Technical guide for genetic advancement of underdeveloped and intractable Clostridium

Biotechnology Advances

Volumn 32, Issue 3, 2014, Pages 623-641

  Pyne, Michael E ^a   Bruder, Mark ^a   Moo Young, Murray ^a   Chung, Duane A ^a,b   Chou, C Perry ^a  

^a UNIVERSITY OF WATERLOO   (Canada)

^b Algaeneers Inc   (Canada)

Author keywords

Biofuels; Clostridia; Clostridium; Gene knockout; Genetic engineering; Industrial biotechnology; Medical biotechnology; Overexpression; Transformation

Indexed keywords

BIOFUELS; CHROMOSOMES; CLOSTRIDIUM; GENE TRANSFER; GENETIC ENGINEERING; INDUSTRIAL CHEMICALS; PHYSIOLOGY; TOOLS;

GENE KNOCKOUT; INDUSTRIAL BIOTECHNOLOGY; MEDICAL BIOTECHNOLOGY; OVER-EXPRESSION; TRANSFORMATION;

BIOTECHNOLOGY;

BACTERIUM; BIOFUEL; BIOTECHNOLOGY; BIOTRANSFORMATION; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC ENGINEERING; GENOME; VIRULENCE;

BACTERIA (MICROORGANISMS); CLOSTRIDIA; CLOSTRIDIUM; CLOSTRIDIUM DIFFICILE;

BIOFUEL;

BACTERIAL GENOME; CLOSTRIDIUM; GENETIC ENGINEERING; GENETICS; MICROBIOLOGY; PHYSIOLOGY;

BIOFUELS; CLOSTRIDIUM; GENETIC ENGINEERING; GENOME, BACTERIAL; INDUSTRIAL MICROBIOLOGY;

EID: 84900563461     PISSN: 07349750     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.biotechadv.2014.04.003     Document Type: Review

References (192)

