Buffering effects of nonspecifically DNA-bound RNA polymerases 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 buffer the free RNAP concentration and mitigate the crosstalk between rRNA and mRNA transcription. We verify our theory using mean-field models and an agent-based model of transcription, showing that the buffering effects are robust against the interaction between RNAPs and sigma factors and the spatial fluctuation and temporal noise of RNAP concentration. We analyze the relevant parameters of Escherichia coli and find that the buffering effects are significant across different growth rates at a low cost, suggesting that nonspecifically DNA-bound RNAPs are evolutionarily advantageous.