Complete genome sequence of Archaeoglobus profundus type strain (AV18 T)

Standards in Genomic Sciences

Volumn 2, Issue 3, 2010, Pages 327-346

  von Jan, Mathias ^a   Lapidus, Alla ^b   del Rio, Tijana Glavina ^b   Copeland, Alex ^b   Tice, Hope ^b   Cheng, Jan Fang ^b   Lucas, Susan ^b   Chen, Feng ^b   Nolan, Matt ^b   Goodwin, Lynne ^b,c   Han, Cliff ^b,c   Pitluck, Sam ^b   Liolios, Konstantinos ^b   Ivanova, Natalia ^b   Mavromatis, Konstantinos ^b   Ovchinnikova, Galina ^b   Chertkov, Olga ^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   Saunders, Elizabeth ^b   Brettin, Thomas ^b,c   Detter, John C ^b,c   Chain, Patrick ^b,d   Eichinger, Konrad ^f   Huber, Harald ^f   Spring, Ste fan ^a   Rohde, Manfred ^g   Göker, Markus ^a   Wirth, Reinhard ^f   Woyke, Tanja ^b   Bristow, Jim ^b   Eisen, Jonathan A ^b,h   Markowitz, Victor ^d   Hugenholtz, Philip ^b   Kyrpides, Nikos C ^b   Klenk, Hans Peter ^a   more..

^a LEIBNIZ INSTITUTE DSMZ GERMAN COLLECTION OF MICROORGANISMS AND CELL CULTURES   (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 UNIVERSITY OF REGENSBURG   (Germany)

^g HELMHOLTZ CENTRE FOR INFECTION RESEARCH   (Germany)

^h UNIVERSITY OF CALIFORNIA   (United States)

Author keywords

Archaeoglobaceae; GEBA; Hydrogen utili zation; Hydrothermal systems; Hyperthermophilic; Marine; Strictly anaerobic; Sulfate respiration

Indexed keywords

ARCHAEA; ARCHAEOGLOBACEAE; ARCHAEOGLOBALES; ARCHAEOGLOBI; ARCHAEOGLOBUS; ARCHAEOGLOBUS PROFUNDUS; BACTERIA (MICROORGANISMS); GEOGLOBUS;

EID: 79955013798     PISSN: 19443277     EISSN: None     Source Type: Journal    
DOI: 10.4056/sigs.942153     Document Type: Article

References (100)

