The hidden function of nonspecifically DNA-bound RNA polymerases: a buffer of resource competition in bacteria

Abstract

RNA polymerase (RNAP) is the workhorse of bacterial gene expression, transcribing rRNA and mRNA. Experiments found that a significant fraction of RNAPs in bacteria are nonspecifically bound to DNA, which is puzzling as these idle RNAPs could have produced more RNAs. Whether nonspecifically DNA-bound RNAPs have any function or are merely a consequence of passive interaction between RNAP and DNA is unclear. In this work, we propose that nonspecifically DNA-bound RNAPs mitigate the crosstalk between rRNA and mRNA transcription. They buffer the free RNAP concentration change upon the regulation of rRNA genes, thus reducing its impact on the mRNA transcription and vice versa. We verify our theory using mean-field models and an agent-based model of transcription. We show that the buffering effects are robust against the finite number of sigma factors and spatial fluctuations of RNAP concentration. We analyze the relevant data ofEscherichia coliand show that its number and affinity of nonspecific binding sites are in the range where the buffering effects are significant, in concert with our theories.