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.

Draft Genome Sequence of a Multi-Metal Resistant Bacterium Pseudomonas putida ATH-43 Isolated from Greenwich Island, Antarctica

“…In fact, higher tRNA genes content seem to be related with specific cold adaption mechanisms, as determined by comparative genomics analysis (Dutta and Chaudhuri, 2010). In addition, the number of genes involved in signal transduction mechanisms and inorganic ion transport and metabolism (two COG categories) in this bacterium's genome, is similar to other P. putida strains but exceeds that displayed by other Gammaproteobacteria (Wu et al, 2011).…”

Auxiliary tRNAs: large-scale analysis of tRNA genes reveals patterns of tRNA repertoire dynamics

“…While several studies in both archaea (58) and bacteria (59,60) have shown that the nucleotide content of tRNA genes does not comply with the genomic GC content but is rather restricted by habitat temperature through constraints on folding stability, the wobble position, which does not contribute to structure stability, might be free from these constraints and conform to nucleotide content bias.…”

tRNA Modifications: Impact on Structure and Thermal Adaptation

“…In thermophilic organisms, a bias towards GC-rich sequences is frequently observed, and the corresponding tRNAs are GC-rich as well [18,59,60,61,62]. This introduces a folding problem similar to the one observed for AU-rich sequences.…”

“…Hence, organisms thriving at high temperatures have an urgent need for thermal stabilization of their tRNAs. One predominant temperature-dependent adaptation is the increase of the GC-content especially in the stems of the cloverleaf structure [60,61]. Oshima reported that an increase of 5% in the GC-content raises the melting temperature of a tRNA by 1.5 °C [62].…”