Skip to main content

Molecular Evolutionary Analysis of Vertebrate Transducins: A Role for Amino Acid Variation in Photoreceptor Deactivation

Abstract

Transducin is a heterotrimeric G protein that plays a critical role in phototransduction in the rod and cone photoreceptor cells of the vertebrate retina. Rods, highly sensitive cells that recover from photoactivation slowly, underlie dim-light vision, whereas cones are less sensitive, recover more quickly, and underlie bright-light vision. Transducin deactivation is a critical step in photoreceptor recovery and may underlie the functional distinction between rods and cones. Rods and cones possess distinct transducin α subunits, yet they share a common deactivation mechanism, the GTPase activating protein (GAP) complex. Here, we used codon models to examine patterns of sequence evolution in rod (GNAT1) and cone (GNAT2) α subunits. Our results indicate that purifying selection is the dominant force shaping GNAT1 and GNAT2 evolution, but that GNAT2 has additionally been subject to positive selection operating at multiple phylogenetic scales; phylogeny-wide analysis identified several sites in the GNAT2 helical domain as having substantially elevated dN/dS estimates, and branch-site analysis identified several nearby sites as targets of strong positive selection during early vertebrate history. Examination of aligned GNAT and GAP complex crystal structures revealed steric clashes between several positively selected sites and the deactivating GAP complex. This suggests that GNAT2 sequence variation could play an important role in adaptive evolution of the vertebrate visual system via effects on photoreceptor deactivation kinetics and provides an alternative perspective to previous work that focused instead on the effect of GAP complex concentration. Our findings thus further the understanding of the molecular biology, physiology, and evolution of vertebrate visual systems.

This is a preview of subscription content, access via your institution.

Fig. 1
Fig. 2
Fig. 3
Fig. 4
Fig. 5

References

  • Abascal F, Zardoya R, Posada D (2005) Prottest: selection of best-fit models of protein evolution. Bioinformatics 21:2104–2105

    CAS  PubMed  Article  Google Scholar 

  • Alfaro ME, Santini F, Brock C, Alamillo H, Dornburg A, Rabosky DL, Carnevale G, Harmon LJ (2009) Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates. Proc Natl Acad Sci 106:13410–13414

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Anisimova M, Liberles DA (2012) Detecting and understanding natural selection. In: Cannarozzi GM, Schneider A (eds) Codon evolution: mechanisms and models. Oxford University Press, Oxford, pp 73–96

    Chapter  Google Scholar 

  • Anisimova M, Bielawski JP, Yang Z (2001) Accuracy and power of the likelihood ratio test in detecting adaptive molecular evolution. Mol Biol Evol 18:1585–1592

    CAS  PubMed  Article  Google Scholar 

  • Bielawski JP, Yang ZH (2004) A maximum likelihood method for detecting functional divergence at individual codon sites, with application to gene family evolution. J Mol Evol 59:121–132

    CAS  PubMed  Article  Google Scholar 

  • Burns ME, Pugh EN (2009) Rgs9 concentration matters in rod phototransduction. Biophys J 97:1538–1547

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Burns ME, Pugh EN (2010) Lessons from photoreceptors: turning off g-protein signaling in living cells. Physiology 25:72–84

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Carretero-Paulet L, Albert VA, Fares MA (2013) Molecular evolutionary mechanisms driving functional diversification of the hsp90a family of heat shock proteins in eukaryotes. Mol Biol Evol 30:2035–2043

    CAS  PubMed  Article  Google Scholar 

  • Cheever ML, Snyder JT, Gershburg S, Siderovski DP, Harden TK, Sondek J (2008) Crystal structure of the multifunctional g beta 5-rgs9 complex. Nat Struct Mol Biol 15:155–162

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Chen CK, Woodruff ML, Chen FS, Shim H, Cilluffo MC, Fain GL (2010) Replacing the rod with the cone transducin alpha subunit decreases sensitivity and accelerates response decay. J Physiol (London) 588:3231–3241

    CAS  Article  Google Scholar 

  • Cowan CW, Fariss RN, Sokal I, Palczewski K, Wensel TG (1998) High expression levels in cones of rgs9, the predominant gtpase accelerating protein of rods. Proc Natl Acad Sci USA 95:5351–5356

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Delport W, Poon AFY, Frost SDW, Pond SLK (2010) Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 26:2455–2457

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Ebrey T, Koutalos Y (2001) Vertebrate photoreceptors. Prog Retin Eye Res 20:49–94

