa K. In situ study of tetrachloroethylene bioremediation with different microbial community shifting. Environ Technol 2009, 30:1607-1614.
44. Martins M., Faleiro M.L., Chaves S., Tenreiro R., Santos E., Costa M.C. Anaerobic bio-removal of uranium (VI) and chromium (VI): comparison of microbial community structure. J Hazard Mater 2010, 176:1065-1072.
45. Francis A.J., Dodge C.J. Bioreduction of uranium(VI) complexed with citric acid by Clostridia affects its structure and solubility. Environ Sci Technol 2008, 42:8277-8282.
46. Bowman K.S., Dupre R.E., Rainey F.A., Moe W.M. Clostridium hydrogeniformans sp. nov. and Clostridium cavendishii sp. nov., hydrogen-producing bacteria from chlorinated solvent-contaminated groundwater. Int J Syst Evol Microbiol 2010, 60:358-363.
47. Bowman K.S., Rainey F.A., Moe W.M. Production of hydrogen by Clostridium species in the presence of chlorinated solvents. FEMS Microbiol Lett 2009, 290:188-194.
48. Ezeji T., Blaschek H.P. Fermentation of dried distillers' grains and solubles (DDGS) hydrolysates to solvents and value-added products by solventogenic clostridia. Bioresour Technol 2008, 99:5232-5242.
49. Mitchell W.J., Albasheri K.A., Yazdanian M. Factors affecting utilization of carbohydrates by clostridia. FEMS Microbiol Rev 1995, 17:317-329.
50. Fujita Y. Carbon catabolite control of the metabolic network in Bacillus subtilis. Biosci Biotechnol Biochem 2009, 73:245-259.
51. Ren C., Gu Y., Hu S., Wu Y., Wang P., Yang Y., Yang C., Yang S., Jiang W. Identification and inactivation of pleiotropic regulator CcpA to eliminate glucose repression of xylose utilization in Clostridium acetobutylicum. Metab Eng 2010, 12:446-454.
52. Tangney M., Galinier A., Deutscher J., Mitchell W.J. Analysis of the elements of catabolite repression in Clostridium acetobutylicum ATCC 824. J Mol Microbiol Biotechnol 2003, 6:6-11.
53. Gu Y., Li J., Zhang L., Chen J., Niu L., Yang Y., Yang S., Jiang W. Improvement of xylose utilization in Clostridium acetobutylicum via expression of the talA gene encoding transaldolase from Escherichia coli. J Biotechnol 2009, 143:284-287.
54. Qureshi N., Li X.L., Hughes S., Saha B.C., Cotta M.A. Butanol production from corn fiber xylan using Clostridium acetobutylicum. Biotechnol Prog 2006, 22:673-680.
55. Qureshi N., Saha B.C., Cotta M.A. Butanol production from wheat straw hydrolysate using Clostridium beijerinckii. Bioprocess Biosyst Eng 2007, 30:419-427.
56. Liu Z., Ying Y., Li F., Ma C., Xu P. Butanol production by Clostridium beijerinckii ATCC 55025 from wheat bran. J Ind Microbiol Biotechnol 2010, 37:495-501.
57. Heluane H., Evans M.R., Dagher S.F., Bruno-Barcena J.M. Meta-analysis and functional validation of nutritional requirements of solventogenic clostridia growing under butanol stress conditions and coutilization of d-glucose and d-xylose. Appl Environ Microbiol 2011, 77:4473-4485.
58. Gold N.D., Martin V.J. Global view of the Clostridium thermocellum cellulosome revealed by quantitative proteomic analysis. J Bacteriol 2007, 189:6787-6795.
59. Stevenson D.M., Weimer P.J. Expression of 17 genes in Clostridium thermocellum ATCC 27405 during fermentation of cellulose or cellobiose in continuous culture. Appl Environ Microbiol 2005, 71:4672-4678.
60. Zhang Y.H., Lynd L.R. Regulation of cellulase synthesis in batch and continuous cultures of Clostridium thermocellum. J Bacteriol 2005, 187:99-106.
61. Abdou L., Boileau C., de Philip P., Pages S., Fierobe H.P., Tardif C. Transcriptional regulation of the Clostridium cellulolyticum cip-cel operon: a complex mechanism involving a catabolite-responsive element. J Bacteriol 2008, 190:1499-1506.
