Complete genome sequence of Desulfurococcus mucosus type strain (O7/1 T)

Standards in Genomic Sciences

Volumn 4, Issue 2, 2011, Pages 173-182

  Wirth, Reinhard ^a   Chertkov, Olga ^b,c   Held, Brittany ^b,c   Lapidus, Alla ^b   Nolan, Matt ^b   Lucas, Susan ^b   Hammon, Nancy ^b   Deshpande, Shweta ^b   Cheng, Jan Fang ^b   Tapia, Roxane ^b,c   Han, Cliff ^b,c   Goodwin, Lynne ^b,c   Pitluck, Sam ^b   Liolios, Konstantinos ^b   Ioanna, Pagani ^b   Ivanova, Natalia ^b   Mavromatis, Konstantinos ^b   Mikhailova, Natalia ^b   Pati, Amrita ^b   Chen, Amy ^d   Palaniappan, Krishna ^d   Land, Miriam ^b,e   Hauser, Loren ^b,e   Chang, Yun Juan ^b,e   Jeffries, Cynthia D ^b,e   Bilek, Yvonne ^a   Hader, Thomas ^a   Rohde, Manfred ^f   Spring, Stefan ^g   Sikorski, Johannes ^g   Göker, Markus ^g   Woyke, Tanja ^b   Bristow, James ^b   Eisen, Jonathan A ^b,h   Markowitz, Victor ^d   Hugenholtz, Philip ^b,i   Kyrpides, Nikos C ^b   Klenk, Hans Peter ^g   more..

^a UNIVERSITY OF REGENSBURG   (Germany)

^b DOE JOINT GENOME INSTITUTE   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^e OAK RIDGE NATIONAL LABORATORY   (United States)

^f HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^g LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (Germany)

^h UNIVERSITY OF CALIFORNIA   (United States)

ⁱ UNIVERSITY OF QUEENSLAND   (Australia)

Author keywords

Anaerobic; Desulfurococcaceae; Extracellular enzymes; GEBA; Hyperthermophile; Non motile; Organotroph; Spheroid shaped; Sulfur respiration

Indexed keywords

ARCHAEA; BACTERIA (MICROORGANISMS); CRENARCHAEOTA; DESULFUROCOCCACEAE; DESULFUROCOCCUS; DESULFUROCOCCUS MUCOSUS;

EID: 80053368415     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.1644004     Document Type: Article

References (48)