1. Burggraf S, Jannasch HW, Nicolaus B, Stetter KO. Archaeoglobus profundus sp. nov., represents a new species within the sulfate-reducing archae-bacteria. Syst Appl Microbiol 1990; 13:24-28.
2. Validation List no. 34. Validation of the publica-tion of new names and new combinations pre-viously effectively published outside the IJSB. Int J Syst Bacteriol 1990; 40:320-321. doi:10.1099/00207713-40-3-320
3. Stetter KO. Archaeoglobus fulgidus gen. nov., sp. nov.: a new taxon of extremely thermophilic arc-haebacteria. Syst Appl Microbiol 1988; 10:172-173.
4. Hafenbradl D, Keller M, Dirmeier R, Rachel R, Roßnagel P, Burggraf S, Huber H, Stetter KO. Fer-roglobus placidus gen. nov., sp. nov., a novel hyperthermophilic archaeum that oxidizes Fe2+ at neutral pH under anoxic conditions. Arch Micro-biol 1996; 166:308-314. PubMed doi:10.1007/s002030050388
5. Kashefi K, Tor JM, Holmes DE, Gaw Van Praagh CV, Reysenbach AL, Lovley DE. Geoglobus ahan-gari gen. nov., sp. nov., a novel hyperthermophil-ic archaeon capable of oxidizing organic acids and growing autotrophically on hydrogen with Fe(III) serving as sole electron acceptor. Int J Syst Evol Microbiol 2002; 52:719-728. PubMed doi:10.1099/ijs.0.01953-0
6. Slobodkina GB, Kolganova TV, Querellou J, Bonch-Osmolovskaya EA, Slobodkin AI. Geoglo-bus acetivorans sp. nov., an iron(III)-reducing archaeon from a deep-sea hydrothermal vent. Int J Evol Microbiol 2009; 59:2880-2883. doi:10.1099/ijs.0.011080-0
7. Huber H, Jannasch H, Rachel R, Fuchs T, Stetter KO. Archaeoglobus veneficus sp. nov., a novel facultative chemolithoautotrophic hyperthermo-philic sulfide reducer, isolated from abyssal black smokers. Syst Appl Microbiol 1997; 20:374-380.
8. Mori K, Maruyama A, Urabe T, Suzuki K, Hanada S. Archaeoglobus infectus sp. nov., a novel ther-mophilic chemolithoheterotrophic archaeon iso-lated from a deep-sea rock collected at Suiyo Seamount, Izu-Bonin Arc, western Pacific Ocean. Int J Syst Evol Microbiol 2008; 58:810-816. PubMed doi:10.1099/ijs.0.65422-0
9. Steinsbu BO, Thorseth IH, Nakagawa S, Inagaki F, Lever MA, Engelen B, Øvreås L, Pedersen RB. Archaeoglobus sulfaticallidus sp. nov., a novel thermophilic and facultatively lithoautotrophic sulfate-reducer isolated from black rust exposed to hot ridge flank crustal fluids. Int J Syst Evol Mi-crobiol 2010; PubMed doi:10.1099/ijs.0.016105-0
10. Stetter KO, Huber R, Blöchl E, Kurr M, Eden RD, Fielder M, Cash H, Vance I. Hyperthermophilic archaea are thriving in deep North Sea and Alaskan oil reservoirs. Nature 1993; 365:743-745. doi:10.1038/365743a0
11. Chun J, Lee JH, Jung Y, Kim M, Kim S, Kim BK, Lim YW. EzTaxon: a web-based tool for the iden-tification of prokaryotes based on 16S ribosomal RNA gene sequences. Int J Syst Evol Microbiol 2007; 57:2259-2261. PubMed doi:10.1099/ijs.0.64915-0
12. Reysenbach AL, Longnecker K, Kirshtein J. Novel bacterial and archaeal lineages from an in situ growth chamber deployed at a mid-atlantic ridge hydrothermal vent. Appl Environ Microbiol 2000; 66:3798-3806. PubMed doi:10.1128/AEM.66.9.3798-3806.2000
13. Voordeckers JW, Do MH, Hügler M, Ko V, Sievert SM, Vetriani C. Culture dependent and indepen-dent ATP citrate lyase genes: a comparison of mi-crobial communities from different black smoker chimneys on the Mid-Atlantic Ridge. Extremo-philes 2008; 12:627-640. PubMed doi:10.1007/s00792-008-0167-5
14. Nercessian O, Reysenbach AL, Prieur D, Jeanthon C. Archaeal diversity associated with in situ sam-plers deployed in hydrothermal vents on the East Pacific Rise (13°N). Environ Microbiol 2003; 5:492-502. PubMed doi:10.1046/j.1462-2920.2003.00437.x
