Expansion of the genetic toolkit for metabolic engineering of Clostridium pasteurianum: Chromosomal gene disruption of the endogenous CpaAI restriction enzyme

Biotechnology for Biofuels

Volumn 7, Issue 1, 2014, Pages

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

^a UNIVERSITY OF WATERLOO   (Canada)

^b MCMASTER UNIVERSITY   (Canada)

^c Neemo Inc   (Canada)

Author keywords

Biofuel; Clostridium; Gene disruption; Intron; Metabolic engineering; Restriction modification

Indexed keywords

ALKYLATION; BIOFUELS; CLOSTRIDIUM; ESCHERICHIA COLI; GENE ENCODING; METABOLISM;

CLOSTRIDIUM PASTEURIANUM; ELECTROTRANSFORMATION; GENE DISRUPTIONS; INTRON; RECOGNITION SEQUENCE; RESTRICTION ENZYMES; RESTRICTION-MODIFICATION; TYPE II RESTRICTION ENDONUCLEASE;

METABOLIC ENGINEERING;

BACTERIUM; BIOFUEL; CHROMOSOME; ENZYME; GENETIC ENGINEERING;

CLOSTRIDIUM; CLOSTRIDIUM PASTEURIANUM; ESCHERICHIA COLI; LACTOCOCCUS;

EID: 84988876848     PISSN: 17546834     EISSN: None     Source Type: Journal    
DOI: 10.1186/s13068-014-0163-1     Document Type: Article

References (48)

