Regulons are the basic units of cellular response systems in bacterial cells, and represent a most basic concept in bacterial studies. A bacterial regulon is a group of operons that are transcriptionally co-regulated by the same regulatory machinery, consisting of trans regulators (transcription factors or simply TFs) and cis regulatory binding elements in the promoters of the operons they regulate. Operationally, a regulon contains operons regulated by one same transcription factor. Since the term regulon was first proposed in 1964, 173 regulons have been fully or partially identified in E. coli K12 and many more in other bacteria e.g. B. subtilis.
Loosely speaking, regulons can be categorized into two classes: local and global regulons, with the former corresponding to regulons consisting of only a few component operons and the latter having a relatively large number of operons. While the functionalities of the known regulons have been well studied, very little is known about how regulons are organized in a bacterial genome.
This paper examines the organizational principles of regulons in bacterial genomes, looking at E. coli K12 and Bacillus subtilis. The key findings are (1) operons of each regulon tend to form a few closely located clusters along with genome; (2) TFs are under stronger evolutionary constraints than their TGs; and (3) the global arrangement of the component operons of all the (known) regulons in a genome tend to minimize a simple scoring function.
Genomic Arrangement of Regulons in Bacterial Genomes. (2012) PLoS ONE 7(1): e29496. doi:10.1371/journal.pone.0029496
Regulons, as groups of transcriptionally co-regulated operons, are the basic units of cellular response systems in bacterial cells. While the concept has been long and widely used in bacterial studies since it was first proposed in 1964, very little is known about how its component operons are arranged in a bacterial genome. We present a computational study to elucidate of the organizational principles of regulons in a bacterial genome, based on the experimentally validated regulons of E. coli and B. subtilis. Our results indicate that (1) genomic locations of transcriptional factors (TFs) are under stronger evolutionary constraints than those of the operons they regulate so changing a TF’s genomic location will have larger impact to the bacterium than changing the genomic position of any of its target operons; (2) operons of regulons are generally not uniformly distributed in the genome but tend to form a few closely located clusters, which generally consist of genes working in the same metabolic pathways; and (3) the global arrangement of the component operons of all the regulons in a genome tends to minimize a simple scoring function, indicating that the global arrangement of regulons follows simple organizational principles. Tweet