1. Ackermann G., Tang Y.J., Henderson J.P., Rodloff A.C., Silva J., Cohen S.H. Electroporation of DNA sequences from the pathogenicity locus (PaLoc) of toxigenic Clostridium difficile into a non-toxigenic strain. Mol Cell Probes 2001, 15:301-306.
2. Al-Hinai M.A., Fast A.G., Papoutsakis E.T. Novel system for efficient isolation of Clostridium double-crossover allelic exchange mutants enabling markerless chromosomal gene deletions and DNA integration. Appl Environ Microbiol 2012, 78:8112-8121.
3. Allen S.P., Blaschek H.P. Electroporation-induced transformation of intact cells of Clostridium perfringens. Appl Environ Microbiol 1988, 54:2322-2324.
4. Allen S.P., Blaschek H.P. Factors involved in the electroporation-induced transformation of Clostridium perfringens. FEMS Microbiol Lett 1990, 70:217-220.
5. Alsaker K.V., Spitzer T.R., Papoutsakis E.T. Transcriptional analysis of spo0A overexpression in Clostridium acetobutylicum and its effect on the cell's response to butanol stress. J Bacteriol 2004, 186:1959-1971.
6. Argyros D.A., Tripathi S.A., Barrett T.F., Rogers S.R., Feinberg L.F., Olson D.G., et al. High ethanol titers from cellulose by using metabolically engineered thermophilic, anaerobic microbes. Appl Environ Microbiol 2011, 77:8288-8294.
7. Assad-Garcia J.S., Bonnin-Jusserand M., Garmyn D., Guzzo J., Alexandre H., Grandvalet C. An improved protocol for electroporation of Oenococcus oeni ATCC BAA-1163 using ethanol as immediate membrane fluidizing agent. Lett Appl Microbiol 2008, 47:333-338.
8. Aune T.E.V., Aachmann F.L. Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Appl Microbiol Biotechnol 2010, 85:1301-1313.
9. Awad M.M., Rood J.I. Isolation of alpha-toxin, theta-toxin and kappa-toxin mutants of Clostridium perfringens by Tn916 mutagenesis. Microb Pathog 1997, 22:275-284.
10. Awang G.M., Jones G.A., Ingledew W.M. The actone-butanol-ethanol fermentation. Crit Rev Microbiol 1988, 15:S33-S67.
11. Barash J.R., Arnon S.S. A novel strain of Clostridium botulinum that produces Type B and Type H botulinum toxins. J Infect Dis 2014, 209(2):183-191. 10.1093/infdis/jit449.
12. Bashir A., Klammer A.A., Robins W.P., Chin C.S., Webster D., Paxinos E., et al. A hybrid approach for the automated finishing of bacterial genomes. Nat Biotechnol 2012, 30:701-707.
13. Birrer G.A., Chesbro W.R., Zsigray R.M. Electrotransformation of Clostridium beijerinckii B-592 with shuttle plasmid pHR106 and recombinant derivatives. Appl Microbiol Biotechnol 1994, 41:32-38.
14. Blumberg P.M., Stroming Jl Interaction of penicillin with the bacterial cell: penicillin-binding proteins and penicillin-sensitive enzymes. Bacteriol Rev 1974, 38:291-335.
15. Brown D.P., Ganovaraeva L., Green B.D., Wilkinson S.R., Young M., Youngman P. Characterization of spo0A homologs in diverse Bacillus and Clostridium species identifies a probable DNA-binding domain. Mol Microbiol 1994, 14:411-426.
16. Cai G.Q., Jin B., Saint C., Monis P. Genetic manipulation of butyrate formation pathways in Clostridium butyricum. J Biotechnol 2011, 155:269-274.
17. Cai G.Q., Jin B., Monis P., Saint C. A genetic and metabolic approach to redirection of biochemical pathways of Clostridium butyricum for enhancing hydrogen production. Biotechnol Bioeng 2013, 110:338-342.
18. Carere C.R., Sparling R., Cicek N., Levin D.B. Third generation biofuels via direct cellulose fermentation. Int J Mol Sci 2008, 9:1342-1360.
19. Carter G.P., Awad M.M., Hao Y.B., Thelen T., Bergin I.L., Howarth P.M., et al. TcsL ss an essential virulence factor in Clostridium sordellii ATCC 9714. Infect Immun 2011, 79:1025-1032.
20. Cartman S.T., Minton N.P. A mariner-based transposon system for in vivo random mutagenesis of Clostridium difficile. Appl Environ Microbiol 2010, 76:1103-1109.
21. Cartman S.T., Kelly M.L., Heeg D., Heap J.T., Minton N.P. Precise manipulation of the Clostridium difficile chromosome reveals a lack of association between the tcdC genotype and toxin production. Appl Environ Microbiol 2012, 78:4683-4690.
22. Chalmers J.D., Al-Khairalla M., Short P.M., Fardon T.C., Winter J.H. Proposed changes to management of lower respiratory tract infections in response to the Clostridium difficile epidemic. J Antimicrob Chemother 2010, 65:608-618.
23. Chanal A., Mingardon F., Bauzan M., Tardif C., Fierobe H.P. Scaffoldin modules serving as "cargo" domains to promote the secretion of heterologous cellulosomal cellulases by Clostridium acetobutylicum. Appl Environ Microbiol 2011, 77:6277-6280.
24. Chassy B.M. Gentle method for lysis of oral streptococci. Biochem Biophys Res Commun 1976, 68:603-608.
25. Chen Y., McClane B.A., Fisher D.J., Rood J.I., Gupta P. Construction of an alpha toxin gene knockout mutant of Clostridium perfringens type A by use of a mobile group II intron. Appl Environ Microbiol 2005, 71:7542-7547.
26. Chin C.S., Alexander D.H., Marks P., Klammer A.A., Drake J., Heiner C., et al. Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data. Nat Methods 2013, 10:563-569.
