Abstract
BackgroundThe evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, particularly with the availability of many complete genomes. Are there specific properties associated with lifestyles and phylogenies? What are the underlying evolutionary trends? One of the simplest analyses to address such questions concerns characterization of proteomes at the amino acids composition level.ResultsIn this work, amino acid compositions of a large set of 208 proteomes, with significant number of representatives from the three phylogenetic domains and different lifestyles are analyzed, resorting to an appropriate multidimensional method: Correspondence analysis. The analysis reveals striking discrimination between eukaryotes, prokaryotic mesophiles and hyperthemophiles-themophiles, following amino acid usage. In sharp contrast, no similar discrimination is observed for psychrophiles. The observed distributional properties are compared with various inferred chronologies for the recruitment of amino acids into the genetic code. Such comparisons reveal correlations between the observed segregations of species following amino acid usage, and the separation of amino acids following early or late recruitment.ConclusionA simple description of proteomes according to amino acid compositions reveals striking signatures, with sharp segregations or on the contrary non-discriminations following phylogenies and lifestyles. The distribution of species, following amino acid usage, exhibits a discrimination between [high GC]-[high optimal growth temperatures] and [low GC]-[moderate temperatures] characteristics. This discrimination appears to coincide closely with the separation of amino acids following their inferred early or late recruitment into the genetic code. Taken together the various results provide a consistent picture for the evolution of proteomes, in terms of amino acid usage.
Highlights
The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, with the availability of many complete genomes
We used Correspondence analysis to compare amino acid compositions of 208 predicted proteomes with large representations of the three phylogenetic domains as well as various lifestyles (20 hyperthermophiles, 7 thermophiles, 8 psychrophiles and 173 mesophiles including 53 eukaryotes; detailed list is in Additional file 1)
It is important to stress that GC content and optimal growth temperatures are not included in the set of analysed parameters, but correspond rather to observations underlying the distributions of species as obtained from their amino acid compositions
Summary
The evolutionary characterization of species and lifestyles at global levels is nowadays a subject of considerable interest, with the availability of many complete genomes. At the DNA level the simplest analyses concern the GC compositions and, at the proteomes level the simplest analyses concern the amino acid compositions Even such simple comparative descriptions can reveal important evolutionary properties for the genomes. In comparison to the simple one-dimensional linearity associated with DNA, the analysis of compositional properties in proteomes makes it necessary to resort to appropriate multi-dimensional representations for the data. Such analyses have been performed from different perspectives, trying for example to identify signatures associated with different lifestyles. Analyses of amino acid compositions in a limited number of proteomes (as available at the time [1,6,7,8]) revealed a discrimination of hypethermophiles
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