Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.
Bottom Line: Qualitatively similar results were obtained for 49 fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions.Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome.Thus, evolutionary shifts in overall AAC appear to occur almost exclusively through factors shaping the global oligonucleotide content of the genome.
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.Show MeSH
Mentions: Next, we visualize the distributions of selected dinucleotide frequencies of thermophilic and mesophilic protein-coding genes in all three codon positions (fig. 7). Here, the codon positions and can be compared qualitatively, in terms of direction and magnitude of change. Indeed, differences between the codon positions can be observed, where, for instance, the second codon position shifts toward higher GpA/TpC values in thermophiles, whereas this trend is reversed in the third codon position. These differences are not evident in randomized data (supplementary fig. S7, Supplementary Material online). Similar visualizations reveal significant differences between codon positions in dinucleotide frequency shifts between halophiles and non-halophiles (fig. 7B), strict anaerobes and aerotolerant organisms (fig. 7C), psychrophiles and non-psychrophiles (fig. 7D), and other niches (not shown).Fig. 7.—
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.