1.A.110.  The Channel-forming Otopetrin (OTOP) Family 

Otopertrin1 of Danio rerio inhibits P2Y purinoceptors. It may modulate calcium homeostasis and influx of calcium in response to extracellular ATP. It is essential for the formation of otoliths in the inner ear of developing larvae and for the perception of gravity and acceleration (Söllner et al. 2004).  Otoliths in bony fishes and otoconia in mammals are composite crystals consisting of calcium carbonate and proteins. These biominerals are part of the gravity and linear acceleration detection system of the inner ear. Mutations in otopetrin 1 result in lack of otoconia in tilted and mergulhador mutant mice. Söllner et al. 2004 showed that a mutation in the otop1 gene in zebrafish is responsible for the complete absence of otoliths. They examined the localization of Starmaker, a secreted protein that is abundant in otoliths in backstroke mutants. The starmaker protein accumulated within cells of the otic epithelium, indicating a possible defect in secretion. Otopetrin-1 and Otopetrin-2 are constituents of otoliths, biological crystals formed by a layer of calcium carbonate crystal that adhere to the ciliary surface of the utricular and saccular receptors in the vestibule of all vertebrates inner ears (Huang and Qian 2022).

The fish inner ear contains three large extracellular biomineral particles, otoliths, which have evolved to transduce the force of gravity into neuronal signals. Mammalian ears contain thousands of small particles called otoconia that serve a similar function. Loss or displacement of these structures can be lethal for fish and is responsible for benign paroxysmal positional vertigo (BPPV) in humans. The distinct morphologies of otoconial particles and otoliths suggest divergent developmental mechanisms. Mutations in Otopetrin 1 result in nonsyndromic otoconial agenesis and a severe balance disorder in mice. Hughes et al. 2004 showed that in zebrafish,  Otop1 is essential for otolith formation. Morpholino-mediated knockdown of zebrafish Otop1 led to otolith agenesis without affecting the sensory epithelium or other structures within the inner ear. Otop1 regulates cellular Ca2+ (Hughes et al. 2007). The OTOP family was previously the DUF270 or pfam03189 family. The members of this family have three 'Otopetrin Domains' that are highly conserved between vertebrates, arthropods and nematodes, as well as a constrained predicted loop structure (Hughes et al. 2008). 

By comparative transcriptome analysis of mouse taste receptor cells, Tu et al. 2018 identified OTOP1 as a proton-selective ion channel. They found that murine OTOP1 is enriched in acid-detecting taste receptor cells and is required for their zinc-sensitive proton conductance. Two related murine genes, Otop2 and Otop3, and a Drosophila ortholog also encode proton channels. Evolutionary conservation of the gene family and its widespread tissue distribution suggest a broad role for proton channels in physiology and pathophysiology (Tu et al. 2018). Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels have been analyzed (Teng et al. 2022).

Chen et al. 2019 presented the cryo-EM structure of OTOP3 from Xenopus tropicalis (XtOTOP3) along with functional characterization of the channel. XtOTOP3 forms a homodimer with each subunit containing 12 TMSs that can be divided into two structurally homologous halves, each half assembling as an alpha-helical barrel that could serve as a proton conduction pore. Both pores open from the extracellular half before becoming occluded at a central constriction point consisting of three highly conserved residue pairs - Gln232/585-Asp262/Asn623-Tyr322/666 (the constriction triads). Mutagenesis showed that the constriction triad from the second pore is less amenable to perturbation than that of the first pore, suggesting an unequal contribution between the two pores to proton transport. Several key residues at the interface between the two pores that are functionally important, particularly Asp509, which confers intracellular pH-dependent desensitization to OTOP channels, were also identified (Chen et al. 2019). 

