A distinct abundant group of microbial rhodopsins discovered using functional metagenomics

Abstract

Many organisms capture or sense sunlight using rhodopsin pigments, which are integral membrane proteins that bind retinal chromophores. Rhodopsins comprise two distinct protein families , 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 helix. 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 . 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.

Heliorhodopsins are absent in diderm (Gram‐negative) bacteria: Some thoughts and possible implications for activity

“…Binning of contigs assembled from metagenomes, is an error‐prone which can result in spurious sequences containing fragments of multiple unrelated organisms (Sharon and Banfield, ). Contigs deposited in GenBank as diderms were re‐classified after manual validation (Supporting Information Table S5), confirming our previous observation with cultured proteobacteria representatives (Pushkarev et al ., ) that heliorhodopsins are mostly absent in diderms.…”

“…Based on microbial rhodopsin sequences (Supporting Information Table S1) previously reported (Pushkarev et al, 2018) we created a graftM (Boyd et al, 2018) gene classification package to identify and classify proteins into rhodopsins or heliorhodopsins. GraftM is a tool for fast and accurate phylogenetically informed classification of genes, which employs hidden Markov Models (HMM) (Boyd et al, 2018;Potter et al, 2018).…”

“…The orientation of heliorhodopsins in the membrane is opposite to that of type-1 or type-2 rhodopsins, with the N-terminus facing the cell cytoplasm. Heliorhodopsins show photocycles longer than 1 s, additionally they are largely constrained to the photic zone which is suggestive of light sensory activity (Pushkarev et al, 2018).…”

“…Rhodopsins are currently divided to two distinct protein families (Spudich et al, 2000): type-1 (microbial rhodopsins) and type-2 (animal rhodopsins) which share similar topologies with seven trans-membrane (TM) helices but show little or no sequence similarity to each other. Recently, heliorhodopsins, a novel rhodopsin family, were discovered using functional metagenomics (Pushkarev et al, 2018). The orientation of heliorhodopsins in the membrane is opposite to that of type-1 or type-2 rhodopsins, with the N-terminus facing the cell cytoplasm.…”

“…Heliorhodopsins are found in diverse bacteria, archaea, unicellular eukarya and algal viruses (Pushkarev et al, 2018). These microbes range from psychrophiles, mesophiles and even hyperthermophiles originating from soil, freshwater, marine and hypersaline environments.…”