Plasticity in oligomerization, operator architecture, and DNA binding in the mode of action of a bacterial B₁₂-based...

Newly discovered bacterial photoreceptors called CarH sense light by using 5'-deoxyadenosylcobalamin (AdoCbl). They repress their own expression and that of genes for carotenoid synthesis by binding in the dark to operator DNA as AdoCbl-bound tetramers, whose light-induced disassembly relieves repression. High-resolution structures of Thermus thermophilus CarH_Tt have provided snapshots of the dark and light states and have revealed a unique DNA-binding mode whereby only three of four DNA-binding domains contact an operator comprising three tandem direct repeats. To gain further insights into CarH photoreceptors and employing biochemical, spectroscopic, mutational, and computational analyses, here we investigated CarH_Bm from Bacillus megaterium We found that apoCarH_Bm, unlike monomeric apoCarH_Tt, is an oligomeric molten globule that forms DNA-binding tetramers in the dark only upon AdoCbl binding, which requires a conserved W-X₉-EH motif. Light relieved DNA binding by disrupting CarH_Bm tetramers to dimers, rather than to monomers as with CarH_Tt CarH_Bm operators resembled that of CarH_Tt, but were larger by one repeat and overlapped with the -35 or -10 promoter elements. This design persisted in a six-repeat, multipartite operator we discovered upstream of a gene encoding an Spx global redox-response regulator whose photoregulated expression links photooxidative and general redox responses in B. megaterium Interestingly, CarH_Bm recognized the smaller CarH_Tt operator, revealing an adaptability possibly related to the linker bridging the DNA- and AdoCbl-binding domains. Our findings highlight a remarkable plasticity in the mode of action of B₁₂-based CarH photoreceptors, important for their biological functions and development as optogenetic tools.