Recurring cluster and operon assembly for Phenylacetate degradation genes

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 co-localise 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.

Figure 1

Schematic for the degradation of phenylacetate, including genes involved and the cluster and operon structures in E. coli K12 and P. putida KT2440.

Figure 2

An exhaustive list of all observed operons in the dataset of 102 genomes examined. Each arrow represents a gene, with the name of the gene being given in the legend. I.G. refers to an intervening gene, which is a gene in the cluster that is not involved in the degradation of phenylacetate.

Figure 3

On the left is the gene tree for paaC, in the middle are the clusters of genes in which the respective paaC genes are found, with the paaC genes aligned to one another and facing away from the tree. On the right are the organism abbreviations (see supplementary information for list of organisms and abbreviations) and the gene number for the paaC gene, which indicates how many genes between it and the origin of replication for the genome in which it is found.

Figure 4

The same layout as figure 3, but the information represented is based upon the paaK gene.