Construction of a Stable Replicating Shuttle Vector for Caldicellulosiruptor Species: Use for Extending Genetic Methodologies to Other Members of This Genus

PLoS ONE

Volumn 8, Issue 5, 2013, Pages

  Chung, Daehwan ^a,b   Cha, Minseok ^a,b   Farkas, Joel ^a,b,c   Westpheling, Janet ^a,b  

^a University of Georgia ^*  (United States)

^b OAK RIDGE NATIONAL LABORATORY   (United States)

^c OHIO STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

APRAMYCIN; METHYLTRANSFERASE; PLASMID DNA; PROTEIN S30EA; RIBOSOME PROTEIN; UNCLASSIFIED DRUG; BACTERIAL PROTEIN;

ARTICLE; BACTERIAL GENE; BACTERIUM ISOLATION; BACTERIUM TRANSFORMATION; CALDICELLULOSIRUPTOR; CALDICELLULOSIRUPTOR BESCII; CALDICELLULOSIRUPTOR HYDROTHERMALIS; CARBOHYDRATE ANALYSIS; CLONING VECTOR; CONTROLLED STUDY; DELETION MUTANT; DNA METHYLATION; ESCHERICHIA COLI; GENE CASSETTE; GENE LOCUS; GENE REARRANGEMENT; GENE REPLICATION; GENETIC ANALYSIS; GENETIC COMPLEMENTATION; GENETIC SELECTION; IN VITRO STUDY; MOLECULAR CLONING; NONHUMAN; PLASMID; PYRF GENE; SHUTTLE VECTOR; THERMOPHILIC BACTERIUM; TRANSCRIPTION REGULATION; ANAEROBIC BACTERIUM; BIOMASS; CHEMISTRY; ENZYMOLOGY; FERMENTATION; GENE VECTOR; GENETICS; GRAM POSITIVE BACTERIUM; HEAT; METABOLISM; PLANT;

CALDICELLULOSIRUPTOR;

BACTERIA, ANAEROBIC; BACTERIAL PROTEINS; BIOMASS; CLONING, MOLECULAR; DNA METHYLATION; ESCHERICHIA COLI; FERMENTATION; GENETIC VECTORS; GRAM-POSITIVE BACTERIA; HOT TEMPERATURE; PLANTS; PLASMIDS; RIBOSOMAL PROTEINS; TRANSFORMATION, BACTERIAL;

EID: 84877056036     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0062881     Document Type: Article

References (38)