62. Shen G.J., Shieh J.S., Grethlein A.J., Jain M.K., Zeikus J.G. Biochemical basis for carbon monoxide tolerance and butanol production by Butyribacterium methylotrophicum. Appl Microbiol Biotechnol 1999, 51:827-832.
63. Kerby R., Zeikus J.G. Catabolic enzymes of the acetogen Butyribacterium methylotrophicum grown on single-carbon substrates. J Bacteriol 1987, 169:5605-5609.
64. Ragsdale S.W. Enzymology of the Wood-Ljungdahl pathway of acetogenesis. Ann N Y Acad Sci 2008, 1125:129-136.
65. 2 fixation. Biochim Biophys Acta 2008, 1784:1873-1898.
66. Ljungdahl L.G. A life with acetogens, thermophiles, and cellulolytic anaerobes. Ann Rev Microbiol Annu Rev 2009, 1-25.
67. Köpke M., Mihalcea C., Bromley J.C., Simpson S.D. Fermentative production of ethanol from carbon monoxide. Curr Opin Biotechnol 2011, 22:320-325.
68. Wilkins M.R., Atiyeh H.K. Microbial production of ethanol from carbon monoxide. Curr Opin Biotechnol 2011, 22:326-330.
69. Parkhill J., Sebaihia M., Wren B.W., Mullany P., Fairweather N.F., Minton N., Stabler R., Thomson N.R., Roberts A.P., Cerdeno-Tarrraga A.M., et al. The multidrug-resistant human pathogen Clostridium difficile has a highly mobile, mosaic genome. Nat Genet 2006, 38:779-786.
70. Paul D., Austin F.W., Arick T., Bridges S.M., Burgess S.C., Dandass Y.S., Lawrence M.L. Genome sequence of the solvent-producing bacterium Clostridium carboxidivorans strain P7T. J Bacteriol 2010, 192:5554-5555.
71. Ragsdale S.W., Pierce E., Xie G., Barabote R.D., Saunders E., Han C.S., Detter J.C., Richardson P., Brettin T.S., Das A., et al. The complete genome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 2008, 10:2550-2573.
72. Drake H.L., Daniel S.L. Physiology of the thermophilic acetogen Moorella thermoacetica. Res Microbiol 2004, 155:422-436.
73. Muller V. Energy conservation in acetogenic bacteria. Appl Environ Microbiol 2003, 69:6345-6353.
74. Das A., Hugenholtz J., Vanhalbeek H., Ljungdahl L.G. Structure and function of a menaquinone involved in electron-transport in membranes of Clostridium thermoautotrophicum and Clostridium thermoaceticum. J Bacteriol 1989, 171:5823-5829.
75. Wohlfarth G., Diekert G. Thermodynamics of methylenetetrahydrofolate reduction to methyltetrahydrofolate and its implications for the energy-metabolism of homoacetogenic bacteria. Arch Microbiol 1991, 155:378-381.
76. Muller V., Schmidt S., Biegel E. The ins and outs of Na(+) bioenergetics in Acetobacterium woodii. Biochim Biophys Acta 2009, 1787:691-696.
77. Phillips J.R., Clausen E.C., Gaddy J.L. Synthesis gas as substrate for the biological production of fuels and chemicals. Appl Biochem Biotechnol 1994, 45-6:145-157.
78. Papoutsakis E.T. Equations and calculations for fermentations of butyric acid bacteria. Biotechnol Bioeng 1984, 26:174-187.
79. Abrini J., Naveau H., Nyns E.J. Clostridium autoethanogenum, sp. nov., an anaerobic bacterium that produces rthanol from carbon monoxide. Arch Microbiol 1994, 161:345-351.
80. Hunke RL, Lewis RS, Tanner RS: Isolation and characterization of novel clostridial species. US Patent Application 20080057554 A1 2008.
81. Liou J.S., Balkwill D.L., Drake G.R., Tanner R.S. Clostridium carboxidivorans, sp. nov., a solvent-producing clostridium isolated from an agricultural settling lagoon, and reclassification of the acetogen Clostridium scatologenes strain SL1 as Clostridium drakei, sp. nov. Int J Syst Evol Microbiol 2005, 55:2085-2091.