1. Zillig W, Stetter KO, Prangishvilli D, Schäfer W, Wunderl S, Janekovic D, Holz I, Palm P. Desulfu-rococcaceae, the second family of the extremely thermophilic, anaerobic, sulfur-respiring Thermo-proteales. Zentralbl Bakteriol 1982; 3:304-317.
2. Garrity G. NamesforLife. BrowserTool takes ex-pertise out of the database and puts it right in the browser. Microbiol Today 2010; 37:9.
3. List Editor. Validation List no. 10. Validation of the publication of new names and new combina-tions previously effectively published outside the IJSB. Int J Syst Bacteriol 1983; 33:438-440. doi:10.1099/00207713-33-2-438
4. Tu JK, Prangishvilli D, Huber H, Wildgruber G, Zillig W, Stetter KO. Taxonomic relations be-tween Archaebacteria including 6 novel genera examined by cross hybridization of DNAs and 16S rRNAs. Mol Evol 1982; 18:109-114. PubMed doi:10.1007/BF01810829
5. Klenk HP, Haas B, Schwass V, Zillig W. Hybridi-zation homology: a new parameter for the analy-sis of phylogenetic relations, demonstrated with the urkingdom of the Archaebacteria. J Mol Evol 1986; 24:167-173. doi:10.1007/BF02099964
6. Prangishvilli D, Zillig W, Gierl A, Biesert L, Holz I. DNA-dependent RNA polymerase of thermoa-cidophilic archaebacteria. Eur J Biochem 1982; 122:471-477. PubMed doi:10.1111/j.1432-1033.1982.tb06461.x
7. Thurl S, Witke W, Buhrow I, Schäfer W. Qui-nones from archaebacteria, II. Different types of quinones from sulphur-dependent archaebacteria. Biol Chem Hoppe Seyler 1986; 367:191-197. PubMed doi:10.1515/bchm3.1986.367.1.191
8. Cowan DA, Smolenski KA, Daniel RM, Morgan HW. An extracellular proteinase from a strain of the archaebacterium Desulfurococcus growing at 88 degrees C. Biochem J 1987; 247:121-133. PubMed
9. Duffner F, Bertoldo C, Andersen JT, Wagner K, Antranikian G. A new thermoactive pullulanase from Desulfurococcus mucosus: cloning, se-quencing, purification, and characterization of the recombinant enzyme ofter expression in Bacil-lus subtilis. J Bacteriol 2000; 182:6331-6338. PubMed doi:10.1128/JB.182.22.6331-6338.2000
10. DeSantis TZ, Hugenholtz P, Larsen N, Rojas M, Brodie E, Keller K, Huber T, Dalevi D, Hu P, An-dersen G. Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB. Appl Environ Microbiol 2006; 72:5069-5072. PubMed doi:10.1128/AEM.03006-05
11. Porter MF. An algorithm for suffix stripping. Pro-gram: electronic library and information systems 1980; 14:130-137. doi:10.1108/eb046814
12. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
13. Lee C, Grasso C, Sharlow MF. Multiple sequence alignment using partial order graphs. Bioinformat-ics 2002; 18:452-464. PubMed doi:10.1093/bioinformatics/18.3.452
14. Stamatakis A, Hoover P, Rougemont J. A rapid bootstrap algorithm for the RAxML Web servers. Syst Biol 2008; 57:758-771. PubMed doi:10.1080/10635150802429642
15. Pattengale ND, Alipour M, Bininda-Emonds ORP, Moret BME, Stamatakis A. How many bootstrap replicates are necessary? Lect Notes Comput Sci 2009; 5541:184-200. doi:10.1007/978-3-642-02008-7_13
16. Liolios K, Chen IM, Mavromatis K, Tavernarakis N, Hugenholtz P, Markowitz VM, Kyrpides NC. The Genomes On Line Database (GOLD) in 2009: status of genomic and metagenomic projects and their associated metadata. Nucleic Acids Res 2009; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
17. Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG. Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon De-sulfurococcus kamchatkensis. J Bacteriol 2009; 191:2371-2379. PubMed doi:10.1128/JB.01525-08
18. Anderson IJ, Sun H, Lapidus A, Copeland A, Glavina Del Rio T, Tice H, Dalin E, Lucas S, Barry K, Land M, et al. Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1. Stand Genomic Sci 2009; 1:183-188. PubMed doi:10.4056/sigs.30527
19. Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP. The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic crenarchaeote growing up to 108 °C. Archaea 2007; 2:127-135. PubMed doi:10.1155/2007/745987
20. Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, et al. Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1T). Stand Genomic Sci 2010; 3:66-75. PubMed doi:10.4056/sigs.1072907
21. Podar M, Anderson I, Makarova KS, Elkins JG, Ivanova N, Wall MA, Lykidis A, Mavromatis K, Sun H, Hudson ME, et al. A genomic analysis of the archaeal system Ignicoccus hospitalis-Nanoarchaeum equitans. Genome Biol 2008; 9:R158. PubMed doi:10.1186/gb-2008-9-11-r158
22. Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, et al. Complete genome sequence of Ther-mosphaera aggregans type strain (M11TLT). Stand Genomic Sci 2010; 2:245-259. PubMed doi:10.4056/sigs.821804
23. Huber H, Stetter KO. 2006. Desulfurococcales In: M Dworkin, S Falkow, E Rosenberg, KH Schleifer E Stackebrandt (eds), The Prokaryotes, 3. ed, vol. 3. Springer, New York, p. 52-68.
