Recurring cluster and operon assembly for Phenylacetate degradation genes

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.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.The aerobic degradation of phenylacetic acid in E. coli K12 occurs via a series of five reactions, involving eleven catabolic paa genes [1], two of which are distant paralogs, with the rest showing no sequence homology (figure 1). The first step of the pathway is catalysed by the product of the paaK gene, a CoA ligase that catalyses the conversion of phenylacetate into phenylacetyl-CoA. The second step involves a ring-oxygenase complex formed from the gene products of paaABCDE. This heteromer converts phenylacetyl-CoA into 2'-OH-phenylacetyl-CoA. The third step, where 2'-OH-phenylacetyl-CoA is converted to 3-hydroxyadipyl-CoA, is jointly catalysed by paaJ, paaG and paaZ. The fourth step sees the conversion of 3-hydroxyadipyl-CoA by paaF and paaH to β-ketoadipyl-CoA. The final step is catalysed by paaJ, which converts β-ketoadipyl-CoA to succinyl-CoA,