Skip Navigation

Nucleic Acids Research 2005 33(10):3125-3132; doi:10.1093/nar/gki631
This Article
Right arrow Full Text Freely available
Right arrow Print PDF (390K) Freely available
Right arrow Screen PDF (229K) Freely available
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (17)
Right arrow Commercial Re-use Guidelines
for Open Access NAR Content
Google Scholar
Right arrow Articles by Lerat, E.
Right arrow Articles by Ochman, H.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Lerat, E.
Right arrow Articles by Ochman, H.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

Published online 2 June 2005

© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

Recognizing the pseudogenes in bacterial genomes

Emmanuelle Lerat and Howard Ochman1,*

Department of Ecology and Evolutionary Biology, University of Arizona Tucson, AZ 87521, USA 1Department of Biochemistry and Molecular Biophysics, University of Arizona Tucson, AZ 87521, USA

*To whom correspondence should be addressed. Tel: +1 520 626 8355; Fax: +1 520 621 3709; Email: hochman{at}email.arizona.edu

Received December 25, 2004. Revised March 1, 2005. Accepted May 15, 2005.

Pseudogenes are now known to be a regular feature of bacterial genomes and are found in particularly high numbers within the genomes of recently emerged bacterial pathogens. As most pseudogenes are recognized by sequence alignments, we use newly available genomic sequences to identify the pseudogenes in 11 genomes from 4 bacterial genera, each of which contains at least 1 human pathogen. The numbers of pseudogenes range from 27 in Staphylococcus aureus MW2 to 337 in Yersinia pestis CO92 (e.g. 1–8% of the annotated genes in the genome). Most pseudogenes are formed by small frameshifting indels, but because stop codons are A + T-rich, the two low-G + C Gram-positive taxa (Streptococcus and Staphylococcus) have relatively high fractions of pseudogenes generated by nonsense mutations when compared with more G + C-rich genomes. Over half of the pseudogenes are produced from genes whose original functions were annotated as ‘hypothetical’ or ‘unknown’; however, several broadly distributed genes involved in nucleotide processing, repair or replication have become pseudogenes in one of the sequenced Vibrio vulnificus genomes. Although many of our comparisons involved closely related strains with broadly overlapping gene inventories, each genome contains a largely unique set of pseudogenes, suggesting that pseudogenes are formed and eliminated relatively rapidly from most bacterial genomes.


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Appl. Environ. Microbiol.Home page
M. F. Romine, T. S. Carlson, A. D. Norbeck, L. A. McCue, and M. S. Lipton
Identification of Mobile Elements and Pseudogenes in the Shewanella oneidensis MR-1 Genome
Appl. Envir. Microbiol., May 15, 2008; 74(10): 3257 - 3265.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
S. J. Hinchliffe, S. L. Howard, Y. H. Huang, D. J. Clarke, and B. W. Wren
The importance of the Rcs phosphorelay in the survival and pathogenesis of the enteropathogenic yersiniae
Microbiology, April 1, 2008; 154(4): 1117 - 1131.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
R. D. Magnuson
Hypothetical Functions of Toxin-Antitoxin Systems
J. Bacteriol., September 1, 2007; 189(17): 6089 - 6092.
[Full Text] [PDF]

Home page
 Infect. Immun.Home page
L. Rohmer, M. Brittnacher, K. Svensson, D. Buckley, E. Haugen, Y. Zhou, J. Chang, R. Levy, H. Hayden, M. Forsman, et al.
Potential Source of Francisella tularensis Live Vaccine Strain Attenuation Determined by Genome Comparison
Infect. Immun., December 1, 2006; 74(12): 6895 - 6906.
[Abstract] [Full Text] [PDF]

Home page
 ScienceHome page
H. Ochman and L. M. Davalos
The nature and dynamics of bacterial genomes.
Science, March 24, 2006; 311(5768): 1730 - 1733.
[Abstract] [Full Text] [PDF]

Home page
 Proc. Natl. Acad. Sci. USAHome page
H. Ochman
Genomes on the shrink
PNAS, August 23, 2005; 102(34): 11959 - 11960.
[Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.