An integrated analysis of the genome of the hyperthermophilic archaeon Pyrococcus abyssi

Abstract

SummaryThe hyperthermophilic euryarchaeon Pyrococcus abyssi and the related species Pyrococcus furiosus and Pyrococcus horikoshii , whose genomes have been completely sequenced, are presently used as model organisms in different laboratories to study archaeal DNA replication and gene expression and to develop genetic tools for hyperthermophiles. We have performed an extensive re-annotation of the genome of P. abyssi to obtain an integrated view of its phylogeny, molecular biology and physiology. Many new functions are predicted for both informational and operational proteins. Moreover, several candidate genes have been identified that might encode missing links in key metabolic pathways, some of which have unique biochemical features. The great majority of Pyrococcus proteins are typical archaeal proteins and their phylogenetic pattern agrees with its position near the root of the archaeal tree. However, proteins probably from bacterial origin, including some from mesophilic bacteria, are also present in the P. abyssi genome.

Insights on the Evolution of Metabolic Networks of Unicellular Translationally Biased Organisms from Transcriptomic Data and Sequence Analysis

“…Among its most biased genes, besides ribosomal proteins and elongation factors, we find ferrodoxin (CAI(fdxA)=0.71), ferredoxin oxidoreductase (CAI(for)=0.63), and keto-valine-ferredoxin oxidoreductase c-chain (CAI(PAB1470)=0.62). Ferredoxin appears to be the major metabolic electron carrier in pyrococci (Cohen et al 2003). After reduction during peptide or sugar degradation, it is mainly reoxidized by a membrane-bound hydrogenase (Silva et al 2000), potentially generating membrane potential.…”

tRNA synthetase paralogs: Evolutionary links in the transition from tRNA-dependent amino acid biosynthesis to de novo biosynthesis

“…These studies establish unambiguously that P. abyssi possesses an AsnA homolog that is based on a class II catalytic fold related to asparaginyl-tRNA synthetase. Accordingly, the combination of AsnRS and AsnRS2 constitute a direct pathway for asparagine synthesis and aminoacyltRNA synthesis, rationalizing the absence of a nondiscriminating AspRS and GatCAB transamidase in the P. abyssi genome (16). This direct pathway for asparagine synthesis͞incorporation is limited to the Pyrococcus, Thermoplasma, and Pyrobaculum genera; other archaea employ indirect pathways for asparaginyl-tRNA synthesis (16).…”

Genome sequence of the deep-sea γ-proteobacterium Idiomarina loihiensis reveals amino acid fermentation as a source of carbon and energy

“…and Pyrococcus spp. (7)(8)(9), I. loihiensis inhabits partially oxygenated cold waters at the periphery of the vent, surviving a wide range of growth temperatures (from 4°C to 46°C) and salinities (from 0.5% to 20% NaCl). We report here the complete genome sequence of I. loihiensis, deep-sea ␥-proteobacterium.…”