Genome sequence of the mesophilic Thermotogales bacterium Mesotoga prima MesG1.Ag.4.2 reveals the largest Thermotogales genome to date

Genome Biology and Evolution

Volumn 4, Issue 8, 2012, Pages 700-708

  Zhaxybayeva, Olga ^a,b   Swithers, Kristen S ^c   Foght, Julia ^d   Green, Anna G ^c   Bruce, David ^e   Detter, Chris ^e   Han, Shunsheng ^e   Teshima, Hazuki ^e   Han, James ^f   Woyke, Tanja ^f   Pitluck, Sam ^f   Nolan, Matt ^f   Ivanova, Natalia ^f   Pati, Amrita ^f   Land, Miriam L ^g   Dlutek, Marlena ^h   Doolittle, W Ford ^h   Noll, Kenneth M ^c   Nesbø, Camilla L ^d,i  

^a WEST VIRGINIA UNIVERSITY   (United States)

^b DARTMOUTH COLLEGE   (United States)

^c UNIVERSITY OF CONNECTICUT   (United States)

^d UNIVERSITY OF ALBERTA   (Canada)

^e LOS ALAMOS NATIONAL LABORATORY   (United States)

^f DOE JOINT GENOME INSTITUTE   (United States)

^g OAK RIDGE NATIONAL LABORATORY   (United States)

^h DALHOUSIE UNIVERSITY   (Canada)

ⁱ UNIVERSITY OF OSLO   (Norway)

Author keywords

Lateral gene transfer; Mesophilic; Temperature adaptation; Thermotogales

Indexed keywords

BACTERIA (MICROORGANISMS); LANGAT VIRUS; OLEARIA; THERMOTOGALES;

EID: 84866374347     PISSN: None     EISSN: 17596653     Source Type: Journal    
DOI: 10.1093/gbe/evs059     Document Type: Article

References (40)