15. Moussard H, Moreira D, Cambon-Bonavita MA, López-García P, Jeanthon C. Uncultured Archaea in a hydrothermal microbial assemblage: phylo-genetic diversity and characterization of a ge-nome fragment from a euryarchaeote. FEMS Mi-crobiol Ecol 2006; 57:452-469. PubMed doi:10.1111/j.1574-6941.2006.00128.x
16. Higashi Y, Sunamura M, Kitamura K, Nakamura K, Kurusu Y, Ishibashi J, Urabe T, Maruyama A. Microbial diversity in hydrothermal environments of Suiyo Seamount, Izu-Bonin Arc, using a cathe-ter-type in situ growth chamber. FEMS Microbiol Ecol 2004; 47:327-336. PubMed doi:10.1016/S0168-6496(04)00004-2
17. Nakagawa S, Takai K, Inagaki F, Chiba H, Ishiba-shi J, Kataoka S, Hirayama H, Nunoura T, Horiko-shi K, Sako Y. Variability in microbial community and venting chemistry in a sediment-hosted back-arc hydrothermal system: Impacts of subseafloor phase-separation. FEMS Microbiol Ecol 2005; 54:141-155. PubMed doi:10.1016/j.femsec.2005.03.007
18. Takai K, Horikoshi K. Genetic diversity of archaea in deep-sea hydrothermal vent environments. Genetics 1999; 152:1285-1297. PubMed
19. Teske A, Hinrichs KU, Edgcomb V, de Vera Go-mez A, Kysela D, Sylva SP, Sogin ML, Jannasch HW. Microbial diversity of hydrothermal sedi-ments in the Guaymas Basin: evidence for anae-robic methanotrophic communities. Appl Environ Microbiol 2002; 68:1994-2007. PubMed doi:10.1128/AEM.68.4.1994-2007.2002
20. Pagé A, Tivey MK, Stakes DS, Reysenbach AL. Temporal and spacial archaeal colonization of hydrothermal vent deposits. Environ Microbiol 2008; 10:874-884. PubMed doi:10.1111/j.1462-2920.2007.01505.x
21. Nakagawa S, Inagaki F, Suzuki Y, Steinsbu BO, Lever MA, Takai K, Engelen B, Sako Y, Wheat CG, Horikoshi K and Integrated Ocean Drilling Program Expedition 301 Scientists. Microbial community in black rust exposed to hot ridge flank crustal fluids. Appl Environ Microbiol 2006; 72:6789-6799. PubMed doi:10.1128/AEM.01238-06
22. Gittel A, Sørensen KB, Skovhus TL, Ingvorsen K, Schramm A. Prokaryotic community structure and sulfate reducer activity in water from high-temperature oil reservoirs with and without nitrate treatment. Appl Environ Microbiol 2009; 75:7086-7096. PubMed doi:10.1128/AEM.01123-09
23. Kormas KA, Tamaki H, Hanada S, Kamagata Y. Apparent richness and community composition of Bacteria and Archaea in geothermal springs. Aquat Microb Ecol 2009; 57:113-122. doi:10.3354/ame01333
24. Spear JR, Walker JJ, McCollom TM, Pace NR. Hy-drogen and bioenergetics in the Yellowstone geo-thermal ecosystem. Proc Natl Acad Sci USA 2005; 102:2555-2560. doi:10.1073/pnas.0409574102
25. Costa KC, Navarro JB, Shock EL, Zhang CL, Sou-kup D, Hedlund BP. Microbiology and geochemi-stry of great boiling and mud hot springs in the United States Great Basin. Extremophiles 2009; 13:447-459. PubMed doi:10.1007/s00792-009-0230-x
26. Vick TJ, Dodsworth JA, Costa KC, Shock EL, Hed-lund BP. Microbiology and geochemistry of Little Hot Creek, a hot spring environment in the Long Valley Caldera. Geobiology 2010; 8:140-154. PubMed doi:10.1111/j.1472-4669.2009.00228.x
27. Kanokratana P, Chanapan S, Pootanakit K, Eurwi-laichtr L. Diversity and abundance of Bacteria and Archaea in the Bor Khuleng Hot Spring in Thailand. J Basic Microbiol 2004; 44:430-444. doi:10.1002/jobm.200410388
28. 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
29. Castresana J. Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis. Mol Biol Evol 2000; 17:540-552. PubMed
30. 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
