Recreating a functional ancestral archosaur visual pigment.

The ancestors of the archosaurs, a major branch of the diapsid reptiles, originated more than 240 MYA near the dawn of the Triassic Period. We used maximum likelihood phylogenetic ancestral reconstruction methods and explored different models of evolution for inferring the amino acid sequence of a putative ancestral archosaur visual pigment. Three different types of maximum likelihood models were used: nucleotide-based, amino acid-based, and codon-based models. Where possible, within each type of model, likelihood ratio tests were used to determine which model best fit the data. Ancestral reconstructions of the ancestral archosaur node using the best-fitting models of each type were found to be in agreement, except for three amino acid residues at which one reconstruction differed from the other two. To determine if these ancestral pigments would be functionally active, the corresponding genes were chemically synthesized and then expressed in a mammalian cell line in tissue culture. The expressed artificial genes were all found to bind to 11-cis-retinal to yield stable photoactive pigments with lambda(max) values of about 508 nm, which is slightly redshifted relative to that of extant vertebrate pigments. The ancestral archosaur pigments also activated the retinal G protein transducin, as measured in a fluorescence assay. Our results show that ancestral genes from ancient organisms can be reconstructed de novo and tested for function using a combination of phylogenetic and biochemical methods.

[1]  M. Gouy,et al.  A nonhyperthermophilic common ancestor to extant life forms. , 1999, Science.

[2]  R. Crouch.  Photosensitive pigments formed with rat opsin. , 1976, Investigative ophthalmology.

[3]  Donoghue,et al.  Recreating ancestral proteins. , 2000, Trends in ecology & evolution.

[4]  G A Churchill,et al.  Methods for inferring phylogenies from nucleic acid sequence data by using maximum likelihood and linear invariants. , 1991, Molecular biology and evolution.

[5]  S. Yokoyama,et al.  Rhodopsin from the fish, Astyanax: role of tyrosine 261 in the red shift. , 1995, Investigative ophthalmology & visual science.

[6]  A. Yasui,et al.  Isolation and characterization of lamprey rhodopsin cDNA. , 1991, Biochemical and biophysical research communications.

[7]  D. Hyde,et al.  Cloning and characterization of six zebrafish photoreceptor opsin cDNAs and immunolocalization of their corresponding proteins , 1999, Visual Neuroscience.

[8]  M. Nei,et al.  Color vision of ancestral organisms of higher primates. , 1997, Molecular biology and evolution.

[9]  S. Kawamura,et al.  Functional characterization of visual and nonvisual pigments of American chameleon (Anolis carolinensis) , 1998, Vision Research.

[10]  S. Yokoyama,et al.  Molecular evolution of the rhodopsin gene of marine lamprey, Petromyzon marinus. , 1997, Gene.

[11]  N. Goldman,et al.  A codon-based model of nucleotide substitution for protein-coding DNA sequences. , 1994, Molecular biology and evolution.

[12]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[13]  J. Huelsenbeck.  Is the Felsenstein zone a fly trap? , 1997, Systematic biology.

[14]  T. Sakmar,et al.  The Amino Terminus of the Fourth Cytoplasmic Loop of Rhodopsin Modulates Rhodopsin-Transducin Interaction* , 2000, The Journal of Biological Chemistry.

[15]  D. Zack,et al.  Cloning and characterization of rod opsin cDNA from the Old World monkey, Macaca fascicularis. , 1995, Investigative ophthalmology & visual science.

[16]  J. Bowmaker,et al.  Visual pigments and oil droplets from six classes of photoreceptor in the retinas of birds , 1997, Vision Research.

[17]  K. Palczewski,et al.  Alligator rhodopsin: sequence and biochemical properties. , 1995, Experimental eye research.

[18]  Ziheng Yang.  Estimating the pattern of nucleotide substitution , 1994, Journal of Molecular Evolution.

[19]  J. Nathans,et al.  Isolation and nucleotide sequence of the gene encoding human rhodopsin. , 1984, Proceedings of the National Academy of Sciences of the United States of America.