    CAS  PubMed  Article  Google Scholar 

  • Fain GL, Hardie R, Laughlin SB (2010) Phototransduction and the evolution of photoreceptors. Curr Biol 20:R114–R124

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Fletcher W, Yang Z (2010) The effect of insertions, deletions, and alignment errors on the branch-site test of positive selection. Mol Biol Evol 27:2257–2267

    CAS  PubMed  Article  Google Scholar 

  • Fritsches KA, Brill RW, Warrant EJ (2005) Warm eyes provide superior vision in swordfishes. Curr Biol 15:55–58

    CAS  PubMed  Article  Google Scholar 

  • Gharib WH, Robinson-Rechavi M (2013) The branch-site test of positive selection is surprisingly robust but lacks power under synonymous substitution saturation and variation in gc. Mol Biol Evol 30:1675–1686

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Gojobori T (1983) Codon substitution in evolution and the “saturation” of synonymous changes. Genetics 105:1011–1027

    PubMed Central  CAS  PubMed  Google Scholar 

  • Goldman N, Whelan S (2000) Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics. Mol Biol Evol 17:975–978

    CAS  PubMed  Article  Google Scholar 

  • Goldman N, Yang ZH (1994) Codon-based model of nucleotide substitution for protein-coding DNA-sequences. Mol Biol Evol 11:725–736

    CAS  PubMed  Google Scholar 

  • Gopalakrishna KN, Boyd KK, Artemyev NO (2012) Comparative analysis of cone and rod transducins using chimeric galpha subunits. Biochemistry 51:1617–1624

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • He W, Cowan CW, Wensel TG (1998) Rgs9, a gtpase accelerator for phototransduction. Neuron 20:95–102

    PubMed  Article  Google Scholar 

  • Hu G, Wensel TG (2002) R9ap, a membrane anchor for the photoreceptor gtpase accelerating protein, rgs9-1. Proc Natl Acad Sci USA 99:9755–9760

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Huelsenbeck JP, Rannala B (1997) Phylogenetic methods come of age: testing hypotheses in an evolutionary context. Science 276:227–232

    CAS  PubMed  Article  Google Scholar 

  • Hughes AL (2007) Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level. Heredity (Edinb) 99:364–373

    CAS  Article  Google Scholar 

  • Jones DT, Taylor WR, Thornton JM (1992) The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci 8:275–282

    CAS  PubMed  Google Scholar 

  • Jordan G, Goldman N (2012) The effects of alignment error and alignment filtering on the sitewise detection of positive selection. Mol Biol Evol 29:1125–1139

    CAS  PubMed  Article  Google Scholar 

  • Kosakovsky Pond SL, Murrell B, Fourment M, Frost SDW, Delport W, Scheffler K (2011) A random effects branch-site model for detecting episodic diversifying selection. Mol Biol Evol 28:3033–3043

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Lagman D, Sundstrom G, Ocampo Daza D, Abalo XM, Larhammar D (2012) Expansion of transducin subunit gene families in early vertebrate tetraploidizations. Genomics 100:203–211

    CAS  PubMed  Article  Google Scholar 

  • Lamb TD (1984) Effects of temperature changes on toad rod photocurrents. J Physiol 346:557–578

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Lambright DG, Noel JP, Hamm HE, Sigler PB (1994) Structural determinants for activation of the alpha-subunit of a heterotrimeric g-protein. Nature 369:621–628

    CAS  PubMed  Article  Google Scholar 

  • Laskowski RA, Macarthur MW, Moss DS, Thornton JM (1993) Procheck—a program to check the stereochemical quality of protein structures. J Appl Crystallogr 26:283–291

    CAS  Article  Google Scholar 

  • Leipe DD, Wolf YI, Koonin EV, Aravind L (2002) Classification and evolution of p-loop gtpases and related atpases. J Mol Biol 317:41–72

    CAS  PubMed  Article  Google Scholar 

  • Lerea CL, Somers DE, Hurley JB, Klock IB, Buntmilam AH (1986) Identification of specific transducin alpha-subunits in retinal rod and cone photoreceptors. Science 234:77–80

    CAS  PubMed  Article  Google Scholar 

  • Li W-H, Wu C-I, Luo C-C (1985) A new method for estimating synonymous and nonsynonymous rates of nucleotide substitution considering the relative likelihood of nucleotide and codon changes. Mol Biol Evol 2:150–174

