Skip Navigation



MBE Advance Access published online on July 13, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi211
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow Supplementary Material
Right arrow All Versions of this Article:
22/11/2147    most recent
msi211v1
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 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 arrowRequest Permissions
Google Scholar
Right arrow Articles by Fang, G.
Right arrow Articles by Danchin, A.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Fang, G.
Right arrow Articles by Danchin, A.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oupjournals.org
Accepted June 30, 2005

Research Article

How Essential are Non-essential Genes?

Gang Fang 1, Eduardo Rocha 2, and Antoine Danchin 1*

1 Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 Rue du Dr Roux, 75724 Paris Cedex 15, Frances
2 Unité Génétique des Génomes Bactériens, Institut Pasteur, 28 Rue du Dr Roux, 75724 Paris Cedex 15, Frances; Atelier de Bioinformatique, Université Pierre et Marie Curie, 12, Rues Cuvier, 75005 Paris, France

* To whom correspondence should be addressed.
Antoine Danchin, E-mail: adanchin{at}pasteur.fr


  Abstract

Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knock-outs in rich media. Comparing 55 genomes of Firmicutes and Gamma-proteobacteria to identify the genes which, while persistent among genomes, do not lead to a lethal phenotype when inactivated, we show that the characteristics of persistence, conservation, expression and location are shared between persistent non-essential genes and experimentally essential genes. Persistent non-essential genes show an over-representation of genes related to maintenance and stress response. This outlines the limits of current experimental techniques to define gene essentiality and highlights the essential role of genes implicated in maintenance which, although dispensable for growth, are not dispensable from an evolutionary point of view. Firmicutes and Gamma-proteobacteria are mostly differing in the construction of the cell envelope, DNA replication and proofreading, and RNA degradation. In addition to suggesting functions for persistent genes that had until now resisted identification, we show that these genes have many characters in common with experimentally identified essential genes. They should then be regarded as truly essential genes.

Keywords: Bacterial evolution; essentiality; gene expression; gene strand bias; protein evolution; gene content.
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
 GeneticsHome page
W. Hao and G. B. Golding
Does Gene Translocation Accelerate the Evolution of Laterally Transferred Genes?
Genetics, August 1, 2009; 182(4): 1365 - 1375.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
V. Barbe, S. Cruveiller, F. Kunst, P. Lenoble, G. Meurice, A. Sekowska, D. Vallenet, T. Wang, I. Moszer, C. Medigue, et al.
From a consortium sequence to a unified sequence: the Bacillus subtilis 168 reference genome a decade later
Microbiology, June 1, 2009; 155(6): 1758 - 1775.
[Abstract] [Full Text] [PDF]

Home page
 MicrobiologyHome page
J. C. Karst, A.-E. Foucher, T. L. Campbell, A.-M. Di Guilmi, D. Stroebel, C. S. Mangat, E. D. Brown, and J.-M. Jault
The ATPase activity of an 'essential' Bacillus subtilis enzyme, YdiB, is required for its cellular function and is modulated by oligomerization
Microbiology, March 1, 2009; 155(3): 944 - 956.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
B. Gao, R. Mohan, and R. S. Gupta
Phylogenomics and protein signatures elucidating the evolutionary relationships among the Gammaproteobacteria
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 234 - 247.
[Abstract] [Full Text] [PDF]

Home page
 Int. J. Syst. Evol. Microbiol.Home page
R. S. Gupta and B. Gao
Phylogenomic analyses of clostridia and identification of novel protein signatures that are specific to the genus Clostridium sensu stricto (cluster I)
Int J Syst Evol Microbiol, February 1, 2009; 59(2): 285 - 294.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
A. Wellner and U. Gophna
Neutrality of Foreign Complex Subunits in an Experimental Model of Lateral Gene Transfer
Mol. Biol. Evol., September 1, 2008; 25(9): 1835 - 1840.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
M. Ohnishi, M. Saito, S. Wakabayashi, M. Ishizuka, K. Nishimura, Y. Nagata, and S. Kasai
Purification and Characterization of Serine Racemase from a Hyperthermophilic Archaeon, Pyrobaculum islandicum
J. Bacteriol., February 15, 2008; 190(4): 1359 - 1365.
[Abstract] [Full Text] [PDF]

Home page
 Mol Biol EvolHome page
M. Touchon and E. P. C. Rocha
Causes of Insertion Sequences Abundance in Prokaryotic Genomes
Mol. Biol. Evol., April 1, 2007; 24(4): 969 - 981.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. M. Watt, J. Wang, M. Leong, H.-f. Kung, K. S.E. Cheah, D. Liu, A. Danchin, and J.-D. Huang
Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes
Nucleic Acids Res., March 19, 2007; 35(6): e37 - e37.
[Abstract] [Full Text] [PDF]

Home page
 J. Bacteriol.Home page
H. B. Thomaides, E. J. Davison, L. Burston, H. Johnson, D. R. Brown, A. C. Hunt, J. Errington, and L. Czaplewski
Essential Bacterial Functions Encoded by Gene Pairs
J. Bacteriol., January 15, 2007; 189(2): 591 - 602.
[Abstract] [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.