82. Park D.H., Laivenieks M., Guettler M.V., Jain M.K., Zeikus J.G. Microbial utilization of electrically reduced neutral red as the sole electron donor for growth and metabolite production. Appl Environ Microbiol 1999, 65:2912-2917.
83. Green E.M. Fermentative production of butanol - the industrial perspective. Curr Opin Biotechnol 2011, 22:337-343.
84. Lee S.Y., Park J.H., Jang S.H., Nielsen L.K., Kim J., Jung K.S. Fermentative butanol production by Clostridia. Biotechnol Bioeng 2008, 101:209-228.
85. Lütke-Eversloh T., Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 2011, 22:634-647.
86. Papoutsakis E.T. Engineering solventogenic clostridia. Curr Opin Biotechnol 2008, 19:420-429.
87. Dürre P. Fermentative production of butanol - the academic perspective. Curr Opin Biotechnol 2011, 22:331-336.
88. Jeon B.S., Kim B.C., Um Y., Sang B.I. Production of hexanoic acid from d-galactitol by a newly isolated Clostridium sp. BS-1. Appl Microbiol Biotechnol 2010, 88:1161-1167.
89. Steinbusch K.J.J., Hamelers H.V.M., Plugge C.M., Buisman C.J.N. Biological formation of caproate and caprylate from acetate: fuel and chemical production from low grade biomass. Energy Environ Sci 2011, 4:216-224.
90. Hetzel M., Brock M., Selmer T., Pierik A.J., Golding B.T., Buckel W. Acryloyl-CoA reductase from Clostridium propionicumi - an enzyme complex of propionyl-CoA dehydrogenase and electron-transferring flavoprotein. Eur J Biochem 2003, 270:902-910.
91. Papoutsakis E.T., Meyer C.L. Fermentation equations for propionic-acid bacteria and production of assorted oxychemicals from various sugars. Biotechnol Bioeng 1985, 27:67-80.
92. Selmer T., Willanzheimer A., Hetzel M. Propionate CoA-transferase from Clostridium propionicum - cloning of the gene and identification of glutamate 324 at the active site. Eur J Biochem 2002, 269:372-380.
93. Obrien D.J., Panzer C.C., Eisele W.P. Biological production of acrylic acid from cheese whey by resting cells of Clostridium propionicum. Biotechnol Prog 1990, 6:237-242.
94. Shaw AJ, Rajgarhia V: Mesophilic and thermophilic organisms modified to produce acrylat, and methods of use thereof. International Application PCT/US2010/027190 2010.
95. Barbirato F., Chedaille D., Bories A. Propionic acid fermentation from glycerol: comparison with conventional substrates. Appl Microbiol Biotechnol 1997, 47:441-446.
96. Hettinga D.H., Reinbold G.W. Propionic-acid bacteria - review 2. Metabolism. J Milk Food Technol 1972, 35. 358-&.
97. Wood H.G. Metabolic cycles in the fermentation by propionic acid bacteria. Curr Top Cell Regul 1981, 18:255-287.
98. Mermelstein L.D., Welker N.E., Bennett G.N., Papoutsakis E.T. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. Biotechnology (N Y) 1992, 10:190-195.
99. Desai R.P., Papoutsakis E.T. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl Environ Microbiol 1999, 65:936-945.
100. Tummala S.B., Welker N.E., Papoutsakis E.T. Development and characterization of a gene expression reporter system for Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 1999, 65:3793-3799.
101. Girbal L., Mortier-Barriere I., Raynaud F., Rouanet C., Croux C., Soucaille P. Development of a sensitive gene expression reporter system and an inducible promoter-repressor system for Clostridium acetobutylicum. Appl Environ Microbiol 2003, 69:4985-4988.
102. Hartman A.H., Liu H.L., Melville S.B. Construction and characterization of a lactose-inducible promoter system for controlled gene expression in Clostridium perfringens. Appl Environ Microbiol 2011, 77:471-478.
103. Heap J.T., Pennington O.J., Cartman S.T., Carter G.P., Minton N.P. The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods 2007, 70:452-464.
104. Shao L., Hu S., Yang Y., Gu Y., Chen J., Jiang W., Yang S. Targeted gene disruption by use of a group II intron (targetron) vector in Clostridium acetobutylicum. Cell Res 2007, 17:963-965.
