Shozo Yokoyama

Summary

Affiliation: Emory University
Country: USA

Publications

  1. pmc Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA 30322, USA Electronic address
    Gene 534:93-9. 2014
  2. pmc Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes
    Christine E Schnitzler
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Biol 10:107. 2012
  3. pmc Synthetic biology of phenotypic adaptation in vertebrates: the next frontier
    Shozo Yokoyama
    Department of Biology, Emory University, USA
    Mol Biol Evol 30:1495-9. 2013
  4. ncbi request reprint The molecular basis of adaptive evolution of squirrelfish rhodopsins
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia, USA
    Mol Biol Evol 21:2071-8. 2004
  5. ncbi request reprint Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, USA
    Mol Biol Evol 22:968-75. 2005
  6. ncbi request reprint Molecules, biodiversity, and adaptive evolution
    S Yokoyama
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    J Hered 96:169-70. 2005
  7. pmc Elephants and human color-blind deuteranopes have identical sets of visual pigments
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Genetics 170:335-44. 2005
  8. pmc A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei)
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    Gene 396:196-202. 2007
  9. doi request reprint Evolution of dim-light and color vision pigments
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Annu Rev Genomics Hum Genet 9:259-82. 2008
  10. pmc Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Genetics 179:2037-43. 2008

Research Grants

  1. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2009
  2. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2007
  3. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2006
  4. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2002
  5. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2002
  6. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2001
  7. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2000
  8. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 1999
  9. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2010

