Abstract
BackgroundStudies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. Although the general hypothesis of an increased molecular flexibility in the cold is widely accepted, the results of thermal adaptation are still difficult to detect at proteomic down to the genomic sequence level. Approaches towards a more detailed picture emerge with the advent of new sequencing technologies. Only small changes in primary protein structure have been shown to modify kinetic and thermal properties of enzymes, but likewise for interspecies comparisons a high genetic identity is still essential to specify common principles. The present study uses comprehensive transcriptomic sequence information to uncover general patterns of thermal adaptation on the RNA as well as protein primary structure.ResultsBy comparing orthologous sequences of two closely related zoarcid fish inhabiting different latitudinal zones (Antarctica: Pachycara brachycephalum, temperate zone: Zoarces viviparus) we were able to detect significant differences in the codon usage. In the cold-adapted species a lower GC content in the wobble position prevailed for preserved amino acids. We were able to estimate 40-60% coverage of the functions represented within the two compared zoarcid cDNA-libraries on the basis of a reference genome of the phylogenetically closely related fish Gasterosteus aculeatus. A distinct pattern of amino acid substitutions could be identified for the non-synonymous codon exchanges, with a remarkable surplus of serine and reduction of glutamic acid and asparagine for the Antarctic species.ConclusionBased on the differences between orthologous sequences from confamiliar species, distinguished mainly by the temperature regimes of their habitats, we hypothesize that temperature leaves a signature on the composition of biological macromolecules (RNA, proteins) with implications for the transcription and translation level. As the observed pattern of amino acid substitutions only partly support the flexibility hypothesis further evolutionary forces may be effective at the global transcriptome level.
Highlights
Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles
A classification of P. brachycephalum and Z. viviparus by molecular analyses of selected sequence data was used to determine the phylogenetic relationship with various bony fish species from widespread geographical regions
The present approach includes a comprehensive set of transcriptomic sequence pairs from confamiliar species inhabiting thermally distinct realms differing by about 10°C optimal growth temperature (OGT)
Summary
Studies of temperature-induced adaptation on the basis of genomic sequence data were mainly done in extremophiles. The general hypothesis of an increased molecular flexibility in the cold is widely accepted, the results of thermal adaptation are still difficult to detect at proteomic down to the genomic sequence level. The present study uses comprehensive transcriptomic sequence information to uncover general patterns of thermal adaptation on the RNA as well as protein primary structure. Different temperature adaptations and dependencies of the kinetics of single enzymes like the phosphoglycerate kinase [6,7], chitobiase [7] or the lactate dehydrogenase [8] were studied intensively complemented by comparative analyses at the amino acid sequence level [9], discussing thermal acclimation up to adaptation at the molecular level
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