Skip to main content

Advertisement

SpringerLink
Log in

Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function

  • Original Paper
  • Published:
Extremophiles Aims and scope Submit manuscript

Abstract

The complete genome of the obligately anaerobic crenarchaeote Fervidicoccus fontis Kam940T, a terrestrial hot spring inhabitant with a growth optimum of 65–70 °C, has been sequenced and analyzed. The small 1.3-Mb genome encodes several extracellular proteases and no other extracellular hydrolases. No complete pathways of carbohydrate catabolism were found. Genes coding for enzymes necessary for amino acid transamination and further oxidative decarboxylation are present. The genome encodes no mechanisms of acyl-CoA and acetyl-CoA oxidation. Two [NiFe]-hydrogenases are encoded: a membrane-bound energy-converting hydrogenase and a cytoplasmic one. The ATP-synthase is H+-dependent as inferred from the amino acid sequence of the membrane rotor subunit. On the whole, genome analysis shows F. fontis to be a peptidolytic heterotroph with a restricted biosynthetic potential, which is in accordance with its phenotypic properties. The analysis of phylogenetic markers and of the distribution of best blastp hits of F. fontis proteins in the available genomes of Crenarchaeota supports distinct phylogenetic position of the order Fervidicoccales as a separate lineage adjoining the heterogeneous order Desulfurococcales. In addition, certain F. fontis genomic features correlate with its adaptation to temperatures of 60–80 °C, which are lower than temperatures preferred by Desulfurococcales.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

Similar content being viewed by others

References

  • Abu-Qarn M, Yurist-Doutsch S, Giordano A, Trauner A, Morris HR, Hitchen P, Medalia O, Dell A, Eichler J (2007) Haloferax volcanii AglB and AglD are involved in N-glycosylation of the S-layer glycoprotein and proper assembly of the surface layer. J Mol Biol 374:1224–1236

    Article  CAS  PubMed  Google Scholar 

  • Adams MW, Holden JF, Menon AL, Schut GJ, Grunden AM, Hou C, Hutchins AM, Jenney FE Jr, Kim C, Ma K, Pan G, Roy R, Sapra R, Story SV, Verhagen MF (2001) Key role for sulfur in peptide metabolism and in regulation of three hydrogenases in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 183:716–724

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anderson I, Rodriguez J, Susanti D, Porat I, Reich C, Ulrich LE, Elkins JG, Mavromatis K, Lykidis A, Kim E, Thompson LS, Nolan M, Land M, Copeland A, Lapidus A, Lucas S, Detter C, Zhulin IB, Olsen GJ, Whitman W, Mukhopadhyay B, Bristow J, Kyrpides N (2008) Genome sequence of Thermofilum pendens reveals an exceptional loss of biosynthetic pathways without genome reduction. J Bacteriol 190:2957–2965

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Anderson IJ, Dharmarajan L, Rodriguez J, Hooper S, Porat I, Ulrich LE, Elkins JG, Mavromatis K, Sun H, Land M, Lapidus A, Lucas S, Barry K, Huber H, Zhulin IB, Whitman WB, Mukhopadhyay B, Woese C, Bristow J, Kyrpides N (2009) The complete genome sequence of Staphylothermus marinus reveals differences in sulfur metabolism among heterotrophic Crenarchaeota. BMC Genomics 10:145

    Article  PubMed Central  PubMed  Google Scholar 

  • Aono R, Sato T, Yano A, Yoshida S, Nishitani Y, Miki K, Imanaka T, Atomi H (2012) Enzymatic characterization of AMP phosphorylase and ribose-1,5-bisphosphate isomerase functioning in an archaeal AMP metabolic pathway. J Bacteriol 194:6847–6855

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Auchtung TA, Shyndriayeva G, Cavanaugh CM (2011) 16S rRNA phylogenetic analysis and quantification of Korarchaeota indigenous to the hot springs of Kamchatka, Russia. Extremophiles 15:105–116