1. Himmel ME, Ding SY, Johnson DK, Adney WS, Nimlos MR, et al. (2007) Biomass recalcitrance: engineering plants and enzymes for biofuels production. Science 315: 804-807.
2. McCann MC, Carpita NC, (2008) Designing the deconstruction of plant cell walls. Curr Opin Plant Biol 11: 314-320.
3. Wilson DB, (2008) Three microbial strategies for plant cell wall degradation. Ann N Y Acad Sci 1125: 289-297.
4. Wyman CE, (2007) What is (and is not) vital to advancing cellulosic ethanol. Trends Biotechnol 25: 153-157.
5. Zhang YH, Ding SY, Mielenz JR, Cui JB, Elander RT, et al. (2007) Fractionating recalcitrant lignocellulose at modest reaction conditions. Biotechnol Bioeng 97: 214-223.
6. Negro MJ, Manzanares P, Ballesteros I, Oliva JM, Cabanas A, et al. (2003) Hydrothermal pretreatment conditions to enhance ethanol production from poplar biomass. Appl Biochem Biotechnol 105-108: 87-100.
7. Blumer-Schuette SE, Giannone RJ, Zurawski JV, Ozdemir I, Ma Q, et al. (2012) Caldicellulosiruptor core and pangenomes reveal determinants for noncellulosomal thermophilic deconstruction of plant biomass. J Bacteriol 194: 4015-4028.
8. Blumer-Schuette SE, Kataeva I, Westpheling J, Adams MW, Kelly RM, (2008) Extremely thermophilic microorganisms for biomass conversion: status and prospects. Curr Opin Biotechnol 19: 210-217.
9. Yang SJ, Kataeva I, Hamilton-Brehm SD, Engle NL, Tschaplinski TJ, et al. (2009) Efficient degradation of lignocellulosic plant biomass, without pretreatment, by the thermophilic anaerobe "Anaerocellum thermophilum" DSM 6725. Appl Environ Microbiol 75: 4762-4769.
10. Bredholt S, Sonne-Hansen J, Nielsen P, Mathrani IM, Ahring BK, (1999) Caldicellulosiruptor kristjanssonii sp. nov., a cellulolytic, extremely thermophilic, anaerobic bacterium. Int J Syst Bacteriol 49 Pt 3: 991-996.
11. Hamilton-Brehm SD, Mosher JJ, Vishnivetskaya T, Podar M, Carroll S, et al. (2010) Caldicellulosiruptor obsidiansis sp. nov., an anaerobic, extremely thermophilic, cellulolytic bacterium isolated from Obsidian Pool, Yellowstone National Park. Appl Environ Microbiol 76: 1014-1020.
12. Huang CY, Patel BK, Mah RA, Baresi L, (1998) Caldicellulosiruptor owensensis sp. nov., an anaerobic, extremely thermophilic, xylanolytic bacterium. Int J Syst Bacteriol 48 Pt 1: 91-97.
13. Miroshnichenko ML, Kublanov IV, Kostrikina NA, Tourova TP, Kolganova TV, et al. (2008) Caldicellulosiruptor kronotskyensis sp. nov. and Caldicellulosiruptor hydrothermalis sp. nov., two extremely thermophilic, cellulolytic, anaerobic bacteria from Kamchatka thermal springs. Int J Syst Evol Microbiol 58: 1492-1496.
14. Rainey FA, Donnison AM, Janssen PH, Saul D, Rodrigo A, et al. (1994) Description of Caldicellulosiruptor saccharolyticus gen. nov., sp. nov: an obligately anaerobic, extremely thermophilic, cellulolytic bacterium. FEMS Microbiol Lett 120: 263-266.
15. Svetlichnyi VA, Svetlichnaya TP, Chernykh NA, Zavarzin GA, (1990) Anaerocellum Thermophilum Gen. Nov Sp. Nov. an Extremely Thermophilic Cellulolytic Eubacterium Isolated from Hot-Springs in the Valley of Geysers. Microbiology 59: 598-604.
16. Blumer-Schuette SE, Lewis DL, Kelly RM, (2010) Phylogenetic, microbiological, and glycoside hydrolase diversities within the extremely thermophilic, plant biomass-degrading genus Caldicellulosiruptor. Appl Environ Microbiol 76: 8084-8092.
17. Dam P, Kataeva I, Yang SJ, Zhou F, Yin Y, et al. (2011) Insights into plant biomass conversion from the genome of the anaerobic thermophilic bacterium Caldicellulosiruptor bescii DSM 6725. Nucleic Acids Res 39: 3240-3254.
18. VanFossen AL, Ozdemir I, Zelin SL, Kelly RM, (2011) Glycoside hydrolase inventory drives plant polysaccharide deconstruction by the extremely thermophilic bacterium Caldicellulosiruptor saccharolyticus. Biotechnol Bioeng 108: 1559-1569.
19. Chung D, Farkas J, Huddleston JR, Olivar E, Westpheling J, (2012) Methylation by a Unique α-class N4-Cytosine Methyltransferase Is Required for DNA Transformation of Caldicellulosiruptor bescii DSM6725. PLoS One 7: e43844.
