Evidence of a large novel gene pool associated with prokaryotic genomic Islands

Abstract

Microbial genes that are "novel" (no detectabie homologs in other species) have become of increasing interest as environmental sampiing suggests thai there are many more such novel genes in yet-ta-be-csjityred microorganisms. By analyzing known mkrobiaS gersomk islands and praphages, we developed criteria for systematic identification of putative genamic islands (dusters of genes of probabie horizontal origin in a prokaryotic genome) in 63 prokaryotlc genomes, and then characterized the distribution of novel genes and other features. AH but a few of the genomes examined contained sSgnafacantuy higher proportions of novel genes "m their predicted genomic islands compared with the rest of their genome {Paired t test - 4.43E-14 to 1.27E-18, depending on method), IVSoreover, the reverse observation {i.e., higher proportions of nove! genes outside of islands) never reached statistical significance in any organism examined. We show that this higher proportion of nave! genes in predicted genomic islands is not due to !ess accurate gene prediction in genomic isiand regions, but !ike!y reflects a genuine increase in rsoveS genes in these regions for both bacteria and arehaea. This represents the first comprehensive arsaiysis of novei genes in prokaryoiic genomic isSands and provides dues regarding the origan of novel genes. Our coilective results impiy that there are different gene poois associated with recently horizontauy transmitted genomic regions versus regions that are primariiy vertically inherited. Moreover, there are more novel genes within the gene pooi associated with genomic islands. Since genornic islands are frequentay associated with a particular microbiai adaptation, such as antibiotic resistance, pathogen virulence, or rneta! resistance, this suggests that microbes may have access to a larger "arsenal!" of novel genes for adaptation than previousSy thought. Copyright:©2005 Hsiao et al.