Cation and Anion Channelrhodopsins: Sequence Motifs and Taxonomic Distribution

Abstract

Channelrhodopsins are widely used in neuroscience and cardiology as research tools and are considered prospective therapeutics, but their natural diversity and mechanisms remain poorly characterized. Genomic and metagenomic sequencing projects are producing an ever-increasing wealth of data, whereas biophysical characterization of the encoded proteins lags behind.

Emerging Diversity of Channelrhodopsins and Their Structure-Function Relationships

“…Their retinal-binding pockets show a distinctly different residue pattern as compared to that of Chrimson, indicating that the red spectral shift is achieved in RubyACRs by a different biophysical mechanism. Yet another residue pattern was found in two prasinophyte CCRs with the spectra red-shifted to 585 nm (Govorunova et al, 2021 ).…”

“…An important insight gained from recent studies on ChR diversity is that channel function cannot always be deduced from the primary sequence alone, i.e., several ChR families exist that show very low sequence homology to each other yet similar function (Govorunova et al, 2021 ). A striking example is the family of cryptophyte CCRs known as “bacteriorhodopsin-like CCRs” (BCCRs; Sineshchekov et al, 2017 ).…”

“…A group of rhodopsin sequences from dinoflagellates of the genera Ansanella, Pelagodinum, Breviolum , and Symbiodinium contain the Thr-Cys-Pro motif in the middle of TM3 that is conserved in most so far known ChRs. Two of such rhodopsins from the coral endosymbiont Symbiodinium microadriaticum exhibited channel activity upon heterologous expression (Govorunova et al, 2021 ). Their spectral sensitivity roughly matched that of phototactic accumulation observed in the Symbiodiniaceae and unclassified coral symbiotic dinoflagellates (Hollingsworth et al, 2005 ; Aihara et al, 2019 ), which suggests their photoreceptor role for this response.…”

“…Cafeteria roenbergensis is a globally distributed marine bacterivorous flagellate that belongs to the same stramenopile class Bygira as Labyrinthulea (Hackl et al, 2020 ). ChRs from several Labyrinthulea species of the order Thraustochytrida, C. roenbergensis and the unclassified stramenopile strain TOSAG 23-3 have been functionally characterized by heterologous expression and patch clamp electrophysiology (Govorunova et al, 2020 , 2021 ). ChRs from the latter source are highly homologous to metagenomically identified ChRs known as MerMAIDs (Metagenomically discovered, Marine, Anion-conducting and Intensely Desensitizing channelrhodopsins; Oppermann et al, 2019 ), which suggests that MerMAIDs also originate from stramenopiles.…”

“…Most so far tested cryptophyte BCCRs also have an increased Na + /H + permeability ratio (e.g., ~5 × 10 −5 in Gt CCR4), as compared to Cr ChR2 (~10 −6 ) (Govorunova et al, 2016b ; Shigemura et al, 2019 ). A number of chlorophyte and cryptophyte CCRs are almost purely H + channels (Berthold et al, 2008 ; Tsunoda and Hegemann, 2009 ; Zhang et al, 2011 ; Govorunova et al, 2021 ). Some CCRs are also permeable for Ca 2+ , although to a lesser extent than for monovalent metal cations, e.g., the Ca 2+ /Na + permeability ratio of Cr ChR2 is ~0.15 (Kleinlogel et al, 2011 ).…”