1. Demirbas A: Political, economic and environmental impacts of biofuels: a review. Appl Energy 2009, 86:S108-S117.
2. Behzadi S, Farid MM: Review: examining the use of different feedstock for the production of biodiesel. Asia Pac J Chem Eng 2007, 2:480-486.
3. Tilman D, Socolow R, Foley JA, Hill J, Larson E, Lynd L, Pacala S, Reilly J, Searchinger T, Somerville C, Williams R: Beneficial biofuels-the food, energy, and environment trilemma. Science 2009, 325:270-271.
4. Carere CR, Sparling R, Cicek N, Levin DB: Third generation biofuels via direct cellulose fermentation. Int J Mol Sci 2008, 9:1342-1360.
5. da Silva GP, Mack M, Contiero J: Glycerol: a promising and abundant carbon source for industrial microbiology. Biotechnol Adv 2009, 27:30-39.
6. Johnson DT, Taconi KA: The glycerin glut: options for the value-added conversion of crude glycerol resulting from biodiesel production. Environ Prog 2007, 26:338-348.
7. Yang FX, Hanna MA, Sun RC: Value-added uses for crude glycerol-a byproduct of biodiesel production. Biotechnol Biofuels 2012, 5:13.
8. Yazdani SS, Gonzalez R: Anaerobic fermentation of glycerol: a path to economic viability for the biofuels industry. Curr Opin Biotechnol 2007, 18:213-219.
9. Biebl H: Fermentation of glycerol by Clostridium pasteurianum - Batch and continuous culture studies. J Ind Microbiol Biotechnol 2001, 27:18-26.
10. Dabrock B, Bahl H, Gottschalk G: Parameters affecting solvent production by Clostridium pasteurianum. Appl Environ Microbiol 1992, 58:1233-1239.
11. Taconi KA, Venkataramanan KP, Johnson DT: Growth and solvent production by Clostridium pasteurianum ATCC (R) 6013 (TM) utilizing biodiesel-derived crude glycerol as the sole carbon source. Environ Prog Sustainable Energy 2009, 28:100-110.
12. Jensen TO, Kvist T, Mikkelsen MJ, Christensen PV, Westermann P: Fermentation of crude glycerol from biodiesel production by Clostridium pasteurianum. J Ind Microbiol Biotechnol 2012, 39:709-717.
13. Jensen TO, Kvist T, Mikkelsen MJ, Westermann P: Production of 1,3-PDO and butanol by a mutant strain of Clostridium pasteurianum with increased tolerance towards crude glycerol. AMB Express 2012, 2:44.
14. Malaviya A, Jang YS, Lee SY: Continuous butanol production with reduced byproducts formation from glycerol by a hyper producing mutant of Clostridium pasteurianum. Appl Microbiol Biotechnol 2012, 93:1485-1494.
15. Pyne ME, Moo-Young M, Chung DA, Chou CP: Development of an electrotransformation protocol for genetic manipulation of Clostridium pasteurianum. Biotechnol Biofuels 2013, 6:50.
16. Papoutsakis ET: Engineering solventogenic clostridia. Curr Opin Biotechnol 2008, 19:420-429.
17. Pyne ME, Bruder M, Moo-Young M, Chung DA, Chou CP: Technical guide for genetic advancement of underdeveloped and intractable Clostridium. Biotechnol Adv 2014, 32:623-641.
18. Heap JT, Kuehne SA, Ehsaan M, Cartman ST, Cooksley CM, Scott JC, Minton NP: The ClosTron: mutagenesis in Clostridium refined and streamlined. J Microbiol Methods 2010, 80:49-55.
19. Heap JT, Pennington OJ, Cartman ST, Carter GP, Minton NP: The ClosTron: a universal gene knock-out system for the genus Clostridium. J Microbiol Methods 2007, 70:452-464.
20. 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.
21. Cai GQ, Jin B, Saint C, Monis P: Genetic manipulation of butyrate formation pathways in Clostridium butyricum. J Biotechnol 2011, 155:269-274.
22. Cui GZ, Hong W, Zhang J, Li WL, Feng YG, Liu YJ, Cui Q: Targeted gene engineering in Clostridium cellulolyticum H10 without methylation. J Microbiol Methods 2012, 89:201-208.
23. Li YC, Tschaplinski TJ, Engle NL, Hamilton CY, Rodriguez M, Liao JC, Schadt CW, Guss AM, Yang YF, Graham DE: 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.
24. Mohr G, Hong W, Zhang J, Cui GZ, Yang YF, Cui Q, Liu YJ, Lambowitz AM: A targetron system for gene targeting in thermophiles and its application in Clostridium thermocellum. PLoS One 2013, 8:e69032.
25. Tolonen AC, Chilaka AC, Church GM: Targeted gene inactivation in Clostridium phytofermentans shows that cellulose degradation requires the family 9 hydrolase Cphy3367. Mol Microbiol 2009, 74:1300-1313.
26. Aune TEV, Aachmann FL: Methodologies to increase the transformation efficiencies and the range of bacteria that can be transformed. Appl Microbiol Biotechnol 2010, 85:1301-1313.
27. Roberts RJ: Restriction enzymes and their isoschizomers. Nucleic Acids Res 1987, 15:R189-R215.
28. Richards DF, Linnett PE, Oultram JD, Young M: Restriction endonucleases in Clostridium pasteurianum ATCC 6013 and C. thermohydrosulfuricum DSM 568. J Gen Microbiol 1988, 134:3151-3157.
29. Matsuura M, Saldanha R, Ma HW, Wank H, Yang J, Mohr G, Cavanagh S, Dunny GM, Belfort M, Lambowitz AM: 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.
30. Guo HT, Karberg M, Long M, Jones JP, Sullenger B, Lambowitz AM: Group II introns designed to insert into therapeutically relevant DNA target sites in human cells. Science 2000, 289:452-457.
31. Guss AM, Olson DG, Caiazza NC, Lynd LR: Dcm methylation is detrimental to plasmid transformation in Clostridium thermocellum. Biotechnol Biofuels 2012, 5:1-6.
32. Leang C, Ueki T, Nevin KP, Lovley DR: A genetic system for Clostridium ljungdahlii: a chassis for autotrophic production of biocommodities and a model homoacetogen. Appl Environ Microbiol 2013, 79:1102-1109.
33. Pyne ME, Utturkar S, Brown SD, Moo-Young M, Chung DA, Chou CP: Improved draft genome sequence of Clostridium pasteurianum strain ATCC 6013 (DSM 525) using a hybrid next-generation sequencing approach. Genome Announc 2014, 2:e00790-14.
34. Roberts RJ, 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.
35. Dong HJ, Zhang YP, Dai ZJ, Li Y: Engineering Clostridium strain to accept unmethylated DNA. PLoS One 2010, 5:e9038.
36. Jennert KCB, Tardif C, Young DI, Young M: Gene transfer to Clostridium cellulolyticum ATCC 35319. Microbiology 2000, 146:3071-3080.
37. Liu SC, Minton NP, Giaccia AJ, Brown JM: Anticancer efficacy of systemically delivered anaerobic bacteria as gene therapy vectors targeting tumor hypoxia/necrosis. Gene Ther 2002, 9:291-296.
38. 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.
39. Oultram JD, Loughlin M, Swinfield TJ, Brehm JK, Thompson DE, Minton NP: Introduction of plasmids into whole cells of Clostridium acetobutylicum by electroporation. FEMS Microbiol Lett 1988, 56:83-88.
40. Roberts RJ, Belfort M, Bestor T, Bhagwat AS, Bickle TA, Bitinaite J, Blumenthal RM, Degtyarev SK, Dryden DTF, Dybvig K, Firman K, Gromova ES, Gumport RI, Halford SE, Hattman S, Heitman J, Hornby DP, Janulaitis A, Jeltsch A, Josephsen J, Kiss A, Klaenhammer TR, Kobayashi I, Kong H, Krüger DH, Lacks S, Marinus MG, Miyahara M, Morgan RD, Murray NE, et al: A nomenclature for restriction enzymes, DNA methyltransferases, homing endonucleases and their genes. Nucleic Acids Res 2003, 31:1805-1812.
41. Cui GZ, Zhang J, Hong W, Xu CG, Feng YG, Cui Q, Liu YJ: Improvement of ClosTron for successive gene disruption in Clostridium cellulolyticum using a pyrF-based screening system. Appl Microbiol Biotechnol 2014, 98:313-323.
42. Al-Hinai MA, Fast AG, Papoutsakis ET: 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.
43. Jang YS, Im JA, Choi SY, Lee JI, Lee SY: Metabolic engineering of Clostridium acetobutylicum for butyric acid production with high butyric acid selectivity. Metab Eng 2014, 23:165-174.
44. Mermelstein LD, Welker NE, Bennett GN, Papoutsakis ET: Expression of cloned homologous fermentative genes in Clostridium acetobutylicum ATCC 824. Nat Biotech 1992, 10:190-195.
45. Heap JT, Pennington OJ, Cartman ST, Minton NP: A modular system for Clostridium shuttle plasmids. J Microbiol Methods 2009, 78:79-85.
46. Kell DB, Peck MW, Rodger G, Morris JG: On the permeability to weak acids and bases of the cytoplasmic membrane of Clostridium pasteurianum. Biochem Biophys Res Commun 1981, 99:81-88.
47. Wilkinson SR, Young M: Wide diversity of genome size among different strains of Clostridium acetobutylicum. J Gen Microbiol 1993, 139:1069-1076.
48. Sambrook J, Fritsch EF, Maniatis T: Molecular Cloning: A Laboratory Manual. 2nd edition. Cold Spring Harbor: Cold Spring Harbor Press; 1989.