    PubMed  Google Scholar 

  • Lochrie MA, Hurley JB, Simon MI (1985a) Sequence of the alpha subunit of photoreceptor g protein: homologies between transducin, ras, and elongation factors. Science 228:96–99

    CAS  PubMed  Article  Google Scholar 

  • Lochrie MA, Hurley JB, Simon MI (1985b) Sequence of the alpha-subunit of photoreceptor-g protein—homologies between transducin, ras, and elongation-factors. Science 228:96–99

    CAS  PubMed  Article  Google Scholar 

  • Long JA, Gordon MS (2004) The greatest step in vertebrate history: a paleobiological review of the fish-tetrapod transition. Physiol Biochem Zool 77:700–719

    PubMed  Article  Google Scholar 

  • Loytynoja A, Goldman N (2005) An algorithm for progressive multiple alignment of sequences with insertions. Proc Natl Acad Sci USA 102:10557–10562

    PubMed Central  PubMed  Article  Google Scholar 

  • Loytynoja A, Vilella AJ, Goldman N (2012) Accurate extension of multiple sequence alignments using a phylogeny-aware graph algorithm. Bioinformatics 28:1684–1691

    PubMed Central  PubMed  Article  Google Scholar 

  • Lythgoe JN (1979) The ecology of vision. Clarendon Press, Oxford

    Google Scholar 

  • Lyubarsky A, Chen CK, Naarendorp F, Zhang X, Wensel T, Simon M, Pugh E (2001) Rgs9-1 is required for normal inactivation of mouse cone phototransduction. Mol Vis 7:71–78

    CAS  PubMed  Google Scholar 

  • Maddison DR, Schulz K-S (eds) (2007) The tree of life web project. http://tolweb.org

  • Makino ER, Handy JW, Li TS, Arshavsky VY (1999) The gtpase activating factor for transducin in rod photoreceptors is the complex between rgs9 and type 5 g protein beta subunit. Proc Natl Acad Sci USA 96:1947–1952

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Mao W, Miyagishima KJ, Yao Y, Soreghan B, Sampath AP, Chen J (2013) Functional comparison of rod and cone galphat on the regulation of light sensitivity. J Biol Chem 288:5257–5267

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Maynard Smith J (1994) Estimating selection by comparing synonymous and substitutional changes. J Mol Evol 39:123–128

    Google Scholar 

  • Miyata T, Yasunaga T (1980) Molecular evolution of mRNA: a method for estimating evolutionary rates of synonymous and amino acid substitutions from homologous nucleotide sequences and its application. J Mol Evol 16:23–36

    CAS  PubMed  Article  Google Scholar 

  • Muradov H, Kerov V, Boyd KK, Artemyev NO (2008) Unique transducins expressed in long and short photoreceptors of lamprey petromyzon marinus. Vis Res 48:2302–2308

    PubMed Central  PubMed  Article  Google Scholar 

  • Muse SV, Gaut BS (1994) A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. Mol Biol Evol 11:715–724

    CAS  PubMed  Google Scholar 

  • Nagai H, Terai Y, Sugawara T, Imai H, Nishihara H, Hori M, Okada N (2011) Reverse evolution in rh1 for adaptation of cichlids to water depth in Lake Tanganyika. Mol Biol Evol 28:1769–1776

    CAS  PubMed  Article  Google Scholar 

  • Nei M, Gojobori T (1986) Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 3:418–426

    CAS  PubMed  Google Scholar 

  • Noel JP, Hamm HE, Sigler PB (1993) The 2.2-angstrom crystal-structure of transducin-alpha complexed with gtp-gamma-s. Nature 366:654–663

    CAS  PubMed  Article  Google Scholar 

  • Nordstrom K, Larsson TA, Larhammar D (2004) Extensive duplications of phototransduction genes in early vertebrate evolution correlate with block (chromosome) duplications. Genomics 83:852–872

    CAS  PubMed  Article  Google Scholar 

  • Nozawa M, Suzuki Y, Nei M (2009) Reliabilities of identifying positive selection by the branch-site and the site-prediction methods. Proc Natl Acad Sci USA 106:6700–6705

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Oldham WM, Hamm HE (2008) Heterotrimeric g protein activation by g-protein-coupled receptors. Nat Rev Mol Cell Bio 9:60–71

    CAS  Article  Google Scholar 

  • Penn O, Privman E, Ashkenazy H, Landan G, Graur D, Pupko T (2010a) Guidance: a web server for assessing alignment confidence scores. Nucleic Acids Res 38:W23–W28