Otopetrins (Otop1-Otop3) comprise one of two known eukaryotic proton-selective channel families. Otop1 is required for otoconia formation and a candidate mammalian sour taste receptor. Saotome et al. 2019 reported cryo-EM structures of zebrafish Otop1 and chicken Otop3 in lipid nanodiscs. The structures have a dimeric architecture, with each subunit forming 12 TMSs, divided into structurally similar amino (N) and carboxy (C) domains. Cholesterol-like molecules occupy various sites in Otop1 and Otop3 and occlude a central tunnel. In molecular dynamics simulations, hydrophilic vestibules formed by the N- and C-domains and in the intrasubunit interface between N- and C-domains form conduits for water entry into the membrane core, suggesting three potential proton conduction pathways. By mutagenesis, Saotome et al. 2019  tested the roles of charged residues in each putative permeation pathway. The results provided a structural basis for understanding selective proton permeation and gating of this conserved family of proton channels.


 

References:

Chen, Q., W. Zeng, J. She, X.C. Bai, and Y. Jiang. (2019). Structural and functional characterization of an otopetrin family proton channel. Elife 8:.

Danmaliki, G.I. and P.M. Hwang. (2020). Solution NMR spectroscopy of membrane proteins. Biochim. Biophys. Acta. Biomembr 1862: 183356. [Epub: Ahead of Print]

Huang, S. and S. Qian. (2022). Advances in otolith-related protein research. Front Neurosci 16: 956200.

Hughes, I., B. Blasiole, D. Huss, M.E. Warchol, N.P. Rath, B. Hurle, E. Ignatova, J.D. Dickman, R. Thalmann, R. Levenson, and D.M. Ornitz. (2004). Otopetrin 1 is required for otolith formation in the zebrafish Danio rerio. Dev Biol 276: 391-402.

Hughes, I., J. Binkley, B. Hurle, E.D. Green, , A. Sidow, and D.M. Ornitz. (2008). Identification of the Otopetrin Domain, a conserved domain in vertebrate otopetrins and invertebrate otopetrin-like family members. BMC Evol Biol 8: 41.

Hughes, I., M. Saito, P.H. Schlesinger, and D.M. Ornitz. (2007). Otopetrin 1 activation by purinergic nucleotides regulates intracellular calcium. Proc. Natl. Acad. Sci. USA 104: 12023-12028.

Hurle, B., T. Marques-Bonet, F. Antonacci, I. Hughes, J.F. Ryan, , E.E. Eichler, D.M. Ornitz, and E.D. Green. (2011). Lineage-specific evolution of the vertebrate Otopetrin gene family revealed by comparative genomic analyses. BMC Evol Biol 11: 23.

Li, B., Y. Wang, A. Castro, C. Ng, Z. Wang, H. Chaudhry, Z. Agbaje, G.A. Ulloa, and Y. Yu. (2022). The roles of two extracellular loops in proton sensing and permeation in human Otop1 proton channel. Commun Biol 5: 1110.

Saotome, K., B. Teng, C.C.A. Tsui, W.H. Lee, Y.H. Tu, J.P. Kaplan, M.S.P. Sansom, E.R. Liman, and A.B. Ward. (2019). Structures of the otopetrin proton channels Otop1 and Otop3. Nat Struct Mol Biol 26: 518-525.

Söllner, C., H. Schwarz, R. Geisler, and T. Nicolson. (2004). Mutated otopetrin 1 affects the genesis of otoliths and the localization of Starmaker in zebrafish. Dev Genes Evol 214: 582-590.

Teng, B., J.P. Kaplan, Z. Liang, Z. Krieger, Y.H. Tu, B. Burendei, A.B. Ward, and E.R. Liman. (2022). Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels. Elife 11:.

Tu, Y.H., A.J. Cooper, B. Teng, R.B. Chang, D.J. Artiga, H.N. Turner, E.M. Mulhall, W. Ye, A.D. Smith, and E.R. Liman. (2018). An evolutionarily conserved gene family encodes proton-selective ion channels. Science 359: 1047-1050.

Examples:

TC#NameOrganismal TypeExample
1.A.110.1.1

OTOP1 of 600 aas and 12 TMSs in a 5 + 5 + 2 arrangement.  OTOP1 is a pH-sensitive proton-selective ion channel enriched in acid-detecting taste receptor cells and is required for their zinc-sensitive proton conductance (Tu et al. 2018). Two related murine genes, Otop2 and Otop3, and a Drosophila ortholog also encode proton channels. Evolutionary conservation of the gene family and its widespread tissue distribution suggest a broad role for proton channels in physiology and pathophysiology (Tu et al. 2018). Structural motifs for subtype-specific pH-sensitive gating of vertebrate otopetrin proton channels have been analyzed (Teng et al. 2022).

