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: Consistent with previous work (Singer and Hickey 2000; Lightfield et al. 2011), we find that G + C content alone can explain some of the AAC variation between genomes (fig. 1; median R2 over amino acids = 0.555) but leaves a substantial fraction of variance unexplained. This is not surprising as G + C variation has a single degree of freedom, insufficient to capture the diversity in AAC (and ecological preferences) among microbes, as illustrated by the seven amino acids with balanced G + C across codons (THEVDQC): AAC for this subset of amino acids is poorly predictable from G + C alone (fig. 1; median R2 = 0.115). In more general terms, we estimate that our data set has at least 6 and 7 degrees of freedom for the AAC and ecological preference, respectively (supplementary fig. S1, Supplementary Material online). This is important to note because in cases where AAC correlates with ecological parameters, but G + C does not—such as for thermophilicity (Hurst and Merchant 2001; Zeldovich et al. 2007) and halophilicity (Paul et al. 2008)—this should not be taken as sufficient evidence for adaptation at the amino acid level. Rather, absence of a clear association might reflect intrinsic limitations of G + C content as a predictor.Fig. 1.—
Affiliation: Division of Electronics, Rudjer Boskovic Institute, Zagreb, Croatia Molecular Basis of Ageing, Mediterranean Institute for Life Sciences (MedILS), Split, Croatia.