31. Yarza P, Richter M, Peplies J, Euzeby J, Amann R, Schleifer KH, Ludwig W, Glöckner FO, Rosselló-Móra R. The all-species living tree project: a 16S rRNA-based phylogenetic tree of all sequenced type strains. Syst Appl Microbiol 2007; 31:241-250. doi:10.1016/j.syapm.2008.07.001
32. 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 2010; 38:D346-D354. PubMed doi:10.1093/nar/gkp848
33. Bult CJ, White O, Olsen GJ, Zhou L, Fleischmann RD, Sutton GG, Blake JA, FitzGerald LM, Clayton RA, Gocayne JD, et al. Complete genome se-quence of the methanogenic archaeon Methano-coccus jannaschii. Science 1996; 273:1058-1073. PubMed doi:10.1126/science.273.5278.1058
34. Klenk HP, Clayton RA, Tomb JF, White O, Nelson KE, Ketchum KA, Dodson RJ, Gwinn M, Hickey EK, Peterson JD, et al. The complete genome se-quence of the hyperthermophilic, sulphate-reducing archaeon Archaeoglobus fulgidus. Nature 1997; 390:364-370. PubMed doi:10.1038/37052
35. Felsenstein J. Evolutionary trees from DNA se-quences: a maximum likelihood approach. J Mol Evol 1981; 17:368-376. PubMed doi:10.1007/BF01734359
36. Field D, Garrity G, Gray T, Morrison N, Selengut J, Sterk P, Tatusova T, Tompson 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
37. Tor JM, Lovley DR. Anaerobic degradation of aromatic compounds coupled to Fe(III) reduction by Ferroglobus placidus. Environ Microbiol 2001; 3:281-287. PubMed doi:10.1046/j.1462-2920.2001.00192.x
38. 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
39. Garrity GM, Holt JG. Phylum AII. Euryarchaeota phy. nov. In: Bergey's Manual of Systematic Bac-teriology, vol. 1. 2nd ed. Edited by: Garrity GM, Boone DR, Castenholz RW. Springer, New York; 2001; pp 211-355.
40. Garrity GM, Holt JG. Class VI. Archaeoglobi class. nov. In: Bergey's Manual of Systematic Bac-teriology, vol. 1. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York; 2001; pp 349.
41. Huber H, Stetter KO. Order I. Archaeoglobales ord.: Bergey's Manual of Systematic Bac-teriology, second edition vol. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York; 2001; pp 349.
42. 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 un-ification of biology. The Gene Ontology Consor-tium. Nat Genet 2000; 25:25-29. PubMed doi:10.1038/75556
43. Hartzell P, Reed DW. The genus Archaeoglobus. In: Falkow S, Rosenberg E, Schleifer K-H, Stacke-brandt E. (eds.), Prokaryotes, Third Edition, Sprin-ger, New York 2006; 3:82-100.
44. 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
45. Wu D, Hugenholtz P, Mavromatis K, Pukall R, Dalin E, Ivanova N, Kunin V, Goodwin L, Wu M, Tindall BJ, et al. A phylogeny-driven genomic en-cyclopedia of Bacteria and Archaea. Nature 2009; 462:1056-1060. PubMed doi:10.1038/nature08656
46. List of growth media used at DSMZ: http://www.dsmz.de/microorganisms/media_list.php
47. Sims D, Brettin T, Detter JC, Han C, Lapidus A, Copeland A, Glavina Del Rio T, Nolan M, Chen F, Lucas S, et al. Complete genome sequence of Kytococcus sedentarius type strain (541T). Stand Genomic Sci 2009; 1:12-20. doi:10.4056/sigs.761
48. 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
49. Pati A, Ivanova N, Mikhailova N, Ovchinikova G, Hooper SD, Lykidis A, Kyrpides NC. GenePRIMP: A Gene Prediction Improvement Pipeline for mi-crobial genomes. Nat Methods 2010; 7:455-457. PubMed
50. Markowitz VM, Mavromatis K, Ivanova NN, Chen IM, Chu K, Kyrpides NC. IMG ER: a system for microbial genome annotation expert review and curation. Bioinformatics 2009; 25:2271-2278. PubMed doi:10.1093/bioinformatics/btp393
