ArticleBMC evolutionary biology2009
Recurring cluster and operon assembly for Phenylacetate degradation genes.
Article in BMC evolutionary biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed, 31 citations in OpenAlex.
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- A new selective force driving metabolic gene clustering.mSystems · 2024Article
- The evolutionary life cycle of the polysaccharide biosynthetic gene cluster based on the Sphingomonadaceae.Scientific reports · 2017Article
- Convergent evolution of the arginine deiminase pathway: the ArcD and ArcE arginine/ornithine exchangers.MicrobiologyOpen · 2017Article
- Horizontally transferred genes cluster spatially and metabolically.Biology direct · 2015Article
- The role of thionins in rice defence against root pathogens.Molecular plant pathology · 2015Article
- An event-driven approach for studying gene block evolution in bacteria.Bioinformatics (Oxford, England) · 2015Article
- A systematic computational analysis of biosynthetic gene cluster evolution: lessons for engineering biosynthesis.PLoS computational biology · 2014Article
- Phenylacetic acid catabolism and its transcriptional regulation in Corynebacterium glutamicum.Applied and environmental microbiology · 2012Article
- Goods-thinking vs. tree-thinking: Finding a place for mobile genetic elements.Mobile genetic elements · 2011Article
- Regulation of phenylacetic acid uptake is σ54 dependent in Pseudomonas putida CA-3.BMC microbiology · 2011Article
- PR-1 gene family of grapevine: a uniquely duplicated PR-1 gene from a Vitis interspecific hybrid confers high level resistance to bacterial disease in transgenic tobacco.Plant cell reports · 2011Article
- Evolutionary origins of metabolic compartmentalization in eukaryotes.Philosophical transactions of the Royal Society of London. Series B, Biological sciences · 2010Review
- Conditions for the evolution of gene clusters in bacterial genomes.PLoS computational biology · 2010Article
- Stochasticity in protein levels drives colinearity of gene order in metabolic operons of Escherichia coli.PLoS biology · 2009Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA 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 co-localise protein products and that operon formation is not an inevitable conclusion of the process.
resultsWe 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.
conclusionOur 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.
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