20. Lynd LR, van Zyl WH, McBride JE, Laser M, (2005) Consolidated bioprocessing of cellulosic biomass: an update. Curr Opin Biotechnol 16: 577-583.
21. Mai V, Lorenz WW, Wiegel J, (1997) Transformation of Thermoanaerobacterium sp. strain JW/SL-YS485 with plasmid pIKM1 conferring kanamycin resistance. FEMS Microbiol Lett 148: 163-167.
22. Jennert KC, Tardif C, Young DI, Young M, (2000) Gene transfer to Clostridium cellulolyticum ATCC 35319. Microbiology 146 Pt 12: 3071-3080.
23. Imanaka T, Fujii M, Aramori I, Aiba S, (1982) Transformation of Bacillus stearothermophilus with plasmid DNA and characterization of shuttle vector plasmids between Bacillus stearothermophilus and Bacillus subtilis. J Bacteriol 149: 824-830.
24. Tripathi SA, Olson DG, Argyros DA, Miller BB, Barrett TF, et al. (2010) Development of pyrF-based genetic system for targeted gene deletion in Clostridium thermocellum and creation of a pta mutant. Appl Environ Microbiol 76: 6591-6599.
25. Tsoi TV, Chuvil'skaia NA, Atakishieva I, Dzhavakhishvili T, Akimenko VK (1987) [Clostridium thermocellum-a new object of genetic studies]. Mol Gen Mikrobiol Virusol: 18-23.
26. Clausen A, Mikkelsen MJ, Schroder I, Ahring BK, (2004) Cloning, sequencing, and sequence analysis of two novel plasmids from the thermophilic anaerobic bacterium Anaerocellum thermophilum. Plasmid 52: 131-138.
27. Farkas JCD, Cha M, Grayeski P, Westpheling J (2012) Improved Growth Media and Culture Techniques for Genetic Analysis and Assessment of Biomass Utilization by Caldicellulosiruptor bescii. Journal of industrial Microbiology & Biotechnology. In press.
28. Sambrook J, Russell D (2001) Molecular Cloning: A Laboratory Manual: Cold Spring Harbor Laboratory Press.
29. Lipscomb GL, Stirrett K, Schut GJ, Yang F, Jenney FE Jr, et al. (2011) Natural competence in the hyperthermophilic archaeon Pyrococcus furiosus facilitates genetic manipulation: construction of markerless deletions of genes encoding the two cytoplasmic hydrogenases. Appl Environ Microbiol 77: 2232-2238.
30. Chung DH, Huddleston JR, Farkas J, Westpheling J, (2011) Identification and characterization of CbeI, a novel thermostable restriction enzyme from Caldicellulosiruptor bescii DSM 6725 and a member of a new subfamily of HaeIII-like enzymes. J Ind Microbiol Biotechnol 38: 1867-1877.
31. Boeke JD, LaCroute F, Fink GR, (1984) A positive selection for mutants lacking orotidine-5'-phosphate decarboxylase activity in yeast: 5-fluoro-orotic acid resistance. Mol Gen Genet 197: 345-346.
32. Zwick ME, Joseph SJ, Didelot X, Chen PE, Bishop-Lilly KA, et al. (2012) Genomic characterization of the Bacillus cereus sensu lato species: backdrop to the evolution of Bacillus anthracis. Genome Res 22: 1512-1524.
33. Kurusu Y, Yoshimura S, Tanaka M, Nakamura T, Maruyama A, et al. (2001) Genetic transformation system for a psychrotrophic deep-sea bacterium: isolation and characterization of a psychrotrophic plasmid. Mar Biotechnol (NY) 3: 96-99.
34. Espinosa M, del Solar G, Rojo F, Alonso JC, (1995) Plasmid rolling circle replication and its control. FEMS Microbiol Lett 130: 111-120.
35. Chung D, Farkas J, Westpheling J (2013) Detection of a novel active transposable element in Caldicellulosiruptor hydrothermalis and a new search for elements in this genus. J Ind Microbiol Biotechnol: doi:10.1007/s10295-10013-11244-z.
36. Gruss A, Ehrlich SD, (1989) The family of highly interrelated single-stranded deoxyribonucleic acid plasmids. Microbiol Rev 53: 231-241.
37. Karita S, Ohtaki A, Noborikawa M, Nakasaki K, (2001) A cryptic plasmid, pAO1, from a compost bacterium, Bacillus sp. Biosci Biotechnol Biochem 65: 226-228.
38. Roberts RJ, Vincze T, Posfai J, Macelis D, (2010) REBASE-a database for DNA restriction and modification: enzymes, genes and genomes. Nucleic Acids Res 38: D234-236.