Cyclic-di-GMP interferes with DNA-MucR-DNA bridging to derepress genes targeted by the xenogeneic silencer MucR

The tradeoff between the benefits and costs of maintaining AT-rich accessory genes is vital in bacterial ecology and evolution. MucR is a conserved xenogeneic silencer for AT-rich accessory genes within α-proteobacteria, but its anti-silencing mechanisms remain unknown. By focusing on Sinorhizobium fredii, a facultative nitrogen-fixing microsymbiont of diverse legumes, this work reports that elevated c-di-GMP promotes the condition-dependent expression of various MucR1-targets, while downregulating the energy production and conversion pathway and reducing the NAD+/NADH ratio under both free-living and symbiotic conditions. Among the MucR1 targets responsive to c-di-GMP, an accessory module directing the biosynthesis of costly exopolysaccharides has been further studied. This anti-silencing process involves the sequential disruption of the DNA-MucR1-DNA bridging complex and the activation of a local transcriptional activator, CuxR. c-di-GMP directly binds to the C-terminal DNA-binding domain of MucR1, thereby facilitating intra- and inter-molecular interactions of MucR1. These interactions effectively alleviate the DNA-MucR-DNA bridging in the promoter region of target genes. This consequently enables the recruitment of the CuxR-c-di-GMP complex to the specific CuxR binding sites, which subsequently activates gene transcription. Collectively, accessory functions that are energetically costly and repressed by MucR1 can be harnessed by the ubiquitous messenger c-di-GMP through an integrated global-local signaling pathway.