51. López-García P, Forterre P, van der Oost J, Erauso G. Plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled. J Bacteriol 2000; 182:4998-5000. PubMed doi:10.1128/JB.182.17.4998-5000.2000
52. Gao F, Zhang CT. Ori-Finder: a web-based sys-tem for finding oriCs in unannotated bacterial ge-nomes. BMC Bioinformatics 2008; 9:79. PubMed doi:10.1186/1471-2105-9-79
53. Grigoriev A. Analyzing genomes with cumulative skew diagrams. Nucleic Acids Res 1998; 26:2286-2290. PubMed doi:10.1093/nar/26.10.2286
54. Mrázek J, Karlin S. Strand compositional asymme-try in bacterial and large viral genomes. Proc Natl Acad Sci USA 1998; 95:3720-3725. PubMed doi:10.1073/pnas.95.7.3720
55. Salzberg SL, Salzberg AJ, Kerlavage AR, Tomb JF. Skewed oligomers and origins of replication. Gene 1998; 217:57-67. PubMed doi:10.1016/S0378-1119(98)00374-6
56. Lopez P, Philippe H, Myllykallio H, Forterre P. Identification of putative chromosomal origins of replication in archaea. Mol Microbiol 1999; 32:883-886. PubMed doi:10.1046/j.1365-2958.1999.01370.x
57. Rocha EPC, Danchin A, Viari A. Universal repli-cation biases in bacteria. Mol Microbiol 1999; 32:11-16. PubMed doi:10.1046/j.1365-2958.1999.01334.x
58. Maisnier-Patin S, Malandrin L, Birkeland NK, Bernander R. Chromosome replication patterns in the hyperthermophilic euryarchaea Archaeoglo-bus fulgidus and Methanocaldococcus (Methano-coccus) jannaschii. Mol Microbiol 2002; 45:1443-1450. PubMed doi:10.1046/j.1365-2958.2002.03111.x
59. Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD. Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 2004; 116:25-38. PubMed doi:10.1016/S0092-8674(03)01034-1
60. Shine J, Dalgarno L. The 3'-terminal sequence of Escherichia coli 16S ribosomal RNA: Complemen-tarity to nonsense triplets and ribosome binding sites. Proc Natl Acad Sci USA 1974; 71:1342-1346. PubMed doi:10.1073/pnas.71.4.1342
61. van Helden J, André B, Collado-Vides J. Extract-ing regulatory sites from the upstream region of yeast genes by computational analysis of oligo-nucleotide frequencies. J Mol Biol 1998; 281:827-842. PubMed doi:10.1006/jmbi.1998.1947
62. Münch R, Hiller K, Barg H, Heldt D, Linz S, Win-gender E, Jahn D. PRODORIC: prokaryotic data-base of gene regulation. Nucleic Acids Res 2003; 31:266-269. PubMed doi:10.1093/nar/gkg037
63. Bakke P, Carney N, DeLoache W, Gearing M, Ingvorsen K, Lotz M, McNair J, Penumetcha P, Simpson S, Voss L, et al. Evaluation of three au-tomated genome annotations for Halorhabdus utahensis. PLoS ONE 2009; 4:e6291. PubMed doi:10.1371/journal.pone.0006291
64. Anderson I, Tindall BJ, Pomrenke H, Göker M, Lapidus A, Nolan M, Copeland A, Glavina Del Rio T, Chen F, Tice H, et al. Complete genome sequence of Halorhabdus utahensis type strain (AX-2T). Stand Genomic Sci 2009; 1:218-225. doi:10.4056/sigs.31864
65. Torarinsson E, Klenk HP, Garrett RA. Divergent transcriptional and translational signals in arc-haea. Environ Microbiol 2005; 7:47-54. PubMed doi:10.1111/j.1462-2920.2004.00674.x
66. Korostelev A, Trakhanov S, Asahata H, Laurberg M, Lancaster L, Noller HF. Interactions and dy-namics of the Shine Dalgarno helix in the 70S ri-bosome. Proc Natl Acad Sci USA 2007; 104:16840-16843. PubMed doi:10.1073/pnas.0707850104
67. Lowe TM, Eddy SR. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 1997; 25:955-964. PubMed doi:10.1093/nar/25.5.955
68. Ikeuchi Y, Kimura S, Numata T, Nakamura D, Yokogawa T, Ogata T, Wada T, Suzuki T, Suzuki T. Agmatine-conjugated cytidine in a tRNA anti-codon is essential for AUA decoding in archaea. Nat Chem Biol 2010; 6:277-282. PubMed doi:10.1038/nchembio.323
69. Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Anderson I, Lyki-dis A, Mavromatis K, et al. The integrated micro-bial genomes system: an expanding comparative analysis resource. Nucleic Acids Res 2010; 38(Database issue):D382-D390. PubMed doi:10.1093/nar/gkp887
70. Kanehisa M, Goto S. KEGG: Kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000; 28:27-30. PubMed doi:10.1093/nar/28.1.27
71. Chang A, Scheer M, Grote A, Schomburg I, Schomburg D. BRENDA, AMENDA and FRENDA the enzyme information system: new content and tools in 2009. Nucleic Acids Res 2009; 37(Database issue):D588-D592. PubMed doi:10.1093/nar/gkn820
72. Caspi R, Altman T, Dale JM, Dreher K, Fulcher CA, Gilham F, Kaipa P, Karthikeyan AS, Kothari A, Krummenacker M, et al. The MetaCyc data-base of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases. Nucleic Acids Res 2010; 38(Database is-sue):D473-D479. PubMed doi:10.1093/nar/gkp875
73. Altschul SF, Gish W, Miller W, Myers EW, Lip-man DJ. Basic local alignment search tool. J Mol Biol 1990; 215:403-410. PubMed
74. Hunter S, Apweiler R, Attwood TK, Bairoch A, Bateman A, Binns D, Bork P, Das U, Daugherty L, Duquenne L, et al. InterPro: the integrative pro-tein signature database. Nucleic Acids Res 2009; 37(Database issue):D211-D215. PubMed doi:10.1093/nar/gkn785
75. Tahirov TH, Makarova KS, Rogozin IB, Pavlov YI, Koonin EV. Evolution of DNA polymerases: an inactivated polymerase-exonuclease module in Pol ε and a chimeric origin of eukaryotic polyme-rases from two classes of archaeal ancestors. Biol Direct 2009; 4:11. PubMed doi:10.1186/1745-6150-4-11
76. Castrec B, Rouillon C, Henneke G, Flament D, Querellou J, Raffin JP. Binding to PCNA in eu-ryarchaeal DNA replication requires two PIP mo-tifs for DNA polymerase D and one PIP motif for DNA polymerase B. J Mol Biol 2009; 394:209-218. PubMed doi:10.1016/j.jmb.2009.09.044
77. Pisani FM, De Martino C, Rossi MA. DNA poly-merase from the archaeon Sulfolobus solfataricus shows sequence similarity to family B DNA po-lymerases. Nucleic Acids Res 1992; 20:2711-2716. PubMed doi:10.1093/nar/20.11.2711
78. Prangishvili DA. DNA-dependent DNA polyme-rases of the thermoacidophilic archaebacterium Sulfolobus acidocaldarius. Mol Biol USSR 1986; 20:477-488.
79. Edgell DR, Klenk HP, Doolittle WF. Gene dupli-cations in evolution of archaeal family B DNA polymerases. J Bacteriol 1997; 179:2632-2640. PubMed
80. Klenk HP, Zillig W. DNA-dependent RNA poly-merase subunit B as a tool for phylogenetic re-constructions: branching topology of the archaeal domain. J Mol Evol 1994; 38:420-432. PubMed doi:10.1007/BF00163158
81. Edgar RC. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 2004; 32:1792-1797. PubMed doi:10.1093/nar/gkh340
82. Brochier C, Forterre P, Gribaldo S. Archaeal phy-logeny based on proteins of the transcription and translation machineries: tackling the Methanopy-rus kandleri paradox. Genome Biol 2004; 5:R17. PubMed doi:10.1186/gb-2004-5-3-r17
83. Jansen R, Embden JD, Gaastra W, Schouls LM. Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 2002; 43:1565-1575. PubMed doi:10.1046/j.1365-2958.2002.02839.x
84. Horvath P, Barrangou R. CRISPR/Cas, the immune system of bacteria and archaea. Science 2010; 327:167-170. PubMed doi:10.1126/science.1179555
85. Ng SY, Chaban B, Jarrell KF. Archaeal flagella, bacterial flagella and type IV pili: a comparison of genes and posttranslational modifications. J Mol Microbiol Biotechnol 2006; 11:167-191. PubMed doi:10.1159/000094053