105. Mohr G., Smith D., Belfort M., Lambowitz A.M. Rules for DNA target-site recognition by a lactococcal group II intron enable retargeting of the intron to specific DNA sequences. Genes Dev 2000, 14:559-573.
106. Zhong J., Karberg M., Lambowitz A.M. Targeted and random bacterial gene disruption using a group II intron (targetron) vector containing a retrotransposition-activated selectable marker. Nucleic Acids Res 2003, 31:1656-1664.
107. Heap J.T., Kuehne S.A., Ehsaan M., Cartman S.T., Cooksley C.M., Scott J.C., Minton N.P. The ClosTron: mutagenesis in Clostridium refined and streamlined. J Microbiol Methods 2010, 80:49-55.
108. Tracy B.P., Jones S.W., Papoutsakis E.T. Inactivation of sigmaE and sigmaG in Clostridium acetobutylicum illuminates their roles in clostridial-cell-form biogenesis, granulose synthesis, solventogenesis, and spore morphogenesis. J Bacteriol 2011, 193:1414-1426.
109. Rocha E.P., Cornet E., Michel B. Comparative and evolutionary analysis of the bacterial homologous recombination systems. PLoS Genet 2005, 1:e15.
110. Bi C., Jones S.W., Hess D.R., Tracy B.P., Papoutsakis E.T. SpoIIE is necessary for asymmetric division, sporulation, and the expression of sigmaF, sigmaE, and sigmaG, but does not control solvent production in Clostridium acetobutylicum. J Bacteriol 2011, 193:5130-5137.
111. Jones S.W., Tracy B.P., Gaida S.M., Papoutsakis E.T. Inactivation of sigmaF in Clostridium acetobutylicum ATCC 824 blocks sporulation prior to asymmetric division and abolishes sigmaE and sigmaG protein expression but does not block solvent formation. J Bacteriol 2011, 193:2429-2440.
112. Tripathi S.A., Olson D.G., Argyros D.A., Miller B.B., Barrett T.F., Murphy D.M., McCool J.D., Warner A.K., Rajgarhia V.B., Lynd L.R., et al. Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant. Appl Environ Microbiol 2010, 76:6591-6599.
113. Nariya H., Miyata S., Suzuki M., Tamai E., Okabe A. Development and application of a method for counterselectable in-frame deletion in Clostridium perfringens. Appl Environ Microbiol 2011, 77:1375-1382.
114. 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.
115. Kosugi A., Murashima K., Doi R.H. Characterization of xylanolytic enzymes in Clostridium cellulovorans: expression of xylanase activity dependent on growth substrates. J Bacteriol 2001, 183:7037-7043.
116. Mohand-Oussaid O., Payot S., Guedon E., Gelhaye E., Youyou A., Petitdemange H. The extracellular xylan degradative system in Clostridium cellulolyticum cultivated on xylan: evidence for cell-free cellulosome production. J Bacteriol 1999, 181:4035-4040.
117. Morag E., Bayer E.A., Lamed R. Relationship of cellulosomal and noncellulosomal xylanases of Clostridium thermocellum to cellulose-degrading enzymes. J Bacteriol 1990, 172:6098-6105.
118. Lamed R., Naimark J., Morgenstern E., Bayer E.A. Specialized cell surface structures in cellulolytic bacteria. J Bacteriol 1987, 169:3792-3800.
119. Bayer E.A., Belaich J.P., Shoham Y., Lamed R. The cellulosomes: multienzyme machines for degradation of plant cell wall polysaccharides. Annu Rev Microbiol 2004, 58:521-554.
120. Warnick T.A., Methe B.A., Leschine S.B. Clostridium phytofermentans sp. nov., a cellulolytic mesophile from forest soil. Int J Syst Evol Microbiol 2002, 52:1155-1160.
121. Feinberg L., Foden J., Barrett T., Davenport K.W., Bruce D., Detter C., Tapia R., Han C., Lapidus A., Lucas S., et al. Complete genome sequence of the cellulolytic thermophile Clostridium thermocellum DSM1313. J Bacteriol 2011, 193:2906-2907.
122. Hemme C.L., Mouttaki H., Lee Y.J., Zhang G., Goodwin L., Lucas S., Copeland A., Lapidus A., Glavina del Rio T., Tice H., et al. Sequencing of multiple clostridial genomes related to biomass conversion and biofuel production. J Bacteriol 2010, 192:6494-6496.
