Targeted gene engineering in Clostridium cellulolyticum H10 without methylation

Journal of Microbiological Methods

Volumn 89, Issue 3, 2012, Pages 201-208

  Cui, Gu Zhen ^a   Hong, Wei ^a   Zhang, Jie ^a   Li, Wen Li ^b   Feng, Yingang ^a   Liu, Ya Jun ^a   Cui, Qiu ^a  

^a QINGDAO INSTITUTE OF BIOENERGY AND BIOPROCESS TECHNOLOGY   (China)

^b Ocean University of China   (China)

Author keywords

Acetate kinase; ClosTron; Lactate dehydrogenase; Methylation free; MspI; Oxygen independent green fluorescence protein

Indexed keywords

ACETATE KINASE; AMPICILLIN; ENDONUCLEASE; GLYCINE; ISONIACIN; LACTATE DEHYDROGENASE; MSPI ENDONUCLEASE; NICOTINIC ACID DERIVATIVE; PHOSPHATE ACETYLTRANSFERASE; THREONINE; UNCLASSIFIED DRUG;

ARTICLE; BACTERIAL GENE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM MUTANT; BIOFUEL PRODUCTION; CCEL2136 GENE; CCEL2485 GENE; CCEL2866 GENE; CLOSTRIDIUM CELLULOLYTICUM; CONTROLLED STUDY; DNA METHYLATION; ELECTROTRANSFORMATION; ENZYME ACTIVITY; ESCHERICHIA COLI; FERMENTATION; GENE DISRUPTION; GENE EXPRESSION; GENE INACTIVATION; GENE TARGETING; GENETIC MANIPULATION; NONHUMAN; NUCLEOTIDE SEQUENCE; PPFBFP GENE; PRIORITY JOURNAL; PROTEIN EXPRESSION; REPORTER GENE;

CLOSTRIDIUM CELLULOLYTICUM; DEOXYRIBONUCLEASE HPAII; DNA METHYLATION; DNA, BACTERIAL; GENE KNOCKOUT TECHNIQUES; GENE TARGETING; GENES, REPORTER; GENETIC ENGINEERING; GREEN FLUORESCENT PROTEINS; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; TRANSFORMATION, BACTERIAL;

CLOSTRIDIUM CELLULOLYTICUM;

EID: 84860364258     PISSN: 01677012     EISSN: 18728359     Source Type: Journal    
DOI: 10.1016/j.mimet.2012.02.015     Document Type: Article

References (55)