[20]  D. Baylor,et al.  The photocurrent, noise and spectral sensitivity of rods of the monkey Macaca fascicularis. , 1984, The Journal of physiology.

[21]  Fumio Tokunaga,et al.  Isolation and sequence determination of the chicken rhodopsin gene , 1988, Vision Research.

[22]  W. Messier,et al.  Episodic adaptive evolution of primate lysozymes , 1997, Nature.

[23]  W. D. de Jong,et al.  Molecules remodel the mammalian tree. , 1998, Trends in ecology & evolution.

[24]  J M Gale,et al.  Localization and DNA sequence of a replication origin in the rhodopsin gene locus of Chinese hamster cells. , 1992, Journal of molecular biology.

[25]  D. Baylor,et al.  Spectral tuning in salamander visual pigments studied with dihydroretinal chromophores. , 1999, Biophysical journal.

[26]  David L. Swofford,et al.  Are Guinea Pigs Rodents? The Importance of Adequate Models in Molecular Phylogenetics , 1997, Journal of Mammalian Evolution.

[27]  J. Martinko,et al.  The deduced amino-acid sequence of opsin from rabbit rod photoreceptors. , 1995, Gene.

[28]  N. Blow,et al.  Molecular evolution of color vision of zebra finch. , 2000, Gene.

[29]  H. Khorana,et al.  Total synthesis of a gene for bovine rhodopsin. , 1986, Proceedings of the National Academy of Sciences of the United States of America.

[30]  T. Sakmar,et al.  Rhodopsin: structural basis of molecular physiology. , 2001, Physiological reviews.

[31]  L. Paulin,et al.  The introns of the canine rod opsin gene show higher sequence homology to the human than to the rodent introns. , 1997, DNA sequence : the journal of DNA sequencing and mapping.

[32]  K. Donner,et al.  Measurement of thermal contribution to photoreceptor sensitivity , 2000, Nature.

[33]  S. Pääbo,et al.  DNA damage and DNA sequence retrieval from ancient tissues. , 1996, Nucleic acids research.

[34]  C. Kuo,et al.  Molecular cloning of the common carp (Cyprinus carpio) rhodopsin cDNA. , 1994, Comparative biochemistry and physiology. Part B, Biochemistry & molecular biology.

[35]  L. Stryer,et al.  Cyclic GMP cascade of vision. , 1986, Annual review of neuroscience.

[36]  W. W. Jong.  Molecules remodel the mammalian tree , 1998 .

[37]  T. Sakmar,et al.  Synthetic gene technology: applications to ancestral gene reconstruction and structure-function studies of receptors. , 2002, Methods in enzymology.

[38]  T. Reuter,et al.  Rod pigment and rod noise in the European toad Bufo bufo , 1998, Vision Research.

[39]  N. Goldman,et al.  Comparison of models for nucleotide substitution used in maximum-likelihood phylogenetic estimation. , 1994, Molecular biology and evolution.

[40]  S. Archer,et al.  Absorbance spectra and molecular structure of the blue-sensitive rod visual pigment in the conger eel (Conger conger) , 1996, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[41]  J G Bishop,et al.  Rapid evolution in plant chitinases: molecular targets of selection in plant-pathogen coevolution. , 2000, Proceedings of the National Academy of Sciences of the United States of America.

[42]  M. Al-Ubaidi,et al.  Molecular cloning of a rod opsin cDNA from the skate retina. , 1997, Gene.

[43]  M. Hasegawa,et al.  Phylogenetic place of guinea pigs: no support of the rodent-polyphyly hypothesis from maximum-likelihood analyses of multiple protein sequences. , 1994, Molecular biology and evolution.

[44]  J. Kleinschmidt,et al.  Visual pigments in the sea lamprey, Petromyzon marinus , 1993, Visual Neuroscience.

[45]  J. Bowmaker,et al.  The rod and green cone opsins of two avian species, the budgerigar, Melopsittacus undulatus, and the mallard duck, Anas platyrhynchus. , 1997, Gene.