27. Coleman J.P., Hudson L.L. Cloning and characterization of a conjugated bile-acid hydrolase gene from Clostridium perfringens. Appl Environ Microbiol 1995, 61:2514-2520.
28. Cooksley C.M., Zhang Y., Wang H.Z., Redl S., Winzer K., Minton N.P. Targeted mutagenesis of the Clostridium acetobutylicum acetone-butanol-ethanol fermentation pathway. Metab Eng 2012, 14:630-641.
29. Cui G.Z., Hong W., Zhang J., Li W.L., Feng Y.G., Liu Y.J., et al. Targeted gene engineering in Clostridium cellulolyticum H10 without methylation. J Microbiol Methods 2012, 89:201-208.
30. Cui G.Z., Zhang J., Hong W., Xu C.G., Feng Y.G., Cui Q., et al. Improvement of ClosTron for successive gene disruption in Clostridium cellulolyticum using a pyrF-based screening system. Appl Microbiol Biotechnol 2014, 98:313-323.
31. Dang L.H., Bettegowda C., Huso D.L., Kinzler K.W., Vogelstein B. Combination bacteriolytic therapy for the treatment of experimental tumors. Proc Natl Acad Sci U S A 2001, 98:15155-15160.
32. Datsenko K.A., Wanner B.L. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A 2000, 97:6640-6645.
33. Datta S., Costantino N., Zhou X.M., Court D.L. Identification and analysis of recombineering functions from Gram-negative and Gram-positive bacteria and their phages. Proc Natl Acad Sci U S A 2008, 105:1626-1631.
34. Davis T.O., Henderson I., Brehm J.K., Minton N.P. Development of a transformation and gene reporter system for group II, non-proteolytic Clostridium botulinum type B strains. J Mol Microbiol Biotechnol 2000, 2:59-69.
35. Desai R.P., Papoutsakis E.T. Antisense RNA strategies for metabolic engineering of Clostridium acetobutylicum. Appl Environ Microbiol 1999, 65:936-945.
36. Dong H.J., Tao W.W., Zhang Y.P., Li Y. Development of an anhydrotetracycline-inducible gene expression system for solvent-producing Clostridium acetobutylicum: a useful tool for strain engineering. Metab Eng 2012, 14:59-67.
37. Dong H.J., Tao W.W., Gong F., Li Y., Zhang Y. A functional recT gene for recombineering of Clostridium. J Biotechnol 2014, 10.1016/j.jbiotec.2013.12.011.
38. Dornenburg J.E., DeVita A.M., Palumbo M.J., Wade J.T. Widespread antisense transcription in Escherichia coli. mBio 2010, 1:1-4.
39. Ellis H.M., Yu D.G., DiTizio T., Court D.L. High efficiency mutagenesis, repair, and engineering of chromosomal DNA using single-stranded oligonucleotides. Proc Natl Acad Sci U S A 2001, 98:6742-6746.
40. Feustel L., Nakotte S., Durre P. Characterization and development of two reporter gene systems for Clostridium acetobutylicum. Appl Environ Microbiol 2004, 70:798-803.
41. Finegold S.M., Song Y.L., Liu C.X. Taxonomy - general comments and update on taxonomy of clostridia and anaerobic cocci. Anaerobe 2002, 8:283-285.
42. Flusberg B.A., Webster D.R., Lee J.H., Travers K.J., Olivares E.C., Clark T.A., et al. Direct detection of DNA methylation during single-molecule, real-time sequencing. Nat Methods 2010, 7:461-U72.
43. Forbes N.S. Engineering the perfect (bacterial) cancer therapy. Nat Rev Cancer 2010, 10:784-793.
44. Georg J., Hess W.R. cis-Antisense RNA, another level of gene regulation in bacteria. Microbiol Mol Biol Rev 2011, 75:286-300.
45. Gheshlaghi R., Scharer J.M., Moo-Young M., Chou C.P. Metabolic pathways of clostridia for producing butanol. Biotechnol Adv 2009, 27:764-781.
46. 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.
47. Girbal L., von Abendroth G., Winkler M., Benton P.M.C., Meynial-Salles I., Croux C., et al. Homologous and heterologous overexpression in Clostridium acetobutylicum and characterization of purified clostridial and algal Fe-only hydrogenases with high specific activities. Appl Environ Microbiol 2005, 71:2777-2781.
48. Gonzalez-Pajuelo M., Meynial-Salles I., Mendes F., Andrade J.C., Vasconcelos I., Soucaille P. Metabolic engineering of Clostridium acetobutylicum for the industrial production of 1,3-propanediol from glycerol. Metab Eng 2005, 7:329-336.
49. Gonzalez-Pajuelo M., Meynial-Salles I., Mendes F., Soucaille P., Vasconcelos I. Microbial conversion of glycerol to 1,3-propanediol: physiological comparison of a natural producer, Clostridium butyricum VPI 3266, and an engineered strain, Clostridium acetobutylicum DG1(pSPD5). Appl Environ Microbiol 2006, 72:96-101.
50. Gottschalk G., Andreesen J.R., Hippe H. The genus Clostridium (non-medical aspects). The prokaryotes, a handbook on habitats, isolation and identification of bacteria 1981, 1767-1803. Springer-Verlag, New York. M.P. Starr, H. Stolp, H.C. Truper, A. Balows, H.G. Schlegel (Eds.).
51. Gouy M., Gautier C. Codon usage in bacteria - correlation with gene expressivity. Nucleic Acids Res 1982, 10:7055-7074.
52. Green E.M., Boynton Z.L., Harris L.M., Rudolph F.B., Papoutsakis E.T., Bennett G.N. Genetic manipulation of acid formation pathways by gene inactivation in Clostridium acetobutylicum ATCC 824. Microbiology 1996, 142:2079-2086.
