Track the topics, authors, and articles important to you. Sign up for PNAS Online eTocs
Link: Info for AuthorsLink: Editorial BoardLink: AboutLink: SubscribeLink: AdvertiseLink: ContactLink: Sitemap Link: PNAS Home
Proceedings of the National Academy of Sciences
Link: Current Issue "" Link: Archives "" Link: Online Submission ""  Link: Advanced Search


PNAS | April 2, 2002 | vol. 99 | no. 7 | 4644-4649
This Article
Right arrow Full Text
Right arrow Full Text (PDF)
Right arrow Supporting Information
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Right arrow Citation Map
Services
Right arrow Email this article to a colleague
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My File Cabinet
Right arrow Download to citation manager
Right arrow Request Copyright Permission
Citing Articles
Right arrow Citing Articles via HighWire
Right arrow Citing Articles via CrossRef
Right arrow Citing Articles via ISI Web of Science (124)
Right arrow Citing Articles via Google Scholar
Google Scholar
Right arrow Articles by Slesarev, A. I.
Right arrow Articles by Kozyavkin, S. A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Slesarev, A. I.
Right arrow Articles by Kozyavkin, S. A.
Right arrowPubmed/NCBI databases
*Gene*Genome
*Nucleotide*Protein
Social Bookmarking
Add to CiteULike   Add to Complore   Add to Connotea   Add to Del.icio.us   Add to Digg  
What's this?

 Previous Article  | Table of Contents |  Next Article 

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

Alexei I. Slesarev*,dagger ,Dagger , Katja V. Mezhevaya*, Kira S. Makarova§, Nikolai N. Polushin*, Olga V. Shcherbinina*, Vera V. Shakhova*, Galina I. BelovaDagger , L. Aravind§, Darren A. Natale§, Igor B. Rogozin§, Roman L. Tatusov§, Yuri I. Wolf§, Karl O. Stetter, Andrei G. Malykh*, Eugene V. Koonin§, and Sergei A. Kozyavkin*

* Fidelity Systems, Gaithersburg, MD 20879: § National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894; Dagger  M. M. Shemyakin and Yu. A. Ovchinnikov Institute of Bioorganic Chemistry, Russian Academy of Sciences, Moscow 117871, Russia; and  Department of Microbiology, University of Regensburg, Regensburg, D-93053, Germany

Communicated by Dieter Söll, Yale University, New Haven, CT, December 14, 2001 (received for review December 3, 2001)

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 (3.3×) 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.

dagger To whom reprint requests should be addressed. E-mail: alex{at}fidelitysystems.com.

www.pnas.org/cgi/doi/10.1073/pnas.032671499
Add to CiteULike CiteULike   Add to Complore Complore   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us   Add to Digg Digg    What's this?


This article has been cited by other articles in HighWire Press-hosted journals:


Home page
 Nucleic Acids ResHome page
K. Sheppard, J. Yuan, M. J. Hohn, B. Jester, K. M. Devine, and D. Soll
From one amino acid to another: tRNA-dependent amino acid biosynthesis
Nucleic Acids Res., April 1, 2008; 36(6): 1813 - 1825.
[Abstract] [Full Text] [PDF]

Home page
 Ann. N. Y. Acad. Sci.Home page
I. D. WAGNER and J. WIEGEL
Diversity of Thermophilic Anaerobes
Ann. N.Y. Acad. Sci., March 1, 2008; 1125(1): 1 - 43.
[Abstract] [Full Text] [PDF]

Home page
 Ann. N. Y. Acad. Sci.Home page
Y. LIU and W. B. WHITMAN
Metabolic, Phylogenetic, and Ecological Diversity of the Methanogenic Archaea
Ann. N.Y. Acad. Sci., March 1, 2008; 1125(1): 171 - 189.
[Abstract] [Full Text] [PDF]

