The Role of Gene Duplication and Unconstrained Selective Pressures in the Melanopsin Gene Family Evolution and Vertebrate Circadian Rhythm Regulation

Antunes A (2012) The Role of Gene Duplication and Unconstrained Selective Pressures in the Melanopsin Gene Family Evolution and Vertebrate Circadian Rhythm Regulation. PLoS ONE 7(12): e52413. doi:10.1371/journal.pone.0052413 The Role of Gene Duplication and Unconstrained Selective Pressures in the Melanopsin Gene Family Evolution and Vertebrate Circadian Rhythm Regulation Rui Borges 0 Warren E. Johnson 0 Stephen J. O'Brien 0 Vitor Vasconcelos 0 Agostinho Antunes 0 Stephen R. Proulx, University of California Santa Barbara, United States of America 0 1 CIMAR/CIIMAR, Centro Interdisciplinar de Investigac a o Marinha e Ambiental, Universidade do Porto , Rua dos Bragas, Porto , Portugal , 2 Departamento de Biologia, Faculdade de Ciencias, Universidade do Porto , Rua do Campo Alegre, Porto , Portugal , 3 Laboratory of Genomic Diversity, National Cancer Institute , Frederick , Maryland, United States of America, 4 Theodosius Dobzhansky Center for Genome Bioinformatics, St. Petersburg State University , St. Petersburg , Russia Melanopsin is a photosensitive cell protein involved in regulating circadian rhythms and other non-visual responses to light. The melanopsin gene family is represented by two paralogs, OPN4x and OPN4m, which originated through gene duplication early in the emergence of vertebrates. Here we studied the melanopsin gene family using an integrated gene/protein evolutionary approach, which revealed that the rhabdomeric urbilaterian ancestor had the same amino acid patterns (DRY motif and the Y and E conterions) as extant vertebrate species, suggesting that the mechanism for light detection and regulation is similar to rhabdomeric rhodopsins. Both OPN4m and OPN4x paralogs are found in vertebrate genomic paralogons, suggesting that they diverged following this duplication event about 600 million years ago, when the complex eye emerged in the vertebrate ancestor. Melanopsins generally evolved under negative selection (v = 0.171) with some minor episodes of positive selection (proportion of sites = 25%) and functional divergence (hI = 0.349 and hII = 0.126). The OPN4m and OPN4x melanopsin paralogs show evidence of spectral divergence at sites likely involved in melanopsin light absorbance (200F, 273S and 276A). Also, following the teleost lineage-specific whole genome duplication (3R) that prompted the teleost fish radiation, type I divergence (hI = 0.181) and positive selection (affecting 11% of sites) contributed to amino acid variability that we related with the photo-activation stability of melanopsin. The melanopsin intracellular regions had unexpectedly high variability in their coupling specificity of G-proteins and we propose that Gq/11 and Gi/o are the two G-proteins most-likely to mediate the melanopsin phototransduction pathway. The selection signatures were mainly observed on retinal-related sites and the third and second intracellular loops, demonstrating the physiological plasticity of the melanopsin protein group. Our results provide new insights on the phototransduction process and additional tools for disentangling and understanding the links between melanopsin gene evolution and the specializations observed in vertebrates, especially in teleost fish. - Funding: The authors acknowledge the Portuguese Foundation for Science and Technology (FCT) for financial support to RB (SFRH/BD/79850/2011) and the projects PTDC/AAC-AMB/104983/2008 (FCOMP-01-0124-FEDER-008610) and PTDC/AAC-AMB/121301/2010 (FCOMP-01-0124-FEDER-019490) to AA. This research received support by the Intramural Research Program of the National Institutes of Health, National Cancer Institute to WEJ and SJO. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: The authors have declared that no competing interests exist. Vertebrates have a wide range of strategies to respond to light in different photic environments [1]. The evolution of these diverse light-signalling processes and the link between photoreceptors and adaptive strategies are not fully understood. One of the mostrecently discovered groups of photoreceptors, melanopsin (OPN4), was first described in the dermal melanophores of Xenopus laevis [2]. Its main functions are non-image forming, including the regulation of circadian rhythms, the pupillary light reflex and melatonin synthesis [35]. Melanopsins are sensitive to low wavelength light with maximum sensitivities near to 480 nm [6,7]. Within vertebrate genomes there are two variants of the melanopsin gene: the mammalian-like melanopsin (OPN4m) and the Xenopus-like melanopsin (OPN4x) [8]. In mammals, only the OPN4m gene has been described, suggesting that the OPN4x variant was lost during mammalian evolution [9]. Mammalian melanopsin is expressed in a subset of intrinsically photosensitive retinal ganglion cells (ipRGCs) of the eye [10] while the nonmammalian vertebrates also express melanopsin in intraocular p (...truncated)