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Supporting Information Supporting Information Tong et al. 10.1073/pnas.0904571106 SI Results Arrestin-Beta. The arrestin-beta gene sequence of E. scolopes predicted a protein longer than that of L. pealei. Both visual and Characteristics of the E. scolopes Sequences Characterized in nonvisual arrestins have been identified in both invertebrates this Study and vertebrates, but thus far, only the visual system-specific R-Opsin. Sequences in the eye and light organ were identical to arrestin has been identified in cephalopods (7). The derived each other and to the sequence for E. scolopes visual rhodopsin amino acid sequence of the E. scolopes light-organ arrestin that had already been reported (1), a finding demonstrating that contains the 5 fingerprint regions that are characteristic of these the same isoform of this protein probably occurs in both the eyes proteins; in these regions, the overall identity is 89%. In addition, and light organs of this squid species. Comparisons of the 5 polar core residues, which are present in the bovine and L. sequence with that of rhodopsins of other cephalopod species pealei visual arrestins, occur in the same positions in the E. confirmed the presence of conserved amino acids, e.g., a lysine scolopes protein. in the seventh transmembrane region, presumably the site of retinal binding, a glycosylation site in the N terminus, a rho- Squid Retinal-Binding Protein. The EST database had a clone that encoded the C-terminal portion of the squid retinal-binding dopsin kinase phosphorylation site, and proline-rich repeats in protein (RALBP), with 82% identity in the region of alignment. the C terminus. Similar to that portion of the RALBP of another squid species (8), the E. scolopes RALBP-like fragment is composed of highly Gq Alpha. We report 2 genes, both with high blast similarity (97% hydrophilic and acidic amino acid residues. identical) to published Loligo pealei proteins of the Gq class (2). In E. scolopes, 1 gene is expressed in the eye; the other is G Alpha i. The same isoform of G alpha i was expressed in both expressed in its light organ. In maximum likelihood phylogenetic the eye and the light organ of E. scolopes. The E. scolopes gene analyses, both these genes fall within a clade of cephalopod Gq reported here is most closely related (87% identical) to an proteins. Most genes closely related to the E. scolopes genes are octopus gene isolated from a hemisected eye (GenBank known to be expressed in retinas by study of eye-specific cDNA #BAA93636). (2). These studies did not address expression outside the eye. Visual G Protein Beta. Unlike mammals, which have 3 distinct PLC-Beta. The E. scolopes gene is related (Ϸ89% identical) to G-beta subunit types, cephalopods have a single type (9). This PLC genes that have been isolated from eyes of other cephalo- protein is a subunit of the phosphatidylinositol-specific phos- pods (e.g., L. pealei and Watasenia scintillans). Hallmarks of PLC pholipase C-directed GTP-binding protein of cephalopod pho- genes include a pleckstrin homology domain, EF-hand homology toreceptor cells. The beta subunit of the G protein is highly domain, bipartite catalytic domain, C2 homology domain, and P conserved in vertebrates and invertebrates, including E. scolopes box and G box, which are required for functional interaction with (a 1% change in the amino acid sequence approximately every Gq alpha (3). These domains are present in the inferred E. 40 million years). scolopes protein sequence. In L. pealei, PLC is stimulated by activated squid Gq alpha and is expressed ‘‘uniquely’’ in photo- Phosphodiesterase. The phosphodiesterase (PDE) sequence of E. receptors (4). These features provide strong evidence that the L. scolopes shares identity with sequences in mammalian PDE pealei gene is involved in phototransduction and, by the argu- families. For example, of 22 amino acids conserved among all ment of conserved function, from a common ancestor; the E. mammalian PDE1–8 families, 21 also are conserved in the E. scolopes gene(s) are also phototransduction genes. scolopes PDE sequence. The single change is a conservative Tyr to Phe at amino acid 24 of the catalytic domain (amino acid 89). Transient Receptor Potential-Canonical. Transient Receptor Potential- A 266-amino acid region near the C terminus of PDE in the E. Canonical (TRPC). TRP-like proteins have been identified in L. scolopes sequence is homologous to the catalytic region of the forbesi and have 3 conserved domains: the ankyrin repeat mammalian PDE, which shares 72.2% amino acid sequence identity with the human sequence in the catalytic domain. Also domain (amino acid residues 47–147), the TRP2 domain (amino conserved in the E. scolopes PDE sequence are 2 divalent acid residues 155–217), and the ion transport