    Article  CAS  PubMed  Google Scholar 

  • Barrangou R, Fremaux C, Deveau H, Richards M, Boyaval P, Moineau S, Romero DA, Horvath P (2007) CRISPR provides acquired resistance against viruses in prokaryotes. Science 315:1709–1712

    Article  CAS  PubMed  Google Scholar 

  • Bridger SL, Clarkson SM, Stirrett K, DeBarry MB, Lipscomb GL, Schut GJ, Westpheling J, Scott RA, Adams MW (2011) Deletion strains reveal metabolic roles for key elemental sulfur-responsive proteins in Pyrococcus furiosus. J Bacteriol 193:6498–6504

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brochier-Armanet C, Forterre P (2007) Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers. Archaea 2:83–93

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Brochier-Armanet C, Forterre P, Gribaldo S (2011) Phylogeny and evolution of the Archaea: one hundred genomes later. Curr Opin Microbiol 14:274–281

    Article  PubMed  Google Scholar 

  • Brügger K (2007) The Sulfolobus database. Nucleic Acids Res 35:D413–D415

    Article  PubMed Central  PubMed  Google Scholar 

  • Brügger K, Chen L, Stark M, Zibat A, Redder P, Ruepp A, Awayez M, She Q, Garrett RA, Klenk HP (2007) The genome of Hyperthermus butylicus: a sulfur-reducing, peptide fermenting, neutrophilic Crenarchaeote growing up to 108 degrees C. Archaea 2:127–135

    Article  PubMed Central  PubMed  Google Scholar 

  • Burgess EA, Unrine JM, Mills GL, Romanek CS, Wiegel J (2012) Comparative geochemical and microbiological characterization of two thermal pools in the Uzon Caldera, Kamchatka, Russia. Microb Ecol 63:471–489

    Article  PubMed  Google Scholar 

  • Cantarel BL, Coutinho PM, Rancurel C, Bernard T, Lombard V, Henrissat B (2009) The Carbohydrate-Active EnZymes database (CAZy): an expert resource for Glycogenomics. Nucleic Acids Res 37:D233–D238

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Childs AM, Mountain BW, O’Toole R, Stott MB (2008) Relating microbial community and physicochemical parameters of a hot spring: Champagne Pool, Wai-o-tapu, New Zealand. Geomicrobiol J 25:441–453

    Article  CAS  Google Scholar 

  • Delcher AL, Harmon D, Kasif S, White O, Salzberg SL (1999) Improved microbial gene identification with GLIMMER. Nucleic Acids Res 27:4636–4641

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Desmond E, Brochier-Armanet C, Gribaldo S (2007) Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure. BMC Evol Biol 7:106

    Article  PubMed Central  PubMed  Google Scholar 

  • Devine E, Holmqvist M, Stensjö K, Lindblad P (2009) Diversity and transcription of proteases involved in the maturation of hydrogenases in Nostoc punctiforme ATCC 29133 and Nostoc sp. strain PCC 7120. BMC Microbiol 9:53

    Article  PubMed Central  PubMed  Google Scholar 

  • Elbein AD, Pan YT, Pastuszak I, Carroll D (2003) New insights on trehalose: a multifunctional molecule. Glycobiology 13:17R–27R

    Article  CAS  PubMed  Google Scholar 

  • Fuchs G (2011) Alternative pathways of carbon dioxide fixation: insights into the early evolution of life? Annu Rev Microbiol 65:631–658

    Article  CAS  PubMed  Google Scholar 

  • Fukui T, Atomi H, Kanai T, Matsumi R, Fujiwara S, Imanaka T (2005) Complete genome sequence of the hyperthermophilic archaeon Thermococcus kodakaraensis KOD1 and comparison with Pyrococcus genomes. Genome Res 15:352–363

