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Literature DB >> 14566062

The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism.

Elizabeth Waters¹, Michael J Hohn, Ivan Ahel, David E Graham, Mark D Adams, Mary Barnstead, Karen Y Beeson, Lisa Bibbs, Randall Bolanos, Martin Keller, Keith Kretz, Xiaoying Lin, Eric Mathur, Jingwei Ni, Mircea Podar, Toby Richardson, Granger G Sutton, Melvin Simon, Dieter Soll, Karl O Stetter, Jay M Short, Michiel Noordewier.

Abstract

The hyperthermophile Nanoarchaeum equitans is an obligate symbiont growing in coculture with the crenarchaeon Ignicoccus. Ribosomal protein and rRNA-based phylogenies place its branching point early in the archaeal lineage, representing the new archaeal kingdom Nanoarchaeota. The N. equitans genome (490,885 base pairs) encodes the machinery for information processing and repair, but lacks genes for lipid, cofactor, amino acid, or nucleotide biosyntheses. It is the smallest microbial genome sequenced to date, and also one of the most compact, with 95% of the DNA predicted to encode proteins or stable RNAs. Its limited biosynthetic and catabolic capacity indicates that N. equitans' symbiotic relationship to Ignicoccus is parasitic, making it the only known archaeal parasite. Unlike the small genomes of bacterial parasites that are undergoing reductive evolution, N. equitans has few pseudogenes or extensive regions of noncoding DNA. This organism represents a basal archaeal lineage and has a highly reduced genome.

Entities: Chemical Disease Species

Keywords: Non-programmatic

Mesh：

Substances：
DNA, Archaeal

Year: 2003 PMID： 14566062 PMCID： PMC240731 DOI： 10.1073/pnas.1735403100

Source DB: PubMed Journal: Proc Natl Acad Sci U S A ISSN： 0027-8424 Impact factor: 11.205

45 in total

1. Isolation of a complete A1AO ATP synthase comprising nine subunits from the hyperthermophile Methanococcus jannaschii.

Authors: Astrid Lingl; Harald Huber; Karl O Stetter; Frank Mayer; Josef Kellermann; Volker Müller
Journal: Extremophiles Date: 2003-04-09 Impact factor: 2.395

2. Improved microbial gene identification with GLIMMER.

Authors: A L Delcher; D Harmon; S Kasif; O White; S L Salzberg
Journal: Nucleic Acids Res Date: 1999-12-01 Impact factor: 16.971

3. Assembly of a class I tRNA synthetase from products of an artificially split gene.

Authors: J J Burbaum; P Schimmel
Journal: Biochemistry Date: 1991-01-15 Impact factor: 3.162

4. Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal.

Authors: J Lyons-Weiler; G A Hoelzer; R J Tausch
Journal: Mol Biol Evol Date: 1996-07 Impact factor: 16.240

5. The exon theory of genes.

Authors: W Gilbert
Journal: Cold Spring Harb Symp Quant Biol Date: 1987

6. Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

Authors: N A Moran
Journal: Proc Natl Acad Sci U S A Date: 1996-04-02 Impact factor: 11.205

7. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

Authors: J D Thompson; D G Higgins; T J Gibson
Journal: Nucleic Acids Res Date: 1994-11-11 Impact factor: 16.971

8. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria.

Authors: Y Andachi; F Yamao; A Muto; S Osawa
Journal: J Mol Biol Date: 1989-09-05 Impact factor: 5.469

9. DNA recovery from soils of diverse composition.

Authors: J Zhou; M A Bruns; J M Tiedje
Journal: Appl Environ Microbiol Date: 1996-02 Impact factor: 4.792