24. Stetter KO, Zillig W. 1985. Thermoplasma and the thermophilic sulfur-dependent archaebacteria. In: Woese CR, and Wolfe RS (eds) The Bacteria. Academic Press. New York, NY. 8:100-201.
25. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Thomson N, Allen MJ, An-giuoli SV, et al. The minimum information about a genome sequence (MIGS) specification. Nat Biotechnol 2008; 26:541-547. PubMed doi:10.1038/nbt1360
26. Woese CR, Kandler O, Wheelis ML. Towards a natural system of organisms: proposal for the do-mains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci USA 1990; 87:4576-4579. PubMed doi:10.1073/pnas.87.12.4576
27. Validation list 85: Validation of publication of new names and new combinations previously ef-fectively published outside the IJSEM. Int J Syst Evol Microbiol 2002; 52:685-690. PubMed doi:10.1099/ijs.0.02358-0
28. Garrity GM, Holt JG. 2001. Phylum AI. Crenar-chaeota phy. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Syste-matic Bacteriology, Second Edition, Volume 1, Springer, New York, p. 169-210.
29. Reysenbach AL. 2001. Class I. Thermoprotei class. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Systematic Bacteri-ology, Second Edition, Volume 1, Springer, New York, p.169.
30. Huber H, Stetter O. 2001. Order II. Desulfuro-coccales ord. nov. In: Garrity GM, Boone DR, Castenholz RW (eds), Bergey's Manual of Syste-matic Bacteriology, Second Edition, Volume 1, Springer, New York, p. 179-180.
31. Burggraf S, Huber H, Stetter KO. Reclassification of the crenarchael orders and families in accor-dance with 16S rRNA sequence data. Int J Syst Bacteriol 1997; 47:657-660. PubMed doi:10.1099/00207713-47-3-657
32. Perevalova AA, Svetlichny VA, Kublanov IV, Chernyh NA, Kostrikina NA, Tourova TP, Kuznet-sov BB, Bonch-Osmolovskaya EA. Desulfurococ-cus fermentans sp. nov., a novel hyperthermo-philic archaeon from a Kamchatka hot spring, and emended description of the genus Desulfurococ-cus. Int J Syst Evol Microbiol 2005; 55:995-999. PubMed doi:10.1099/ijs.0.63378-0
33. Classification of. Bacteria and Archaea in risk groups. www.baua.deTRBA466.
34. Ashburner M, Ball CA, Blake JA, Botstein D, But-ler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, et al. Gene Ontology: tool for the unification of biology. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
35. Kjems J, Garrett RA. Novel splicing mechanism for the ribosomal RNA intron in the archaebacte-rium Desulfurococcus mobilis. Cell 1988; 54:693-703. PubMed doi:10.1016/S0092-8674(88)80014-X
36. Lanzotti V, De Rosa M, Trincone A, Basso AL, Gambacorta A, Zillig W. Complex lipids from Desulfurococcus mobilis, a sulfur-reducing arc-haebacterium. Biochim Biophys Acta 1987; 922:95-102.
37. Klenk HP, Göker M. En route to a genome-based classification of Archaea and Bacteria? Syst Appl Microbiol 2010; 33:175-182. PubMed doi:10.1016/j.syapm.2010.03.003
38. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova NN, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic encyclopaedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed doi:10.1038/nature08656
39. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php.
40. Gemeinholzer B, Dröge G, Zetzsche H, Haszpru-nar G, Klenk HP, Güntsch A, Berendsohn WG, Wägele JW. The DNA Bank Network: the start from a German initiative. Biopreservation and Biobanking 2011; 9:51-55. doi:10.1089/bio.2010.0029
41. DOE Joint Genome Institute. http://www.jgi.doe.gov
42. Phrap and Phred for Windows, MacOS, Linux, and Unix. http://www.phrap.com
43. Zerbino DR, Birney E. Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res 2008; 18:821-829. PubMed doi:10.1101/gr.074492.107
44. Han C, Chain P. 2006. Finishing repeat regions automatically with Dupfinisher. In: Proceeding of the 2006 international conference on bioinfor-matics & computational biology. Edited by Hamid R. Arabnia & Homayoun Valafar, CSREA Press. June 26-29, 2006: 141-146.
45. Lapidus A, LaButti K, Foster B, Lowry S, Trong S, Goltsman E. POLISHER: An effective tool for us-ing ultra short reads in microbial genome assem-bly and finishing. AGBT, Marco Island, FL, 2008.
46. Hyatt D, Chen GL, LoCascio PF, Land ML, Lari-mer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identifi-cation. BMC Bioinformatics 2010; 11:119. PubMed doi:10.1186/1471-2105-11-119
47. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, Lykidis A, Kyrpides NC. Gene-PRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 2010; 7:455-457. PubMed doi:10.1038/nmeth.1457
48. Markowitz VM, Ivanova NN, Chen IMA, Chu K, Kyrpides NC. IMG ER: a system for microbial ge-nome annotation expert review and curation. Bio-informatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393