Preferred codons and amino acid couples in hyperthermophiles.
BACKGROUND
Most organisms grow at temperatures from 20 to 50 degrees C but some prokaryotes, including Archaea and Bacteria, are capable of withstanding higher temperatures, from 60 to >100 degrees C. What makes these cells so resistant to heat? Their biomolecules must be sufficiently stable, especially proteins, to work under these extreme conditions, but the bases for thermostability remains elusive.


RESULTS
The preferential usage of certain couples of amino acids and codons in thermal adaptation was investigated, by comparative proteome analysis, using 28 complete genomes from 18 mesophiles, 4 thermophiles, and 6 hyperthermophiles. In the hyperthermophiles proteomes, whenever the percent of Glu (E) and Lys (K) Increased, the percent of Gln (Q) and His (H) decreased, so that the E+K/Q+H ratio was > 4,5; in the mesophiles proteomes, it was < 2,5 and in the thermophiles an intermediary value was observed. The E+K/Q+H ratios for chaperonins, potentially thermostable proteins, were higher than their proteome ratios whereas, for DNA ligases, not necessarily thermostable, they followed the proteome ones. Analysis of codon usage revealed that hyperthermophiles preferred AGR codons for Arg in detriment of CGN codons, which were preferred by mesophiles.


CONCLUSIONS
The results suggested that the E+K/Q+H ratio may provide a useful mark for distinguishing hyperthermophilic, thermophilic and mesophilic prokaryotes and that the high percent of the amino acid couple E+K, consistently associated to the low percent of the pair Q+H, could contribute to protein thermostability. Second, the preference for AGR codons for Arg was a signature of all hyperthermophilics so far analyzed.
De Farias
Sávio Torres
ST
Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa-PB, 58059-900, Brazil.
Bonato
Maria Christina Manhães
MC
D000596:Amino Acids / Q000235:genetics*; D000818:Animals; D029681:Arabidopsis Proteins / Q000737:chemistry / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry* / Q000235:genetics*; D001120:Arginine / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry* / Q000235:genetics*; D001482:Base Composition; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000235:genetics; D018833:Chaperonins / Q000737:chemistry / Q000235:genetics; D003062:Codon / Q000235:genetics*; D011088:DNA Ligases / Q000737:chemistry / Q000235:genetics; D017238:Genes, Helminth / Q000235:genetics; D020745:Genome, Archaeal; D016680:Genome, Bacterial; D016681:Genome, Fungal; D018745:Genome, Plant; D006358:Hot Temperature; D020543:Proteome / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics
D000596:Amino Acids; D029681:Arabidopsis Proteins; D019843:Archaeal Proteins; D001426:Bacterial Proteins; D029742:Caenorhabditis elegans Proteins; D003062:Codon; D020543:Proteome; D029701:Saccharomyces cerevisiae Proteins; D001120:Arginine; D018833:Chaperonins; D011088:DNA Ligases