53. Gu Y., Li J., Zhang L., Chen J., Niu L., Yang Y., et al. 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. Guedon E., Desvaux M., Petitdemange H. Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering. Appl Environ Microbiol 2002, 68:53-58.
55. Guo H.T., Karberg M., Long M., Jones J.P., Sullenger B., Lambowitz A.M. Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 2000, 289:452-457.
56. Gupta R.S., Gao B. Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I). Int J Syst Evol Microbiol 2009, 59:285-294.
57. Gustafsson C., Govindarajan S., Minshull J. Codon bias and heterologous protein expression. Trends Biotechnol 2004, 22:346-353.
58. Hammes W., Schleife Kh., Kandler O. Mode of action of glycine on biosynthesis of peptidoglycan. J Bacteriol 1973, 116:1029-1053.
59. 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.
60. 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.
61. 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.
62. Heap J.T., Pennington O.J., Cartman S.T., Minton N.P. A modular system for Clostridium shuttle plasmids. J Microbiol Methods 2009, 78:79-85.
63. Heap J.T., Kuehne S.A., Ehsaan M., Cartman S.T., Cooksley C.M., Scott J.C., et al. The ClosTron: mutagenesis in Clostridium refined and streamlined. J Microbiol Methods 2010, 80:49-55.
64. Heap J.T., Ehsaan M., Cooksley C.M., Ng Y.K., Cartman S.T., Winzer K., et al. Integration of DNA into bacterial chromosomes from plasmids without a counter-selection marker. Nucleic Acids Res 2012, 40.
65. Hermans J., Boschloo J.G., Debont J.A.M. Transformation of Mycobacterium aurum by electroporation - the use of glycine, lysozyme and isonicotinic acid hydrazide in enhancing transformation efficiency. FEMS Microbiol Lett 1990, 72:221-224.
66. Higashide W., Li Y.C., Yang Y.F., Liao J.C. Metabolic engineering of Clostridium cellulolyticum for production of isobutanol from cellulose. Appl Environ Microbiol 2011, 77:2727-2733.
67. Iacobino A., Scalfaro C., Franciosa G. Structure and genetic content of the megaplasmids of neurotoxigenic Clostridium butyricum Type E strains from Italy. PLoS One 2013, 8.
68. Jennert K.C.B., Tardif C., Young D.I., Young M. Gene transfer to Clostridium cellulolyticum ATCC 35319. Microbiology 2000, 146:3071-3080.
69. Jo J.H., Jeon C.O., Lee S.Y., Lee D.S., Park J.M. Molecular characterization and homologous overexpression of FeFe-hydrogenase in Clostridium tyrobutyricum JM1. Int J Hydrogen Energy 2010, 35:1065-1073.
70. Jones D.T., Woods D.R. Acetone-butanol fermentation revisited. Microbiol Rev 1986, 50:484-524.
71. Karberg M., Guo H.T., Zhong J., Coon R., Perutka J., Lambowitz A.M. Group II introns as controllable gene targeting vectors for genetic manipulation of bacteria. Nat Biotechnol 2001, 19:1162-1167.
72. Kelly C.P., LaMont J.T. Clostridium difficile-more difficult than ever. N Engl J Med 2008, 359:1932-1940.
73. Kennedy C.L., Krejany E.O., Young L.F., O'Connor J.R., Awad M.M., Boyd R.L., et al. The alpha-toxin of Clostridium septicum is essential for virulence. Mol Microbiol 2005, 57:1357-1366.
74. Kim A.Y., Blaschek H.P. Construction of an Escherichia coli-Clostridium perfringens shuttle vector and plasmid transformation of Clostridium perfringens. Appl Environ Microbiol 1989, 55:360-365.
75. Klapatch T.R., Demain A.L., Lynd L.R. Restriction endonuclease activity in Clostridium thermocellum and Clostridium thermosaccharolyticum. Appl Microbiol Biotechnol 1996, 45:127-131.
76. Klapatch T.R., Guerinot M.L., Lynd L.R. Electrotransformation of Clostridium thermosaccharolyticum. J Ind Microbiol 1996, 16:342-347.
77. Klein M., Ansorge-Schumacher M.B., Fritsch M., Hartmeier W. Influence of hydrogenase overexpression on hydrogen production of Clostridium acetobutylicum DSM 792. Enzyme Microb Technol 2010, 46:384-390.
78. Kopke M., Held C., Hujer S., Liesegang H., Wiezer A., Wollherr A., et al. Clostridium ljungdahlii represents a microbial production platform based on syngas. Proc Natl Acad Sci U S A 2010, 107:13087-13092.
79. Kovacs K., Willson B.J., Schwarz K., Heap J.T., Jackson A., Bolam D.N., et al. Secretion and assembly of functional mini-cellulosomes from synthetic chromosomal operons in Clostridium acetobutylicum ATCC 824. Biotechnol Biofuels 2013, 6.
80. Kuehne S.A., Cartman S.T., Heap J.T., Kelly M.L., Cockayne A., Minton N.P. The role of toxin A and toxin B in Clostridium difficile infection. Nature 2010, 467:711-713.
81. Lanckriet A., Timbermont L., Happonen L.J., Pajunen M.I., Pasmans F., Haesebrouck F., et al. Generation of single-copy transposon insertions in Clostridium perfringens by electroporation of phage Mu DNA transposition complexes. Appl Environ Microbiol 2009, 75:2638-2642.
82. Lawson P.A., Llopperez P., Hutson R.A., Hippe H., Collins M.D. Towards a phylogeny of the clostridia based on 16S ribosomal-RNA sequences. FEMS Microbiol Lett 1993, 113:87-92.
83. Leang C., Ueki T., Nevin K.P., Lovley D.R. A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen. Appl Environ Microbiol 2013, 79:1102-1109.
