Large-scale comparative genomic ranking of taxonomically restricted genes (TRGs) in bacterial and archaeal genomes

• Published in: PloS one Vol. 2; no. 3; p. e324
• Main Authors: Wilson, Gareth A, Feil, Edward J, Lilley, Andrew K, Field, Dawn
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 28-03-2007; Public Library of Science (PLoS)
• Subjects: Adaptation; Analysis; Archaea; Archaea - classification; Archaeal Proteins - genetics; Archaeal Proteins - standards; Bacteria; Bacteria - classification; Bacterial genetics; Bacterial Proteins - genetics; Bacterial Proteins - standards; Comparative Genomic Hybridization - methods; Computational Biology; Computational Biology/Genomics; Data processing; Datasets; E coli; Ecological adaptation; Ecology; Escherichia coli; Escherichia coli K12 - genetics; Evolutionary Biology/Bioinformatics; Evolutionary Biology/Microbial Evolution and Genomics; Genes; Genetics and Genomics/Bioinformatics; Genetics and Genomics/Genome Projects; Genetics and Genomics/Microbial Evolution and Genomics; Genome, Archaeal - genetics; Genome, Bacterial - genetics; Genomes; Genomics; Homology; Hydrology; Microbiology/Microbial Evolution and Genomics; Mutation; Niches; Organisms; Proteins; Proteome - genetics; Ranking; Rickettsia; Taxonomy
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0000324

Lineage-specific, or taxonomically restricted genes (TRGs), especially those that are species and strain-specific, are of special interest because they are expected to play a role in defining exclusive ecological adaptations to particular niches. Despite this, they are relatively poorly studied and little understood, in large part because many are still orphans or only have homologues in very closely related isolates. This lack of homology confounds attempts to establish the likelihood that a hypothetical gene is expressed and, if so, to determine the putative function of the protein.
We have developed "QIPP" ("Quality Index for Predicted Proteins"), an index that scores the "quality" of a protein based on non-homology-based criteria. QIPP can be used to assign a value between zero and one to any protein based on comparing its features to other proteins in a given genome. We have used QIPP to rank the predicted proteins in the proteomes of Bacteria and Archaea. This ranking reveals that there is a large amount of variation in QIPP scores, and identifies many high-scoring orphans as potentially "authentic" (expressed) orphans. There are significant differences in the distributions of QIPP scores between orphan and non-orphan genes for many genomes and a trend for less well-conserved genes to have lower QIPP scores.
The implication of this work is that QIPP scores can be used to further annotate predicted proteins with information that is independent of homology. Such information can be used to prioritize candidates for further analysis. Data generated for this study can be found in the OrphanMine at http://www.genomics.ceh.ac.uk/orphan_mine.