Schizorhodopsins: A family of rhodopsins from Asgard archaea that function as light-driven inward H ⁺ pumps

Abstract

Schizorhodopsins (SzRs), a rhodopsin family first identified in Asgard archaea, the archaeal group closest to eukaryotes, are present at a phylogenetically intermediate position between typical microbial rhodopsins and heliorhodopsins. However, the biological function and molecular properties of SzRs have not been reported. Here, SzRs from Asgardarchaeota and from a yet unknown microorganism are expressed in Escherichia coli and mammalian cells, and ion transport assays and patch clamp analyses are used to demonstrate SzR as a novel type of light-driven inward H+ pump. The mutation of a cytoplasmic glutamate inhibited inward H+ transport, suggesting that it functions as a cytoplasmic H+ acceptor. The function, trimeric structure, and H+ transport mechanism of SzR are similar to that of xenorhodopsin (XeR), a light-driven inward H+ pumping microbial rhodopsins, implying that they evolved convergently. The inward H+ pump function of SzR provides new insight into the photobiological life cycle of the Asgardarchaeota.

Crystal structure of schizorhodopsin reveals mechanism of inward proton pumping

“…The alkalization was largely eliminated by the addition of a protonophore, 10 μM CCCP (carbonyl cyanide m-chlorophenylhydrazone), suggesting that SzR4 functions as an inward H + pump as reported previously 13 . The purified SzR4 showed a maximum absorption wavelength (λmax) at 557 nm, identical to that of SzR1 13 (Fig. 1c).…”

“…Asgard archaea are the closest prokaryotic species to ancestral eukaryotes 11 and have many genes unique to eukaryotes. Recently, a new microbial rhodopsin group, schizorhodopsin (SzR), was found in the assembled genomes of Asgard archaea and the metagenomic sequences of unknown microbial species 12,13 . A molecular phylogenetic analysis suggested that SzRs are located at an intermediate position between typical microbial rhodopsins, also called "type-1 rhodopsins" 14 , and HeR 5 , and thus they were named "schizo-(meaning "split" in Greek)" rhodopsin.…”

“…A molecular phylogenetic analysis suggested that SzRs are located at an intermediate position between typical microbial rhodopsins, also called "type-1 rhodopsins" 14 , and HeR 5 , and thus they were named "schizo-(meaning "split" in Greek)" rhodopsin. Especially, the transmembrane helix (TM) 3 of SzR is more similar to that of HeR than type-1, whereas TM6 and 7 of SzR and type-1 share many identical residues; e.g., W154, P158, T161, A184, and F191, which are not conserved in HeR 13 . SzRs heterologously expressed in E. coli and mammalian cells displayed light-driven inward H + pump activity 13 .…”

“…Especially, the transmembrane helix (TM) 3 of SzR is more similar to that of HeR than type-1, whereas TM6 and 7 of SzR and type-1 share many identical residues; e.g., W154, P158, T161, A184, and F191, which are not conserved in HeR 13 . SzRs heterologously expressed in E. coli and mammalian cells displayed light-driven inward H + pump activity 13 . As SzRs are phylogenetically distant from XeRs (~18% identity and ~44% similarity), these two rhodopsin families with similar functions have convergently evolved.…”

“…In the case of XeR from the marine bacterium Parvularcula oceani (PoXeR), the H + is transferred to the cytoplasmic aspartate (PoXeR D216, H + acceptor) in TM7, and then released to the cytoplasmic bulk phase 10 . By contrast, the H + acceptor of SzR was considered to be E81 in TM3, since the mutation of E81 to glutamine abolished the inward H + transport 13 .…”