    Article  CAS  PubMed  Google Scholar 

  • Göker M, Held B, Lapidus A, Nolan M, Spring S, Yasawong M, Lucas S, Glavina Del Rio T, Tice H, Cheng JF, Goodwin L, Tapia R, Pitluck S, Liolios K, Ivanova N, Mavromatis K, Mikhailova N, Pati A, Chen A, Palaniappan K, Brambilla E, Land M, Hauser L, Chang YJ, Jeffries CD, Brettin T, Detter JC, Han C, Rohde M, Sikorski J, Woyke T, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP (2010) Complete genome sequence of Ignisphaera aggregans type strain (AQ1.S1). Stand Genomic Sci 3:66–75

    Article  PubMed Central  PubMed  Google Scholar 

  • Grissa I, Vergnaud G, Pourcel C (2007) CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats. Nucleic Acids Res 35:W52–W57

    Article  PubMed Central  PubMed  Google Scholar 

  • Grunden AM, Jenney FE Jr, Ma K, Ji M, Weinberg MV, Adams MW (2005) In vitro reconstitution of an NADPH-dependent superoxide reduction pathway from Pyrococcus furiosus. Appl Environ Microbiol 71:1522–1530

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Guiral M, Tron P, Aubert C, Gloter A, Iobbi-Nivol C, Giudici-Orticoni MT (2005) A membrane-bound multienzyme, hydrogen-oxidizing, and sulfur-reducing complex from the hyperthermophilic bacterium Aquifex aeolicus. J Biol Chem 280:42004–42015

    Article  CAS  PubMed  Google Scholar 

  • Hagen WR, Silva PJ, Amorim MA, Hagedoorn PL, Wassink H, Haaker H, Robb FT (2000) Novel structure and redox chemistry of the prosthetic groups of the iron-sulfur flavoprotein sulfide dehydrogenase from Pyrococcus furiosus; evidence for a [2Fe-2S] cluster with Asp(Cys)3 ligands. J Biol Inorg Chem 5:527–534

    Article  CAS  PubMed  Google Scholar 

  • Henz SR, Huson DH, Auch AF, Nieselt-Struwe K, Schuster SC (2005) Whole-genome prokaryotic phylogeny. Bioinformatics 21:2329–2335

    Article  CAS  PubMed  Google Scholar 

  • Jansen R, Embden JD, Gaastra W, Schouls LM (2002) Identification of genes that are associated with DNA repeats in prokaryotes. Mol Microbiol 43:1565–1575

    Article  CAS  PubMed  Google Scholar 

  • Jormakka M, Yokoyama K, Yano T, Tamakoshi M, Akimoto S, Shimamura T, Curmi P, Iwata S (2008) Molecular mechanism of energy conservation in polysulfide respiration. Nat Struct Mol Biol 7:730–737

    Article  Google Scholar 

  • Kim YJ, Lee HS, Kim ES, Bae SS, Lim JK, Matsumi R, Lebedinsky AV, Sokolova TG, Kozhevnikova DA, Cha SS, Kim SJ, Kwon KK, Imanaka T, Atomi H, Bonch-Osmolovskaya EA, Lee JH, Kang SG (2010) Formate-driven growth coupled with H2 production. Nature 467:352–355

    Article  CAS  PubMed  Google Scholar 

  • Kim SM, Paek KH, Lee SB (2012) Characterization of NADP+-specific L-rhamnose dehydrogenase from the thermoacidophilic archaeon Thermoplasma acidophilum. Extremophiles 16:447–454

    Article  CAS  PubMed  Google Scholar 

  • Koonin EV, Wolf YI (2008) Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world. Nucleic Acids Res 36:6688–6719

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Koski LB, Gray MW, Lang BF, Burger G (2005) AutoFACT: an automatic functional annotation and classification tool. BMC Bioinformatics 6:151

    Article  PubMed Central  PubMed  Google Scholar 

  • Krafft T, Bokranz M, Klimmek O, Schröder I, Fahrenholz F, Kojro E, Kröger A (1992) Cloning and nucleotide sequence of the psrA gene of Wolinella succinogenes polysulphide reductase. Eur J Biochem 206:503–510

