Saccharibacteria harness light energy using type-1 rhodopsins that may rely on retinal sourced from microbial hosts.

Alexander L Jaffe, Masae Konno, Yuma Kawasaki, Chihiro Kataoka, Oded Béjà, Hideki Kandori, Keiichi Inoue, Jillian F Banfield

Journal: The ISME journal 2022;16(8):2056-2059

PMID: 35440729

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Abstract

Microbial rhodopsins are a family of photoreceptive membrane proteins with a wide distribution across the Tree of Life. Within the candidate phyla radiation (CPR), a diverse group of putatively episymbiotic bacteria, the genetic potential to produce rhodopsins appears to be confined to a small clade of organisms from sunlit environments. Here, we characterize the metabolic context and biophysical features of Saccharibacteria Type-1 rhodopsin sequences derived from metagenomic surveys and show that these proteins function as outward proton pumps. This provides one of the only known mechanisms by which CPR can generate a proton gradient for ATP synthesis. These Saccharibacteria do not encode the genetic machinery to produce all-trans-retinal, the chromophore essential for rhodopsin function, but their rhodopsins are able to rapidly uptake this cofactor when provided in experimental assays. We found consistent evidence for the capacity to produce retinal from β-carotene in microorganisms co-occurring with Saccharibacteria, and this genetic potential was dominated by members of the Actinobacteria, which are known hosts of Saccharibacteria in other habitats. If Actinobacteria serve as hosts for Saccharibacteria in freshwater environments, exchange of retinal for use by rhodopsin may be a feature of their associations.

Address: Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA.; The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan.; PRESTO, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan.; The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan.; Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.; Faculty of Biology, Technion - Israel Institute of Technology, Haifa, Israel.; Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.; OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya, Japan.; The Institute for Solid State Physics, The University of Tokyo, Kashiwa, Chiba, Japan. [email protected].; Innovative Genomics Institute, University of California, Berkeley, CA, USA. [email protected].; Department of Earth and Planetary Science, University of California, Berkeley, CA, USA. [email protected].; Department of Environmental Science, Policy, and Management, University of California, Berkeley, CA, USA. [email protected].

DOI: 10.1038/s41396-022-01231-w

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MeSH Terms: Actinobacteria, Bacteria, Light, Proton Pumps, Rhodopsin, Rhodopsins, Microbial