The silencing of pseudogenes

Institute:University of Miguel Hernández, Alicante, SPAIN
Programming Language:PERL, C
Operating System:Linux Fedora Core 2
Software Tools:CVS, gnuplot
Bioinformatics Tools:BioInfoSend, DNAMaster
Team Size:2
Duration:Aug. 2004 - Jan. 2005


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 binding strength at Shine-Dalgarno sequences and the prevalence of σ70 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.


Mira A. and Pushker R. (2005) The silencing of pseudogenes. Molecular Biology and Evolution , 22(11):2135-2138.