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.

Figure 1. Characterization of different environments by their relative amino acid composition.

A) scatter plot by Principal Component Analysis according to the type of environment; B) Hierarchical clustering analysis. The length of branches represents the degree of dissimilarity between clusters. The x-axis of the heat map represents the 20 amino acids by alphabetical order of the three-letter code name. Determinations of Asp/Asn and Glu/Gln were considered together for the analysis, because environmental measurements did not distinguish between the two amino acids in the pairs. The y- axis of the heatmap represents the individual environments where amino acid abundance was determined. Over- and under-representation of amino acid residues in each environment are represented in green and red colored squares, respectively.

Figure 2. Characterization of the relative amino acid composition of the proteomes from different organisms.

A) scatter plot by Principal Component Analysis according to the type of environment; B) Hierarchical clustering analysis. The length of branches represents the degree of dissimilarity between clusters. The x-axis of the heat map represents the 20 amino acids by alphabetical order of the three-letter code name. The y- axis of the heatmap represents the individual organisms where amino acid abundance was estimated. Over- and under-representation of amino acid residues in each organism are represented in green and red colored squares, respectively.

Figure 3. Relative amino acid composition, weighted by δ index, of each organism plotted against average GC content.

Figure 4. Spearman Rank Correlations between the RAAA of organisms and environments.

Asterisks represent significance at p<0.01 (**) and p<0.001 (***).