A distinct lineage of giant viruses brings a rhodopsin photosystem to unicellular marine predators

Abstract

Giant viruses are remarkable for their large genomes, often rivaling those of small bacteria, and for having genes thought exclusive to cellular life. Most isolated to date infect nonmarine protists, leaving their strategies and prevalence in marine environments largely unknown. Using eukaryotic single-cell metagenomics in the Pacific, we discovered a Mimiviridae lineage of giant viruses, which infects choanoflagellates, widespread protistan predators related to metazoans. The ChoanoVirus genomes are the largest yet from pelagic ecosystems, with 442 of 862 predicted proteins lacking known homologs. They are enriched in enzymes for modifying organic compounds, including degradation of chitin, an abundant polysaccharide in oceans, and they encode 3 divergent type-1 rhodopsins (VirR) with distinct evolutionary histories from those that capture sunlight in cellular organisms. One (VirRDTS) is similar to the only other putative rhodopsin from a virus (PgV) with a known host (a marine alga). Unlike the algal virus, ChoanoViruses encode the entire pigment biosynthesis pathway and cleavage enzyme for producing the required chromophore, retinal. We demonstrate that the rhodopsin shared by ChoanoViruses and PgV binds retinal and pumps protons. Moreover, our 1.65-Å resolved VirRDTS crystal structure and mutational analyses exposed differences from previously characterized type-1 rhodopsins, all of which come from cellular organisms. Multiple VirR types are present in metagenomes from across surface oceans, where they are correlated with and nearly as abundant as a canonical marker gene from Mimiviridae. Our findings indicate that light-dependent energy transfer systems are likely common components of giant viruses of photosynthetic and phagotrophic unicellular marine eukaryotes.

Viral channelrhodopsins: calcium-dependent Na+/K+ selective light-gated channels

“…Here we present the results of a comprehensive structure-function study of two homologous proteins from the VR1 group, OLPVR1 and VirChR1. We show that unlike previously reported data (Needham et al, 2019), VirChR1 demonstrate sodium/potassium-selective channelrhodopsin activity when expressed in human neuroblastoma cells. Upon light absorption, VirChR1 depolarizes cell membranes to a level sufficient to fire neurons.…”

“…Under acidic conditions the absorption spectra of both proteins undergo a reversible transition to the protonated state, associated with red-shifted absorption maximum at around 530 nm, similar to those for other microbial rhodopsins (Tsukamoto et al, 2013). In contrast to previously reported data, we did not observe any significant ion translocation ability of viral rhodopsins in pH change experiments with protein-containing liposomes (Needham et al, 2019). Under continuous bright light illumination, OLPVR1 liposomes have not showed any substantial pH change of the external solvent ( Figure 2g).…”

“…The constriction sites regions are almost identical in OLPVR1 and DTS-motif rhodopsin from Phaeocystis globosa virus 12T (Needham et al, 2019), therefore we consider them as characteristic feature of the group 1 of viral rhodopsins. Hence, we assume that they are also essential for the ion channeling.…”

“…To decipher the molecular mechanism of ion channeling, the structure of viral channelrhodopsin from group 1 is essential. One crystal structure of the DTS-motif rhodopsin from Phaeocystis globosa virus 12T was recently reported (Needham et al, 2019). However, from the only one available structure it is not possible to distinguish the features of the entire group.…”

“…Phylogenetic analysis shows that, within the rhodopsin superfamily, viral rhodopsins form a monophyletic group that consists of two distinct branches, VR1 and VR2 (López et al, 2017). Recently, a DTS-rhodopsin from VR1 group was reported to pump protons when expressed in E.coli plasma membrane (Needham et al, 2019). In contrast to VR1 group, the OLPVRII protein from VR2 group was shown to have pentameric organization that resembles ligand-gated channels and second-scale photocycle .…”