84. Lee J.M., Zhang S.H., Saha S., Anna S.S., Jiang C., Perkins J. RNA expression analysis using an antisense Bacillus subtilis genome array. J Bacteriol 2001, 183:7371-7380.
85. 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.
86. Lee J.Y., Jang Y.-S., Lee J., Papoutsakis E.T., Lee S.Y. Metabolic engineering of Clostridium acetobutylicum M5 for highly selective butanol production. Biotechnol J 2009, 4:1432-1440.
87. Lee J., Jang Y.S., Choi S.J., Im J.A., Song H., Cho J.H., et al. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for isopropanol-butanol-ethanol fermentation. Appl Environ Microbiol 2012, 78:1416-1423.
88. Lehmann K., Schmidt U. Group II introns: structure and catalytic versatility of large natural ribozymes. Crit Rev Biochem Mol Biol 2003, 38:249-303.
89. Li Y.C., Tschaplinski T.J., Engle N.L., Hamilton C.Y., Rodriguez M., Liao J.C., et al. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. Biotechnol Biofuels 2012, 5.
90. Lin Y.L., Blaschek H.P. Transformation of heat-treated Clostridium acetobutylicum protoplasts with pUB110 plasmid DNA. Appl Environ Microbiol 1984, 48:737-742.
91. Liu S.C., Minton N.P., Giaccia A.J., Brown J.M. Anticancer efficacy of systemically delivered anaerobic bacteria as gene therapy vectors targeting tumor hypoxia/necrosis. Gene Ther 2002, 9:291-296.
92. Liu L., Li Y.H., Li S.L., Hu N., He Y.M., Pong R., et al. Comparison of next-generation sequencing systems. J Biomed Biotechnol 2012, 1-11. 10.1155/2012/251364.
93. Liyanage H., Young M., Kashket E.R. Butanol tolerance of Clostridium beijerinckii NCIMB 8052 associated with down-regulation of gldA by antisense RNA. J Mol Microbiol Biotechnol 2000, 2:87-93.
94. Lofblom J., Kronqvist N., Uhlen M., Stahl S., Wernerus H. Optimization of electroporation-mediated transformation: Staphylococcus carnosus as model organism. J Appl Microbiol 2007, 102:736-747.
95. Ludwig W., Schleifer K.H., Whitman W.B. Revised road map to the phylum Firmicutes. Bergey's manual of systematic bacteriology 2009, 1-8. Springer, New York. 2nd ed. P. De Vos, G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey (Eds.).
96. Lunnen K.D., Barsomian J.M., Camp R.R., Card C.O., Chen S.Z., Croft R., et al. Cloning Type II restriction and modification genes. Gene 1988, 74:25-32.
97. Lutke-Eversloh T., Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr Opin Biotechnol 2011, 22:634-647.
98. Lyras D., Rood J.I. Conjugative transfer of RP4-oriT shuttle vectors from Escherichia coli to Clostridium perfringens. Plasmid 1998, 39:160-164.
99. Malmgren R.A., Flanigan C.C. Localization of the vegetative form of Clostridium tetani in mouse tumors following intravenous spore administration. Cancer Res 1955, 15:473-478.
100. Mani N., Dupuy B. Regulation of toxin synthesis in Clostridium difficile by an alternative RNA polymerase sigma factor. Proc Natl Acad Sci U S A 2001, 98:5844-5849.
101. Mani N., Lyras D., Barroso L., Howarth P., Wilkins T., Rood J.I., et al. Environmental response and autoregulation of Clostridium difficile TxeR, a sigma factor for toxin gene expression. J Bacteriol 2002, 184:5971-5978.
102. Marvaud J.C., Eisel U., Binz T., Niemann H., Popoff M.R. TetR is a positive regulator of the tetanus toxin gene in Clostridium tetani and is homologous to BotR. Infect Immun 1998, 66:5698-5702.
103. Marvaud J.C., Gibert M., Inoue K., Fujinaga Y., Oguma K. Popoff MR. botR/A is a positive regulator of botulinum neurotoxin and associated non-toxin protein genes in Clostridium botulinum A. Mol Microbiol 1998, 29:1009-1018.
104. Matamouros S., England P., Dupuy B. Clostridium difficile toxin expression is inhibited by the novel regulator TcdC. Mol Microbiol 2007, 64:1274-1288.
105. Matsushita C., Matsushita O., Koyama M., Okabe A. A Clostridium perfringens vector for the selection of promoters. Plasmid 1994, 31:317-319.
106. Matsuura M., Saldanha R., Ma H.W., Wank H., Yang J., Mohr G., et al. A bacterial group II intron encoding reverse transcriptase, maturase, DNA endonuclease activities: biochemical demonstration of maturase activity and insertion of new genetic information within the intron. Genes Dev 1997, 11:2910-2924.
107. Matsuura M., Noah J.W., Lambowitz A.M. Mechanism of maturase-promoted group II intron splicing. Embo J 2001, 20:7259-7270.
108. Mavromatis K., Land M.L., Brettin T.S., Quest D.J., Copeland A., Clum A., et al. The fast changing landscape of sequencing technologies and their impact on microbial genome assemblies and annotation. PLoS One 2012, 7.
109. McFarland L.V., Mulligan M.E., Kwok R.Y.Y., Stamm W.E. Nosocomial acquisition of Clostridium difficile infection. N Engl J Med 1989, 320:204-210.
110. Mermelstein L.D., Papoutsakis E.T. In vivo methylation in Escherichia coli by the Bacillus subtilis phage phi-3TI methyltransferase to protect plasmids from restriction upon transformation of Clostridium acetobutylicum ATCC 824. Appl Environ Microbiol 1993, 59:1077-1081.
