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

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.

SUBMITTER: Waters E

PROVIDER: S-EPMC240731 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature

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

Waters Elizabeth E Hohn Michael J MJ Ahel Ivan I Graham David E DE Adams Mark D MD Barnstead Mary M Beeson Karen Y KY Bibbs Lisa L Bolanos Randall R Keller Martin M Kretz Keith K Lin Xiaoying X Mathur Eric E Ni Jingwei J Podar Mircea M Richardson Toby T Sutton Granger G GG Simon Melvin M Soll Dieter D Stetter Karl O KO Short Jay M JM Noordewier Michiel M

Proceedings of the National Academy of Sciences of the United States of America 20031017 22

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 seque ...[more]

PMID: 14566062

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Project description:BackgroundNanoarchaeum equitans, the only known hyperthermophilic archaeon exhibiting parasitic life style, has raised some new questions about the evolution of the Archaea and provided a model of choice to study the genome landmarks correlated with thermo-parasitic adaptation. In this context, we have analyzed the genome and proteome composition of N. equitans and compared the same with those of other mesophiles, hyperthermophiles and obligatory host-associated organisms.ResultsAnalysis of nucleotide, codon and amino acid usage patterns in N. equitans indicates the presence of distinct selective constraints, probably due to its adaptation to a thermo-parasitic life-style. Among the conspicuous characteristics featuring its hyperthermophilic adaptation are overrepresentation of purine bases in protein coding sequences, higher GC-content in tRNA/rRNA sequences, distinct synonymous codon usage, enhanced usage of aromatic and positively charged residues, and decreased frequencies of polar uncharged residues, as compared to those in mesophilic organisms. Positively charged amino acid residues are relatively abundant in the encoded gene-products of N. equitans and other hyperthermophiles, which is reflected in their isoelectric point distribution. Pairwise comparison of 105 orthologous protein sequences shows a strong bias towards replacement of uncharged polar residues of mesophilic proteins by Lys/Arg, Tyr and some hydrophobic residues in their Nanoarchaeal orthologs. The traits potentially attributable to the symbiotic/parasitic life-style of the organism include the presence of apparently weak translational selection in synonymous codon usage and a marked heterogeneity in membrane-associated proteins, which may be important for N. equitans to interact with the host and hence, may help the organism to adapt to the strictly host-associated life style. Despite being strictly host-dependent, N. equitans follows cost minimization hypothesis.ConclusionThe present study reveals that the genome and proteome composition of N. equitans are marked with the signatures of dual adaptation--one to high temperature and the other to obligatory parasitism. While the analysis of nucleotide/amino acid preferences in N. equitans offers an insight into the molecular strategies taken by the archaeon for thermo-parasitic adaptation, the comparative study of the compositional characteristics of mesophiles, hyperthermophiles and obligatory host-associated organisms demonstrates the generality of such strategies in the microbial world.

Dataset Information

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

Publications

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

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