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. 1999 Aug;152(4):1299–1305. doi: 10.1093/genetics/152.4.1299

Divergence of the hyperthermophilic archaea Pyrococcus furiosus and P. horikoshii inferred from complete genomic sequences.

D L Maeder 1, R B Weiss 1, D M Dunn 1, J L Cherry 1, J M González 1, J DiRuggiero 1, F T Robb 1
PMCID: PMC1460691  PMID: 10430560

Abstract

Divergence of the hyperthermophilic Archaea, Pyrococcus furiosus and Pyrococcus horikoshii, was assessed by analysis of complete genomic sequences of both species. The average nucleotide identity between the genomic sequences is 70-75% within ORFs. The P. furiosus genome (1.908 mbp) is 170 kbp larger than the P. horikoshii genome (1.738 mbp) and the latter displays significant deletions in coding regions, including the trp, his, aro, leu-ile-val, arg, pro, cys, thr, and mal operons. P. horikoshii is auxotrophic for tryptophan and histidine and is unable to utilize maltose, unlike P. furiosus. In addition, the genomes differ considerably in gene order, displaying displacements and inversions. Six allelic intein sites are common to both Pyrococcus genomes, and two intein insertions occur in each species and not the other. The bacteria-like methylated chemotaxis proteins form a functional group in P. horikoshii, but are absent in P. furiosus. Two paralogous families of ferredoxin oxidoreductases provide evidence of gene duplication preceding the divergence of the Pyrococcus species.

