Relative Amino Acid Composition Signatures of Organisms and Environments

Abstract

BackgroundIdentifying organism-environment interactions at the molecular level is crucial to understanding how organisms adapt to and change the chemical and molecular landscape of their habitats. In this work we investigated whether relative amino acid compositions could be used as a molecular signature of an environment and whether such a signature could also be observed at the level of the cellular amino acid composition of the microorganisms that inhabit that environment.Methodologies/Principal FindingsTo address these questions we collected and analyzed environmental amino acid determinations from the literature, and estimated from complete genomic sequences the global relative amino acid abundances of organisms that are cognate to the different types of environment. Environmental relative amino acid abundances clustered into broad groups (ocean waters, host-associated environments, grass land environments, sandy soils and sediments, and forest soils), indicating the presence of amino acid signatures specific for each environment. These signatures correlate to those found in organisms. Nevertheless, relative amino acid abundance of organisms was more influenced by GC content than habitat or phylogeny.ConclusionsOur results suggest that relative amino acid composition can be used as a signature of an environment. In addition, we observed that the relative amino acid composition of organisms is not highly determined by environment, reinforcing previous studies that find GC content to be the major factor correlating to amino acid composition in living organisms.

Analysis of five complete genome sequences for members of the class Peribacteria in the recently recognized Peregrinibacteria bacterial phylum

“…This value is significantly larger than those reported for bacteria from aquatic and terrestrial environments (average values of 0.05% and 0.15%, although these previously published data indicate substantial within-environment variation) (Moura, Savageau & Alves, 2013). Notably, 19% of these cysteines are incorporated into twenty proteins including a 14-gene cluster (7.2 ± 2.4% cysteine) (Supplementary Table S4).…”

Variations in amino acid composition in bacterial single stranded DNA–binding proteins correlate with GC content

“…However, it is much higher (up to 60 %, on average 30 %) than it has been expected from the reported proteome analyses; i.e. up to 10 % of Gly residues were found in GC rich proteomes (35). This suggests that elevated Gly accumulation in the Ct domain evolved with some specific functional request of SSBs to high GC content genomes.…”

“…Next, although it has been expected that high GC content bacteria will accumulate Pro due to the GC codon enrichment (35), OB folds from high GC content bacteria (Table 4) do not show this trend. This could be ascribed to the fact that proline, due to its unique chemical and structural properties, belongs to the group of the aas known to have "disorder-promoting" residues, and as such Pro can have a negative influence on the classical secondary elements which form OB-fold (38).…”

“…Composition of amino acids in SSB proteins in our dataset were compared to composition of aas in the overall proteomes of 961 species (35), as shown in Table 4. Observed changes in aa content reported for 961 proteomes were explained with enrichment of GC rich/poor codons (35). Significant correlation between genomic GC composition and proteome aa content was well documented (36,37).…”

“…It was reported that AT-rich genome would encode proteins rich in the Phe, Tyr, Met, Ile, Asn, and Lys (FYMINK), whereas GC-rich genomes would encode proteins rich in the Gly, Ala, Arg, and Pro (GARP) (36). Indeed, this trend is present in SSB proteins (Table 4) (34,35). As shown previously for a trial sample ( Table 2) the changes were much more pronounced for Ct domain.…”