123. Miller D.A., Suen G., Bruce D., Copeland A., Cheng J.F., Detter C., Goodwin L.A., Han C.S., Hauser L.J., Land M.L., et al. Complete genome sequence of the cellulose-degrading bacterium Cellulosilyticum lentocellum. J Bacteriol 2011, 193:2357-2358.
124. Tamaru Y., Miyake H., Kuroda K., Nakanishi A., Matsushima C., Doi R.H., Ueda M. Comparison of the mesophilic cellulosome-producing Clostridium cellulovorans genome with other cellulosome-related clostridial genomes. Microb Biotechnol 2011, 4:64-73.
125. Tamaru Y., Miyake H., Kuroda K., Nakanishi A., Kawade Y., Yamamoto K., Uemura M., Fujita Y., Doi R.H., Ueda M. Genome sequence of the cellulosome-producing mesophilic organism Clostridium cellulovorans 743B. J Bacteriol 2010, 192:901-902.
126. Hu S., Zheng H., Gu Y., Zhao J., Zhang W., Yang Y., Wang S., Zhao G., Yang S., Jiang W. Comparative genomic and transcriptomic analysis revealed genetic characteristics related to solvent formation and xylose utilization in Clostridium acetobutylicum EA 2018. BMC Genomics 2011, 12:93.
127. Raman B., McKeown C.K., Rodriguez M., Brown S.D., Mielenz J.R. Transcriptomic analysis of Clostridium thermocellum ATCC 27405 cellulose fermentation. BMC Microbiol 2011, 11:134.
128. Riederer A., Takasuka T.E., Makino S., Stevenson D.M., Bukhman Y.V., Elsen N.L., Fox B.G. Global gene expression patterns in Clostridium thermocellum as determined by microarray analysis of chemostat cultures on cellulose or cellobiose. Appl Environ Microbiol 2011, 77:1243-1253.
129. Tolonen A.C., Haas W., Chilaka A.C., Aach J., Gygi S.P., Church G.M. Proteome-wide systems analysis of a cellulosic biofuel-producing microbe. Mol Syst Biol 2011, 7:461.
130. Cho W., Jeon S.D., Shim H.J., Doi R.H., Han S.O. Cellulosomic profiling produced by Clostridium cellulovorans during growth on different carbon sources explored by the cohesin marker. J Biotechnol 2010, 145:233-239.
131. Fierobe H.P., Mechaly A., Tardif C., Belaich A., Lamed R., Shoham Y., Belaich J.P., Bayer E.A. Design and production of active cellulosome chimeras. Selective incorporation of dockerin-containing enzymes into defined functional complexes. J Biol Chem 2001, 276:21257-21261.
132. Elkins J.G., Raman B., Keller M. Engineered microbial systems for enhanced conversion of lignocellulosic biomass. Curr Opin Biotechnol 2010, 21:657-662.
133. Nölling J., Breton G., Omelchenko M.V., Makarova K.S., Zeng Q., Gibson R., Lee H.M., Dubois J., Qiu D., Hitti J., et al. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 2001, 183:4823-4838.
134. Mingardon F., Chanal A., Tardif C., Fierobe H.P. The issue of secretion in heterologous expression of Clostridium cellulolyticum cellulase-encoding genes in Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 2011, 77:2831-2838.
135. Mingardon F., Perret S., Belaich A., Tardif C., Belaich J.P., Fierobe H.P. Heterologous production, assembly, and secretion of a minicellulosome by Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 2005, 71:1215-1222.
136. Perret S., Casalot L., Fierobe H.P., Tardif C., Sabathe F., Belaich J.P., Belaich A. Production of heterologous and chimeric scaffoldins by Clostridium acetobutylicum ATCC 824. J Bacteriol 2004, 186:253-257.
137. Higashide W., Li Y., Yang Y., Liao J.C. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl Environ Microbiol 2011, 77:2727-2733.
138. Hillmann F., Fischer R.J., Saint-Prix F., Girbal L., Bahl H. PerR acts as a switch for oxygen tolerance in the strict anaerobe Clostridium acetobutylicum. Mol Microbiol 2008, 68:848-860.
139. 2 detoxification in Clostridium acetobutylicum. Microbiology 2009, 155:16-24.