1. Ben Hania W, et al. 2011. Cultivation of the first mesophilic representative ("mesotoga") within the order Thermotogales. System Appl Microbiol. 34:581-585.
2. Chaffron S, Rehrauer H, Pernthaler J, Mering von C. 2010. A global network of coexisting microbes from environmental and whole-genome sequence data. Genome Res. 20:947-959.
3. Charbonnier F, Forterre P. 1994. Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria. J Bacteriol. 176:1251-1259.
4. Desantis TZ, et al. 2006. NAST: a multiple sequence alignment server for comparative analysis of 16S rRNA genes. Nucleic Acids Res. 34: W394-W399.
5. Dipippo JL, et al. 2009. Kosmotoga olearia gen. nov., sp. nov., a thermophilic, anaerobic heterotroph isolated from an oil production fluid. Int J System Evol Microbiol. 59:2991-3000.
6. Donini S, et al. 2006. A threonine synthase homolog from a mammalian genome. Biochem Biophys Res Commun. 350:922-928.
7. Felsenstein J. 1985. Phylogenies and the comparative method. Am Nat. 125:1-15.
8. Giovannoni SJ, et al. 2005. Genome streamlining in a cosmopolitan oceanic bacterium. Science 309:1242-1245.
9. Graham DE, Taylor SM, Wolf RZ, Namboori SC. 2009. Convergent evolution of coenzyme M biosynthesis in the Methanosarcinales: cysteate synthase evolved from an ancestral threonine synthase. Biochem J. 424:467-478.
10. Grigoriev A. 1998. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res. 26:2286-2290.
11. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol. 52: 696-704.
12. Harriott O, Huber R, Stetter K, Betts P, Noll K. 1994. A cryptic miniplasmid from the hyperthermophilic bacterium Thermotoga sp. strain RQ7. J Bacteriol. 176:2759-2762.
13. Holoman TR, Elberson MA, Cutter LA, May HD, Sowers KR. 1998. Characterization of a defined 2,3,5, 6-tetrachlorobiphenyl-orthodechlorinating microbial community by comparative sequence analysis of genes coding for 16S rRNA. Appl Environ Microbiol. 64: 3359-3367.
14. Hu LI, Lima BP, Wolfe AJ. 2010. Bacterial protein acetylation: the dawning of a new age. Mol Microbiol. 77:15-21.
15. Kemp PF, Aller JY. 2004. Bacterial diversity in aquatic and other environments: what 16S rDNA libraries can tell us. FEMS Microbiol Ecol. 47: 161-177.
16. Klotz MG. 2003. The molecular evolution of catalatic hydroperoxidases: evidence formultiple lateral transfer of genes between prokaryota and from bacteria into eukaryota. Mol Biol Evol. 20:1098-1112.
17. Konstantinidis KT, Tiedje JM. 2004. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci. 101:3160-3165.
18. Konstantinidis KT, Tiedje JM. 2005. Towards a genome-based taxonomy for prokaryotes. J Bacteriol. 187:6258-6264.
19. Kuo C-H,Moran NA, Ochman H. 2009. The consequences of genetic drift for bacterial genome complexity. Genome Res. 19:1450-1454.
20. Lynch M. 2006. Streamlining and simplification of microbial genome architecture. Annu Rev Microbiol. 60:327-349.
21. Makarova KS, et al. 2011. Evolution and classification of the CRISPR-Cas systems. Nat Rev Microbiol. 9:467-477.
22. Markowitz VM, et al. 2012. IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res. 40: D115-D122.
23. Meiri S. 2010. Bergmann's Rule - what's in a name? Global Ecol Biogeogr. 20:203-207.
24. Nelson KE, et al. 1999. Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima. Nature 399:323-329.
25. Nesbø CL, et al. 2009. The genome of Thermosipho africanus TCF52B: lateral genetic connections to the Firmicutes and Archaea. J Bacteriol. 191:1974-1978.
26. Nesbø CL, et al. 2012. Mesotoga prima gen. nov., sp. nov., the first described mesophilic species of the Thermotogales. Extremophiles 16:387-93.
27. Nesbø CL, Dlutek M, Zhaxybayeva O, Doolittle WF. 2006. Evidence for existence of "mesotogas," members of the order Thermotogales adapted to low-temperature environments. Appl Environ Microbiol. 72:5061-5068.
28. Nesbø CL, Kumaraswamy R, Dlutek M, Doolittle WF, Foght JM. 2010. Searching for mesophilic Thermotogales bacteria: "mesotogas" in the wild. Appl Environ Microbiol. 76:4896-4900.
29. Podell S, Gaasterland T. 2007. DarkHorse: a method for genome-wideprediction of horizontal gene transfer. Genome Biol. 8:R16.
30. Rice P, Longden I, Bleasby A. 2000. EMBOSS: The European Molecular Biology Open Software Suite. Trends Genet. 16:276-277.
31. Saillard C, et al. 2008. The abundant extrachromosomal DNA content of the Spiroplasma citri GII3-3X genome. BMC Genomics 9:195.
32. Smidt H, de Vos WM. 2004. Anaerobic microbial dehalogenation. Annu Rev Microbiol. 58:43-73.
33. Smillie CS, et al. 2011. Ecology drives a global network of gene exchange connecting the human microbiome. Nature 480:241-244.
34. Sogin ML, et al. 2006. Microbial diversity in the deep sea and the underexplored "rare biosphere." Proc Natl Acad Sci U S A. 103: 12115-12120.
35. Straight PD, Kolter R. 2009. Interspecies chemical communication in bacterial development. Annu Rev Microbiol. 63:99-118.
36. Suhre K, Claverie J-M. 2003. Genomic correlates of hyperthermostability, an update. J Biol Chem. 278:17198-17202.
37. Tatusov RL, et al. 2001. The COG database: new developments in phylogenetic classification of proteins from complete genomes. Nucleic Acids Res. 29:22-28.
38. Whittaker RH. 1975. Communities and ecosystems, 2nd ed. New York: Macmillan Co.
39. Zeldovich KB, Berezovsky IN, Shakhnovich EI. 2007. Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol. 3:e5.
40. Zhaxybayeva O, et al. 2009. On the chimeric nature, thermophilic origin, and phylogenetic placement of the Thermotogales. Proc Natl Acad Sci. 106:5865-5870.