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PMID: 11930014 Published · ppublish English Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, U.S. Gov't, P.H.S.

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 ·Vol. 99 ·No. 7 ·2002-04-02 ·Pages 4644-9

Slesarev AI, Mezhevaya KV, Makarova KS, Polushin NN, Shcherbinina OV, Shakhova VV, Belova GI, Aravind L, Natale DA, Rogozin IB, Tatusov RL, Wolf YI, Stetter KO, Malykh AG, Koonin EV, Kozyavkin SA

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 and Methanothermobacter thermoautotrophicum. These findings indicate that archaeal methanogens are monophyletic. A distinctive feature of M. kandleri is the paucity of proteins involved in signaling and regulation of gene expression. Also, M. kandleri appears to have fewer genes acquired via lateral transfer than other archaea. These features might reflect the extreme habitat of this organism.

MeSH Terms
Base Sequence Euryarchaeota/classification,genetics,metabolism Genome, Archaeal Molecular Sequence Data Operon Phylogeny
Authors & Affiliations
16 authors, click to expand affiliations / ORCID
Slesarev Alexei I
Fidelity Systems, Gaithersburg, MD 20879, USA. [email protected]
Mezhevaya Katja V
Makarova Kira S
Polushin Nikolai N
Shcherbinina Olga V
Shakhova Vera V
Belova Galina I
Aravind L
Natale Darren A
Rogozin Igor B
Tatusov Roman L
Wolf Yuri I
Stetter Karl O
Malykh Andrei G
Koonin Eugene V
Kozyavkin Sergei A
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Article Info
Journal
Proceedings of the National Academy of Sciences of the United States of America
Abbr.
Proc Natl Acad Sci U S A
ISSN
0027-8424
DOI
10.1073/pnas.032671499
Email
[email protected]
Published
2002-04-02
Pages
4644-9
Language
English
Region
United States
NLM ID
7505876
PMCID
PMC123701
Subset
IM
Grants
NHGRI NIH HHS · R43HG02186 · United States
NIGMS NIH HHS · R44GM55485 · United States
Databases
GENBANK
AE009439
External Links
PubMed source DOI: 10.1073/pnas.032671499 PMC Full Text View journal details
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