Collaborators

Detail Information

Publications45

  1. pmc Extraordinarily low evolutionary rates of short wavelength-sensitive opsin pseudogenes
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA 30322, USA Electronic address
    Gene 534:93-9. 2014
    ..4 × 10(-9)/site/year) of the pseudogenes of these aquatic species as well as some prosimian and bat species are much smaller than the previous estimates for the globin and immunoglobulin pseudogenes...
  2. pmc Genomic organization, evolution, and expression of photoprotein and opsin genes in Mnemiopsis leidyi: a new view of ctenophore photocytes
    Christine E Schnitzler
    National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA
    BMC Biol 10:107. 2012
    ..We combined our genomic survey with gene trees, developmental expression patterns, and functional protein assays of photoproteins and opsins to provide a comprehensive view of light production and light reception in Mnemiopsis...
  3. pmc Synthetic biology of phenotypic adaptation in vertebrates: the next frontier
    Shozo Yokoyama
    Department of Biology, Emory University, USA
    Mol Biol Evol 30:1495-9. 2013
    ....
  4. ncbi request reprint The molecular basis of adaptive evolution of squirrelfish rhodopsins
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia, USA
    Mol Biol Evol 21:2071-8. 2004
    ....
  5. ncbi request reprint Statistical and molecular analyses of evolutionary significance of red-green color vision and color blindness in vertebrates
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, USA
    Mol Biol Evol 22:968-75. 2005
    ....
  6. ncbi request reprint Molecules, biodiversity, and adaptive evolution
    S Yokoyama
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    J Hered 96:169-70. 2005
  7. pmc Elephants and human color-blind deuteranopes have identical sets of visual pigments
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Genetics 170:335-44. 2005
    ..During the day, therefore, elephants seem to have the dichromatic color vision of deuteranopes. During the night, however, they are likely to use RH1 and SWS1 pigments and detect light at 420-490 nm...
  8. pmc A novel spectral tuning in the short wavelength-sensitive (SWS1 and SWS2) pigments of bluefin killifish (Lucania goodei)
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    Gene 396:196-202. 2007
    ..Moreover, the larger the individual effects of amino acid changes on the lambda(max)-shift are, the larger the synergistic effects tend to be generated, revealing a novel mechanism of spectral tuning of visual pigments...
  9. doi request reprint Evolution of dim-light and color vision pigments
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Annu Rev Genomics Hum Genet 9:259-82. 2008
    ....
  10. pmc Molecular basis of spectral tuning in the red- and green-sensitive (M/LWS) pigments in vertebrates
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Genetics 179:2037-43. 2008
    ..Our findings demonstrate that the evolutionary method should be used in elucidating the mechanisms of spectral tuning of four other pigment groups and, for that matter, functional differentiations of any other proteins...
  11. pmc Evolutionary dynamics of rhodopsin type 2 opsins in vertebrates
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, USA
    Mol Biol Evol 27:133-41. 2010
    ..25 x 10(-9)/site/year, which increased to approximately 1 x 10(-9) to 3 x 10(-9)/site/year in euteleost lineages and to approximately 0.3 x 10(-9) to 0.5 x 10(-9)/site/year in coelacanth and tetrapods...
  12. pmc Modulation of the absorption maximum of rhodopsin by amino acids in the C-terminus
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA, USA
    Photochem Photobiol 83:236-41. 2007
    ..We anticipate our analyses to be a starting point for viewing the spectral tuning of visual pigments as interactions between the retinal and key amino acids that are distributed throughout the entire pigment...
  13. pmc Elucidation of phenotypic adaptations: Molecular analyses of dim-light vision proteins in vertebrates
    Shozo Yokoyama
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Proc Natl Acad Sci U S A 105:13480-5. 2008
    ....
  14. pmc Tertiary structure and spectral tuning of UV and violet pigments in vertebrates
    Shozo Yokoyama
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    Gene 365:95-103. 2006
    ..Both mutagenesis analyses of E113Q and quantum chemical calculations strongly suggest that unprotonated Schiff base-linked chromophore is responsible for detecting UV light...
  15. pmc Molecular analysis of the evolutionary significance of ultraviolet vision in vertebrates
    Yongsheng Shi
    Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Proc Natl Acad Sci U S A 100:8308-13. 2003
    ..The use of UV vision is associated strongly with UV-dependent behaviors of organisms. When UV light is not available or is unimportant to organisms, the SWS1 gene can become nonfunctional, as exemplified by coelacanth and dolphin...
  16. pmc Evolutionary replacement of UV vision by violet vision in fish
    Takashi Tada
    Department of Biology, Emory University, Atlanta, GA 30322, USA
    Proc Natl Acad Sci U S A 106:17457-62. 2009
    ....
  17. pmc Spectral tuning in visual pigments: an ONIOM(QM:MM) study on bovine rhodopsin and its mutants
    Ahmet Altun
    Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
    J Phys Chem B 112:6814-27. 2008
    ..The protonation state and conformation of mutated residues affect electronic spectrum significantly. The present QM/MM calculations estimate not only the experimental excitation energies but also the source of spectral shifts in mutants...
  18. pmc H-bond network around retinal regulates the evolution of ultraviolet and violet vision
