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Deposited research article

Preferred codons and amino acid couples in hyperthermophiles

Sávio Torres de Farias and Maria Christina Manhães Bonato

Departamento de Biologia Molecular, Universidade Federal da Paraíba, João Pessoa-PB, 58059-900, Brazil

author email corresponding author email

Genome Biology 2002, 3:preprint0006.1-0006.18doi:10.1186/gb-2002-3-8-preprint0006

Published:	19 July 2002

This is the first version of this article to be made available publicly, and no other version is available at present. This article was submitted to Genome Biology for peer review.

Subject areas: Bioinformatics, Microbiology and parasitology, Evolution

Abstract

Background

Most organisms grow at temperatures from 20 to 50°C but some prokaryotes, including Archaea and Bacteria, are capable of withstanding higher temperatures, from 60 to >100°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.