Keeping foreign DNA silent - the role of DNA sequences and molecular backups

In a paper, just published in Molecular Biosystems, we report that both DNA sequences and the need for back-up mechanisms for gene silencing in Escherichia coli might be selected for targeting highly transcribable genes. Much of the experimental work was performed by Rajalakshmi Srinivasan, who was helped at various points by Deepti Chandraprakash, Revathy Krishnamurthi, Parul Singh and Vittore Scolari. Sandeep Krishna contributed to several discussions on this work.


The abstract reads as follows:

A barrier for horizontal gene transfer is high gene expression, which is metabolically expensive. Silencing of horizontally-acquired genes in the bacterium Escherichia coli is caused by the global transcriptional repressor H-NS. The activity of H-NS is enhanced or diminished by other proteins including its homologue StpA, and Hha and YdgT. The interconnections of H-NS with these regulators and their role in silencing gene expression in E. coli are not well understood on a genomic scale. In this study, we use transcriptome sequencing to show that there is a bi-layered gene silencing system – involving the homologous H-NS and StpA – operating on horizontally-acquired genes among others. We show that H-NS-repressed genes belong to two types, termed “epistatic” and “unilateral”. In the absence of H-NS, the expression of “epistatically controlled genes” is repressed by StpA, whereas that of “unilaterally controlled genes” is not. Epistatic genes show a higher tendency to be non-essential and recently acquired, when compared to unilateral genes. Epistatic genes reach much higher expression levels than unilateral genes in the absence of the silencing system. Finally, epistatic genes contain more high affinity H-NS binding motifs than unilateral genes. Therefore, both the DNA binding sites of H-NS as well as the function of StpA as a backup system might be selected for silencing highly transcribable genes.