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Selected References

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  1. Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. Basic local alignment search tool. J Mol Biol. 1990 Oct 5;215(3):403–410. doi: 10.1016/S0022-2836(05)80360-2. [DOI] [PubMed] [Google Scholar]
  2. Andersson S. G., Zomorodipour A., Andersson J. O., Sicheritz-Pontén T., Alsmark U. C., Podowski R. M., Näslund A. K., Eriksson A. S., Winkler H. H., Kurland C. G. The genome sequence of Rickettsia prowazekii and the origin of mitochondria. Nature. 1998 Nov 12;396(6707):133–140. doi: 10.1038/24094. [DOI] [PubMed] [Google Scholar]
  3. Aravalli R. N., Garrett R. A. Shuttle vectors for hyperthermophilic archaea. Extremophiles. 1997 Nov;1(4):183–191. doi: 10.1007/s007920050032. [DOI] [PubMed] [Google Scholar]
  4. Aravind L., Tatusov R. L., Wolf Y. I., Walker D. R., Koonin E. V. Evidence for massive gene exchange between archaeal and bacterial hyperthermophiles. Trends Genet. 1998 Nov;14(11):442–444. doi: 10.1016/s0168-9525(98)01553-4. [DOI] [PubMed] [Google Scholar]
  5. Balch W. E., Fox G. E., Magrum L. J., Woese C. R., Wolfe R. S. Methanogens: reevaluation of a unique biological group. Microbiol Rev. 1979 Jun;43(2):260–296. doi: 10.1128/mr.43.2.260-296.1979. [DOI] [PMC free article] [PubMed] [Google Scholar]
  6. Bayley D. P., Florian V., Klein A., Jarrell K. F. Flagellin genes of Methanococcus vannielii: amplification by the polymerase chain reaction, demonstration of signal peptides and identification of major components of the flagellar filament. Mol Gen Genet. 1998 Jun;258(6):639–645. doi: 10.1007/s004380050777. [DOI] [PubMed] [Google Scholar]
  7. Bult C. J., White O., Olsen G. J., Zhou L., Fleischmann R. D., Sutton G. G., Blake J. A., FitzGerald L. M., Clayton R. A., Gocayne J. D. Complete genome sequence of the methanogenic archaeon, Methanococcus jannaschii. Science. 1996 Aug 23;273(5278):1058–1073. doi: 10.1126/science.273.5278.1058. [DOI] [PubMed] [Google Scholar]
  8. Cannio R., Contursi P., Rossi M., Bartolucci S. An autonomously replicating transforming vector for Sulfolobus solfataricus. J Bacteriol. 1998 Jun;180(12):3237–3240. doi: 10.1128/jb.180.12.3237-3240.1998. [DOI] [PMC free article] [PubMed] [Google Scholar]
  9. Charlebois R. L., St Jean A. Supercoiling and map stability in the bacterial chromosome. J Mol Evol. 1995 Jul;41(1):15–23. doi: 10.1007/BF00174037. [DOI] [PubMed] [Google Scholar]
  10. DiRuggiero J., Santangelo N., Nackerdien Z., Ravel J., Robb F. T. Repair of extensive ionizing-radiation DNA damage at 95 degrees C in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 1997 Jul;179(14):4643–4645. doi: 10.1128/jb.179.14.4643-4645.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  11. Doolittle W. F. A paradigm gets shifty. Nature. 1998 Mar 5;392(6671):15–16. doi: 10.1038/32033. [DOI] [PubMed] [Google Scholar]
  12. González J. M., Masuchi Y., Robb F. T., Ammerman J. W., Maeder D. L., Yanagibayashi M., Tamaoka J., Kato C. Pyrococcus horikoshii sp. nov., a hyperthermophilic archaeon isolated from a hydrothermal vent at the Okinawa Trough. Extremophiles. 1998 May;2(2):123–130. doi: 10.1007/s007920050051. [DOI] [PubMed] [Google Scholar]
  13. Hoaki T., Nishijima M., Kato M., Adachi K., Mizobuchi S., Hanzawa N., Maruyama T. Growth requirements of hyperthermophilic sulfur-dependent heterotrophic archaea isolated from a shallow submarine geothermal system with reference to their essential amino acids. Appl Environ Microbiol. 1994 Aug;60(8):2898–2904. doi: 10.1128/aem.60.8.2898-2904.1994. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Hoff W. D., Jung K. H., Spudich J. L. Molecular mechanism of photosignaling by archaeal sensory rhodopsins. Annu Rev Biophys Biomol Struct. 1997;26:223–258. doi: 10.1146/annurev.biophys.26.1.223. [DOI] [PubMed] [Google Scholar]
  15. Jacobs K. L., Grogan D. W. Rates of spontaneous mutation in an archaeon from geothermal environments. J Bacteriol. 1997 May;179(10):3298–3303. doi: 10.1128/jb.179.10.3298-3303.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  16. Kawarabayasi Y., Sawada M., Horikawa H., Haikawa Y., Hino Y., Yamamoto S., Sekine M., Baba S., Kosugi H., Hosoyama A. Complete sequence and gene organization of the genome of a hyper-thermophilic archaebacterium, Pyrococcus horikoshii OT3. DNA Res. 1998 Apr 30;5(2):55–76. doi: 10.1093/dnares/5.2.55. [DOI] [PubMed] [Google Scholar]
  17. Mayr E. Two empires or three? Proc Natl Acad Sci U S A. 1998 Aug 18;95(17):9720–9723. doi: 10.1073/pnas.95.17.9720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Menon A. L., Hendrix H., Hutchins A., Verhagen M. F., Adams M. W. The delta-subunit of pyruvate ferredoxin oxidoreductase from Pyrococcus furiosus is a redox-active, iron-sulfur protein: evidence for an ancestral relationship with 8Fe-type ferredoxins. Biochemistry. 1998 Sep 15;37(37):12838–12846. doi: 10.1021/bi980979p. [DOI] [PubMed] [Google Scholar]
  19. Ng W. L., Kothakota S., DasSarma S. Structure of the gas vesicle plasmid in Halobacterium halobium: inversion isomers, inverted repeats, and insertion sequences. J Bacteriol. 1991 Mar;173(6):1958–1964. doi: 10.1128/jb.173.6.1958-1964.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  20. Ng W. V., Ciufo S. A., Smith T. M., Bumgarner R. E., Baskin D., Faust J., Hall B., Loretz C., Seto J., Slagel J. Snapshot of a large dynamic replicon in a halophilic archaeon: megaplasmid or minichromosome? Genome Res. 1998 Nov;8(11):1131–1141. doi: 10.1101/gr.8.11.1131. [DOI] [PubMed] [Google Scholar]
  21. Peak M. J., Robb F. T., Peak J. G. Extreme resistance to thermally induced DNA backbone breaks in the hyperthermophilic archaeon Pyrococcus furiosus. J Bacteriol. 1995 Nov;177(21):6316–6318. doi: 10.1128/jb.177.21.6316-6318.1995. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. She Q., Phan H., Garrett R. A., Albers S. V., Stedman K. M., Zillig W. Genetic profile of pNOB8 from Sulfolobus: the first conjugative plasmid from an archaeon. Extremophiles. 1998 Nov;2(4):417–425. doi: 10.1007/s007920050087. [DOI] [PubMed] [Google Scholar]
  23. Smith D. R., Doucette-Stamm L. A., Deloughery C., Lee H., Dubois J., Aldredge T., Bashirzadeh R., Blakely D., Cook R., Gilbert K. Complete genome sequence of Methanobacterium thermoautotrophicum deltaH: functional analysis and comparative genomics. J Bacteriol. 1997 Nov;179(22):7135–7155. doi: 10.1128/jb.179.22.7135-7155.1997. [DOI] [PMC free article] [PubMed] [Google Scholar]
  24. Woese C. R., Kandler O., Wheelis M. L. Towards a natural system of organisms: proposal for the domains Archaea, Bacteria, and Eucarya. Proc Natl Acad Sci U S A. 1990 Jun;87(12):4576–4579. doi: 10.1073/pnas.87.12.4576. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Zillig W., Arnold H. P., Holz I., Prangishvili D., Schweier A., Stedman K., She Q., Phan H., Garrett R., Kristjansson J. K. Genetic elements in the extremely thermophilic archaeon Sulfolobus. Extremophiles. 1998 Aug;2(3):131–140. doi: 10.1007/s007920050052. [DOI] [PubMed] [Google Scholar]

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