Global Shifts in Genome and Proteome Composition Are Very Tightly Coupled.
Bottom Line: We disentangle these effects by systematically evaluating the correspondence between intergenic nucleotide composition, where protein-level selection is absent, the AAC, and ecological parameters of 909 prokaryotes.Moreover, highly expressed genes do not exhibit more prominent environment-related AAC signatures than lowly expressed genes, despite contributing more to the effective proteome.We discuss these results in light of contravening evidence from biophysical data and further reading frame-specific analyses that suggest that adaptation takes place at the protein level.
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.Show MeSH
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Mentions: Next, we examined the genomes and proteomes of 49 fungi, of which 13 were thermophilic. Results are broadly consistent with our findings in prokaryotes: The G + C content of noncoding DNA—here encompassing introns and intergenic regions—can explain 60% of the variability in AAC across fungi (fig. 4A and B). Incorporating di- and trinucleotide composition as features in the regression leads to enhanced predictive power (R2 = 0.73), with the further addition of phylogenetic categories leading to 80% of variance in proteome composition being accounted for. As observed for prokaryotes, thermophilic fungi can be recognized with high accuracy from the AAC of their proteomes (AUROC = 0.940; fig. 4C), whereas prediction from AAC residuals after nucleotide composition is factored out is considerably less accurate (AUROC = 0.639; fig. 4C). These findings indicate that the putatively adaptive signatures in AAC emanate from the nucleotide level not only in prokaryotes but also in eukaryotes.Fig. 4.—
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.