140. Zhu L., Dong H., Zhang Y., Li Y. Engineering the robustness of Clostridium acetobutylicum by introducing glutathione biosynthetic capability. Metab Eng 2011, 13:426-434.
141. 2 by metal-catalysed histidine oxidation. Nature 2006, 440:363-367.
142. Helmann J.D., Wu M.F., Gaballa A., Kobel P.A., Morshedi M.M., Fawcett P., Paddon C. The global transcriptional response of Bacillus subtilis to peroxide stress is coordinated by three transcription factors. J Bacteriol 2003, 185:243-253.
143. 2-affected gene expression of Clostridium acetobutylicum. J Bacteriol 2009, 191:6082-6093.
144. Carmel-Harel O., Storz G. Roles of the glutathione- and thioredoxin-dependent reduction systems in the Escherichia coli and Saccharomyces cerevisiae responses to oxidative stress. Annu Rev Microbiol 2000, 54:439-461.
145. Li Y., Hugenholtz J., Abee T., Molenaar D. Glutathione protects Lactococcus lactis against oxidative stress. Appl Environ Microbiol 2003, 69:5739-5745.
146. Jones D.T., van der Westhuizen A., Long S., Allcock E.R., Reid S.J., Woods D.R. Solvent production and morphological changes in Clostridium acetobutylicum. Appl Environ Microbiol 1982, 43:1434-1439.
147. Tracy B.P., Gaida S.M., Papoutsakis E.T. Development and application of flow-cytometric techniques for analyzing and sorting endospore-forming clostridia. Appl Environ Microbiol 2008, 74:7497-7506.
148. Harris L.M., Welker N.E., Papoutsakis E.T. Northern, morphological, and fermentation analysis of spo0A inactivation and overexpression in Clostridium acetobutylicum ATCC 824. J Bacteriol 2002, 184:3586-3597.
149. Hilbert D.W., Piggot P.J. Compartmentalization of gene expression during Bacillus subtilis spore formation. Microbiol Mol Biol Rev 2004, 68:234-262.
150. Scotcher M.C., Bennett G.N. SpoIIE regulates sporulation but does not directly affect solventogenesis in Clostridium acetobutylicum ATCC 824. J Bacteriol 2005, 187:1930-1936.
151. Bennett GN, Scotcher MC: Blocking sporulation by inhibiting SpoIIE. US Patent 7,432,090 2008.
152. Jain MK, Beacon D, Datta R: Mutant strain of C. acetobutylicum and process for making butanol. US Patent 5,192,673 1993.
153. Lemme CJ, Frankiewicz JR: Strain of Clostridium acetobutylicum and process for its preparation. US Patent 4,521,516 1985.
154. Blanchard J, Leschine S, Petit E, Fabel J: Methods and compositions for regulating sporulation. US Patent Application 20100105114 2010.
155. Desvaux M., Petitdemange H. Sporulation of Clostridium cellulolyticum while grown in cellulose-batch and cellulose-fed continuous cultures on a mineral-salt based medium. Microbial Ecol 2002, 43:271-279.
156. Harris L.M., Blank L., Desai R.P., Welker N.E., Papoutsakis E.T. Fermentation characterization and flux analysis of recombinant strains of Clostridium acetobutylicum with an inactivated solR gene. J Ind Microbiol Biotechnol 2001, 27:322-328.
157. Harris L.M., Desai R.P., Welker N.E., Papoutsakis E.T. Characterization of recombinant strains of the Clostridium acetobutylicum butyrate kinase inactivation mutant: need for new phenomenological models for solventogenesis and butanol inhibition?. Biotechnol Bioeng 2000, 67:1-11.
158. Borden J.R., Papoutsakis E.T. Dynamics of genomic-library enrichment and identification of solvent tolerance genes for Clostfidium acetobutylicum. Appl Environ Microbiol 2007, 73:3061-3068.
159. Tomas C.A., Welker N.E., Papoutsakis E.T. Overexpression of groESL in Clostridium acetobutylicum results in increased solvent production and tolerance, prolonged metabolism, and large changes in the cell's transcriptional program. Appl Environ Microbiol 2003, 69:4951-4965.
160. 2- and CO-dependent chemolithotrophic potentials of the acetogens Clostridium thermoaceticum and Acetogenium kivui. J Bacteriol 1990, 172:4464-4471.