Iron Availability Tied to Carbon Metabolism in Cyanobacteria

The Science

Cyanobacteria have photosynthetic and respiratory pathways that are physically interlinked, whereas in plants these pathways are separated into different organelles. In cyanobacteria, multiple enzymatic complexes, including the well-characterized type I and type II NADH dehydrogenases and succinate dehydrogenase (Sdh), contribute electrons into both the photosynthetic and respiratory pathways through their participation in the redox poising of the plastoquinone pool. The enzymatic complexes share iron-dependent electron carriers between the photosynthetic and respiratory electron transfer chains. This adds an extra regulatory burden on the cell, which needs to tightly coordinate iron homeostasis with photosynthesis and respiration.

Scientists from Brookhaven National Laboratory, SLAC National Accelerator Laboratory, and Lawrence Berkeley National Laboratory have discovered a new highly conserved protein from the cyanobacterium Synechocystis sp. PCC 6803 that jointly regulates these two pathways with iron homeostasis. The protein, called Dri1 (for Domain related to Iron 1), uses a never-before-seen heme-binding structural motif.

Using macromolecular crystallography, small-angle X-ray scattering, and Fe K-edge X-ray absorption spectroscopy, researchers were able to characterize Dri1, finding a novel Zinc-mirror heme-binding site within. Dri1 was found to regulate Sdh, which requires many iron-containing cofactors to function. Under conditions of iron limitation, monomeric Dri1 binds to a subunit of Sdh, preventing the formation of the functional protein complex and inhibiting its contribution to the electron transfer chain. When iron isn’t limiting, Dri1 binds iron in the form of a heme-Dri1 dimer; when Zn is also bound, it tightly coordinates the heme, preventing its release back into the cytosol and inhibiting the interaction between Dri1and Sdh.

The Impact

The discovery of Dri1 and its role in the regulation of photosynthesis and respiration in cyanobacteria provides new insight into how CO₂ removal via photosynthesis is dependent on iron availability. Since iron is often limited in marine environments where many species of cyanobacteria are located, the discovery of this regulatory mechanism offers an explanation into how these abundant organisms are able to thrive under these nutrient limited conditions, and offers insight into how iron homeostasis and carbon metabolism are interlinked.

The Summary

This study presents a new protein, Dri1, conserved in cyanobacteria, which links iron homeostasis with carbon metabolism. The structure of this protein reveals a novel Zn-mirror heme-binding motif, wherein Zn binding aligns two histidine residues to tightly coordinate the heme iron. When heme is bound, Dri1 is no longer able to interact with the succinate dehydrogenase (Sdh) subunit SdhB. This allows formation of the fully functional Sdh complex, which is then able to participate as an electron donor for the photosynthetic and respiratory metabolic pathways.

Funding

This work was supported by the U.S. Department of Energy, Office of Science, Office of Biological and Environmental Research, as part of the Quantitative Plant Science Initiative SFA at Brookhaven National Laboratory. E.F.Y. and K.C. are supported by Brookhaven National Laboratory LDRD (21-038). The work (Award DOI 10.46936/10.25585/ 60000750) conducted by the U.S. Department of Energy Joint Genome Institute (https://ror.org/04xm1d337), a DOE Office of Science User Facility, is supported by the Office of Science of the U.S. Department of Energy operated under Contract No. DE-AC02-05CH11231. This research used beamlines 16-ID, 17-ID−1, and 17-ID-2 of the National Synchrotron Light Source II, a U.S. Department of Energy (DOE) Office of Science User Facility operated for the DOE Office of Science by Brookhaven National Laboratory under Contract No. DE-SC0012704. The Center for BioMolecular Structure (CBMS) is primarily supported by the National Institutes of Health, National Institute of General Medical Sciences (NIGMS) through a Center Core P30 Grant (P30GM133893), and by the DOE Office of Biological and Environmental Research (KP1605010). Use of the Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, is supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences under Contract No. DE-AC02-76SF00515. The SSRL Structural Molecular Biology Program is supported by the DOE Office of Biological and Environmental Research, and by the National Institutes of Health, National Institute of General Medical Sciences (P30GM133894). This research was supported by the U.S. Department of Energy, Office of Science, Office of Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division, Physical Biosciences Program through FWP 100593. The contents of this publication are solely the responsibility of the authors and do not necessarily represent the official views of NIGMS or NIH. CW-EPR experiments were run at the National Biomedical Resource for Advanced ESR Spectroscopy (ACERT) at Cornell University, under NIGMS grant 1R24GM146107. We thank Jack H. Freed, Siddarth Chandrasekaran, and Alex L. Lai for their assistance in performing these experiments. The work conducted at Washington University in St Louis was supported by the U.S. Department of Energy (DOE), Office of Basic Energy Sciences, grant DE-FG02-99ER20350 to H.B.P. M.I. was supported by the U.S. Department of Energy, Office of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and Biosciences Division under field work proposal 449B. K.K.N. is an investigator of the Howard Hughes Medical Institute. Crystallization screening of the His21Ala-Heme dimer (PDB 8FM6) was accomplished at the National Crystallization Center at HWI and supported through NIH grant R24GM141256.

Related Links

• BER Resource: Structural Molecular Biology Resource
• BER Resource: Center for BioMolecular Structure

References

Grosjean, N.; Yee, E. F.; Kumaran, D.; Chopra, K.; Abernathy, M.; Biswas, S.; Byrnes, J.; Kreitler, D. F.; Cheng, J.-F.; Ghosh, A.; Almo, S. C.; Iwai, M.; Niyogi, K. K.; Pakrasi, H. B.; Sarangi, R.; van Dam, H.; Yang, L.; Blaby, I. K.; and Blaby-Haas, C. E. 2024. “A Hemoprotein with a Zinc-Mirror Heme Site Ties Heme Availability to Carbon Metabolism in Cyanobacteria.” Nature Communications 15(1), 3167. DOI: 10.1038/s41467-024-47486-z.