Protein languages differ depending on microorganism lifestyle.
Few quantitative measures of genome architecture or organization exist to support assumptions of differences between microorganisms that are broadly defined as being free-living or pathogenic. General principles about complete proteomes exist for codon usage, amino acid biases and essential or core genes. Genome-wide shifts in amino acid usage between free-living and pathogenic microorganisms result in fundamental differences in the complexity of their respective proteomes that are size and gene content independent. These differences are evident across broad phylogenetic groups-a result of environmental factors and population genetic forces rather than phylogenetic distance. A novel comparative analysis of amino acid usage-utilizing linguistic analyses of word frequency in language and text-identified a global pattern of higher peptide word repetition in 376 free-living versus 421 pathogen genomes across broad ranges of genome size, G+C content and phylogenetic ancestry. This imprint of repetitive word usage indicates free-living microorganisms have a bias for repetitive sequence usage compared to pathogens. These findings quantify fundamental differences in microbial genomes relative to life-history function.
Division of Earth and Ecosystem Sciences, Desert Research Institute, Reno, Nevada, United States of America.
Joseph J
JJ
Grzymski
Center for Bioinformatics and Computational Biology, Marine Biological Sciences, University of Delaware, Lewes, Delaware, United States of America.
Adam G
AG
Marsh
D000596:Amino Acids; D001419:Bacteria / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity; D001482:Base Composition; D003062:Codon; D019295:Computational Biology; D059647:Gene-Environment Interaction; D016680:Genome, Bacterial; D054884:Host-Pathogen Interactions; D010802:Phylogeny; D020543:Proteome / Q000235:genetics*; D013045:Species Specificity; D009626:Terminology as Topic; D014774:Virulence
D000596:Amino Acids; D003062:Codon; D020543:Proteome