Relative amino acid composition signatures of organisms and environments

Abstract

Background: Identifying 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 Findings: To 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. Conclusions: Our 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.

AM was supported by Fundação para a Ciência e a Tecnologia, Portugal, through the postdoctoral grant SFRH/BPD/72256/2010. RA was partially supported by the Ministerio de Ciencia e Innovación (Spain) through grant BFU2010-17704, and by the Generalitat de Catalunya through a grant for research group 2009SGR809. MAS was supported in part by a grant from the US Public Health Service (RO1-GM30054). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.