Transcriptional rewiring of the GcrA/CcrM bacterial epigenetic regulatory system in closely related bacteria.

Satish Adhikari,Ivan Erill,Patrick D Curtis,Sean Crosson

doi:10.1371/journal.pgen.1009433

Satish Adhikari, Ivan Erill + Show 2 more

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https://doi.org/10.1371/journal.pgen.1009433

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Abstract

Transcriptional rewiring is the regulation of different target genes by orthologous regulators in different organisms. While this phenomenon has been observed, it has not been extensively studied, particularly in core regulatory systems. Several global cell cycle regulators are conserved in the Alphaproteobacteria, providing an excellent model to study this phenomenon. First characterized in Caulobacter crescentus, GcrA and CcrM compose a DNA methylation-based regulatory system that helps coordinate the complex life cycle of this organism. These regulators are well-conserved across Alphaproteobacteria, but the extent to which their regulatory targets are conserved is not known. In this study, the regulatory targets of GcrA and CcrM were analyzed by SMRT-seq, RNA-seq, and ChIP-seq technologies in the Alphaproteobacterium Brevundimonas subvibrioides, and then compared to those of its close relative C. crescentus that inhabits the same environment. Although the regulators themselves are highly conserved, the genes they regulate are vastly different. GcrA directly regulates 204 genes in C. crescentus, and though B. subvibrioides has orthologs to 147 of those genes, only 48 genes retained GcrA binding in their promoter regions. Additionally, only 12 of those 48 genes demonstrated significant transcriptional change in a gcrA mutant, suggesting extensive transcriptional rewiring between these organisms. Similarly, out of hundreds of genes CcrM regulates in each of these organisms, only 2 genes were found in common. When multiple Alphaproteobacterial genomes were analyzed bioinformatically for potential GcrA regulatory targets, the regulation of genes involved in DNA replication and cell division was well conserved across the Caulobacterales but not outside this order. This work suggests that significant transcriptional rewiring can occur in cell cycle regulatory systems even over short evolutionary distances.

Highlights

Bacterial global regulators can regulate the activity of dozens, if not hundreds, of genes
The degree to which genetic or physiological systems evolve over evolutionary distance is often untested
One can assume that the same system in different organisms will change very little if 1) the evolutionary distance between the organisms is small, 2) the systems

Summary

Introduction

Bacterial global regulators can regulate the activity of dozens, if not hundreds, of genes. It is generally assumed that orthologous global regulators in closely related bacteria regulate similar sets of genes even when the organisms occupy different niches [1]. While this assumption is supported by a few cross organismal studies [2,3], regulon comparison has not been extensively performed. The fourth (4) mechanism of regulatory circuit evolution is the gain or loss of transcription factor binding sites in the target promoters, such that the orthologous regulators have different regulatory targets in different organisms. This fourth mechanism is referred to as “transcriptional rewiring” [1]. There have been only a handful of studies on transcriptional rewiring performed in prokaryotes [2,3]

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