111. Mermelstein L.D., Welker N.E., Bennett G.N., Papoutsakis E.T. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. BioTechnology 1992, 10:190-195.
112. Mermelstein L.D., Papoutsakis E.T., Petersen D.J., Bennett G.N. Metabolic engineering of Clostridium acetobutylicum ATCC 824 for increased solvent production by enhancement of acetone formation enzyme activities using a synthetic acetone operon. Biotechnol Bioeng 1993, 42:1053-1060.
113. 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.
114. 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.
115. Minton N.P. Clostridia in cancer therapy. Nat Rev Microbiol 2003, 1:237-242.
116. 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.
117. Mohr G., Hong W., Zhang J., Cui G.Z., Yang Y.F., Cui Q., et al. A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum. PLoS One 2013, 8.
118. Morimoto K., Kimura T., Sakka K., Ohmiya K. Overexpression of a hydrogenase gene in Clostridium paraputrificum to enhance hydrogen gas production. FEMS Microbiol Lett 2005, 246:229-234.
119. Munasinghe P.C., Khanal S.K. Biomass-derived syngas fermentation into biofuels: opportunities and challenges. Bioresour Technol 2010, 101:5013-5022.
120. Murphy K.C., Campellone K.G. Lambda Red-mediated recombinogenic engineering of enterohemorrhagic and enteropathogenic E. coli. BMC Mol Biol 2003, 4.
121. Musto H., Romero H., Zavala A. Translational selection is operative for synonymous codon usage in Clostridium perfringens and Clostridium acetobutylicum. Microbiology 2003, 149:855-863.
122. Nair R.V., Papoutsakis E.T. Expression of plasmid-encoded aad in Clostridium acetobutylicum M5 restores vigorous butanol production. J Bacteriol 1994, 176:5843-5846.
123. Nair R.V., Green E.M., Watson D.E., Bennett G.N., Papoutsakis E.T. Regulation of the sol locus genes for butanol and acetone formation in Clostridium acetobutylicum ATCC 824 by a putative transcriptional repressor. J Bacteriol 1999, 181:319-330.
124. Nakayama S., Irie R., Kosaka T., Matsuura K., Yoshino S., Furukawa K. New host-vector system in solvent-producing Clostridium saccharoperbutylacetonicum strain N1-4. J Gen Appl Microbiol 2007, 53:53-56.
125. Nakayama S.I., Kosaka T., Hirakawa H., Matsuura K., Yoshino S., Furukawa K. Metabolic engineering for solvent productivity by downregulation of the hydrogenase gene cluster hupCBA in Clostridium saccharoperbutylacetonicum strain N1-4. Appl Microbiol Biotechnol 2008, 78:483-493.
126. Nakotte S., Schaffer S., Bohringer M., Durre P. Electroporation of, plasmid isolation from and plasmid conservation in Clostridium acetobutylicum DSM 792. Appl Microbiol Biotechnol 1998, 50:564-567.
127. 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.
128. Nolling J., Breton G., Omelchenko M.V., Makarova K.S., Zeng Q.D., Gibson R., et al. Genome sequence and comparative analysis of the solvent-producing bacterium Clostridium acetobutylicum. J Bacteriol 2001, 183:4823-4838.
129. Nuyts S., Theys J., Landuyt W., Van Mellaert L., Lambin P., Anne J. Increasing specificity of anti-tumor therapy: cytotoxic protein delivery by non-pathogenic clostridia under regulation of radio-induced promoters. Anticancer Res 2001, 21:857-861.
130. Nuyts S., Van Mellaert L., Theys J., Landuyt W., Bosmans E., Anne J., et al. Radio-responsive recA promoter significantly increases TNF alpha production in recombinant clostridia after 2Gy irradiation. Gene Ther 2001, 8:1197-1201.
131. Oultram J.D., Loughlin M., Swinfield T.J., Brehm J.K., Thompson D.E., Minton N.P. Introduction of plasmids into whole cells of Clostridium acetobutylicum by electroporation. FEMS Microbiol Lett 1988, 56:83-88.
132. Papoutsakis E.T. Engineering solventogenic clostridia. Curr Opin Biotechnol 2008, 19:420-429.
133. Patzel V., Sczakiel G. Theoretical design of antisense RNA structures substantially improves annealing kinetics and efficacy in human cells. Nat Biotechnol 1998, 16:64-68.
134. Perret S., Casalot L., Fierobe H.P., Tardif C., Sabathe F., Belaich J.P., et al. Production of heterologous and chimeric scaffoldins by Clostridium acetobutylicum ATCC 824. J Bacteriol 2004, 186:253-257.
135. Perret S., Maamar H., Belaich J.P., Tardif C. Use of antisense RNA to modify the composition of cellulosomes produced by Clostridium cellulolyticum. Mol Microbiol 2004, 51:599-607.
136. Perutka J., Wang W.J., Goerlitz D., Lambowitz A.M. Use of computer-designed group II introns to disrupt Escherichia coli DExH/D-box protein and DNA helicase genes. J Mol Biol 2004, 336:421-439.
137. Phillips-Jones M.K. Use of a lux reporter system for monitoring rapid changes in alpha-toxin gene expression in Clostridium perfringens during growth. FEMS Microbiol Lett 2000, 188:29-33.
138. Purdy D., O'Keeffe T.A.T., Elmore M., Herbert M., McLeod A., Bokori-Brown M., et al. Conjugative transfer of clostridial shuttle vectors from Escherichia coli to Clostridium difficile through circumvention of the restriction barrier. Mol Microbiol 2002, 46:439-452.
