HeRs and type I rhodopsins also have similar photoreaction dynamics 13.
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See Supplementary Table S1 for the full names of proteins and sequence (NCBI searchable codes). HeRs and type I rhodopsins form distinct branches arising from 80% for 100 replicates. Phylogenetic tree of microbial rhodopsins with representative HeRs and type I rhodopsins.
Interestingly, bioinformatic analysis revealed that HeRs are found in gram positive bacteria and are largely absent in gram negative bacteria 6, 8, although this taxonomic distribution in monoderms and diderms was somewhat debated 5. Moreover, HeRs can be found in psychrophiles, mesophiles, and hyperthermophiles that live in various temperature environments 1, 8. They are globally distributed in marine, hypersaline, freshwater, and soil environments 1, 7. HeRs are found in bacteria, archaea, eukaryota, and algal viruses 1, 5, 7, 8 (Fig. It turns out that HeRs comprise a large and diverse group of rhodopsins. coli screens 3, 4, and over 400 unique HeR sequences have been found from homology searches of whole genomes from microorganisms 5, 6. Now, 22 more HeRs have been discovered through pigmented E. This fosmid had low sequence similarity to known rhodopsins, which attributed to the lack of detection of HeRs in typical bioinformatic searches 1. coli colonies on retinal-containing culture plates 1. Its first member, HeR 48C12, was discovered through functional metagenomics when the marine fosmid KIN48C12 yielded red E. Heliorhodopsins (HeRs) are a newly discovered category of retinal-binding microbial rhodopsins 1, 2. We additionally performed DEER experiments, which suggests that TaHeR forms possible dimer-of-dimer associations which may be integral to its putative functionality as a light sensor in binding a transducer protein. This intramolecular signaling mechanism may be conserved among HeRs, as similar changes were observed for HeR 48C12 between its pH 8.8 and pH 4.3 structures. We corroborated this intramolecular signaling transduction pathway with computational studies, which revealed allosteric network changes propagating from the perturbed SBC to the intracellular and extracellular space, suggesting TaHeR may function as a sensory rhodopsin. Comparison of the two structures at different pH revealed conformational changes connecting the SBC and the extracellular loop linking helices A–B. The low pH structure revealed that the hydrophilic Schiff base cavity (SBC) accommodates a chloride anion to stabilize the protonated retinal Schiff base when its primary counterion (Glu-108) is neutralized. We have determined the 1.97 Å resolution X-ray crystal structure of Thermoplasmatales archaeon SG8-52-1 heliorhodopsin (TaHeR) in the presence of NaCl under acidic conditions (pH 4.5), which complements the known 2.4 Å TaHeR structure acquired at pH 8.0. Within the microbial rhodopsin family, heliorhodopsins (HeRs) form a phylogenetically distinct group of light-harvesting retinal proteins with largely unknown functions.
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