Home page
 Ann. N. Y. Acad. Sci.Home page
F. E. JENNEY JR and M. W. W. ADAMS
Hydrogenases of the Model Hyperthermophiles
Ann. N.Y. Acad. Sci., March 1, 2008; 1125(1): 252 - 266.
[Abstract] [Full Text] [PDF]

Home page
 Ann. N. Y. Acad. Sci.Home page
A. L. VANFOSSEN, D. L. LEWIS, J. D. NICHOLS, and R. M. KELLY
Polysaccharide Degradation and Synthesis by Extremely Thermophilic Anaerobes
Ann. N.Y. Acad. Sci., March 1, 2008; 1125(1): 322 - 337.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
K. Sivaraman, A. Seshasayee, P. M. Tarwater, and A. M. Cole
Codon choice in genes depends on flanking sequence information--implications for theoretical reverse translation
Nucleic Acids Res., February 11, 2008; 36(3): e16 - e16.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
J. Sugahara, N. Yachie, K. Arakawa, and M. Tomita
In silico screening of archaeal tRNA-encoding genes having multiple introns with bulge-helix-bulge splicing motifs
RNA, May 1, 2007; 13(5): 671 - 681.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
K. Makarova, A. Slesarev, Y. Wolf, A. Sorokin, B. Mirkin, E. Koonin, A. Pavlov, N. Pavlova, V. Karamychev, N. Polouchine, et al.
Comparative genomics of the lactic acid bacteria
PNAS, October 17, 2006; 103(42): 15611 - 15616.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
H. Moussard, G. Henneke, D. Moreira, V. Jouffe, P. Lopez-Garcia, and C. Jeanthon
Thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics.
Appl. Envir. Microbiol., March 1, 2006; 72(3): 2268 - 2271.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
W. F. Fricke, H. Seedorf, A. Henne, M. Kruer, H. Liesegang, R. Hedderich, G. Gottschalk, and R. K. Thauer
The Genome Sequence of Methanosphaera stadtmanae Reveals Why This Human Intestinal Archaeon Is Restricted to Methanol and H2 for Methane Formation and ATP Synthesis
J. Bacteriol., January 15, 2006; 188(2): 642 - 658.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
E. F. Johnson and B. Mukhopadhyay
A New Type of Sulfite Reductase, a Novel Coenzyme F420-dependent Enzyme, from the Methanarchaeon Methanocaldococcus jannaschii
J. Biol. Chem., November 18, 2005; 280(46): 38776 - 38786.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. D. Woodson, A. A. Reynolds, and J. C. Escalante-Semerena
ABC Transporter for Corrinoids in Halobacterium sp. Strain NRC-1
J. Bacteriol., September 1, 2005; 187(17): 5901 - 5909.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Diaz-Perales, V. Quesada, J. R. Peinado, A. P. Ugalde, J. Alvarez, M. F. Suarez, F. X. Gomis-Ruth, and C. Lopez-Otin
Identification and Characterization of Human Archaemetzincin-1 and -2, Two Novel Members of a Family of Metalloproteases Widely Distributed in Archaea
J. Biol. Chem., August 26, 2005; 280(34): 30367 - 30375.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
A. Haddad, R. W. Rose, and M. Pohlschroder
The Haloferax volcanii FtsY Homolog Is Critical for Haloarchaeal Growth but Does Not Require the A Domain
J. Bacteriol., June 15, 2005; 187(12): 4015 - 4022.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
J. B. Robbins, M. C. McKinney, C. E. Guzman, B. Sriratana, S. Fitz-Gibbon, T. Ha, and I. K. O. Cann
The Euryarchaeota, Nature's Medium for Engineering of Single-stranded DNA-binding Proteins
J. Biol. Chem., April 15, 2005; 280(15): 15325 - 15339.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
S. Lewenza, R. K. Falsafi, G. Winsor, W. J. Gooderham, J. B. McPhee, F. S.L. Brinkman, and R. E.W. Hancock
Construction of a mini-Tn5-luxCDABE mutant library in Pseudomonas aeruginosa PAO1: A tool for identifying differentially regulated genes
Genome Res., April 1, 2005; 15(4): 583 - 589.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
S. V. Story, C. Shah, F. E. Jenney Jr., and M. W. W. Adams
Characterization of a Novel Zinc-Containing, Lysine-Specific Aminopeptidase from the Hyperthermophilic Archaeon Pyrococcus furiosus
J. Bacteriol., March 15, 2005; 187(6): 2077 - 2083.
[Abstract] [Full Text] [PDF]