    Article  CAS  PubMed  Google Scholar 

  • Kublanov IV, Bidjieva SKh, Mardanov AV, Bonch-Osmolovskaya EA (2009a) Desulfurococcus kamchatkensis sp. nov., a novel hyperthermophilic protein-degrading archaeon isolated from a Kamchatka hot spring. Int J Syst Evol Microbiol 59:1743–1747

    Article  CAS  PubMed  Google Scholar 

  • Kublanov IV, Perevalova AA, Slobodkina GB, Lebedinsky AV, Bidzhieva SK, Kolganova TV, Kaliberda EN, Rumsh LD, Haertlé T, Bonch-Osmolovskaya EA (2009b) Biodiversity of thermophilic prokaryotes with hydrolytic activities in hot springs of Uzon Caldera, Kamchatka (Russia). Appl Environ Microbiol 75:286–291

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Kvist T, Ahring BK, Westermann P (2007) Archaeal diversity in Icelandic hot springs. FEMS Microbiol Ecol 59:71–80

    Article  CAS  PubMed  Google Scholar 

  • Laska S, Lottspeich F, Kletzin A (2003) Membrane-bound hydrogenase and sulfur reductase of the hyperthermophilic and acidophilic archaeon Acidianus ambivalens. Microbiology 149:2357–2371

    Article  CAS  PubMed  Google Scholar 

  • Lee HS, Shockley KR, Schut GJ, Conners SB, Montero CI, Johnson MR, Chou CJ, Bridger SL, Wigner N, Brehm SD, Jenney FE Jr, Comfort DA, Kelly RM, Adams MW (2006) Transcriptional and biochemical analysis of starch metabolism in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 188:2115–2125

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lillestøl RK, Redder P, Garrett RA, Brügger K (2006) A putative viral defence mechanism in archaeal cells. Archaea 2:59–72

    Article  PubMed Central  PubMed  Google Scholar 

  • Lim JK, Kang SG, Lebedinsky AV, Lee JH, Lee HS (2010) Identification of a novel class of membrane-bound [NiFe]-hydrogenases in Thermococcus onnurineus NA1 by in silico analysis. Appl Environ Microbiol 76:6286–6289

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Lin X, Tang J (1990) Purification, characterization, and gene cloning of thermopsin, a thermostable acid protease from Sulfolobus acidocaldarius. J Biol Chem 265:1490–1495

    CAS  PubMed  Google Scholar 

  • Lowe TM, Eddy SR (1997) tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Nucleic Acids Res 25:955–964

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Ma K, Adams MW (1994) Sulfide dehydrogenase from the hyperthermophilic archaeon Pyrococcus furiosus: a new multifunctional enzyme involved in the reduction of elemental sulfur. J Bacteriol 176:6509–6517

    CAS  PubMed Central  PubMed  Google Scholar 

  • Ma K, Adams MW (2001) Ferredoxin:NADP oxidoreductase from Pyrococcus furiosus. Methods Enzymol 334:40–45

    Article  CAS  PubMed  Google Scholar 

  • Ma K, Schicho RN, Kelly RM, Adams MW (1993) Hydrogenase of the hyperthermophile Pyrococcus furiosus is an elemental sulfur reductase or sulfhydrogenase: evidence for a sulfur-reducing hydrogenase ancestor. Proc Natl Acad Sci USA 90:5341–5344

    Article  CAS  PubMed  Google Scholar 

  • Ma K, Hutchins A, Sung SJ, Adams MW (1997) Pyruvate ferredoxin oxidoreductase from the hyperthermophilic archaeon, Pyrococcus furiosus, functions as a CoA-dependent pyruvate decarboxylase. Proc Natl Acad Sci USA 94:9608–9613

    Article  CAS  PubMed  Google Scholar 

  • Mai X, Adams MW (1996) Purification and characterization of two reversible and ADP-dependent acetyl coenzyme A synthetases from the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol 178:5897–5903

