Cyanobacteria, commonly known as blue-green algae, are found almost everywhere in the world—from hot springs to arctic ice to antioxidant smoothies.
Part of their extreme adaptability lies within a unique light-harvesting structure called the phycobilisome. These modular antennae both collect energy from sunlight, and adapt to changing light levels in order to provide a sort of sunscreen for the bacteria.
One important way that phycobilisomes adapt involves an accessory protein to both sense and protect against too much light. But it's not clear just how this tiny protein works.
Understanding photoprotection in phycobilisomes could inspire new biomimetic strategies for engineering plants to improve food security, or even in creating new kinds of adaptable energy technologies.
So when their collaborators in the Kerfeld Lab at Michigan State University reported a surprisingly specific molecular structure for phycobilisomes protected by this protein, University of Chicago Pritzker School of Molecular Engineering (UChicago PME) Asst. Prof. Allison Squires was intrigued.
"There are tons of places where it could bind that look just like the site that our collaborators identified, and phycobilisomes have many different architectures," she said. "So why did it bind at this one site and not other sites? And what happens in other architectures where this specific site is blocked?"
Combining high-precision spectroscopy experiments with computational modeling, Squires and her team found that in fact, this protein binds to distinct but specific sites in different phycobilisome architectures, yet still seems to work the same way, providing the same level of protection.
"It's a really lovely example of an adaptable molecular mechanism, where the protein can easily evolve to do its job under conditions that require different phycobilisome structures," Squires said. "Maybe it started out at one binding site, but then as the architecture changed, it could still do its job at a new site."
The results were published in the Proceedings of the National Academy of Sciences.
Single photon spectroscopy to understand protein binding
The protein, called orange carotenoid protein, helps harvest light by "quenching" sunlight when necessary. If it's too sunny for too long, for example, the protein binds to the phycobilisome and dissipates absorbed energy.
"Too much energy can damage the photosynthetic machinery, so having this protein provides a quick way to protect the cyanobacteria from a sudden change in light," Squires said.
To better understand how the protein bound to the antenna structure, Squires's team—including recent UChicago PhD graduate Ayesha Ejaz, who was the first author on the research—used single particle spectroscopy. This technology allows them to monitor energy transfer at the nanoscale. The team uses a special setup called an Anti-Brownian ELectrokinetic (ABEL) trap, which suspends their specimen in a solution and uses electrodes within a microfluidic cell to keep it in the center. That keeps the protein in place long enough to get a good signal.
They studied how the protein bound to two different kinds of phycobilisomes—one that has a three-barrel structure, and one with a five-barrel structure—and found that the protein did indeed bind at different sites, though still provided the same quenching effect.
They also ran computer simulations that simulated a photon getting absorbed by the bacteria until it performs photosynthesis or runs into the protein.
Together, the results showed that the system "balances modularity with site specificity," Squires said. "That's pretty common in nature, but it really shows off the exquisite evolvability of this system."
Next, the team hopes to delve further into the phycobilisome system to better understand how it regulates energy capture and flow. Beyond the protein, the phycobilisome seems to contain other intrinsic "switches" and "fuses" that protect against changing light conditions by breaking at the right time and location to control energy transfer. Squires and her team want to know how these other mechanisms work, and how their function complements their recent findings regarding the role of the orange carotenoid protein.
"It was very gratifying to see how the precise data obtained from the ABEL trap can be used to gain structural insights into this quenching mechanism," Ejaz said. "I am excited to see what new patterns will emerge once we combine these results with future experiments comparing intrinsic photoprotective mechanisms among phycobilisomes with different structures."
Collaborators on the paper include Markus Sutter, Sigal Lechno-Yossef, and Cheryl A. Kerfeld (Michigan State University and Lawrence Berkeley National Laboratory).
Citation: "Phycobilisome core architecture influences photoprotective quenching by the Orange Carotenoid Protein." Ejaz et al, Proceedings of the National Academy of Sciences, Oct. 7, 2025. DOI: 10.1073/pnas.2420355122
Funding: U.S. Department of Energy, National Science Foundation