Home page
 DNA ResHome page
B. Mallick, J. Chakrabarti, S. Sahoo, Z. Ghosh, and S. Das
Identity Elements of Archaeal tRNA.
DNA Res, January 1, 2005; 12(4): 235 - 246.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
G. Stan, B. R. Brooks, G. H. Lorimer, and D. Thirumalai
Identifying natural substrates for chaperonins using a sequence-based approach
Protein Sci., January 1, 2005; 14(1): 193 - 201.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Hou, J. H. Saw, K. S. Lee, T. A. Freitas, C. Belisle, Y. Kawarabayasi, S. P. Donachie, A. Pikina, M. Y. Galperin, E. V. Koonin, et al.
Genome sequence of the deep-sea {gamma}-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy
PNAS, December 28, 2004; 101(52): 18036 - 18041.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
T. J. G. Ettema, K. S. Makarova, G. L. Jellema, H. J. Gierman, E. V. Koonin, M. A. Huynen, W. M. de Vos, and J. van der Oost
Identification and Functional Verification of Archaeal-Type Phosphoenolpyruvate Carboxylase, a Missing Link in Archaeal Central Carbohydrate Metabolism
J. Bacteriol., November 15, 2004; 186(22): 7754 - 7762.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
M. C. Moffitt and B. A. Neilan
Characterization of the Nodularin Synthetase Gene Cluster and Proposed Theory of the Evolution of Cyanobacterial Hepatotoxins
Appl. Envir. Microbiol., November 1, 2004; 70(11): 6353 - 6362.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
P. Cabello, M. D. Roldan, and C. Moreno-Vivian
Nitrate reduction and the nitrogen cycle in archaea
Microbiology, November 1, 2004; 150(11): 3527 - 3546.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
E. L. Hendrickson, R. Kaul, Y. Zhou, D. Bovee, P. Chapman, J. Chung, E. Conway de Macario, J. A. Dodsworth, W. Gillett, D. E. Graham, et al.
Complete Genome Sequence of the Genetically Tractable Hydrogenotrophic Methanogen Methanococcus maripaludis
J. Bacteriol., October 15, 2004; 186(20): 6956 - 6969.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
B. A. Carlson, X.-M. Xu, G. V. Kryukov, M. Rao, M. J. Berry, V. N. Gladyshev, and D. L. Hatfield
From the Cover: Identification and characterization of phosphoseryl-tRNA[Ser]Sec kinase
PNAS, August 31, 2004; 101(35): 12848 - 12853.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
H. M. Patel, J. L. Kraszewski, and B. Mukhopadhyay
The Phosphoenolpyruvate Carboxylase from Methanothermobacter thermautotrophicus Has a Novel Structure
J. Bacteriol., August 1, 2004; 186(15): 5129 - 5137.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
B. Ruan, H. Nakano, M. Tanaka, J. A. Mills, J. A. DeVito, B. Min, K. B. Low, J. R. Battista, and D. Soll
Cysteinyl-tRNACys Formation in Methanocaldococcus jannaschii: the Mechanism Is Still Unknown
J. Bacteriol., January 1, 2004; 186(1): 8 - 14.
[Abstract] [Full Text] [PDF]

Home page
 RNAHome page
C. MARCK and H. GROSJEAN
Identification of BHB splicing motifs in intron-containing tRNAs from 18 archaea: evolutionary implications
RNA, December 1, 2003; 9(12): 1516 - 1531.
[Abstract] [Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
V. Muller
Energy Conservation in Acetogenic Bacteria
Appl. Envir. Microbiol., November 1, 2003; 69(11): 6345 - 6353.
[Full Text] [PDF]

