Op-gbev150111 1519..1532

The amino acid composition (AAC) of proteomes differs greatly between microorganisms and is associated with the environmental niche they inhabit, suggesting that these changes may be adaptive. Similarly, the oligonucleotide composition of genomes varies and mayconferadvantagesat theDNA/RNA level. These influencesoverlap inprotein-coding sequences,making itdifficult togauge their relative contributions. 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. We find that G + C content, the most frequently used measure of genomic composition, cannot capture diversity in AAC and across ecological contexts. However, di-/trinucleotide composition in intergenic DNA predicts amino acid frequencies of proteomes to the point where very little cross-speciesvariability remainsunexplained (91%ofvarianceaccountedfor).Qualitatively similar resultswereobtainedfor49fungal genomes, where 80% of the variability in AAC could be explained by the composition of introns and intergenic regions. Upon factoring out oligonucleotide composition and phylogenetic inertia, the residual AAC is poorly predictive of the microbes’ ecological preferences, in stark contrast with the original AAC. Moreover, highly expressed genes do not exhibit more prominent environmentrelated AAC signatures than lowly expressed genes, despite contributing more to the effective proteome. Thus, evolutionary shifts in overallAACappear tooccuralmostexclusively throughfactors shapingtheglobaloligonucleotidecontentof thegenome.Wediscuss 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.