Photoreceptor proteins enable organisms to sense and respond to light. The newly discovered CarH-type photoreceptors use a vitamin B₁₂ derivative, adenosylcobalamin, as the light-sensing chromophore to mediate light-dependent gene regulation. Here we present crystal structures of Thermus thermophilus CarH in all three relevant states: in the dark, both free and bound to operator DNA, and after light exposure. These structures provide visualizations of how adenosylcobalamin mediates CarH tetramer formation in the dark, how this tetramer binds to the promoter −35 element to repress transcription, and how light exposure leads to a large-scale conformational change that activates transcription. In addition to the remarkable functional repurposing of adenosylcobalamin from an enzyme cofactor to a light sensor, we find that nature also repurposed two independent protein modules in assembling CarH. These results expand the biological role of vitamin B₁₂ and provide fundamental insight into a new mode of light-dependent gene regulation.

Cobalamin (B ₁₂ ) typically functions as an enzyme cofactor but can also regulate gene expression via RNA-based riboswitches. B ₁₂ -directed gene regulatory mechanisms via protein factors have, however, remained elusive. Recently, we reported down-regulation of a light-inducible promoter in the bacterium Myxococcus xanthus by two paralogous transcriptional repressors, of which one, CarH, but not the other, CarA, absolutely requires B ₁₂ for activity even though both have a canonical B ₁₂ -binding motif. Unanswered were what underlies this striking difference, what is the specific cobalamin used, and how it acts. Here, we show that coenzyme B ₁₂ (5′-deoxyadenosylcobalamin, AdoB ₁₂ ), specifically dictates CarH function in the dark and on exposure to light. In the dark, AdoB ₁₂ -binding to the autonomous domain containing the B ₁₂ -binding motif foments repressor oligomerization, enhances operator binding, and blocks transcription. Light, at various wavelengths at which AdoB ₁₂ absorbs, dismantles active repressor oligomers by photolysing the bound AdoB ₁₂ and weakens repressor–operator binding to allow transcription. By contrast, AdoB ₁₂ alters neither CarA oligomerization nor operator binding, thus accounting for its B ₁₂ -independent activity. Our findings unveil a functional facet of AdoB ₁₂ whereby it serves as the chromophore of a unique photoreceptor protein class acting in light-dependent gene regulation. The prevalence of similar proteins of unknown function in microbial genomes suggests that this distinct B ₁₂ -based molecular mechanism for photoregulation may be widespread in bacteria.

Distant cousin helps spot animal enzyme: In addition to forming the membranes that enclose cells, lipids are important signaling molecules. Plasmalogens, which contain a vinyl ether linkage, are an abundant group of lipids in animals. How these lipids are synthesized from precursors with an alkyl ether linkage has been a mystery. Gallego-García et al. found an enzyme, CarF, in the social bacterium Myxococcus xanthus that produces plasmalogens used in a signaling pathway for singlet oxygen, a marker of photooxidative stress. They then showed that the animal homolog could catalyze the final step in plasmalogen synthesis in bacterial and human cells, thus resolving a source for plasmalogens in animals. Science , this issue p. 128

The coenzyme B₁₂-dependent photoreceptor protein, CarH, is a bacterial transcriptional regulator that controls the biosynthesis of carotenoids in response to light. On binding of coenzyme B₁₂ the monomeric apoprotein forms tetramers in the dark, which bind operator DNA thus blocking transcription. Under illumination the CarH tetramer dissociates, weakening its affinity for DNA and allowing transcription. The mechanism by which this occurs is unknown. Here we describe the photochemistry in CarH that ultimately triggers tetramer dissociation; it proceeds via a cob(III)alamin intermediate, which then forms a stable adduct with the protein. This pathway is without precedent and our data suggest it is independent of the radical chemistry common to both coenzyme B₁₂ enzymology and its known photochemistry. It provides a mechanistic foundation for the emerging field of B₁₂ photobiology and will serve to inform the development of a new class of optogenetic tool for the control of gene expression.

Living organisms sense and respond to light, a crucial environmental factor, using photoreceptors, which rely on bound chromophores such as retinal, flavins, or linear tetrapyrroles for light sensing. The discovery of photoreceptors that sense light using 5′-deoxyadenosylcobalamin, a form of vitamin B₁₂ that is best known as an enzyme cofactor, has expanded the number of known photoreceptor families and unveiled a new biological role of this vitamin. The prototype of these B₁₂-dependent photoreceptors, the transcriptional repressor CarH, is widespread in bacteria and mediates light-dependent gene regulation in a photoprotective cellular response. CarH activity as a transcription factor relies on the modulation of its oligomeric state by 5′-deoxyadenosylcobalamin and light. This review surveys current knowledge about these B₁₂-dependent photoreceptors, their distribution and mode of action, and the structural and photochemical basis of how they orchestrate signal transduction and control gene expression.

To understand the mechanisms involved in homologous recombination, we have performed a search for Saccharomyces cerevisiae mutants unable to carry out plasmid-to-chromosome gene conversion. For this purpose, we have developed a colony color assay in which recombination is induced by the controlled delivery of double-strand breaks (DSBs). Recombination occurs between a chromosomal mutant ade2 allele and a second plasmid-borne ade2 allele where DSBs are introduced via the site-specific HO endonuclease. Besides isolating a number of new alleles in known rad genes, we identified a novel allele of the RFA1 gene, rfa1-44, which encodes the large subunit of the heterotrimeric yeast single-stranded DNA-binding protein RPA. Characterization of rfa1-44 revealed that it is, like members of the RAD52 epistasis group, sensitive to X rays, high doses of UV, and HO-induced DSBs. In addition, rfa1-44 shows a reduced ability to undergo sporulation and HO-induced gene conversion. The mutation was mapped to a single-base substitution resulting in an aspartate at amino acid residue 77 instead of glycine. Moreover, all radiation sensitivities and repair defects of rfa1-44 are suppressed by RAD52 in a dose-dependent manner, and one RAD52 mutant allele, rad52-34, displays nonallelic noncomplementation when crossed with rfa1-44. Presented is a model accounting for this genetic interaction in which Rfa1, in a complex with Rad52, serves to assemble other proteins of the recombination-repair machinery at the site of DSBs and other kinds of DNA damage. We believe that our findings and those of J. Smith and R. Rothstein (Mol. Cell. Biol. 15:1632-1641, 1995) are the first in vivo demonstrations of the involvement of a eukaryotic single-stranded binding protein in recombination and repair processes.