title: 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.
  
  
  RESULTS
  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.
authors.affiliation: Department of Basic Medical Sciences and Institute of Biomedical Research, University of Lleida, Lleida, Spain ; Department of Biology & CESAM, University of Aveiro, Aveiro, Portugal.
authors.forename: Alexandra
authors.initials: A
authors.lastname: Moura
authors.forename: Michael A
authors.initials: MA
authors.lastname: Savageau
authors.forename: Rui
authors.initials: R
authors.lastname: Alves
mesh_terms: D000596:Amino Acids / Q000235:genetics / Q000378:metabolism*; D000818:Animals; D001105:Archaea / Q000737:chemistry / Q000235:genetics*; D001419:Bacteria / Q000737:chemistry / Q000235:genetics*; D001482:Base Composition / Q000235:genetics*; D016000:Cluster Analysis; D017753:Ecosystem; D006801:Humans; D059013:Microbial Consortia / Q000235:genetics; D064307:Microbiota / Q000235:genetics; D009792:Oceans and Seas; D010944:Plants / Q000737:chemistry / Q000235:genetics*; D025341:Principal Component Analysis; D012988:Soil Microbiology; D014871:Water Microbiology
chemical_list: D000596:Amino Acids