10. The genome sequence of Drosophila melanogaster.

Authors: M D Adams; S E Celniker; R A Holt; C A Evans; J D Gocayne; P G Amanatides; S E Scherer; P W Li; R A Hoskins; R F Galle; R A George; S E Lewis; S Richards; M Ashburner; S N Henderson; G G Sutton; J R Wortman; M D Yandell; Q Zhang; L X Chen; R C Brandon; Y H Rogers; R G Blazej; M Champe; B D Pfeiffer; K H Wan; C Doyle; E G Baxter; G Helt; C R Nelson; G L Gabor; J F Abril; A Agbayani; H J An; C Andrews-Pfannkoch; D Baldwin; R M Ballew; A Basu; J Baxendale; L Bayraktaroglu; E M Beasley; K Y Beeson; P V Benos; B P Berman; D Bhandari; S Bolshakov; D Borkova; M R Botchan; J Bouck; P Brokstein; P Brottier; K C Burtis; D A Busam; H Butler; E Cadieu; A Center; I Chandra; J M Cherry; S Cawley; C Dahlke; L B Davenport; P Davies; B de Pablos; A Delcher; Z Deng; A D Mays; I Dew; S M Dietz; K Dodson; L E Doup; M Downes; S Dugan-Rocha; B C Dunkov; P Dunn; K J Durbin; C C Evangelista; C Ferraz; S Ferriera; W Fleischmann; C Fosler; A E Gabrielian; N S Garg; W M Gelbart; K Glasser; A Glodek; F Gong; J H Gorrell; Z Gu; P Guan; M Harris; N L Harris; D Harvey; T J Heiman; J R Hernandez; J Houck; D Hostin; K A Houston; T J Howland; M H Wei; C Ibegwam; M Jalali; F Kalush; G H Karpen; Z Ke; J A Kennison; K A Ketchum; B E Kimmel; C D Kodira; C Kraft; S Kravitz; D Kulp; Z Lai; P Lasko; Y Lei; A A Levitsky; J Li; Z Li; Y Liang; X Lin; X Liu; B Mattei; T C McIntosh; M P McLeod; D McPherson; G Merkulov; N V Milshina; C Mobarry; J Morris; A Moshrefi; S M Mount; M Moy; B Murphy; L Murphy; D M Muzny; D L Nelson; D R Nelson; K A Nelson; K Nixon; D R Nusskern; J M Pacleb; M Palazzolo; G S Pittman; S Pan; J Pollard; V Puri; M G Reese; K Reinert; K Remington; R D Saunders; F Scheeler; H Shen; B C Shue; I Sidén-Kiamos; M Simpson; M P Skupski; T Smith; E Spier; A C Spradling; M Stapleton; R Strong; E Sun; R Svirskas; C Tector; R Turner; E Venter; A H Wang; X Wang; Z Y Wang; D A Wassarman; G M Weinstock; J Weissenbach; S M Williams; K C Worley; D Wu; S Yang; Q A Yao; J Ye; R F Yeh; J S Zaveri; M Zhan; G Zhang; Q Zhao; L Zheng; X H Zheng; F N Zhong; W Zhong; X Zhou; S Zhu; X Zhu; H O Smith; R A Gibbs; E W Myers; G M Rubin; J C Venter
Journal: Science Date: 2000-03-24 Impact factor: 47.728

188 in total

The genome of Nanoarchaeum equitans: insights into early archaeal evolution and derived parasitism.

1. Isolation of a complete A1AO ATP synthase comprising nine subunits from the hyperthermophile Methanococcus jannaschii.

2. Improved microbial gene identification with GLIMMER.

3. Assembly of a class I tRNA synthetase from products of an artificially split gene.

4. Relative apparent synapomorphy analysis (RASA). I: The statistical measurement of phylogenetic signal.

5. The exon theory of genes.

6. Accelerated evolution and Muller's rachet in endosymbiotic bacteria.

7. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice.

8. Codon recognition patterns as deduced from sequences of the complete set of transfer RNA species in Mycoplasma capricolum. Resemblance to mitochondria.

9. DNA recovery from soils of diverse composition.

10. The genome sequence of Drosophila melanogaster.

1. Trans-editing of mischarged tRNAs.

2. Global analysis of predicted proteomes: functional adaptation of physical properties.

3. Reverse gyrase is not a prerequisite for hyperthermophilic life.

Review 4. Determination of the core of a minimal bacterial gene set.

5. In search of RNase P RNA from microbial genomes.

6. Enigmatic, ultrasmall, uncultivated Archaea.

7. The hyperthermophilic euryarchaeon Archaeoglobus fulgidus repairs uracil by single-nucleotide replacement.

Review 8. Archaea--timeline of the third domain.

9. Separate and combined biochemical activities of the subunits of a naturally split reverse gyrase.

10. Menaquinone-specific prenyl reductase from the hyperthermophilic archaeon Archaeoglobus fulgidus.