Журнал бактериологии и паразитологии

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Microbial proteogenomics gains momentum with avalanche of genomic sequences

Jean Armengaud, Celine Bland, Joseph Christie-Oleza and Guylain Miotello

A consensus on the definition of the fundamental unit of biological diversity, the species, has not yet been reached for prokaryotes. Although high-throughput molecular tools for assessing microbial diversity are now available, estimating the total number of bacterial and archaeal species on Earth remains a challenging task due to the vast number of rare species present in environmental samples. Since the first complete cellular genome sequence, that of Haemophilus influenzae in 1995, more than seven thousand complete genomes have been reported. The avalanche of genomic sequences results in exceptional documentation of representatives of numerous taxa. Although annotation of these genomes has gained precision with new gene prediction tools, proteogenomics has proven its ability to aid in the discovery of novel genes, determination of the true translational initiation codon of coding domain sequences, and characterization of protein-level maturation events such as signal peptide processing. Beyond this structural annotation, proteogenomics can also provide significant insights into protein function. Proteogenomics essentially consists of obtaining massive protein sequence data using large-scale proteomic strategies and high-throughput tandem mass spectrometry. Such experimental data are then used to improve genome annotation. Unexpected results such as reversal of gene sequences in different bacteria or the use of non-canonical translation start codons in Deinococcus species are just a few of the many corrections documented so far. Today, proteogenomic analysis of a given set of representatives that completely cover the tree of life would provide a better basis for accurate annotation of new strains. This would improve comparative genomic studies and could help in assessing how closely related species differ.