1. Andersch W., Bahl H., Gottschalk G. Level of enzymes involved in acetate, butyrate, acetone and butanol formation by Clostridium acetobutylicum. Eur. J. Appl. Microbiol. Biotechnol. 1983, 18:327-332.
2. 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.
3. Berndt C., Meier P., Wackernagel W. DNA restriction is a barrier to natural transformation in Pseudomonas stutzeri JM300. Microbiology 2003, 149:895-901.
4. Blouzard J.C., Valette O., Tardif C., de Philip P. Random mutagenesis of Clostridium cellulolyticum by using a Tn1545 derivative. Appl. Environ. Microbiol. 2010, 76:4546-4549.
5. Bradford M.M. A rapid and sensitive method for the quantitation of microgram quantities of protein utilizing the principle of protein-dye binding. Anal. Biochem. 1976, 72:248-254.
6. Chauthaiwale V.M., Vyas P.R., Deshpande V.V. Genetic transformation of Chainia and heat attenuation of its restriction system. Can. J. Microbiol. 1991, 37:713-715.
7. Contag P.R., Williams M.G., Rogers P. Cloning of a lactate dehydrogenase gene from Clostridium acetobutylicum B643 and expression in Escherichia coli. Appl. Environ. Microbiol. 1990, 56:3760-3765.
8. Donahue J.P., Peek R.M. Restriction and modification systems. Helicobacter pylori: Physiology and Genetics 2001, ASM Press, Washington (DC). H.L. Mobley, G.L. Mendz, S.L. Hazell (Eds.).
9. Dong H., Zhang Y., Dai Z., Li Y. Engineering clostridium strain to accept unmethylated DNA. PLoS One 2010, 5:e9038.
10. Dong H., Tao W., Zhu L., Zhang Y., Li Y. CAC2634-disrupted mutant of Clostridium acetobutylicum can be electrotransformed in air. Lett. Appl. Microbiol. 2011, 53:379-382.
11. Drepper T., Eggert T., Circolone F., Heck A., Krauss U., Guterl J.K., Wendorff M., Losi A., Gartner W., Jaeger K.E. Reporter proteins for in vivo fluorescence without oxygen. Nat. Biotechnol. 2007, 25:443-445.
12. Gal L., Pages S., Gaudin C., Belaich A., Reverbel-Leroy C., Tardif C., Belaich J.P. Characterization of the cellulolytic complex (cellulosome) produced by Clostridium cellulolyticum. Appl. Environ. Microbiol. 1997, 63:903-909.
13. Giallo J., Gaudin C., Belaich J.P. Metabolism and solubilization of cellulose by Clostridium cellulolyticum H10. Appl. Environ. Microbiol. 1985, 49:1216-1221.
14. Gorrell R.J., Yang J., Kusters J.G., van Vliet A.H., Robins-Browne R.M. Restriction of DNA encoding selectable markers decreases the transformation efficiency of Helicobacter pylori. FEMS Immunol. Med. Microbiol. 2005, 44:213-219.
15. Gowen C.M., Fong S.S. Exploring biodiversity for cellulosic biofuel production. Chem. Biodivers. 2010, 7:1086-1097.
16. Guedon E., Desvaux M., Petitdemange H. Improvement of cellulolytic properties of Clostridium cellulolyticum by metabolic engineering. Appl. Environ. Microbiol. 2002, 68:53-58.
17. Hammes W., Schleifer K.H., Kandler O. Mode of action of glycine on the biosynthesis of peptidoglycan. J. Bacteriol. 1973, 116:1029-1053.
18. 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.
19. Heap J.T., Cartman S.T., Kuehne S.A., Cooksley C., Minton N.P. ClosTron-targeted mutagenesis. Methods Mol. Biol. 2010, 646:165-182.
20. 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.
21. Higashide W., Li Y., Yang Y., Liao J.C. Metabolic engineering of Clostridium cellulolyticum for isobutanol production from cellulose. Appl. Environ. Microbiol. 2011, 77:2727-2733.
22. Horton R.M., Hunt H.D., Ho S.N., Pullen J.K., Pease L.R. Engineering hybrid genes without the use of restriction enzymes: gene splicing by overlap extension. Gene 1989, 77:61-68.
23. Jennert K.C., Tardif C., Young D.I., Young M. Gene transfer to Clostridium cellulolyticum ATCC 35319. Microbiology 2000, 146:3071-3080.
24. Jia K., Zhu Y., Zhang Y., Li Y. Group II intron-anchored gene deletion in Clostridium. PLoS One 2011, 6:e16693.
25. Jin M., Balan V., Gunawan C., Dale B.E. Consolidated bioprocessing (CBP) performance of Clostridium phytofermentans on AFEX-treated corn stover for ethanol production. Biotechnol. Bioeng. 2011, 108:1290-1297.
26. Johnson E.A., Madia A., Demain A.L. Chemically defined minimal medium for growth of the anaerobic cellulolytic thermophile Clostridium thermocellum. Appl. Environ. Microbiol. 1981, 41:1060-1062.