    Ahmet Altun
    Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, United States
    ACS Chem Biol 6:775-80. 2011
    ..These results establish for the first time the chemical basis of ultraviolet and violet vision in vertebrates...
  19. pmc Color tuning in short wavelength-sensitive human and mouse visual pigments: ab initio quantum mechanics/molecular mechanics studies
    Ahmet Altun
    Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
    J Phys Chem A 113:11685-92. 2009
    ..There is no charge transfer between the SB and beta-ionone terminals of 11-cis-retinal in the ground and first excited states...
  20. pmc Quantum mechanical/molecular mechanical structure, enantioselectivity, and spectroscopy of hydroxyretinals and insights into the evolution of color vision in small white butterflies
    Sivakumar Sekharan
    Department of Chemistry and Cherry L Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
    J Phys Chem B 115:15380-8. 2011
    ....
  21. pmc Mechanisms of spectral tuning in the RH2 pigments of Tokay gecko and American chameleon
    Naomi Takenaka
    Department of Biology, Rollins Research Center, Emory University, 1510 Clifton Road, Atlanta, GA 30322, USA
    Gene 399:26-32. 2007
    ....
  22. ncbi request reprint The spectral tuning in the short wavelength-sensitive type 2 pigments
    Shozo Yokoyama
    Department of Biology, Biological Research Laboratories, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 306:91-8. 2003
    ....
  23. pmc Mechanism of spectral tuning going from retinal in vacuo to bovine rhodopsin and its mutants: multireference ab initio quantum mechanics/molecular mechanics studies
    Ahmet Altun
    Cherry L Emerson Center for Scientific Computation, Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
    J Phys Chem B 112:16883-90. 2008
    ....
  24. pmc Genetic basis of spectral tuning in the violet-sensitive visual pigment of African clawed frog, Xenopus laevis
    Yusuke Takahashi
    Department of Biology, Emory University, Atlanta, Georgia 30322, USA
    Genetics 171:1153-60. 2005
    ....
  25. pmc Quantum mechanical/molecular mechanical studies on spectral tuning mechanisms of visual pigments and other photoactive proteins
    Ahmet Altun
    Cherry L Emerson Center for Scientific Computation and Department of Chemistry, Emory University, Atlanta, GA, USA
    Photochem Photobiol 84:845-54. 2008
    ..We hereby review recent QM/MM results on the phototransduction of bovine rhodopsin, bacteriorhodopsin, sensory rhodopsin II, nonretinal photoactive yellow protein and their mutants...
  26. ncbi request reprint Molecular evolution of color vision in vertebrates
    Shozo Yokoyama
    Department of Biology, Biological Research Laboratories, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 300:69-78. 2002
    ..These hypotheses can then be tested using the in vitro assay. This approach has been a powerful tool in elucidating not only the molecular bases of color vision, but the processes of adaptive evolution at the molecular level...
  27. ncbi request reprint Adaptive evolution of the African and Indonesian coelacanths to deep-sea environments
    S Yokoyama
    Biological Research Laboratories, Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 261:35-42. 2000
    ..Statistical analyses show that the adaptation of the coelacanths toward the deep-sea started as early as 200 million years ago...
  28. pmc Molecular convergence of infrared vision in snakes
    Shozo Yokoyama
    Department of Biology, Emory University
    Mol Biol Evol 28:45-8. 2011
    ..Protein modeling shows that the three amino acid changes alter the structures of the central region of their ankyrin repeats...
  29. ncbi request reprint Color vision of the coelacanth (Latimeria chalumnae) and adaptive evolution of rhodopsin (RH1) and rhodopsin-like (RH2) pigments
    S Yokoyama
    Department of Biology, Syracuse University, NY 13244 1220, USA
    J Hered 91:215-20. 2000
    ..Among these, D83N, E1220, M207L, and A292S are associated strongly with the adaptive blue shifts in the lambda max values of RH1 and RH2 pigments in vertebrates...
  30. pmc Adaptive evolution of color vision of the Comoran coelacanth (Latimeria chalumnae)
    S Yokoyama
    Department of Biology, Syracuse University, Syracuse, NY 13244, USA
    Proc Natl Acad Sci U S A 96:6279-84. 1999
    ..The lambdamax values are shifted about 20 nm toward blue compared with those of the corresponding orthologous pigments. Mutagenesis experiments show that each of these coadapted changes is fully explained by two amino acid replacements...
  31. ncbi request reprint Regeneration of ultraviolet pigments of vertebrates
    S Yokoyama
    Department of Biology, Syracuse University, NY 13244, USA
    FEBS Lett 423:155-8. 1998
    ..The construction and functional assays of the ultraviolet or near-ultraviolet pigments from a wide range of vertebrate species will allow us to study the molecular bases of ultraviolet vision for the first time...
  32. ncbi request reprint Cloning and characterization of the pineal gland-specific opsin gene of marine lamprey (Petromyzon marinus)
    S Yokoyama
    Syracuse University, Department of Biology, NY 13244, USA
    Gene 202:89-93. 1997
    ..These changes in P(Pm) might have been important in achieving marine lamprey-specific interaction between P(Pm) and other proteins in the pineal gland...
  33. ncbi request reprint Molecular genetic basis of adaptive selection: examples from color vision in vertebrates
    S Yokoyama
    Department of Biology, Syracuse University, New York, USA
    Annu Rev Genet 31:315-36. 1997
    ..The identification of potentially important amino acid changes using evolutionary biological means is an indispensable step in elucidating the molecular mechanisms that underlie the spectral tuning of visual pigments...
