Analysis of tRNA composition and folding in psychrophilic, mesophilic and thermophilic genomes: indications for thermal adaptation

Abstract

Comparative genomic studies on several thermophilic archaea and bacteria revealed that a set of coordinated changes are associated with organisms adapted to a higher temperature, among which the dinucleotide composition of genomic DNA, pattern of codon usage and amino acid composition of the proteomes reveal subtle differences between thermophilic and mesophilic organisms. In this context, we have analyzed all tRNA sequences present in the complete genome sequences of 57 organisms belonging to psychrophiles, meophiles, thermophiles and hyperthermophiles. The presence of distinct selective constraints was revealed in the number and distribution of tRNAs and in their folding patterns, which could be correlated with the optimal growth temperature. The tRNA contents of thermophiles were found to be significantly less compared with the two other groups, whereas the tRNA genes of thermophiles exhibit a much higher guanine plus cytosine content. Analysis of the entire data set revealed that tRNAs from thermophiles showed greater structural stability at higher temperatures compared with the other two groups. Repeated cluster analysis applied to two sets of data from tRNA folding, the free energy of folding (dG) and the melting temperature (T(m)), indicated that the thermophiles always had a tendency to cluster together.