139. Pyne M.E., Moo-Young M., Chung D.A., Chou C.P. Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum. Biotechnol Biofuels 2013, 6.
140. Quixley K.W.M., Reid S.J. Construction of a reporter gene vector for Clostridium beijerinckii using a Clostridium endoglucanase gene. J Mol Microbiol Biotechnol 2000, 2:53-57.
141. Rainey F.A., Hollen B.J., Small A. Genus I. Clostridium. Bergey's manual of systematic bacteriology 2009, 738-830. Springer, New York. 2nd ed. P. De Vos, G.M. Garrity, D. Jones, N.R. Krieg, W. Ludwig, F.A. Rainey (Eds.).
142. Raju D., Setlow P., Sarker M.R. Antisense-RNA-mediated decreased synthesis of small, acid-soluble spore proteins leads to decreased resistance of Clostridium perfringens spores to moist heat and UV radiation. Appl Environ Microbiol 2007, 73:2048-2053.
143. Raleigh E.A., Wilson G. Escherichia coli K-12 restricts DNA containing 5-methylcytosine. Proc Natl Acad Sci U S A 1986, 83:9070-9074.
144. Reysset G. Transformation and electrotransformation in clostridia. Genetics and molecular biology of anaerobic bacteria 1993, 111-119. Springer-Verlag, New York. M. Sebald (Ed.).
145. Richards D.F., Linnett P.E., Oultram J.D., Young M. Restriction endonucleases in Clostridium pasteurianum ATCC 6013 and C. thermohydrosulfuricum DSM 568. J Gen Microbiol 1988, 134:3151-3157.
146. Roberts R.J., Vincze T., Posfai J., Macelis D. REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 2010, 38:D234-D236.
147. Sakka K., Kawase M., Baba D., Morimoto K., Karita S., Kimura T., et al. Electrotransformation of Clostridium paraputrificum M-21 with some plasmids. J Biosci Bioeng 2003, 96:304-306.
148. Saunders J.R., Docherty A., Humphreys G.O. Transformation of bacteria by plasmid DNA. Methods Microbiol 1984, 17:61-95.
149. Scallan E., Hoekstra R.M., Angulo F.J., Tauxe R.V., Widdowson M.A., Roy S.L., et al. Foodborne illness acquired in the United States-major pathogens. Emerg Infect Dis 2011, 17:7-15.
150. Scott P.T., Rood J.I. Electroporation-mediated transformation of lysostaphin-treated Clostridium perfringens. Gene 1989, 82:327-333.
151. Shao L., Hu S., Yang Y., Gu Y., Chen J., Jiang W., et al. Targeted gene disruption by use of a group II intron (targetron) vector in Clostridium acetobutylicum. Cell Res 2007, 17:963-965.
152. Sharma A.D., Singh J., Gill P.K. Ethanol mediated enhancement in bacterial transformation. Electron J Biotechnol 2007, 10:166-168.
153. Sharp P.M., Bailes E., Grocock R.J., Peden J.F., Sockett R.E. Variation in the strength of selected codon usage bias among bacteria. Nucleic Acids Res 2005, 33:1141-1153.
154. Shone C.C., Hambleton P. Toxigenic clostridia. Clostridia 1989, 265-292. Plenum Press, New York. N.P. Minton, D.J. Clarke (Eds.).
155. Siemerink M.A.J., Kuit W., Contreras A.M.L., Eggink G., van der Oost J., Kengen S.W.M. d-2,3-Butanediol production due to heterologous expression of an acetoin reductase in Clostridium acetobutylicum. Appl Environ Microbiol 2011, 77:2582-2588.
156. Sillers R., Chow A., Tracy B., Papoutsakis E.T. Metabolic engineering of the non-sporulating, non-solventogenic Clostridium acetobutylicum strain M5 to produce butanol without acetone demonstrate the robustness of the acid-formation pathways and the importance of the electron balance. Metab Eng 2008, 10:321-332.
157. Sillers R., A-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.
158. Skarin H., Hafstrom T., Westerberg J., Segerman B. Clostridium botulinum group III: a group with dual identity shaped by plasmids, phages and mobile elements. BMC Genomics 2011, 12.
159. Taconi K.A., Venkataramanan K.P., Johnson D.T. Growth and solvent production by Clostridium pasteurianum ATCC (R) 6013 (TM) utilizing biodiesel-derived crude glycerol as the sole carbon source. Environ Prog Sustain Energy 2009, 28:100-110.
160. Thiele E.H., Boxer G.E., Arison R.N. Oncolysis by clostridia. III. Effects of clostridia+chemotherapeutic agents on rodent tumors. Cancer Res 1964, 24:222-233.
161. Tolonen A.C., Chilaka A.C., Church G.M. Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol 2009, 74:1300-1313.
162. Tolonen A.C., Petit E., Blanchard J.L., Warnick T., Leschine S.B. Technologies to study plant biomass fermentation using the model bacterium Clostridium phytofermentans. Biological conversion of biomass for fuels and chemicals 2013, 114-139. Royal Society of Chemistry, Cambridge. J. Sun, S.Y. Ding, J.D. Peterson (Eds.).
163. 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 changes in the cell's transcriptional program. Appl Environ Microbiol 2003, 69:4951-4965.
164. Tracy B.P., Jones S.W., Fast A.G., Indurthi D.C., Papoutsakis E.T. Clostridia: the importance of their exceptional substrate and metabolite diversity for biofuel and biorefinery applications. Curr Opin Biotechnol 2012, 23:364-381.
