Complete genome sequence of dehalobacter restrictus PER-K23T

Standards in Genomic Sciences

Volumn 8, Issue 3, 2013, Pages

  Kruse, Thomas ^a   Maillard, Julien ^b   Goodwin, Lynne ^c,d   Woyke, Tanja ^c   Teshima, Hazuki ^c,d   Bruce, David ^c,d   Detter, Chris ^c,d   Tapia, Roxanne ^c,d   Han, Cliff ^c,d   Huntemann, Marcel ^c   Wei, Chia Lin ^c   Han, James ^c   Chen, Amy ^c   Kyrpides, Nikos ^c   Szeto, Ernest ^c   Markowitz, Victor ^c   Ivanova, Natalia ^c   Pagani, Ioanna ^c   Pati, Amrita ^c   Pitluck, Sam ^c   Nolan, Matt ^c   Holliger, Christof ^b   Smidt, Hauke ^a   more..

^a WAGENINGEN UNIVERSITY   (Netherlands)

^b EPFL   (Switzerland)

^c DOE JOINT GENOME INSTITUTE   (United States)

^d LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

Anaerobe; Dehalobacter restrictus type strain; Organohalide respiration; PCE; Reductive dehalogenases; TCE

Indexed keywords

CORRINOID; HYDROGENASE;

ARTICLE; BACTERIAL GENOME; BACTERIAL GROWTH; BACTERIAL STRAIN; BACTERIUM; BACTERIUM CULTURE; BACTERIUM IDENTIFICATION; BACTERIUM ISOLATION; CHROMOSOME ARM; DEHALOBACTER RESTRICTUS; DNA ISOLATION; GENE EXPRESSION; GENE SEQUENCE; GENETIC ASSOCIATION; NONHUMAN; NUCLEOTIDE SEQUENCE; ORGANISMS BY ELECTRON DONOR; RNA GENE; SEQUENCE HOMOLOGY;

EID: 84881056028     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.3787426     Document Type: Article

References (61)

1. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJB. Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol 1998; 169:313-321.
2. Wild A, Hermann R, Leisinger T. Isolation of an anaerobic bacterium which reductively dechlorinates tetrachloroethene and trichloroethene. Biodegradation 1996; 7:507-511.
3. Maphosa F, Van Passel MWJ, De Vos WM, Smidt H. Metagenome analysis reveals yet unexplored reductive dechlorinating potential of Dehalobacter sp. E1 growing in co-culture with Sedimentibacter sp. Environmental Microbiology Reports 2012; 4:604-616.
4. Lee M, Low A, Zemb O, Koenig J, Michaelsen A, Manefield M. Complete chloroform dechlorination by organochlorine respiration and fermentation. Environ Microbiol 2012; 14:883-894.
5. Justicia-Leon SD, Ritalahti KM, Mack EE, Löffler FE. Dichloromethane fermentation by a Dehalobacter sp. in an enrichment culture derived from pristine river sediment. Appl Environ Microbiol 2012; 78:1288-1291.
6. Holliger C, Schraa G, Stams AJ, Zehnder AJ. A highly purified enrichment culture couples the reductive dechlorination of tetrachloroethene to growth. Appl Environ Microbiol 1993; 59:2991-2997.
7. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547.
8. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579.
9. Gibbons NE, Murray RGE. Proposals Concerning the Higher Taxa of Bacteria. Int J Syst Bacteriol 1978; 28:1-6.
10. Garrity GM, Holt JG. The Road Map to the Manual. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 1, Springer, New York, 2001, p. 119-169.
11. Murray RGE. The Higher Taxa, or, a Place for Everything? In: Holt JG (ed), Bergey's Manual of Systematic Bacteriology, First Edition, Volume 1, The Williams and Wilkins Co., Baltimore, 1984, p. 31-34.
12. List of new names and new combinations previously effectively, but not validly, published. List no. 132. Int J Syst Evol Microbiol 2010; 60:469-472.
13. Rainey FA. Class II. Clostridia class nov. In: De Vos P, Garrity G, Jones D, Krieg NR, Ludwig W, Rainey FA, Schleifer KH, Whitman WB (eds), Bergey's Manual of Systematic Bacteriology, Second Edition, Volume 3, Springer-Verlag, New York, 2009, p. 736.
14. Skerman VBD, McGowan V, Sneath PHA. Approved Lists of Bacterial Names. Int J Syst Bacteriol 1980; 30:225-420.
15. Prévot AR. In: Hauderoy P, Ehringer G, Guillot G, Magrou. J., Prévot AR, Rosset D, Urbain A (eds), Dictionnaire des Bactéries Pathogènes, Second Edition, Masson et Cie, Paris, 1953, p. 1-692.
16. Rogosa M. Peptococcaceae, a new family to include the Gram-positive, anaerobic cocci of the genera Peptococcus, Peptostreptococcus and Ruminococcus. Int J Syst Bacteriol 1971; 21:234-237.
17. Validation of publication of new names and new combinations previously effectively published outside the IJSB. List No. 66. Int J Syst Bacteriol 1998; 48:631-632.
18. Holliger C, Hahn D, Harmsen H, Ludwig W, Schumacher W, Tindall B, Vazquez F, Weiss N, Zehnder AJ. Dehalobacter restrictus gen. nov. and sp. nov., a strictly anaerobic bacterium that reductively dechlorinates tetra- and trichloroethene in an anaerobic respiration. Arch Microbiol 1998; 169:313-321.
19. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000; 25:25-29.
20. Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. MEGA5: Molecular Evolutionary Genetics Analysis using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods. Mol Biol Evol 2011.
21. Edgar RC. MUSCLE: Multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-1797.
22. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987; 4:406-425.
23. Takayuki EH. C. The Firmicutes. In: Vos PG, G.; Jones, D.; Krieg, N.R.; Ludwig, W.; Rainey, F.A.; Schleifer, K.-H.; Whitman, W.B., editor. Bergey's Manual of Systematic Bacteriology. Volume 32009. p 969-975.
24. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, Angiuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547.
25. Bennett S. Solexa Ltd. Pharmacogenomics 2004; 5:433-438.
26. Margulies M, Egholm M, Altman WE, Attiya S, Bader JS, Bemben LA, Berka J, Braverman MS, Chen YJ, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005; 437:376-380.
27. The DOE Joint Genome Institute. http://www.jgi.doe.gov
28. Zerbino DR, Birney E. Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829.
29. Ewing B, Hillier L, Wendl MC, Green P. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res 1998; 8:175-185.
30. Ewing B, Green P. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res 1998; 8:186-194.
31. Gordon D, Abajian C, Green P. Consed: A graphical tool for sequence finishing. Genome Res 1998; 8:195-202.
32. Han C, Chain P. 2006 Finishing Repetitive Regions Automatically with Dupfinisher. In Proceedings of the 2006 International Conference on Bioinformatics Computational Biology, BIOCOMP'06.
33. Azai C, Tsukatani Y, Itoh S, Oh-oka H. C-type cytochromes in the photosynthetic electron transfer pathways in green sulfur bacteria and heliobacteria. Photosynth Res 2010; 104:189-199.
34. Paquete CM, Louro RO. Molecular details of multielectron transfer: The case of multiheme cytochromes from metal respiring organisms. Dalton Trans 2010; 39:4259-4266.
35. Hong Y, Gu JD. Bacterial anaerobic respiration and electron transfer relevant to the biotransformation of pollutants. Int Biodeterior Biodegradation 2009; 63:973-980.
36. Gibson J, Harwood CS. Metabolic diversity in aromatic compound utilization by anaerobic microbes. Annu Rev Microbiol 2002; 56:345-369.
