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MBE Advance Access published online on July 13, 2005
Molecular Biology and Evolution, doi:10.1093/molbev/msi209
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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
Accepted June 24, 2005

Letter

The Silencing of Pseudogenes

Alex Mira 1* and Ravindra Pushker 1

1 Evolutionary Genomics Group, Division of Microbiology, Miguel Hernandez University, Apartado 18, San Juan 03550 (Alicante), SPAIN

* To whom correspondence should be addressed.
Alex Mira, E-mail: alex.mira{at}umh.es


  Abstract

Pseudogenes are non-functional DNA sequences that can accumulate in the genomes of some bacterial species, especially those undergoing processes like niche change, host specialization or weak selection strength. They may last for long evolutionary periods, opening the question of how the genome prevents expression of these degenerated or disrupted genes, that would presumably give rise to malfunctioning proteins. We have investigated ribosomal binding strength at Shine-Dalgarno sequences and the prevalence of {sigma}70 promoter regions in pseudogenes across bacteria. It is reported that the RNA polymerase-binding sites and more strongly the ribosome-binding regions of pseudogenes are highly degraded, suggesting that transcription and translation are impaired in non-functional ORFs. This would reduce the metabolic investment on faulty proteins, because although pseudogenes can persist for long time periods, they would be effectively silenced. It is unclear whether mutation accumulation on regulatory regions is neutral or whether it is accelerated by selection.

Keywords: Pseudogene; Shine-Dalgarno; mutation accumulation; promoter; spacer; gene expression.
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