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Penn O, Privman E, Landan G, Graur D, Pupko T (2010b) An alignment confidence score capturing robustness to guide tree uncertainty. Mol Biol Evol 27:1759–1767

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Perler F, Efstratiadis A, Lomedico P, Gilbert W, Kolodner R, Dodgson J (1980) The evolution of genes: the chicken preproinsulin gene. Cell 20:555–566

    CAS  PubMed  Article  Google Scholar 

  • Sali A, Blundell TL (1993) Comparative protein modeling by satisfaction of spatial restraints. J Mol Biol 234:779–815

    CAS  PubMed  Article  Google Scholar 

  • Shen MY, Sali A (2006) Statistical potential for assessment and prediction of protein structures. Protein Sci 15:2507–2524

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Skiba NP, Yang CS, Huang T, Bae H, Hamm HE (1999) The alpha-helical domain of galphat determines specific interaction with regulator of g protein signaling 9. J Biol Chem 274:8770–8778

    CAS  PubMed  Article  Google Scholar 

  • Skiba NP, Martemyanov KA, Elfenbein A, Hopp JA, Bohm A, Simonds WF, Arshavsky VY (2001) Rgs9-g beta 5 substrate selectivity in photoreceptors. Opposing effects of constituent domains yield high affinity of rgs interaction with the g protein-effector complex. J Biol Chem 276:37365–37372

    CAS  PubMed  Article  Google Scholar 

  • Slep KC, Kercher MA, He W, Cowan CW, Wensel TG, Sigler PB (2001) Structural determinants for regulation of phosphodiesterase by a g protein at 2.0 angstrom. Nature 409:1071–1077

    CAS  PubMed  Article  Google Scholar 

  • Sondek J, Lambright DG, Noel JP, Hamm HE, Sigler PB (1994) Gtpase mechanism of g proteins from the 1.7-angstrom crystal-structure of transducin alpha-center-dot-gdp-center-dot-alf4(−). Nature 372:276–279

    CAS  PubMed  Article  Google Scholar 

  • Soundararajan M, Willard FS, Kimple AJ, Turnbull AP, Ball LJ, Schoch GA, Gileadi C, Fedorov OY, Dowler EF, Higman VA, Hutsell SQ, Sundstrom M, Doyle DA, Siderovski DP (2008) Structural diversity in the rgs domain and its interaction with heterotrimeric g protein alpha-subunits. Proc Natl Acad Sci USA 105:6457–6462

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Sprang SR (1997) G protein mechanisms: insights from structural analysis. Annu Rev Biochem 66:639–678

    CAS  PubMed  Article  Google Scholar 

  • Studer RA, Penel S, Duret L, Robinson-Rechavi M (2008) Pervasive positive selection on duplicated and nonduplicated vertebrate protein coding genes. Genome Res 18:1393–1402

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Swanson WJ, Nielsen R, Yang QF (2003) Pervasive adaptive evolution in mammalian fertilization proteins. Mol Biol Evol 20:18–20

    CAS  PubMed  Article  Google Scholar 

  • Tamura K, Dudley J, Nei M, Kumar S (2007) Mega4: molecular evolutionary genetics analysis (mega) software version 4.0. Mol Biol Evol 24:1596–1599

    CAS  PubMed  Article  Google Scholar 

  • Thompson JD, Higgins DG, Gibson TJ (1994) Clustal-w—improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22:4673–4680

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Trezise AE, Collin SP (2005) Opsins: evolution in waiting. Curr Biol 15:R794–R796

    CAS  PubMed  Article  Google Scholar 

  • Walls GL (1942) The vertebrate eye and its adaptive radiation. Oxford, England: Cranbrook Institute of Science, p 785

  • Weadick CJ, Chang BS (2009) Molecular evolution of the œ ≤ œ ≥ lens crystallin superfamily: evidence for a retained ancestral function in œ ≥ n crystallins? Mol Biol Evol 26:1127–1142

    CAS  PubMed  Article  Google Scholar 

  • Weadick CJ, Chang BSW (2012) An improved likelihood ratio test for detecting site-specific functional divergence among clades of protein-coding genes. Mol Biol Evol 29:1297–1300

    CAS  PubMed  Article  Google Scholar 

  • Wiederstein M, Sippl MJ (2007) Prosa-web: interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Res 35:W407–W410

