A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome

Keiichi Homma, Satoshi Fukuchi, Takeshi Kawabata, Motonori Ota, Ken Nishikawa

Research output: Contribution to journalArticlepeer-review

26 Citations (Scopus)


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.

Original languageEnglish
Pages (from-to)25-33
Number of pages9
Issue number1-2
Publication statusPublished - 2002 Jul 10
Externally publishedYes


  • Gram-negative bacteria
  • Horizontal transfer
  • Position-specific iterated basic local alignment search tool
  • Structure prediction
  • Three-dimensional structure

ASJC Scopus subject areas

  • Genetics


Dive into the research topics of 'A systematic investigation identifies a significant number of probable pseudogenes in the Escherichia coli genome'. Together they form a unique fingerprint.

Cite this