    CAS  PubMed Central  PubMed  Google Scholar 

  • Mardanov AV, Svetlitchnyi VA, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG (2010) The genome sequence of the crenarchaeon Acidilobus saccharovorans supports a new order, Acidilobales, and suggests an important ecological role in terrestrial acidic hot springs. Appl Environ Microbiol 76:5652–5657

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mardanov AV, Gumerov VM, Beletsky AV, Perevalova AA, Karpov GA, Bonch-Osmolovskaya EA, Ravin NV (2011a) Uncultured archaea dominate in the thermal groundwater of Uzon Caldera, Kamchatka. Extremophiles 15:365–372

    Article  PubMed  Google Scholar 

  • Mardanov AV, Gumerov VM, Beletsky AV, Prokofeva MI, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG (2011b) Complete genome sequence of the thermoacidophilic crenarchaeon Thermoproteus uzoniensis 768-20. J Bacteriol 193:3156–3157

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Mardanov AV, Kochetkova TV, Beletsky AV, Bonch-Osmolovskaya EA, Ravin NV, Skryabin KG (2012) Complete genome sequence of the hyperthermophilic cellulolytic crenarchaeon “Thermogladius cellulolyticus” 1633. J Bacteriol 194:4446–4447

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Markowitz VM, Chen IM, Palaniappan K, Chu K, Szeto E, Grechkin Y, Ratner A, Jacob B, Huang J, Williams P, Huntemann M, Anderson I, Mavromatis K, Ivanova NN, Kyrpides NC (2012) IMG: the integrated microbial genomes database and comparative analysis system. Nucleic Acids Res 40:D115–D122

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Meyer-Dombard DR, Shock EL, Amend JP (2005) Archaeal and bacterial communities in geochemically diverse hot springs of Yellowstone National Park, USA. Geobiology 3:211–227

    Article  Google Scholar 

  • Mojica FJ, Díez-Villaseñor C, García-Martínez J, Soria E (2005) Intervening sequences of regularly spaced prokaryotic repeats derive from foreign genetic elements. J Mol Evol 60:174–182

    Article  CAS  PubMed  Google Scholar 

  • Moon YJ, Kwon J, Yun SH, Lim HL, Kim MS, Kang SG, Lee JH, Choi JS, Kim SI, Chung YH (2012) Proteome analyses of hydrogen-producing hyperthermophilic archaeon Thermococcus onnurineus NA1 in different one-carbon substrate culture conditions. Mol Cell Proteomics 11(M111):015420

    PubMed  Google Scholar 

  • Nakao A, Yoshihama M, Kenmochi N (2004) RPG: the Ribosomal Protein Gene database. Nucleic Acids Res 32:168–170

    Article  Google Scholar 

  • Pandit SB, Srinivasan N (2004) Identification and analysis of a new family of bacterial serine proteinases. In Silico Biol 4:563–572

    CAS  PubMed  Google Scholar 

  • Perevalova AA, Kolganova TV, Birkeland NK, Schleper C, Bonch-Osmolovskaya EA, Lebedinsky AV (2008) Distribution of Crenarchaeota representatives in terrestrial hot springs of Russia and Iceland. Appl Environ Microbiol 74:7620–7628

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Perevalova AA, Bidzhieva SKh, Kublanov IV, Hinrichs KU, Liu XL, Mardanov AV, Lebedinsky AV, Bonch-Osmolovskaya EA (2010) Fervidicoccus fontis gen. nov., sp. nov., an anaerobic, thermophilic crenarchaeote from terrestrial hot springs, and proposal of Fervidicoccaceae fam. nov. and Fervidicoccales ord. nov. Int J Syst Evol Microbiol 60:2082–2088