    PubMed Central  PubMed  Article  Google Scholar 

  • Williams PD, Pollock DD, Blackburne BP, Goldstein RA (2006) Assessing the accuracy of ancestral protein reconstruction methods. PLoS Comput Biol 2:e69

    PubMed Central  PubMed  Article  Google Scholar 

  • Wittinghofer A (1994) The structure of transducin-g(alpha-t)—more to view than just ras. Cell 76:201–204

    CAS  PubMed  Article  Google Scholar 

  • Yang ZH (1994) Maximum-likelihood phylogenetic estimation from DNA-sequences with variable rates over sites—approximate methods. J Mol Evol 39:306–314

    CAS  PubMed  Article  Google Scholar 

  • Yang ZH (2007) Paml 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol 24:1586–1591

    CAS  PubMed  Article  Google Scholar 

  • Yang Z, dos Reis M (2011) Statistical properties of the branch-site test of positive selection. Mol Biol Evol 28:1217–1228

    CAS  PubMed  Article  Google Scholar 

  • Yang Z, Nielsen R (2000) Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models. Mol Biol Evol 17:32–43

    CAS  PubMed  Article  Google Scholar 

  • Yang ZH, Nielsen R (2002) Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages. Mol Biol Evol 19:908–917

    CAS  PubMed  Article  Google Scholar 

  • Yang ZH, Kumar S, Nei M (1995) A new method of inference of ancestral nucleotide and amino-acid-sequences. Genetics 141:1641–1650

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yang ZH, Nielsen R, Goldman N, Pedersen AMK (2000) Codon-substitution models for heterogeneous selection pressure at amino acid sites. Genetics 155:431–449

    PubMed Central  CAS  PubMed  Google Scholar 

  • Yang ZH, Wong WSW, Nielsen R (2005) Bayes empirical bayes inference of amino acid sites under positive selection. Mol Biol Evol 22:1107–1118

    CAS  PubMed  Article  Google Scholar 

  • Yang Z, Nielsen R, Goldman N (2009) In defense of statistical methods for detecting positive selection. Proc Natl Acad Sci USA 106:E95; author reply E96

  • Yau KW, Hardie RC (2009) Phototransduction motifs and variations. Cell 139:246–264

    PubMed Central  CAS  PubMed  Article  Google Scholar 

  • Yokoyama S, Starmer WT (1992) Phylogeny and evolutionary rates of g protein alpha subunit genes. J Mol Evol 35:230–238

    CAS  PubMed  Article  Google Scholar 

  • Yoshida I, Sugiura W, Shibata J, Ren FR, Yang ZH, Tanaka H (2011) Change of positive selection pressure on hiv-1 envelope gene inferred by early and recent samples. PLoS ONE 6(4):e18630

    Google Scholar 

  • Zhai W, Nielsen R, Goldman N, Yang Z (2012) Looking for Darwin in genomic sequences—validity and success of statistical methods. Mol Biol Evol 29:2889–2893

    CAS  PubMed  Article  Google Scholar 

  • Zhang X, Wensel TG, Kraft TW (2003) Gtpase regulators and photoresponses in cones of the eastern chipmunk. J Neurosci 23:1287–1297

    CAS  PubMed  Google Scholar 

  • Zhang JZ, Nielsen R, Yang ZH (2005) Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level. Mol Biol Evol 22:2472–2479

    CAS  PubMed  Article  Google Scholar 

Download references

Acknowledgments

This work was supported by a Natural Sciences and Engineering Research Council (NSERC) Discovery grant (B.S.W.C.), an NSERC graduate fellowship (C.J.W.), the Vision Science Research Fellowship Program (C.J.W.), and an NSERC Undergraduate Student Research Award (G.L.).

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Belinda S. W. Chang.

Additional information

Y. Gloria Lin and Cameron J. Weadick have contributed equally to this work.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary material 1 (PDF 400 kb)

Rights and permissions

Reprints and Permissions

About this article

Cite this article

G. Lin, Y., Weadick, C.J., Santini, F. et al. Molecular Evolutionary Analysis of Vertebrate Transducins: A Role for Amino Acid Variation in Photoreceptor Deactivation. J Mol Evol 77, 231–245 (2013). https://doi.org/10.1007/s00239-013-9589-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00239-013-9589-5

Keyword

  • G proteins
  • Vision
  • Rhodopsin
  • dN/dS
  • Positive selection
  • Maximum likelihood
  • Codon models