The Roles of Molecular Chaperones Interacting with the σ70 Factor in Global Transcription of the Escherichia coli Genome.

Background/Objectives: The σ factor of bacterial RNA polymerase (RNAP) directs promoter recognition, recruits RNAP to initiate transcription, and is released from the elongation complex to participate in subsequent rounds of initiation. However, the dynamic recycling mechanism of the primary σ factor, σ70 (RpoD), during transcription in Escherichia coli remains poorly understood. Methods: We employed in vivo and in vitro interaction assays to screen for σ70-interacting partners under different growth conditions. Protein localization studies were performed using fluorescence microscopy. The transcriptomic profile of ΔclpB, ΔdnaK, ΔhtpG, or ΔyhgF mutant was assessed by RNA-seq. Results: The molecular chaperones ClpB, DnaK, HtpG, and the RNA-binding protein YhgF interacts with RpoD both in vivo and in vitro, and the interaction in vivo is growth medium-dependent (LB vs. ABTGcasa). During exponential growth, each of these proteins co-localizes with the nucleoid. The transcriptome profile in ΔclpB, ΔhtpG or ΔyhgF mutant is mutant-specific to some extent; differentially expressed genes (DEGs) associated with amino acid metabolism and lipopolysaccharide biosynthesis are down-regulated in ΔclpB, ΔhtpG or ΔyhgF mutant in a manner that is growth medium-dependent, in agreement with the medium-dependent interaction of RpoD with the chaperones and YhgF. In contrast, the absence of DnaK resulted in delays to initiation of replication with a slow growth, and decreases cell motility, accompanied by down-regulated flagellar assembly and up-regulated amino acid metabolism genes. In summary, ClpB, DnaK, HtpG, and YhgF may regulate transcription by directly interacting with σ70. The σ factor recycling guides global transcription to select genes for transcription and subsequently allows cells to cope with the changing environments by responding to the nutrient level as a signal.