U.S. Department of Energy

Pacific Northwest National Laboratory

Proteogenomic analysis of bacteria and archaea: a 46 organism case study.

TitleProteogenomic analysis of bacteria and archaea: a 46 organism case study.
Publication TypeJournal Article
Year of Publication2011
AuthorsVenter E, Smith RD, Payne SH
JournalPLoS One
KeywordsArchaea, Archaeal Proteins, Bacteria, Bacterial Proteins, Computational Biology, Genome, Archaeal, Genome, Bacterial, Mass Spectrometry, Open Reading Frames, Proteome
Abstract

Experimental evidence is increasingly being used to reassess the quality and accuracy of genome annotation. Proteomics data used for this purpose, called proteogenomics, can alleviate many of the problematic areas of genome annotation, e.g. short protein validation and start site assignment. We performed a proteogenomic analysis of 46 genomes spanning eight bacterial and archaeal phyla across the tree of life. These diverse datasets facilitated the development of a robust approach for proteogenomics that is functional across genomes varying in %GC, gene content, proteomic sampling depth, phylogeny, and genome size. In addition to finding evidence for 682 novel proteins, 1336 new start sites, and numerous dubious genes, we discovered sites of post-translational maturation in the form of proteolytic cleavage of 1175 signal peptides. The number of novel proteins per genome is highly variable (median 7, mean 15, stdev 20). Moreover, comparison of novel genes with the current genes did not reveal any consistent abnormalities. Thus, we conclude that proteogenomics fulfills a yet to be understood deficiency in gene prediction. With the adoption of new sequencing technologies which have higher error rates than Sanger-based methods and the advances in proteomics, proteogenomics may become even more important in the future.

DOI10.1371/journal.pone.0027587
Alternate JournalPLoS ONE
PubMed ID22114679
PubMed Central IDPMC3219674
Area of Research: 
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