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
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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.