  34. ncbi request reprint The "five-sites" rule and the evolution of red and green color vision in mammals
    S Yokoyama
    Department of Biology, Syracuse University, New York 13244, USA
    Mol Biol Evol 15:560-7. 1998
    ..The inferred amino acid sequences of ancestral organisms suggest that the extant mammalian red and green pigments appear to have evolved from a single ancestral green-red hybrid pigment by directed amino acid substitutions...
  35. ncbi request reprint Genetic analyses of the green visual pigments of rabbit (Oryctolagus cuniculus) and rat (Rattus norvegicus)
    F B Radlwimmer
    Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 218:103-9. 1998
    ..The inference on the ancestral pigment sequences strongly suggests that the rabbit and rat (and mouse) green pigments attained the extant lambdamax values independently, mainly by the single aa replacement A308S...
  36. ncbi request reprint Molecular evolution of the cone visual pigments in the pure rod-retina of the nocturnal gecko, Gekko gekko
    S Yokoyama
    Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 276:117-25. 2001
    ..The accelerated evolutionary rates reflect not only the transition from cones to rods in the retina but also the blue-shift in the absorption spectra of the gecko pigments...
  37. pmc The molecular genetics and evolution of red and green color vision in vertebrates
    S Yokoyama
    Department of Biology, Syracuse University, New York 13244, USA
    Genetics 158:1697-710. 2001
    ..It is most likely that this "five-sites" rule is the molecular basis of spectral tuning in the MWS and LWS pigments during vertebrate evolution...
  38. ncbi request reprint Molecular evolution of color vision of zebra finch
    S Yokoyama
    Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    Gene 259:17-24. 2000
    ..Molecular evolutionary analyses suggest that specific amino acid replacements in the SWS1 and SWS2 pigments, resulting from accelerated evolution, must have been responsible for their functional divergences among the avian pigments...
  39. ncbi request reprint Genetics and evolution of ultraviolet vision in vertebrates
    S Yokoyama
    Department of Biology, Syracuse University, 130 College Place, Syracuse, NY 13244, USA
    FEBS Lett 486:167-72. 2000
    ..The avian lineage is an exception, where the ancestral pigment lost UV-sensitivity but some descendants regained it by one amino acid replacement at an entirely different site...
  40. ncbi request reprint Molecular evolution of vertebrate visual pigments
    S Yokoyama
    Biological Research Laboratories, Department of Biology, Syracuse University, Syracuse, NY 13244, USA
    Prog Retin Eye Res 19:385-419. 2000
    ..Therefore, both molecular evolutionary analyses of visual pigments and vision science have an important common goal...
  41. pmc The molecular genetics of red and green color vision in mammals
    S Yokoyama
    Department of Biology, Syracuse University, Syracuse, New York 13244, USA
    Genetics 153:919-32. 1999
    ..The additive effects of these amino acid changes fully explain the red-green color vision in a wide range of mammalian species, goldfish, American chameleon (Anolis carolinensis), and pigeon (Columba livia)...
  42. ncbi request reprint The cone visual pigments of an Australian marsupial, the tammar wallaby (Macropus eugenii): sequence, spectral tuning, and evolution
    Samir S Deeb
    Department of Medicine, University of Washington, Seattle, USA
    Mol Biol Evol 20:1642-9. 2003
    ..Introns interrupt the coding sequences of the wallaby, mouse, and human MWS pigment sequences at the same corresponding nucleotide positions. However, the length of introns varies widely among these species...
  43. ncbi request reprint Mutagenesis and reconstitution of middle-to-long-wave-sensitive visual pigments of New World monkeys for testing the tuning effect of residues at sites 229 and 233
    Chihiro Hiramatsu
    Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Seimeitou 502, 5 1 5 Kashiwanoha, Kashiwa, Chiba 277 8562, Japan
    Vision Res 44:2225-31. 2004
    ..These results preclude the necessity of examining exon 4, encoding the residues at sites 229 and 233, of M/LWS pigment genes for colour-vision typing of New World monkeys...
  44. ncbi request reprint Prediction of distant metastasis by using reverse transcriptase-polymerase chain reaction for epithelial and variant CD44 mRNA in the peripheral blood of patients with colorectal cancer
    Shozo Yokoyama
    Second Department of Surgery, Wakayama Medical University, School of Medicine 811 1 Kimiidera, Wakayama 641 8510, Japan
    Arch Surg 137:1069-73. 2002
    ..Molecular detection is thought to provide useful information for the clinical management of postoperative adjuvant therapy regimens...
  45. ncbi request reprint Evaluating adaptive evolution
    Shozo Yokoyama
    Nat Genet 30:350-1. 2002

Research Grants13

  1. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2009
    ..abstract_text> ..
  2. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2007
    ....
  3. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2006
    ....
  4. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2002
    ..abstract_text> ..
  5. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2002
    ..abstract_text> ..
  6. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2001
    ..abstract_text> ..
  7. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 2000
    ..abstract_text> ..
  8. EVOLUTIONARY GENETICS OF VERTEBRATE VISION
    Shozo Yokoyama; Fiscal Year: 1999
    ..abstract_text> ..
  9. Adaptive Evolution of Color Vision
    Shozo Yokoyama; Fiscal Year: 2010
    ..abstract_text> ..