    Article  PubMed  Google Scholar 

  • Prokofeva MI, Kostrikina NA, Kolganova TV, Tourova TP, Lysenko AM, Lebedinsky AV, Bonch-Osmolovskaya EA (2009) Isolation of the anaerobic thermoacidophilic crenarchaeote Acidilobus saccharovorans sp. nov. and proposal of Acidilobales ord. nov., including Acidilobaceae fam. nov. and Caldisphaeraceae fam. nov. Int J Syst Evol Microbiol 59:3116–3122

    Article  CAS  PubMed  Google Scholar 

  • Prokofeva M, Merkel A, Lebedinsky A, Bonch-Osmolovskaya E (2014) The family Acidilobaceae. In: Rosenberg E, DeLong EF, Lory S, Stackebrandt E, Thompson F (eds) The Prokaryotes, 4th edn, vol 11, Other major lineages of Bacteria and the Archaea. Springer, New York (in press)

    Google Scholar 

  • Ravin NV, Mardanov AV, Beletsky AV, Kublanov IV, Kolganova TV, Lebedinsky AV, Chernyh NA, Bonch-Osmolovskaya EA, Skryabin KG (2009) Complete genome sequence of the anaerobic, protein-degrading hyperthermophilic crenarchaeon Desulfurococcus kamchatkensis. J Bacteriol 191:2371–2379

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Rawlings ND, Barrett AJ, Bateman A (2010) MEROPS: the peptidase database. Nucleic Acids Res 38:D227–D233

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Reid SJ, Abratt VR (2005) Sucrose utilisation in bacteria: genetic organisation and regulation. Appl Microbiol Biotechnol 67:312–321

    Article  CAS  PubMed  Google Scholar 

  • Robinson NP, Bell SD (2007) Extrachromosomal element capture and the evolution of multiple replication origins in archaeal chromosomes. Proc Natl Acad Sci USA 104:5806–5811

    Article  CAS  PubMed  Google Scholar 

  • Robinson NP, Dionne I, Lundgren M, Marsh VL, Bernander R, Bell SD (2004) Identification of two origins of replication in the single chromosome of the archaeon Sulfolobus solfataricus. Cell 116:25–38

    Article  CAS  PubMed  Google Scholar 

  • Rodionov DA, Kurnasov OV, Stec B, Wang Y, Roberts MF, Osterman AL (2007) Genomic identification and in vitro reconstitution of a complete biosynthetic pathway for the osmolyte di-myo-inositol-phosphate. Proc Natl Acad Sci USA 104:4279–4284

    Article  CAS  PubMed  Google Scholar 

  • Ryu SI, Park CS, Cha J, Woo EJ, Lee SB (2005) A novel trehalose-synthesizing glycosyltransferase from Pyrococcus horikoshii: molecular cloning and characterization. Biochim Biophys Res Commun 329:429–436

    Article  CAS  Google Scholar 

  • Sambou T, Dinadayala P, Stadthagen G, Barilone N, Bordat Y, Constant P, Levillain F, Neyrolles O, Gicquel B, Lemassu A, Daffé M, Jackson M (2008) Capsular glucan and intracellular glycogen of Mycobacterium tuberculosis: Biosynthesis and impact of the persistence in mice. Mol Microbiol 70:762–774

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Sato T, Atomi H, Imanaka T (2007) Archaeal type III RuBisCOs function in a pathway for AMP metabolism. Science 315:1003–1006

    Article  CAS  PubMed  Google Scholar 

  • Say RF, Fuchs G (2010) Fructose 1,6-bisphosphate aldolase/phosphatase may be an ancestral gluconeogenic enzyme. Nature 464:1077–1081

    Article  CAS  PubMed  Google Scholar 

  • Schut GJ, Zhou J, Adams MW (2001) DNA microarray analysis of the hyperthermophilic archaeon Pyrococcus furiosus: evidence for a new type of sulfur-reducing enzyme complex. J Bacteriol 183:7027–7036

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schut GJ, Brehm SD, Datta S, Adams MW (2003) Whole-genome DNA microarray analysis of a hyperthermophile and an archaeon: Pyrococcus furiosus grown on carbohydrates or peptides. J Bacteriol 185:3935–3947

