A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

Alina Pushkarev, Keiichi Inoue, Shirley Larom, José Flores-Uribe, Manish Singh, Masae Konno, Sahoko Tomida, Shota Ito, Ryoko Nakamura, Satoshi P. Tsunoda, Alon Philosof, Itai Sharon, Natalya Yutin, Eugene V. Koonin, Hideki Kandori () and Oded Béjà ()
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Alina Pushkarev: Technion Israel Institute of Technology
Keiichi Inoue: Nagoya Institute of Technology
Shirley Larom: Technion Israel Institute of Technology
José Flores-Uribe: Technion Israel Institute of Technology
Manish Singh: Nagoya Institute of Technology
Masae Konno: Nagoya Institute of Technology
Sahoko Tomida: Nagoya Institute of Technology
Shota Ito: Nagoya Institute of Technology
Ryoko Nakamura: Nagoya Institute of Technology
Satoshi P. Tsunoda: Nagoya Institute of Technology
Alon Philosof: Technion Israel Institute of Technology
Itai Sharon: Migal Galilee Research Institute
Natalya Yutin: National Institutes of Health
Eugene V. Koonin: National Institutes of Health
Hideki Kandori: Nagoya Institute of Technology
Oded Béjà: Technion Israel Institute of Technology

Nature, 2018, vol. 558, issue 7711, 595-599

Abstract: Abstract Many organisms capture or sense sunlight using rhodopsin pigments1,2, which are integral membrane proteins that bind retinal chromophores. Rhodopsins comprise two distinct protein families 1 , type-1 (microbial rhodopsins) and type-2 (animal rhodopsins). The two families share similar topologies and contain seven transmembrane helices that form a pocket in which retinal is linked covalently as a protonated Schiff base to a lysine at the seventh transmembrane helix2,3. Type-1 and type-2 rhodopsins show little or no sequence similarity to each other, as a consequence of extensive divergence from a common ancestor or convergent evolution of similar structures 1 . Here we report a previously unknown and diverse family of rhodopsins—which we term the heliorhodopsins—that we identified using functional metagenomics and that are distantly related to type-1 rhodopsins. Heliorhodopsins are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of type-1 or type-2 rhodopsins. Heliorhodopsins show photocycles that are longer than one second, which is suggestive of light-sensory activity. Heliorhodopsin photocycles accompany retinal isomerization and proton transfer, as in type-1 and type-2 rhodopsins, but protons are never released from the protein, even transiently. Heliorhodopsins are abundant and distributed globally; we detected them in Archaea, Bacteria, Eukarya and their viruses. Our findings reveal a previously unknown family of light-sensing rhodopsins that are widespread in the microbial world.

Date: 2018
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DOI: 10.1038/s41586-018-0225-9

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