The DUF1013 protein TrcR tracks with RNA polymerase to control bacterial cell cycle and protection against antibiotics (ChIP-seq dataset)

The regulatory roles of proteins associating with DNA-dependent RNA polymerase (RNAP) during transcription elongation are poorly characterized in bacteria. A forward genetic selection for Caulobacter crescentus cell cycle mutants revealed the uncharacterized DUF1013 protein (TrcR, transcriptional cell cycle regulator). TrcR associates with promoters and coding sequences (CDSs) and tracks with active RNAP. Loss of TrcR causes a cell division cycle and growth defect and an insufficiency in the essential cell cycle regulator CtrA. TrcR also protects cells from the quinolone antibiotic nalidixic acid that induces a multi-drug efflux pump and from the RNAP inhibitor rifampicin (Rif) that prevents transcription elongation. TrcR interacts biochemically and genetically with RNAP and no longer associates with chromatin when RNAP is inhibited with Rif. We show that these TrcR functions and its RNAP-dependent chromatin recruitment are conserved in symbiotic Sinorhizobium sp. and pathogenic Brucella sp., indicating that TrcR represents a new antibiotic target. Examination of TrcR, RpoD and RNAP holoenzyme whole genome binding/occupancy (ChIP-Seq) in WT Caulobacter crescentus and mutants in PYE and following Rifampicin and Nalidixic Acid treatments and TrcR whole genome occupancy/binding in WT Sinorhizobium meliloti before and after Rifampicin treatment.