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schut GJ, Bridger SL, Adams MW (2007) Insights into the metabolism of elemental sulfur by the hyperthermophilic archaeon Pyrococcus furiosus: characterization of a coenzyme A- dependent NAD(P)H sulfur oxidoreductase. J Bacteriol 189:4431–4441

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Schut GJ, Boyd ES, Peters JW, Adams MW (2013) The modular respiratory complexes involved in hydrogen and sulfur metabolism by heterotrophic hyperthermophilic archaea and their evolutionary implications. FEMS Microbiol Rev 37:182–203

    CAS  PubMed  Google Scholar 

  • Siebers B, Schönheit P (2005) Unusual pathways and enzymes of central carbohydrate metabolism in Archaea. Curr Opin Microbiol 8:695–705

    Article  CAS  PubMed  Google Scholar 

  • Siebers B, Brinkmann H, Dörr C, Tjaden B, Lilie H, van der Oost J, Verhees CH (2001) Archaeal fructose-1,6-bisphosphate aldolases constitute a new family of archaeal type class I aldolase. J Biol Chem 276(31):28710–28718

    Article  CAS  PubMed  Google Scholar 

  • Siebers B, Tjaden B, Michalke K, Dörr C, Ahmed H, Zaparty M, Gordon P, Sensen CW, Zibat A, Klenk HP, Schuster SC, Hensel R (2004) Reconstruction of the central carbohydrate metabolism of Thermoproteus tenax by use of genomic and biochemical data. J Bacteriol 186:2179–2194

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Siebers B, Zaparty M, Raddatz G, Tjaden B, Albers SV, Bell SD, Blombach F, Kletzin A, Kyrpides N, Lanz C, Plagens A, Rampp M, Rosinus A, von Jan M, Makarova KS, Klenk HP, Schuster SC, Hensel R (2011) The complete genome sequence of Thermoproteus tenax: a physiologically versatile member of the Crenarchaeota. PLoS ONE 6:e24222

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Spring S, Rachel R, Lapidus A, Davenport K, Tice H, Copeland A, Cheng JF, Lucas S, Chen F, Nolan M, Bruce D, Goodwin L, Pitluck S, Ivanova N, Mavromatis K, Ovchinnikova G, Pati A, Chen A, Palaniappan K, Land M, Hauser L, Chang YJ, Jeffries CC, Brettin T, Detter JC, Tapia R, Han C, Heimerl T, Weikl F, Brambilla E, Göker M, Bristow J, Eisen JA, Markowitz V, Hugenholtz P, Kyrpides NC, Klenk HP (2010) Complete genome sequence of Thermosphaera aggregans type strain (M11TL). Stand Genomic Sci 2:245–259

    Article  PubMed Central  PubMed  Google Scholar 

  • Swartz TH, Ikewada S, Ishikawa O, Ito M, Krulwich TA (2005) The Mrp system: a giant among monovalent cation/proton antiporters? Extremophiles 9:345–354

    Article  CAS  PubMed  Google Scholar 

  • Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S (2011) MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol 28:2731–2739

    Article  CAS  PubMed  Google Scholar 

  • Theodoratou E, Huber R, Böck A (2005) [NiFe]-hydrogenase maturation endopeptidase: structure and function. Biochem Soc Trans 33:108–111

    Article  CAS  PubMed  Google Scholar 

  • Vetting MW, Frantom PA, Blanchard JS (2008) Structural and enzymatic analysis of MshA from Corynebacterium glutamicum: substrate-assisted catalysis. J Biol Chem 283:15834–15844

    Article  CAS  PubMed  Google Scholar 

  • Vignais PM, Billoud B (2007) Occurrence, classification, and biological function of hydrogenases: an overview. Chem Rev 107:4206–4272

    Article  CAS  PubMed  Google Scholar 

  • Wagner ID, Wiegel J (2008) Diversity of thermophilic anaerobes. Ann N Y Acad Sci 1125:1–43

