NUI Maynooth

NUIM ePrints and eTheses Archive

NUIM Library

Recurring cluster and operon assembly for Phenylacetate degradation genes

Martin, Fergal J. and McInerney, James O. (2009) Recurring cluster and operon assembly for Phenylacetate degradation genes. BMC Evolutionary Biology, 9. p. 36. ISSN 1471-2148)

[img] Download (955kB)
Official URL: http://www.biomedcentral.com/content/pdf/1471-2148...

Abstract

Background: A large number of theories have been advanced to explain why genes involved in the same biochemical processes are often co-located in genomes. Most of these theories have been dismissed because empirical data do not match the expectations of the models. In this work we test the hypothesis that cluster formation is most likely due to a selective pressure to gradually colocalise protein products and that operon formation is not an inevitable conclusion of the process. Results: We have selected an exemplar well-characterised biochemical pathway, the phenylacetate degradation pathway, and we show that its complex history is only compatible with a model where a selective advantage accrues from moving genes closer together. This selective pressure is likely to be reasonably weak and only twice in our dataset of 102 genomes do we see independent formation of a complete cluster containing all the catabolic genes in the pathway. Additionally, de novo clustering of genes clearly occurs repeatedly, even though recombination should result in the random dispersal of such genes in their respective genomes. Interspecies gene transfer has frequently replaced in situ copies of genes resulting in clusters that have similar content but very different evolutionary histories. Conclusion: Our model for cluster formation in prokaryotes, therefore, consists of a two-stage selection process. The first stage is selection to move genes closer together, either because of macromolecular crowding, chromatin relaxation or transcriptional regulation pressure. This proximity opportunity sets up a separate selection for co-transcription.

Item Type: Article
Keywords: Evolution; Genes; Genome; Genetic; Operon; Phenylacetates; Phylogeny.
Subjects: Science & Engineering > Biology
Item ID: 1901
Identification Number: 10.1186/1471-2148-9-36
Depositing User: Dr. James McInerney
Date Deposited: 29 Mar 2010 14:12
Journal or Publication Title: BMC Evolutionary Biology
Publisher: BioMed Central
Refereed: Yes
URI:

Repository Staff Only(login required)

View Item Item control page

Document Downloads

More statistics for this item...