title: A simple method for studying the molecular mechanisms of ultraviolet and violet reception in vertebrates.
abstract: BACKGROUND
  Many vertebrate species use ultraviolet (UV) reception for such basic behaviors as foraging and mating, but many others switched to violet reception and improved their visual resolution. The respective phenotypes are regulated by the short wavelength-sensitive (SWS1) pigments that absorb light maximally (λmax) at ~360 and 395-440 nm. Because of strong epistatic interactions, the biological significance of the extensive mutagenesis results on the molecular basis of spectral tuning in SWS1 pigments and the mechanisms of their phenotypic adaptations remains uncertain.
  
  
  RESULTS
  The magnitudes of the λmax-shifts caused by mutations in a present-day SWS1 pigment and by the corresponding forward mutations in its ancestral pigment are often dramatically different. To resolve these mutagenesis results, the A/B ratio, in which A and B are the areas formed by amino acids at sites 90, 113 and 118 and by those at sites 86, 90 and 118 and 295, respectively, becomes indispensable. Then, all critical mutations that generated the λmax of a SWS1 pigment can be identified by establishing that 1) the difference between the λmax of the ancestral pigment with these mutations and that of the present-day pigment is small (3 ~ 5 nm, depending on the entire λmax-shift) and 2) the difference between the corresponding A/B ratios is < 0.002.
  
  
  CONCLUSIONS
  Molecular adaptation has been studied mostly by using comparative sequence analyses. These statistical results provide biological hypotheses and need to be tested using experimental means. This is an opportune time to explore the currently available and new genetic systems and test these statistical hypotheses. Evaluating the λmaxs and A/B ratios of mutagenized present-day and their ancestral pigments, we now have a method to identify all critical mutations that are responsible for phenotypic adaptation of SWS1 pigments. The result also explains spectral tuning of the same pigments, a central unanswered question in phototransduction.
authors.affiliation: Department of Biology, Emory University, Atlanta, GA, 30322, USA. syokoya@emory.edu.
authors.forename: Shozo
authors.initials: S
authors.lastname: Yokoyama
authors.affiliation: Department of Biology, Emory University, Atlanta, GA, 30322, USA.
authors.forename: Takashi
authors.initials: T
authors.lastname: Tada
authors.affiliation: Department of Biology, Emory University, Atlanta, GA, 30322, USA.
authors.forename: Yang
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Department of Biology, Emory University, Atlanta, GA, 30322, USA.
authors.forename: Davide
authors.initials: D
authors.lastname: Faggionato
authors.affiliation: Department of Physics, Fatih University, Istanbul, 34500, Turkey.|Department of Genetics and Bioengineering, Fatih University, Istanbul, 34500, Turkey.
authors.forename: Ahmet
authors.initials: A
authors.lastname: Altun
mesh_terms: D000818:Animals; D004843:Epistasis, Genetic; D019143:Evolution, Molecular; D006801:Humans; D008027:Light; D055537:Light Signal Transduction; D016297:Mutagenesis, Site-Directed / Q000379:methods*; D010802:Phylogeny; D012168:Retinal Pigments / Q000235:genetics* / Q000378:metabolism*; D014714:Vertebrates / Q000145:classification* / Q000235:genetics / Q000378:metabolism*
chemical_list: D012168:Retinal Pigments
keywords: Hydrogen-bond network; Mutagenesis analyses; Spectral tuning; UV and violet reception; Visual pigments