OTOP1 of Mus musculus

 
1.A.110.1.10

Otop3 of 600 aas and 12 TMSs in a 5 + 5 + 2 TMS arrangement.  The high resolution 3-d structure has been determined by cryoEM (Saotome et al. 2019) (see family description). Applications of solution NMR for studying structure, dynamics, and interactions of polytopic integral membrane proteins have been reviewed (Danmaliki and Hwang 2020).

Otop3 of Gallus gallus (chicken)

 
1.A.110.1.2

OTOP1 H+ channel of 612 aas and 10 TMSs in an apparent 4 + 4 + 2 TMS arrangement (Tu et al. 2018). OTOP1 is a protein required for development of gravity-sensing otoconia in the vestibular system. It forms a proton-selective ion channel (Tu et al. 2018). Proton channel activity is only weakly-sensitive to voltage and is probably required in cell types that use changes in intracellular pH for cell signaling or to regulate biochemical or developmental processes (Tu et al. 2018). In the vestibular system of the inner ear, it is required for the formation and function of otoconia, calcium carbonate crystals that sense gravity and acceleration. It regulates purinergic control of intracellular calcium in vestibular supporting cells and may be involved in sour taste perception in sour taste cells by mediating entry of protons within the cytosol. It is also involved in energy metabolism, by reducing adipose tissue inflammation and protecting from obesity-induced metabolic dysfunction. Two extracellular loops in the human Otop1 proton channel function in proton sensing and transport (Li et al. 2022).

OTOP1 of Homo sapiens

 
1.A.110.1.3

OTOP2 H+ channel of 562 aas and 10 TMSs in a 5 + 5 + 2 arrangement (Tu et al. 2018).

OTOP2 of Homo sapiens

 
1.A.110.1.4

OTOP3 of 596 aas and 10 TMSs in a 5 + 5 + 2 TMS arrangement (Tu et al. 2018).

OTOP3 of Homo sapiens

 
1.A.110.1.5

Zinc-sensitive proton channel, OTOP1, of 586 aas and 10 TMSs in a 5 + 5 + 2 TMS arrangement (Tu et al. 2018). It inhibits P2Y purinoceptors and modulates calcium homeostasis and influx of calcium in response to extracellular ATP. It is essential for the formation of otoliths in the inner ear of developing larvae and for the perception of gravity and acceleration (Söllner et al. 2004; Hughes et al. 2004). The 3-d structure has been determined by cryoEM (Saotome et al. 2019) (see family description). Mutations in the Otopetrin 1 gene in mice and fish produce an unusual bilateral vestibular pathology that involves the absence of otoconia without hearing impairment (Hurle et al. 2011).

OTOP1 of Danio rerio (Zebrafish) (Brachydanio rerio)

 
1.A.110.1.6

OtoPetrin-like (Otpl6) of 581 aas and 12 TMSs.

Otpl6 of Caenorhabditis elegans

 
1.A.110.1.7

OToPetrin-like protein, isoform D, of 647 aas and 12 or 13 TMSs in a 5 +7 or 8 TMS arrangement.

OTOP, isoform D of Drosophila melanogaster (Fruit fly)

 
1.A.110.1.8

Putative otopetrin of 747 aas and 11 or 12 TMSs in a 1 + 3 + 7 or 8 TMS arrangement.

Putative Otop protein of Schistosoma mansoni (Blood fluke)

 
1.A.110.1.9

The OTOP3 protopn channel protein of 681 aas and 12 TMSs. The cryo-EM structure along with functional characteristics have been described (Chen et al. 2019). XtOTOP3 forms a homodimer with each subunit containing 12 transmembrane helices that can be divided into two structurally homologous halves; each half assembles as an alpha-helical barrel that could serve as a proton conduction pore.

OTOP3 of Xenopus tropicalis