Home page
 Appl. Environ. Microbiol.Home page
K. Pfluger, S. Baumann, G. Gottschalk, W. Lin, H. Santos, and V. Muller
Lysine-2,3-Aminomutase and {beta}-Lysine Acetyltransferase Genes of Methanogenic Archaea Are Salt Induced and Are Essential for the Biosynthesis of N{varepsilon}-Acetyl-{beta}-Lysine and Growth at High Salinity
Appl. Envir. Microbiol., October 1, 2003; 69(10): 6047 - 6055.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. C. Tantalean, M. A. Araya, C. P. Saavedra, D. E. Fuentes, J. M. Perez, I. L. Calderon, P. Youderian, and C. C. Vasquez
The Geobacillus stearothermophilus V iscS Gene, Encoding Cysteine Desulfurase, Confers Resistance to Potassium Tellurite in Escherichia coli K-12
J. Bacteriol., October 1, 2003; 185(19): 5831 - 5837.
[Abstract] [Full Text] [PDF]

Home page
 Protein Sci.Home page
R. I. Sadreyev, D. Baker, and N. V. Grishin
Profile-profile comparisons by COMPASS predict intricate homologies between protein families
Protein Sci., October 1, 2003; 12(10): 2262 - 2272.
[Abstract] [Full Text] [PDF]

Home page
 Genome Res.Home page
N. F.W. Saunders, T. Thomas, P. M.G. Curmi, J. S. Mattick, E. Kuczek, R. Slade, J. Davis, P. D. Franzmann, D. Boone, K. Rusterholtz, et al.
Mechanisms of Thermal Adaptation Revealed From the Genomes of the Antarctic Archaea Methanogenium frigidum and Methanococcoides burtonii
Genome Res., July 1, 2003; 13(7): 1580 - 1588.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
Y. Shen, X.-F. Tang, and I. Matsui
Subunit Interaction and Regulation of Activity through Terminal Domains of the Family D DNA Polymerase from Pyrococcus horikoshii
J. Biol. Chem., May 30, 2003; 278(23): 21247 - 21257.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
S. Kamtekar, W. D. Kennedy, J. Wang, C. Stathopoulos, D. Soll, and T. A. Steitz
The structural basis of cysteine aminoacylation of tRNAPro by prolyl-tRNA synthetases
PNAS, February 18, 2003; 100(4): 1673 - 1678.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
D. Tumbula-Hansen, L. Feng, H. Toogood, K. O. Stetter, and D. Soll
Evolutionary Divergence of the Archaeal Aspartyl-tRNA Synthetases into Discriminating and Nondiscriminating Forms
J. Biol. Chem., September 27, 2002; 277(40): 37184 - 37190.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
I. Ahel, C. Stathopoulos, A. Ambrogelly, A. Sauerwald, H. Toogood, T. Hartsch, and D. Soll
Cysteine Activation Is an Inherent in Vitro Property of Prolyl-tRNA Synthetases
J. Biol. Chem., September 13, 2002; 277(38): 34743 - 34748.
[Abstract] [Full Text] [PDF]

Home page
 J. Biol. Chem.Home page
A. Ambrogelly, I. Ahel, C. Polycarpo, S. Bunjun-Srihari, B. Krett, C. Jacquin-Becker, B. Ruan, C. Kohrer, C. Stathopoulos, U. L. RajBhandary, et al.
Methanocaldococcus jannaschii Prolyl-tRNA Synthetase Charges tRNAPro with Cysteine
J. Biol. Chem., September 13, 2002; 277(38): 34749 - 34754.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
J. W. Scott and M. E. Rasche
Purification, Overproduction, and Partial Characterization of {beta}-RFAP Synthase, a Key Enzyme in the Methanopterin Biosynthesis Pathway{dagger}
J. Bacteriol., August 15, 2002; 184(16): 4442 - 4448.
[Abstract] [Full Text] [PDF]