title: Unique amino acid composition of proteins in halophilic bacteria.
abstract: The amino acid compositions of proteins from halophilic archaea were compared with those from non-halophilic mesophiles and thermophiles, in terms of the protein surface and interior, on a genome-wide scale. As we previously reported for proteins from thermophiles, a biased amino acid composition also exists in halophiles, in which an abundance of acidic residues was found on the protein surface as compared to the interior. This general feature did not seem to depend on the individual protein structures, but was applicable to all proteins encoded within the entire genome. Unique protein surface compositions are common in both halophiles and thermophiles. Statistical tests have shown that significant surface compositional differences exist among halophiles, non-halophiles, and thermophiles, while the interior composition within each of the three types of organisms does not significantly differ. Although thermophilic proteins have an almost equal abundance of both acidic and basic residues, a large excess of acidic residues in halophilic proteins seems to be compensated by fewer basic residues. Aspartic acid, lysine, asparagine, alanine, and threonine significantly contributed to the compositional differences of halophiles from meso- and thermophiles. Among them, however, only aspartic acid deviated largely from the expected amount estimated from the dinucleotide composition of the genomic DNA sequence of the halophile, which has an extremely high G+C content (68%). Thus, the other residues with large deviations (Lys, Ala, etc.) from their non-halophilic frequencies could have arisen merely as "dragging effects" caused by the compositional shift of the DNA, which would have changed to increase principally the fraction of aspartic acid alone.
authors.affiliation: Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Yata 1111, Mishima, Shizuoka 411-8540, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fukuchi
authors.forename: Kazuaki
authors.initials: K
authors.lastname: Yoshimune
authors.forename: Mamoru
authors.initials: M
authors.lastname: Wakayama
authors.forename: Mitsuaki
authors.initials: M
authors.lastname: Moriguchi
authors.forename: Ken
authors.initials: K
authors.lastname: Nishikawa
mesh_terms: D000596:Amino Acids / Q000032:analysis*; D001105:Archaea; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D019295:Computational Biology; D016208:Databases, Factual; D004795:Enzyme Stability; D016680:Genome, Bacterial; D006217:Halobacterium / Q000737:chemistry*; D006358:Hot Temperature; D008958:Models, Molecular; D013499:Surface Properties
chemical_list: D000596:Amino Acids; D001426:Bacterial Proteins