27. Lee S.Y., Bennett G.N., Papoutsakis E.T. Construction of Escherichia coli-Clostridium acetobutylicum shuttle vectors and transformation of Clostridium acetobtylicum strains. Biotechnol. Lett. 1992, 14:427-432.
28. Li Y., Tschaplinski T.J., Engle N.L., Hamilton C.Y., Rodriguez M., Liao J.C., Schadt C.W., Guss A.M., Yang Y., Graham D.E. Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations. Biotechnol. Biofuels 2012, 5:2.
29. Lin L., Song H., Ji Y., He Z., Pu Y., Zhou J., Xu J. Ultrasound-mediated DNA transformation in thermophilic gram-positive anaerobes. PLoS One 2010, 5:e12582.
30. Lobo L.A., Smith C.J., Rocha E.R. Flavin mononucleotide (FMN)-based fluorescent protein (FbFP) as reporter for gene expression in the anaerobe Bacteroides fragilis. FEMS Microbiol. Lett. 2011, 317:67-74.
31. Lutke-Eversloh T., Bahl H. Metabolic engineering of Clostridium acetobutylicum: recent advances to improve butanol production. Curr. Opin. Biotechnol. 2011, 22:634-647.
32. Lynd L.R., Grethlein H.E., Wolkin R.H. Fermentation of cellulosic substrates in batch and continuous culture by Clostridium thermocellum. Appl. Environ. Microbiol. 1989, 55:3131-3139.
33. Lynd L., Zyl W., McBride J., Laser M. Consolidated bioprocessing of cellulosic biomass: an update. Curr. Opin. Biotechnol. 2005, 16:577-583.
34. Maamar H., Valette O., Fierobe H.P., Belaich A., Belaich J.P., Tardif C. Cellulolysis is severely affected in Clostridium cellulolyticum strain cipCMut1. Mol. Microbiol. 2004, 51:589-598.
35. Maamar H., Abdou L., Boileau C., Valette O., Tardif C. Transcriptional analysis of the cip-cel gene cluster from Clostridium cellulolyticum. J. Bacteriol. 2006, 188:2614-2624.
36. 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.
37. Matseliukh A.B. Genetic transformation of Streptomyces globisporus strain 1912: restriction barrier and plasmid compatibility. Mikrobiol. Z. 2001, 63:15-22.
38. Mermelstein L.D., Welker N.E., Bennett G.N., Papoutsakis E.T. Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. Biotechnol. (NY) 1992, 10:190-195.
39. Nathans D., Smith H.O. Restriction endonucleases in the analysis and restructuring of dna molecules. Annu. Rev. Biochem. 1975, 44:273-293.
40. Papoutsakis E.T. Engineering solventogenic clostridia. Curr. Opin. Biotechnol. 2008, 19:420-429.
41. 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.
42. 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.
43. Perutka J., Wang W., 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.
44. Petitdemange E., Caillet F., Giallo J., Gaudin C. Clostridium cellulolyticum sp. nov, a cellulolytic, mesophilic species from decayed grass. Int. J. Syst. Bacteriol. 1984, 34:155-159.
45. Rodriguez S.A., Yu J.J., Davis G., Arulanandam B.P., Klose K.E. Targeted inactivation of Francisella tularensis genes by group II introns. Appl. Environ. Microbiol. 2008, 74:2619-2626.
46. Rose I.A. Acetate kinase of bacteria (acetokinase). Methods Enzymol. 1955, 1:591-595.
47. Sahota G., Stormo G.D. Novel sequence-based method for identifying transcription factor binding sites in prokaryotic genomes. Bioinformatics 2010, 26:2672-2677.
48. Sambrook J., Fritsch E.F., Maniatis T. Molecular cloning: a laboratory manual 1989, Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY. 2nd ed.
49. Shaner N.C., Patterson G.H., Davidson M.W. Advances in fluorescent protein technology. J. Cell Sci. 2007, 120:4247-4260.
50. 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.
51. 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. U. S. A. 2008, 105:13769-13774.
52. Tardif C., Maamar H., Balfin M., Belaich J.P. Electrotransformation studies in Clostridium cellulolyticum. J. Ind. Microbiol. Biotechnol. 2001, 27:271-274.
53. Thomas C.M., Nielsen K.M. Mechanisms of, and barriers to, horizontal gene transfer between bacteria. Nat. Rev. Microbiol. 2005, 3:711-721.
54. Yu M., Zhang Y., Tang I.C., Yang S.T. Metabolic engineering of Clostridium tyrobutyricum for n-butanol production. Metab. Eng. 2011, 13:373-382.
55. Zhang Y.H., Lynd L.R. Cellulose utilization by Clostridium thermocellum: bioenergetics and hydrolysis product assimilation. Proc. Natl. Acad. Sci. U. S. A. 2005, 102:7321-7325.