The complete genome of hyperthermophile Methanopyrus kandleri AV19 and monophyly of archaeal methanogens

Proceedings of the National Academy of Sciences of the United States of America
Alexei I SlesarevSergei A Kozyavkin

Abstract

We have determined the complete 1,694,969-nt sequence of the GC-rich genome of Methanopyrus kandleri by using a whole direct genome sequencing approach. This approach is based on unlinking of genomic DNA with the ThermoFidelase version of M. kandleri topoisomerase V and cycle sequencing directed by 2'-modified oligonucleotides (Fimers). Sequencing redundancy (3.3x) was sufficient to assemble the genome with less than one error per 40 kb. Using a combination of sequence database searches and coding potential prediction, 1,692 protein-coding genes and 39 genes for structural RNAs were identified. M. kandleri proteins show an unusually high content of negatively charged amino acids, which might be an adaptation to the high intracellular salinity. Previous phylogenetic analysis of 16S RNA suggested that M. kandleri belonged to a very deep branch, close to the root of the archaeal tree. However, genome comparisons indicate that, in both trees constructed using concatenated alignments of ribosomal proteins and trees based on gene content, M. kandleri consistently groups with other archaeal methanogens. M. kandleri shares the set of genes implicated in methanogenesis and, in part, its operon organization with Methanococcus jannaschii ...Continue Reading

References

Aug 5, 1991·Journal of Molecular Biology·G A Fichant, C Burks
May 1, 1991·Journal of Molecular Evolution·M HasegawaN Saitou
Jan 1, 1994·Journal of Bacteriology·G J OlsenR Overbeek
Jan 9, 1996·Proceedings of the National Academy of Sciences of the United States of America·R KrahM Gellert
Jan 1, 1996·International Journal of Systematic Bacteriology·M C Rivera, J A Lake
Aug 1, 1996·Trends in Genetics : TIG·A R Mushegian, E V Koonin
Sep 1, 1996·Trends in Genetics : TIG·E V KooninP Bork
Oct 1, 1996·International Journal of Systematic Bacteriology·J NöllingJ N Reeve
Sep 1, 1997·Nucleic Acids Research·S F AltschulD J Lipman
Feb 12, 1998·Nucleic Acids Research·B B RosenblumS M Chen
Oct 24, 1997·Science·R L TatusovD J Lipman
May 16, 1998·Genome Research·R Durbin, S Dear
May 16, 1998·Genome Research·D GordonP Green
May 30, 1998·Proceedings of the National Academy of Sciences of the United States of America·J SchultzC P Ponting
Jan 23, 1999·Nature Genetics·B SnelM A Huynen
Sep 8, 1999·Microbiology and Molecular Biology Reviews : MMBR·G SchäferV Müller
Nov 11, 1999·Nucleic Acids Research·M D StumpR B Weiss
Dec 10, 1999·Microbiology and Molecular Biology Reviews : MMBR·A J MacarioE Conway de Macario
Dec 11, 1999·Nucleic Acids Research·M Kanehisa, S Goto
Jun 27, 2000·Bioinformatics·L J McGuffinD T Jones
Aug 31, 2000·Journal of Molecular Biology·C NotredameJ Heringa
Feb 22, 2001·Methods : a Companion to Methods in Enzymology·Y Li, R R Breaker
Apr 3, 2001·Genome Research·I K JordanE V Koonin
Apr 3, 2001·Genome Research·D GordonP Green
May 9, 2001·Genome Génome / Conseil National De Recherches Canada·M Pfenninger, M Bugert
May 17, 2001·Proceedings of the National Academy of Sciences of the United States of America·G I BelovaA I Slesarev
Jan 1, 1991·Systematic and Applied Microbiology·S BurggrafC R Woese
Sep 7, 2001·Annual Review of Microbiology·E V KooninL Aravind

❮ Previous
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Citations

Oct 6, 2005·Archives of Microbiology·Devarajan Bharanidharan, Namasivayam Gautham
Oct 21, 2009·Journal of Molecular Evolution·Zhiliang YuJ Tze-Fei Wong
May 8, 2013·Applied Microbiology and Biotechnology·Huibin QinHongjiang Yang
Sep 30, 2009·Extremophiles : Life Under Extreme Conditions·Fujihiko MatsunagaYoshizumi Ishino
May 13, 2006·Journal of Bioenergetics and Biomembranes·Volker MüllerMichael Fritz
Feb 3, 2009·Journal of Structural and Functional Genomics·Robert JanowskiManfred S Weiss
Aug 30, 2005·FEMS Microbiology Reviews·David A MillsKira Makarova
Apr 28, 2004·Trends in Biotechnology·Andrey R PavlovAlexei I Slesarev
Aug 15, 2002·Trends in Genetics : TIG·Yuri I WolfEugene V Koonin
Apr 10, 2003·Trends in Genetics : TIG·Kira S MakarovaEugene V Koonin
Sep 23, 2003·Research in Microbiology·Jamie C SnyderMark J Young
Dec 28, 1999·Trends in Cell Biology·W F Doolittle
Jun 29, 2002·Trends in Microbiology·Mohammed SebaihiaJulian Parkhill
Oct 20, 2005·Journal of Bioscience and Bioengineering·Seigo ShimaUlrich Ermler
Mar 24, 2011·Quarterly Reviews of Biophysics·Stephen P MuenchMichael A Harrison
Apr 6, 2004·Nature Biotechnology·Anke HenneHans-Joachim Fritz
Jun 5, 2008·Nature Reviews. Molecular Cell Biology·Adam T McGeoch, Stephen D Bell
May 12, 2005·Nature Reviews. Microbiology·Edward F DeLong
Sep 22, 2005·Nature Reviews. Microbiology·Thijs J G EttemaJohn van der Oost
Feb 16, 2008·Nature Reviews. Microbiology·Céline Brochier-ArmanetPatrick Forterre
Aug 20, 2004·Proceedings of the National Academy of Sciences of the United States of America·Bradley A CarlsonDolph L Hatfield
Feb 24, 2006·Journal of Biomolecular Structure & Dynamics·Bin-Guang MaHong-Yu Zhang
Jul 3, 2009·Molecular Biology and Evolution·Miklós Csurös, István Miklós
Feb 7, 2008·Nucleic Acids Research·Kelly SheppardDieter Söll
Feb 26, 2009·Nucleic Acids Research·Lars SchomacherHans-Joachim Fritz
Jun 7, 2006·Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences·Simonetta Gribaldo, Celine Brochier-Armanet
Jul 14, 2011·Genome Research·Sung Ho YoonNitin S Baliga
Dec 4, 2004·Protein Science : a Publication of the Protein Society·George StanD Thirumalai
May 2, 2009·Science·Lennart RandauDieter Söll
Oct 4, 2011·Applied and Environmental Microbiology·Andrew M KropinskiChristine M Szymanski
Nov 7, 2003·Applied and Environmental Microbiology·Volker Müller

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