domain (amino cation-binding motifs thought to be critical to the catalytic acid residues 396–608) (5). The derived amino acid sequence for activity of PDEs (10). TRP-like proteins from E. scolopes obtained thus far matches the last 33 amino acids in the ion transport domain with 88% Cyclic Nucleotide-Gated Channels. Although thus far only 58 amino identity. acids of the E. scolopes CNG channel have been identified, the CNG fragment groups strongly (aLRT ϭ .99) with other CNG- Rhodopsin Kinase. In L. pealei, the cephalopod species for which beta genes, compared with the outgroup CNG-alpha genes. this protein has been described, squid rhodopsin kinase (SQRK) CNG proteins are the ion channels responsible for hyperpo- has 3 distinct modular domains, a regulator of G protein larization of ciliary photoreceptors, such as the primary eyes signaling (RGS) domain, a serine-threonine kinase catalytic of vertebrates. CNG genes are expressed outside eyes as well. (STKc) domain, and a pleckstrin homology (PH) domain (6). To our knowledge, the ion channel involved in protostome The fragment of the E. scolopes protein has 96% identity to the ciliary photoreceptors is unknown. However, because CNGs entire region of the L. forbesi sequence to which it aligns. It are used in hyperpolarizing vertebrate ciliary receptors, the E. contains the C-terminal half of the STKc domain (98% identity) scolopes CNG would be a prime candidate for protostome and the entire PH domain (98% identity). ciliary phototransduction. Tong et al. www.pnas.org/cgi/content/short/0904571106 1of16 1. Strugnell J, Norman M, Jackson J, Drummond AJ, Cooper A (2005) Molecular phylogeny 7. Mayeenuddin LH, Mitchell J (2003) Squid visual arrestin: cDNA cloning and calcium- of coleoid cephalopods (Mollusca: Cephalopoda) using a multigene approach: The dependent phosphorylation by rhodopsin kinase (SQRK). J Neurochem 85:592–600. effect of data partitioning on resolving phylogenies in a Bayesian framework. Mol 8. Ozaki K, et al. (1994) Molecular characterization and functional expression of squid Phylogenet Evol 37:426–441. retinal-binding protein. A novel species of hydrophobic ligand-binding protein. J Biol 2. Go L, Mitchell J (2003) Palmitoylation is required for membrane association of activated Chem 269:3838–3845. but not inactive invertebrate Gqalpha. Comp Biochem Physiol B Biochem Mol Biol 9. Ryba NJ, Pottinger JD, Keen JN, Findlay JB (1991) Sequence of the beta-subunit of the 135:601–609. phosphatidylinositol-specific phospholipase C-directed GTP-binding protein from 3. Zuker CS (1996) The biology of vision of Drosophila. Proc Natl Acad Sci USA 93:571–576. squid (Loligo forbesi) photoreceptors. Biochem J 273:225–228. 4. Mayeenuddin LH, Bamsey C, Mitchell J (2001) Retinal phospholipase C from squid is a 10. Liscovitch M, Chalifa-Caspi V (1996) Enzymology of mammalian phospholipase D: In regulator of Gq alpha GTPase activity. J Neurochem 78:1350–1358. vitro studies. Chem Phys Lipids 80:37–44. 5. Monk PD, et al. (1996) Isolation, cloning, and characterisation of a trp homologue from squid (Loligo forbesi) photoreceptor membranes. J Neurochem 67:2227–2235. 6. Mayeenuddin LH, Mitchell J (2001) cDNA cloning and characterization of a novel squid rhodopsin kinase encoding multiple modular domains. Visual Neuroscience 18:907– 915. Tong et al. www.pnas.org/cgi/content/short/0904571106 2of16 A. Opsin 0.986000 UniRef50 Q17A90 Opsin 3 Culicidae Proteins 0.987000 UniRef50 P08100 Rhodopsin 385 Vertebrata Protein 0.735000UniRef50 Q1L4C8 Parietopsin 4 Euteleostomi Prote UniRef50 O42266 Parapinopsin 10 Vertebrata Prote Ciliary 0.776000 UniRef50 UPI0000F1FB40 pred simto multiple ti 0.994000 Opsins 0.923000 UniRef50 Q4RRX8 7 SCAF15001 wgs 2 Eut 0.988000UniRef50 Q868G2 Opsin 1 Branchiostoma belcheri P UniRef50 Q868G1 Opsin 1 Branchiostoma belcheri P UniRef50 UPI0000660618 Homolog of Gallus gallus Pe 1.000000 Go 0.802000 UniRef50 O14718 Visual pigmentlike receptor perops UniRef50 Q868G4 Opsin 1 Branchiostoma belcheri P 0.914000 Opsins UniRef50 O15974 Rhodopsin G0coupled 1 Mizuhopecten UniRef50 Q0ZPT9 Opsin 2 Strongylocentrotus Prote UniRef50 UPI0000F20D29 PREDICTED hypothetical prot 0.384000 0.799000 0.999000 UniRef50 Q4T685 Chromosome undetermined SCAF8878 w 1.000000UniRef50 Q6U736 Opsin5 26 Tetrapoda Proteins UniRef50 Q4RF26 Chromosome 14 SCAF15120 wgs 12 E UniRef50 Q25158 Compound eye opsin BCRH2 3 Heter 0.811000 0.998000UniRef50 P35356 Rhodopsin 13 Eumalacostraca Prot 0.926000 UniRef50 P08099 Opsin Rh2 1339 root Proteins 0.997000 1.000000UniRef50 Q9VTU7 CG5638PA 1 Drosophila melanogast UniRef50 Q7QJJ6 ENSANGP00000010731 2 Culicidae P 0.891000 UniRef50 P04950 Opsin Rh3 44 Neoptera Proteins 0.993000 UniRef50 Q26495 Opsin2 22 Neoptera Proteins 0.991000 Rhabdomeric UniRef50 P91657 Opsin Rh5
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