title: A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome.
abstract: Pseudogenes are open reading frames (ORFs) encoding dysfunctional proteins with high homology to known protein-coding genes. Although pseudogenes were reported to exist in the genomes of many eukaryotes and bacteria, no systematic search for pseudogenes in the Escherichia coli genome has been carried out. Genome comparisons of E. coli strains K-12 and O157 revealed that many protein-coding sequences have prematurely terminated orthologs encoding unstable proteins. To systematically screen for pseudogenes, we selected ORFs generated by premature termination of the orthologous protein-coding genes and subsequently excluded those possibly arising from sequence errors. Lastly we eliminated those with close homologs in this and other species, as these shortened ORFs may actually have functions. The process produced 95 and 101 pseudogene candidates in K-12 and O157, respectively. The assigned three-dimensional structures suggest that most of the encoded proteins cannot fold properly and thus are dysfunctional, indicating that they are probably pseudogenes. Therefore, the existence of a significant number of probable pseudogenes in E. coli is predicted, awaiting experimental verification. Most of them were found to be genes with paralogs or horizontally transferred genes or both. We suggest that pseudogenes constitute a small fraction of the genomes of free-living bacteria in general, reflecting the faster elimination than production of pseudogenes.
authors.affiliation: Laboratory of Gene-Product Informatics, Center for Information Biology-DNA Data Bank of Japan, National Institute of Genetics, 1111 Yata, Mishima, 411-8540, Shizuoka, Japan.
authors.forename: Keiichi
authors.initials: K
authors.lastname: Homma
authors.forename: Satoshi
authors.initials: S
authors.lastname: Fukuchi
authors.forename: Takeshi
authors.initials: T
authors.lastname: Kawabata
authors.forename: Motonori
authors.initials: M
authors.lastname: Ota
authors.forename: Ken
authors.initials: K
authors.lastname: Nishikawa
mesh_terms: D000595:Amino Acid Sequence; D001483:Base Sequence; D004926:Escherichia coli / Q000235:genetics*; D019453:Escherichia coli O157 / Q000235:genetics; D018628:Gene Dosage; D020440:Gene Duplication; D016680:Genome, Bacterial; D016366:Open Reading Frames / Q000235:genetics; D011544:Pseudogenes / Q000235:genetics*; D017386:Sequence Homology, Amino Acid; D012689:Sequence Homology, Nucleic Acid