    Article  CAS  PubMed  Google Scholar 

  • Yokooji Y, Sato T, Fujiwara S, Imanaka T, Atomi H (2013) Genetic examination of initial amino acid oxidation and glutamate catabolism in the hyperthermophilic archaeon Thermococcus kodakarensis. J Bacteriol 195:1940–1948

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zaparty M, Siebers B (2011) 4.10 Physiology, metabolism, and enzymology of thermoacidophiles. Reconstruction of the central carbon metabolic network of thermoacidophilic archaea. In: Horikoshi K (ed) Extremophiles handbook. Springer, New York, pp 601–639

    Chapter  Google Scholar 

  • Zeldovich KB, Berezovsky IN, Shakhnovich EI (2007) Protein and DNA sequence determinants of thermophilic adaptation. PLoS Comput Biol 3:e5

    Article  PubMed Central  PubMed  Google Scholar 

  • Zhang R, Zhang CT (2005) Identification and replication origins in archaeal genomes based on the Z-curve method. Archaea 1:335–346

    Article  CAS  PubMed Central  PubMed  Google Scholar 

  • Zivanovic Y, Lopez P, Philippe H, Forterre P (2002) Pyrococcus genome comparison evidences chromosome shuffling-driven evolution. Nucleic Acids Res 30:1902–1910

    Article  CAS  PubMed Central  PubMed  Google Scholar 

Download references

Acknowledgments

We are grateful to Bettina Siebers and Biswarup Mukhopadhyay for helpful discussions. This work was supported by Ministry of Education and Sciences of Russia (contract 02.512.11.2201), the Russian Foundation for Basic Research (projects 11-04-01723-a and 11-04-00671-a), and by the program “Molecular and Cellular Biology” of the Russian Academy of Science within the projects of E.A.B.-O. and N.V.R. The work of I.V.K. on the analysis of hydrolases and glycosyltransferases was supported by grant #MК-7948.2010.4 from the advisory board for the research grants of the President of the Russian Federation.

Author information

Authors and Affiliations

  1. Winogradsky Institute of Microbiology, Russian Academy of Sciences, Prospekt 60-let Oktyabrya, 7/2, Moscow, 117312, Russia

    Alexander V. Lebedinsky, Ilya V. Kublanov, Anna A. Perevalova, Salima Kh. Bidzhieva & Elizaveta A. Bonch-Osmolovskaya

  2. Centre “Bioengineering”, Russian Academy of Sciences, Prospekt 60-let Oktyabrya, 7/1, Moscow, 117312, Russia

    Andrey V. Mardanov, Vadim M. Gumerov, Alexey V. Beletsky, Konstantin G. Skryabin & Nikolai V. Ravin

Authors
  1. Alexander V. Lebedinsky
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Andrey V. Mardanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Ilya V. Kublanov
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Vadim M. Gumerov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Alexey V. Beletsky
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Anna A. Perevalova
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Salima Kh. Bidzhieva
    View author publications

    You can also search for this author in PubMed Google Scholar

  8. Elizaveta A. Bonch-Osmolovskaya
    View author publications

    You can also search for this author in PubMed Google Scholar

  9. Konstantin G. Skryabin
    View author publications

    You can also search for this author in PubMed Google Scholar

  10. Nikolai V. Ravin
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Alexander V. Lebedinsky or Nikolai V. Ravin.

Additional information

Communicated by A. Oren.

A. V. Lebedinsky and A. V. Mardanov contributed equally to this work.

Rights and permissions

Reprints and permissions

About this article

Cite this article

Lebedinsky, A.V., Mardanov, A.V., Kublanov, I.V. et al. Analysis of the complete genome of Fervidococcus fontis confirms the distinct phylogenetic position of the order Fervidicoccales and suggests its environmental function. Extremophiles 18, 295–309 (2014). https://doi.org/10.1007/s00792-013-0616-7

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00792-013-0616-7

Keywords

Search

Navigation