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MBE Advance Access originally published online on July 13, 2005
Molecular Biology and Evolution 2005 22(11):2147-2156; doi:10.1093/molbev/msi211
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© 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

Research Article

How Essential Are Nonessential Genes?

Gang Fang*, Eduardo Rocha*,{dagger} and Antoine Danchin*

* Unité Génétique des Génomes Bactériens, Institut Pasteur, Paris Cedex, France; and {dagger} Atelier de Bioinformatique, Université Pierre et Marie Curie, Paris, France

E-mail: adanchin{at}pasteur.fr.

Gene essentiality in bacteria has been identified in silico, focusing on gene persistence, or experimentally, focusing on the growth of knockouts 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 nonessential (PNE) genes and experimentally essential genes. PNE genes show an overrepresentation 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.

Key Words: bacterial evolution • essentiality • gene expression • gene strand bias • protein evolution • gene content


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