86. Desmond E, Brochier-Armanet C, Gribaldo S. Phylogenomics of the archaeal flagellum: rare ho-rizontal gene transfer in a unique motility struc-ture. BMC Evol Biol 2007; 7:106. PubMed doi:10.1186/1471-2148-7-106
87. Szurmant H, Ordal GW. Diversity in chemotaxis mechanisms among the bacteria and archaea. Microbiol Mol Biol Rev 2004; 68:301-319. PubMed doi:10.1128/MMBR.68.2.301-319.2004
88. Schlesner M, Miller A, Streif S, Staudinger WF, Müller J, Scheffer B, Siedler F, Oesterhelt D. Iden-tification of Archaea-specific chemotaxis proteins which interact with the flagellar apparatus. BMC Microbiol 2009; 9:56. PubMed doi:10.1186/1471-2180-9-56
89. Stetter KO, Huber R. The role of hyperthermophil-ic prokaryotes in oil fields. In: Bell CR, Brylinsky M, Johnson-Green P (eds.), Microbial Biosystems: New Frontiers: Proceedings of the 8th Internation-al Symposium on Microbial Ecology, Atlantic Canada Society for Microbial Ecology, Halifax, Canada 2000, pp. 369-375.
90. Khelifi N, Grossi V, Hamdi M, Dolla A, Tholozan JL, Ollivier B, Hirschler-Réa A. Anaerobic oxida-tion of fatty acids by the hypothermophilic sul-fate-reducing archaeon Archaeoglobus fulgidus. Appl Environ Microbiol 2010; 76:3057-3060. PubMed doi:10.1128/AEM.02810-09
91. Richardson DJ, Berks BC, Russell DA, Spiro S, Taylor CJ. Functional, biochemical and genetic diversity of prokaryotic nitrate reductases. Cell Mol Life Sci 2001; 58:165-178. PubMed doi:10.1007/PL00000845
92. Spring S, Nolan M, Lapidus A, Del Rio TG, Co-peland A, Tice H, Cheng JF, Lucas S, Land M, Chen F, et al. Complete genome sequence of De-sulfohalobium retbaense type strain (HR100T). Stand Genomic Sci 2010; 2:38-48. doi:10.4056/sigs.581048
93. Li X, Luo Q, Wofford NQ, Keller KL, McInerney MJ, Wall JD, Krumholz LR. A molybdopterin oxi-doreductase is involved in H2 oxidation in Desul-fovibrio desulfuricans G20. J Bacteriol 2009; 191:2675-2682. PubMed doi:10.1128/JB.01814-08
94. Kunow J, Linder D, Stetter KO, Thauer RK. F420H2:quinone oxidoreductase from Archaeoglo-bus fulgidus. Characterization of a membrane-bound multisubunit complex containing FAD and iron-sulfur clusters. Eur J Biochem 1994; 223:503-511. PubMed doi:10.1111/j.1432-1033.1994.tb19019.x
95. Brüggemann H, Falinski F, Deppenmeier U. Structure of the F420H2:quinone oxidoreductase of Archaeoglobus fulgidus. Identification and over-production of the F420H2:oxidizing subunit. Eur J Biochem 2000; 267:5810-5814. PubMed doi:10.1046/j.1432-1327.2000.01657.x
96. Pierce E, Xie G, Barabote RD, Saunders E, Han CS, Detter JC, Richardson P, Brettin TS, Das A, Ljungdahl LG, Ragsdale SW. The complete ge-nome sequence of Moorella thermoacetica (f. Clostridium thermoaceticum). Environ Microbiol 2008; 10:2550-2573. PubMed doi:10.1111/j.1462-2920.2008.01679.x
97. Vorholt J, Kunow J, Stetter KO, Thauer RK. En-zymes and coenzymes of the carbon monoxide dehydrogenase pathway for autotrophic CO2 fixa-tion in Archaeoglobus fulgidus and the lack of carbon monoxide dehydrogenase in the hetero-trophic A. profundus. Arch Microbiol 1995; 163:112-118. doi:10.1007/s002030050179
98. Guss AM, Kulkarni G, Metcalf WW. Differences in hydrogenase gene expression between Metha-nosarcina acetivorans and Methanosarcina barke-ri. J Bacteriol 2009; 191:2826-2833. PubMed doi:10.1128/JB.00563-08
99. Huber H, Stetter KO. Family I. Archaeoglobaceae nov. In: Bergey's Manual of Systematic Bac-teriology, second edition vol. The Archaea and the deeply branching and phototrophic Bacteria. Springer, New York; 2001; pp 349.
100. Classification of Bacteria and Archaea in risk groups. http://www.baua.de TRBA 466