The SinR•SlrR heteromer internally attenuates a long transcript of flagellar genes in B. subtilis [RNA-seq]

Bacillus subtilis differentiates into two cell types during growth, dictated by the activity of the alternative sigma factor SigD. The frequency of SigD-ON motile cells is increased when the heteromeric transcription factor SwrA•DegU activates the promoter of the long fla/che operon that encodes SigD. Conversely, the frequency of SigD-ON cells is decreased by the heteromeric transcription factor SinR•SlrR but the mechanism and location of inhibition is poorly understood. Using ChIP-Seq analysis, we determine the binding sites of the SinR•SlrR heteromer, including five sites within the fla/che operon. The first two sites were found to be both necessary and sufficient to attenuate transcript abundance within the operon upstream of the gene that encodes SigD. We conclude that the SinR•SlrR heteromer inhibits SigD accumulation by binding within the operon by causing RNA polymerase to pause and prematurely terminate. Thus, the development of motile cells, and the motility-to-biofilm transition, depends on the expression of a long operon governed by two opposing heteromeric transcription factors that operate at two different stages of the transcription cycle. RNA extraction and sequencing was performed on wild type and mutant cells of Bacillus subtilis 3610 grown in LB at 37C. Before sequencing, ribosomal RNA was depleted.