A Large and Phylogenetically Diverse Class of Type 1 Opsins Lacking a Canonical Retinal Binding Site.
Opsins are photosensitive proteins catalyzing light-dependent processes across the tree of life. For both microbial (type 1) and metazoan (type 2) opsins, photosensing depends upon covalent interaction between a retinal chromophore and a conserved lysine residue. Despite recent discoveries of potential opsin homologs lacking this residue, phylogenetic dispersal and functional significance of these abnormal sequences have not yet been investigated. We report discovery of a large group of putatively non-retinal binding opsins, present in a number of fungal and microbial genomes and comprising nearly 30% of opsins in the Halobacteriacea, a model clade for opsin photobiology. We report phylogenetic analyses, structural modeling, genomic context analysis and biochemistry, to describe the evolutionary relationship of these recently described proteins with other opsins, show that they are expressed and do not bind retinal in a canonical manner. Given these data, we propose a hypothesis that these abnormal opsin homologs may represent a novel family of sensory opsins which may be involved in taxis response to one or more non-light stimuli. If true, this finding would challenge our current understanding of microbial opsins as a light-specific sensory family, and provides a potential analogy with the highly diverse signaling capabilities of the eukaryotic G-protein coupled receptors (GPCRs), of which metazoan type 2 opsins are a light-specific sub-clade.
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Erin A
EA
Becker
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Andrew I
AI
Yao
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Proteome Software, 1340 SW Bertha Blvd., Portland, Oregon, United States of America.
Phillip M
PM
Seitzer
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Tobias
T
Kind
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Ting
T
Wang
California Department of Food and Agriculture, 1220 N St., Sacramento, CA, 95814, United States of America.
Rich
R
Eigenheer
William's College, 880 Main St., Williamstown, MA, 01267, United States of America.
Katie S Y
KS
Shao
Department of Physiology and Membrane Biology, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Vladimir
V
Yarov-Yarovoy
Genome Center, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Microbiology Graduate Group, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.|Department of Biomedical Engineering, One Shields Ave., University of California Davis, Davis, CA, 95616, United States of America.
Marc T
MT
Facciotti
D065638:Absorption, Radiation; D001105:Archaea / Q000378:metabolism; D001419:Bacteria / Q000378:metabolism; D001665:Binding Sites; D017124:Conserved Sequence; D008027:Light; D055355:Opsins / Q000378:metabolism*; D010802:Phylogeny; D012172:Retinaldehyde / Q000378:metabolism*; D015398:Signal Transduction
D055355:Opsins; D012172:Retinaldehyde