165. Tripathi S.A., Olson D.G., Argyros D.A., Miller B.B., Barrett T.F., Murphy D.M., 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.
166. 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.
167. Tummala S.B., Junne S.G., Papoutsakis E.T. Antisense RNA downregulation of coenzyme A transferase combined with alcohol-aldehyde dehydrogenase overexpression leads to predominantly alcohologenic Clostridium acetobutylicum fermentations. J Bacteriol 2003, 185:3644-3653.
168. Tummala S.B., Welker N.E., Papoutsakis E.T. Design of antisense RNA constructs for downregulation of the acetone formation pathway of Clostridium acetobutylicum. J Bacteriol 2003, 185:1923-1934.
169. Tyurin M., Padda R., Huang K.X., Wardwell S., Caprette D., Bennett G.N. Electrotransformation of Clostridium acetobutylicum ATCC 824 using high-voltage radio frequency modulated square pulses. J Appl Microbiol 2000, 88:220-227.
170. Tyurin M.V., Desai S.G., Lynd L.R. Electrotransformation of Clostridium thermocellum. Appl Environ Microbiol 2004, 70:883-890.
171. Van Mellaert L., Barbe S., Anne J. Clostridium spores as anti-tumour agents. Trends Microbiol 2006, 14:190-196.
172. Venkataramanan K.P., Jones S.W., McCormick K.P., Kunjeti S.G., Ralston M.T., Meyers B.C., et al. The Clostridium small RNome that responds to stress: the paradigm and importance of toxic metabolite stress in C. acetobutylicum. BMC Genomics 2013, 14:849.
173. Vidal J.E., Chen J.M., Li J.H., McClane B.A. Use of an EZ-Tn5-based random mutagenesis system to identify a novel toxin regulatory locus in Clostridium perfringens strain 13. PLoS One 2009, 4.
174. Wagner E.G.H., Simons R.W. Antisense RNA control in bacteria, phages, and plasmids. Annu Rev Microbiol 1994, 48:713-742.
175. Walkinshaw M.D., Taylor P., Sturrock S.S., Atanasiu C., Berge T., Henderson R.M., et al. Structure of Ocr from bacteriophage T7, a protein that mimics B-form DNA. Mol Cell 2002, 9:187-194.
176. Wang Y., Li X.Z., Milne C.B., Janssen H., Lin W.Y., Phan G., et al. Development of a gene knockout system using mobile group II introns (Targetron) and genetic disruption of acid production pathways in Clostridium beijerinckii. Appl Environ Microbiol 2013, 79:5853-5863.
177. 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.
178. Wiegel J., Tanner R., Rainey F.A. An introduction to the family Clostridiaceae. The prokaryotes 2006, 654-678. Springer, New York. 3rd ed. M. Dworkin, S. Falkow, E. Rosenberg, K.H. Schleifer, E. Stackebrandt (Eds.).
179. Wilkinson S.R., Young M. Wide diversity of genome size among different strains of Clostridium acetobutylicum. J Gen Microbiol 1993, 139:1069-1076.
180. Williams D.R., Young D.I., Young M. Conjugative plasmid transfer from Escherichia coli to Clostridium acetobutylicum. J Gen Microbiol 1990, 136:819-826.
181. Xiao H., Li Z.L., Jiang Y., Yang Y.L., Jiang W.H., Gu Y., et al. Metabolic engineering of d-xylose pathway in Clostridium beijerinckii to optimize solvent production from xylose mother liquid. Metab Eng 2012, 14:569-578.
182. Xu S.Y., Corvaglia A.R., Chan S.H., Zheng Y., Linder P. A type IV modification-dependent restriction enzyme SauUSI from Staphylococcus aureus subsp. aureus USA300. Nucleic Acids Res 2011, 39:5597-5610.
183. Yu M.R., Zhang Y.L., Tang I.C., Yang S.T. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production. Metab Eng 2011, 13:373-382.
184. Yu M.R., Du Y.M., Jiang W.Y., Chang W.L., Yang S.T., Tang I.C. Effects of different replicons in conjugative plasmids on transformation efficiency, plasmid stability, gene expression and n-butanol biosynthesis in Clostridium tyrobutyricum. Appl Microbiol Biotechnol 2012, 93:881-889.
185. Yutin N., Galperin M.Y. A genomic update on clostridial phylogeny: gram-negative spore formers and other misplaced clostridia. Environ Microbiol 2013, 15:2631-2641.
186. Zhang Y.M., Buchholz F., Muyrers J.P.P., Stewart A.F. A new logic for DNA engineering using recombination in Escherichia coli. Nat Genet 1998, 20:123-128.
187. Zhang G.Q., Bao P., Zhang Y., Deng A.H., Chen N., Wen T.Y. Enhancing electro-transformation competency of recalcitrant Bacillus amyloliquefaciens by combining cell-wall weakening and cell-membrane fluidity disturbing. Anal Biochem 2011, 409:130-137.
188. Zheng Y.N., Li L.Z., Xian M., Ma Y.J., Yang J.M., Xu X., et al. Problems with the microbial production of butanol. J Ind Microbiol Biotechnol 2009, 36:1127-1138.
189. 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.
190. Zhou Y.T., Johnson E.A. Genetic transformation of Clostridium botulinum Hall A by electroporation. Biotechnol Lett 1993, 15:121-126.
191. Zhu Y., Liu X.G., Yang S.T. Construction and characterization of pta gene-deleted mutant of Clostridium tyrobutyricum for enhanced butyric acid fermentation. Biotechnol Bioeng 2005, 90:154-166.
192. Zhuang F.L., Karberg M., Perutka J., Lambowitz A.M. EcI5, a group IIB intron with high retrohoming frequency: DNA target site recognition and use in gene targeting. RNA 2009, 15:432-449.