37. Andrews SC, Berks BC, McClay J, Ambler A, Quail MA, Golby P, Guest A. 12-cistron Escherichia coli operon (hyf) encoding a putative proton-translocating formate hydrogenlyase system. Microbiology 1997; 143:3633-3647.
38. Calusinska M, Happe T, Joris B, Wilmotte A. The surprising diversity of clostridial hydrogenases: A comparative genomic perspective. Microbiology 2010; 156:1575-1588.
39. Hakobyan M, Sargsyan H, Bagramyan K. Proton translocation coupled to formate oxidation in anaerobically grown fermenting Escherichia coli. Biophys Chem 2005; 115:55-61.
40. Hug LA, Maphosa F, Leys D, Loffler FE, Smidt H, Edwards EA, Lorenz A. Overview of organohalide respiration and introduction of a simple classification system for reductive dehalogenases. Philos Trans R Soc Lond B Biol Sci 2012; 368.
41. Campanella JJ, Bitincka L, Smalley J. MatGAT: An application that generates similarity/identity matrices using protein or DNA sequences. BMC Bioinformatics 2003; 4:29.
42. Maillard J, Schumacher W, Vazquez F, Regeard C, Hagen WR, Holliger C. Characterization of the corrinoid iron-sulfur protein tetrachloroethene reductive dehalogenase of Dehalobacter restrictus. Appl Environ Microbiol 2003; 69:4628-4638.
43. Nonaka H, Keresztes G, Shinoda Y, Ikenaga Y, Abe M, Naito K, Inatomi K, Furukawa K, Inui M, Yukawa H. Complete genome sequence of the dehalorespiring bacterium Desulfitobacterium hafniense Y51 and comparison with Dehalococcoides ethenogenes 195. J Bacteriol 2006; 188:2262-2274.
44. Kim SH, Harzman C, Davis J, Hutcheson R, Broderick J, Marsh T, Tiedje J. Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction. BMC Microbiol 2012; 12:21.
45. Siddaramappa S, Challacombe JF, Delano SF, Green LD, Daligault H, Bruce D, Detter C, Tapia R, Han S, Goodwin L, et al. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9 T) and comparison to Dehalococcoides strains. Stand Genomic Sci 2012; 6:251-264.
46. Taş N, Van Eekert MHA, De Vos WM, Smidt H. The little bacteria that can - Diversity, genomics and ecophysiology of "Dehalococcoides" spp. in contaminated environments. Microb Biotechnol 2010; 3:389-402.
47. McMurdie PJ, Behrens SF, Muller JA, Goke J, Ritalahti KM, Wagner R, Goltsman E, Lapidus A, Holmes S, Loffler FE, et al. Localized Plasticity in the Streamlined Genomes of Vinyl Chloride Respiring Dehalococcoides. PLoS Genet 2009.
48. Rupakula A, Kruse T, Boeren S, Holliger C, Smidt H, Maillard J. Evaluation of the restricted metabolism of the obligate organohalide respiring bacterium Dehalobacter restrictus - lessons from a tiered functional genomics approach. Philos Trans R Soc Lond B Biol Sci 2013; 368.
49. Gábor K, Veríssimo CS, Cyran BC, Ter Horst P, Meijer NP, Smidt H, De Vos WM, Van Der Oost J. Characterization of CprK1, a CRP/FNR-type transcriptional regulator of halorespiration from Desulfitobacterium hafniense. J Bacteriol 2006; 188:2604-2613.
50. Duret A, Holliger C, Maillard J. The opportunistic physiology of Desulfitobacterium hafniense strain TCE1 towards organohalide respiration with tetrachloroethene. Appl Environ Microbiol 2012; 78:6121-6127.
51. Maillard J, Regeard C, Holliger C. Isolation and characterization of Tn-Dha1, a transposon containing the tetrachloroethene reductive dehalogenase of Desulfitobacterium hafniense strain TCE1. Environ Microbiol 2005; 7:107-117.
52. Futagami T, Tsuboi Y, Suyama A, Goto M, Furukawa K. Emergence of two types of nondechlorinating variants in the tetrachloroethene-halorespiring Desulfitobacterium sp strain Y51. Appl Microbiol Biotechnol 2006; 70:720-728.
53. Maphosa F, de Vos WM, Smidt H. Exploiting the ecogenomics toolbox for environmental diagnostics of organohalide-respiring bacteria. Trends Biotechnol 2010; 28:308-316.
54. Seshadri R, Adrian L, Fouts DE, Eisen JA, Phillippy AM, Methe BA, Ward NL, Nelson WC, Deboy RT, Khouri HM, et al. Genome sequence of the PCE-dechlorinating bacterium Dehalococcoides ethenogenes. Science 2005; 307:105-108.
55. Smidt H, Song DL, van der Oost J, de Vos WM. Random transposition by Tn916 in Desulfitobacterium dehalogenans allows for isolation and characterization of halorespiration-deficient mutants. J Bacteriol 1999; 181:6882-6888.
56. Morris RM, Sowell S, Barofsky D, Zinder S, Richardson R. Transcription and mass-spectroscopic proteomic studies of electron transport oxidoreductases in Dehalococcoides ethenogenes. Environ Microbiol 2006; 8:1499-1509.
57. Ahsanul Islam M, Edwards EA, Mahadevan R. Characterizing the metabolism of Dehalococcoides with a constraint-based model. PLOS Comput Biol 2010; 6:e1000887.
58. Tang YJ, Yi S, Zhuang WQ, Zinder SH, Keasling JD, Alvarez-Cohen L. Investigation of carbon metabolism in Dehalococcoides ethenogenes strain 195 by use of isotopomer and transcriptomic analyses. J Bacteriol 2009; 191:5224-5231.
59. Childers SE, Ciufo S, Lovley DR. Geobacter metallireducens accesses insoluble Fe(III) oxide by chemotaxis. Nature 2002; 416:767-769.
60. Lovley DR, Ueki T, Zhang T, Malvankar NS, Shrestha PM, Flanagan KA, Aklujkar M, Butler JE, Giloteaux L, Rotaru AE, et al. Geobacter. The Microbe Electric's Physiology, Ecology, and Practical Applications. Adv Microb Physiol 2011; 59:1-100.
61. Tran HT, Krushkal J, Antommattei FM, Lovley DR, Weis RM. Comparative genomics of Geobacter chemotaxis genes reveals diverse signaling function. BMC Genomics 2008; 9:471.