Functional Coupling Between DnaK and Bacterial RNA Polymerase Through a Dedicated J-domain Protein System

J-domain proteins (JDPs) are co-chaperones of Hsp70/DnaK, conferring a broad range of functions to the Hsp70/DnaK chaperone system. The shortest characterized JDP is AtcJ, which is part of an essential four-protein system dedicated to the cold adaptation of the bacterium Shewanella oneidensis. AtcJ connects DnaK to the Atc system that comprises also the proteins AtcA, AtcB, and AtcC. Previous studies have shown that AtcB interacts with RNA polymerase, and that its overproduction leads to toxicity, likely due to the inhibition of transcription. In this study, we explore the interplay between DnaK, the Atc proteins and RNA polymerase in order to elucidate the mechanism of their coordinated function. First, we identified the molecular determinants underlying the interaction between RNA polymerase and AtcB, mapping mutations on the two proteins that abolish binding. Using these mutants, we demonstrated that binding between AtcB and RNA polymerase is crucial for cold growth. Then, to investigate the potential role of the other Atc proteins in coordination with DnaK and AtcB, we leveraged the toxicity phenotype associated with AtcB overproduction. We discovered that the AtcJ-AtcC complex recruits DnaK, thereby suppressing AtcB toxicity by limiting the accumulation of inactive RNA polymerase. Our study demonstrates the coupling between DnaK and RNA polymerase, mediated by the Atc protein system, revealing how this network recruits the chaperone to modulate RNA polymerase activity. While the exact mechanism is still unclear, our study suggests the notion that this system represents a new DnaK-dependent bacterial transcriptional regulatory pathway involved in cold adaptation.