Omega Rhodopsins: A Versatile Class of Microbial Rhodopsins

Abstract

Microbial rhodopsins are a superfamily of photoactive membrane proteins with the covalently bound retinal cofactor. Isomerization of the retinal chromophore upon absorption of a photon triggers conformational changes of the protein to function as ion pumps or sensors. After the discovery of proteorhodopsin in an uncultivated γ-proteobacterium, light-activated proton pumps have been widely detected among marine bacteria and, together with chlorophyll-based photosynthesis, are considered as an important axis responsible for primary production in the biosphere. Rhodopsins and related proteins show a high level of phylogenetic diversity; we focus on a specific class of bacterial rhodopsins containing the ‘3 omega motif.’ This motif forms a stack of three non-consecutive aromatic amino acids that correlates with the B–C loop orientation and is shared among the phylogenetically close ion pumps such as the NDQ motif-containing sodiumpumping rhodopsin, the NTQ motif-containing chloride-pumping rhodopsin, and some protonpumping rhodopsins including xanthorhodopsin. Here, we reviewed the recent research progress on these ‘omega rhodopsins,’ and speculated on their evolutionary origin of functional diversity.

Microbial Rhodopsins: The Last Two Decades

“…Xanthorhodopsins and NQ rhodopsins (NDQ Na + pumps and NTQ Cl − pumps) are phylogenetically close and form a single clade (56) (Figure 3). They share a common structural element consisting of three tacked aromatic residues, the so-called 3-omega motifs, hence the name omega rhodopsins (73).…”

Rhodopsins: An Excitingly Versatile Protein Species for Research, Development and Creative Engineering

“…A large number of excellent reviews on the rhodopsin families have been published, many of which we have referred to where appropriate, along with the most relevant early and recent papers. We refrain from presenting many molecular details, and therefore we refer to the following more recent reviews ( DeGrip and Rothschild, 2000 ; Hofmann, 2000 ; Spudich et al, 2000 ; Hofmann et al, 2009 ; Yizhar et al, 2011 ; Palczewski and Orban, 2013 ; Ernst et al, 2014 ; Imamoto and Shichida, 2014 ; Inoue et al, 2014 ; Deisseroth, 2015 ; Hofmann and Palczewski, 2015 ; Brown and Ernst, 2017 ; Bando et al, 2019 ; El Khatib and Atamian, 2019 ; Dowling, 2020 ; Kandori, 2020 ; Kwon et al, 2020 ; Baillie et al, 2021 ; Moraes et al, 2021 ; Rozenberg et al, 2021 ; Bondar, 2022 ; Broser, 2022 ; Brown, 2022 ; Khelashvili and Menon, 2022 ; Nagata and Inoue, 2022 ).…”