The silencing of pseudogenes

Pseudogenes are nonfunctional 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 sigma70 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 nonfunctional open reading frames. 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.