[46]  W. Baehr,et al.  Primary structure of frog rhodopsin , 1992, FEBS letters.

[47]  J. Nathans,et al.  Cloning and expression of goldfish opsin sequences. , 1993, Biochemistry.

[48]  Steven A. Benner,et al.  Reconstructing the evolutionary history of the artiodactyl ribonuclease superfamily , 1995, Nature.

[49]  J. Partridge,et al.  The molecular basis for the green-blue sensitivity shift in the rod visual pigments of the European eel , 1995, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[50]  K. Palczewski,et al.  Crystal Structure of Rhodopsin: A G‐Protein‐Coupled Receptor , 2002, Chembiochem : a European journal of chemical biology.

[51]  D. Hewett‐Emmett,et al.  Origins and antiquity of X-linked triallelic color vision systems in New World monkeys. , 1998, Proceedings of the National Academy of Sciences of the United States of America.

[52]  A. Sparks,et al.  Molecular resurrection of an extinct ancestral promoter for mouse L1. , 1994, Proceedings of the National Academy of Sciences of the United States of America.

[53]  Robert L. Carroll,et al.  Patterns and Processes of Vertebrate Evolution , 1997 .

[54]  T. Sakmar,et al.  The Effects of Amino Acid Replacements of Glycine 121 on Transmembrane Helix 3 of Rhodopsin* , 1996, The Journal of Biological Chemistry.

[55]  H. Ripps,et al.  Membrane current responses of skate photoreceptors , 1989, The Journal of general physiology.

[56]  J. Nathans,et al.  Isolation, sequence analysis, and intron-exon arrangement of the gene encoding bovine rhodopsin , 1983, Cell.

[57]  N. Blow,et al.  Genetic analyses of visual pigments of the pigeon (Columba livia). , 1999, Genetics.

[58]  S. Karnik,et al.  Angiotensin II-Forming Activity in a Reconstructed Ancestral Chymase , 1996, Science.

[59]  S. Muse,et al.  A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome. , 1994, Molecular biology and evolution.

[60]  M. Stoskopf,et al.  Cardiovascular evidence for an intermediate or higher metabolic rate in an ornithischian dinosaur. , 2000, Science.

[61]  Signore,et al.  Pulmonary function and metabolic physiology of theropod dinosaurs , 1999, Science.

[62]  Brian W. Matthews,et al.  Ancestral lysozymes reconstructed, neutrality tested, and thermostability linked to hydrocarbon packing , 1990, Nature.

[63]  D. Baylor,et al.  Spectral sensitivity of primate photoreceptors , 1988, Visual Neuroscience.

[64]  A. Dean,et al.  Protein engineering reveals ancient adaptive replacements in isocitrate dehydrogenase. , 1997, Proceedings of the National Academy of Sciences of the United States of America.

[65]  W. Baehr,et al.  Isolation and analysis of the mouse opsin gene , 1988, FEBS letters.

[66]  M. Nei,et al.  A new method of inference of ancestral nucleotide and amino acid sequences. , 1995, Genetics.

[67]  J. Lythgoe,et al.  Rod opsin cDNA sequence from the sand goby (Pomatoschistus minutus) compared with those of other vertebrates , 1992, Proceedings of the Royal Society of London. Series B: Biological Sciences.

[68]  K. Donner,et al.  Rhodopsins from three frog and toad species: sequences and functional comparisons. , 1998, Experimental eye research.

[69]  G VonStudnitz,et al.  Photochemistry of vision , 1972 .

[70]  J. Lythgoe,et al.  List of Vertebrate Visual Pigments , 1972 .

[71]  M. Saha,et al.  Early opsin expression in Xenopus embryos precedes photoreceptor differentiation. , 1993, Brain research. Molecular brain research.

[72]  William R. Taylor,et al.  The rapid generation of mutation data matrices from protein sequences , 1992, Comput. Appl. Biosci..