ESRF X-rays capture vitamin B12 sensing light

CarH is a photoreceptor which senses light through a vitamin B12 derivative and regulates carotenoid expression through direct interaction with genes. Bacteria use this remarkable machinery to regulate gene expression and produce carotenoid to protect themselves from photo-damage upon sun exposure. What scientists had never seen before was how tiny photoinduced changes at the vitamin B12 level, propagate into large-scale structural changes triggering a biological response. Now, an international collaboration has managed to film this process in unprecedented detail, with key experiments carried out at the ESRF and at XFELs.

CarH’s role has been clear since around 2015. In the dark, the protein binds to DNA and blocks the production of carotenoids. When light is present, CarH releases the DNA, allowing the cell to produce carotenoids that help defend against light-induced damage.

Previous crystal structures revealed the start and end points of this process. But the crucial missing piece was the journey in between — from the short-lived structural changes that occur immediately after light hits the vitamin B12 molecule to the large-scale conformational changes involving the whole protein structure and its interaction with DNA.

While time-resolved serial femtosecond X-ray crystallography (TR-SFX) experiments performed at XFEL facilities have unveiled the early crucial photochemical events around the vitamin B12 chromophore, time-resolved X-ray solution scattering (TR-XSS) experiments at the ESRF have allowed to follow  CarH structural dynamics directly in solution, where the protein tetrameric structural change and its detachment from DNA could be observed. 

“At the ESRF’s ID09 beamline, we saw for the first time the structural changes at the protein level and the dissociation of the CarH tetramer into monomers”, says Giorgio Schirò, one of the leading scientist of the study and principal investigator of the ANR project “PhotoGene” together with the ID09 scientist Matteo Levantino and the ID09 postdoc Kévin Pounot.

The ESRF measurements provided a bridge between ultrafast techniques, which capture the first billionths of a second localized changes and the large-scale conformational changes occurring in physiological conditions. They revealed how CarH transitions from its light-activated state to the stable configuration that releases DNA and switches genes on.

“The ESRF allowed us to connect the dots,” explains Martin Weik corresponding author of the paper. “We could see how the initial light reaction is converted into a biologically meaningful response.”

Another important contribution of the ESRF to the research was obtained at the BM07-FIP2 beamline. Thanks to its unique capability of combining crystallography and in cristallo UV-Vis absorption spectroscopy, BM07 provided cryogenic data on photoactivated CarH crystals that helped clarifying the chemical nature of a key intermediate.

Why vitamin B12 matters

Vitamin B12 is normally associated with radical chemistry — reactions involving highly reactive molecules that can be dangerous to cells. This raised a long-standing puzzle: why would a cell use such a molecule in a system designed to protect against light-induced damage?

The results showed that CarH carefully controls the chemistry of vitamin B12, steering it away from harmful radical formation. Instead, the protein channels the light reaction into a safe and effective structural signal.

Applications

Beyond solving a long-standing mystery, the work highlights the growing importance of synchrotron X-ray techniques for studying biological processes in real time. By complementing ultrafast laser methods, the ESRF experiments helped turn static snapshots into a molecular movie.

The findings also strengthen interest in B12-based photoreceptors as tools for optogenetics and synthetic biology, where light is used to control cellular behaviour with precision.

Reference:

Rios-Santacruz, R., Poddar, H., Pounot, K. et al. Integrated structural dynamics uncover a new B₁₂ photoreceptor activation mode. Nature (2026). https://doi.org/10.1038/s41586-025-10074-2

Top image: Credits: CEA and Maria Davila Miliani