My Favorite Gene is
Melanopsin
Larissa Felli
University of Washington School of Aquatic and Fishery Sciences
This webpage was developed to satisfy the coursework requirements of FISH 507a, Applied Bioinformatics for Fishery and Aquatic Sciences
Updated 10/31/07
Melanopsin
Larissa Felli
University of Washington School of Aquatic and Fishery Sciences
This webpage was developed to satisfy the coursework requirements of FISH 507a, Applied Bioinformatics for Fishery and Aquatic Sciences
Updated 10/31/07
Summary
Melanopsin, a recently discovered member of the opsin family of photopigment proteins, mediates non-visual light adaptation in mammals (Nayak et al. 2007). In general, opsins are transmembrane G-protein coupled receptors which change conformation when activated by a photon and initiate the "phototransductory cascade," allowing for perception of light and darkness by an animal. First discovered in melanophores (photoreactive skin cells) of the frog Xenopus laevis, a melanopsin ortholog was discovered in mammals present only in the inner retina. Melanopsin was later localized to intrinsically photosensitive retinal ganglion cells (ipRGCs), a subset of ganglion cells which are directly photosensitive but do not convey visual information like rods or cones. Instead, melanopsin has been characterized as the opsin which regulates light adaptation and entrains circadian rhythms in mammals via the ipRGCs. Two gene variants of melanopsin have since been discovered in the eyes and other tissues of other non-mammals including chicken, cod, and zebrafish (Table 1., adapted from Bellingham et al. 2006 ).
Synonyms for Melanopsin: Opn4, opn4c, opn4m2, Opn4m, Opn4x
I have chosen zebrafish (Danio rerio) melanopsin as my favorite gene in order to learn more about its role in circadian rhythms. It has become a popular subject in mammalian circadian rhythm literature, but its potential role in fishes is unknown. My research interests include biological rhythms in fishes and I hope to gain
insight into whether melanopsin may be an important gene on which to focus my salmon research. The first teleost in which melanopsin was identified was the
zebrafish (Bellingham et al. 2002 ), a model organism in developmental and
genomic research. Notably, melanopsin was simultaneously discovered in the Atlantic cod (Drivenes et al. 2003 ). Although this website focuses on zebrafish melanopsin, the future investigation of this gene in other teleosts is far more interesting to me.
Melanopsin and Circadian Rhythms
Without daily entrainment by light, the mammalian circadian clock tends to "free-run" on a period which is different from the 24 hour day:night cycle. Mammals without eyes do not show circadian entrainment, that is, their circadian rhythms start to free-run even when subjected to normal light:dark cycles. This is evidence that they eye is the organ which entrains circadian rhythms. Interestingly, photoadaptation occurs normally in mammals whose eyes that are intact but have complete loss of rods and cones. This is the first line of evidence to suggest that a novel, non-rod, non-cone opsin mediates photoadaptation in mammals (see Nayak et al. 2007 for historical review). Efforts to elucidate the pathways regulating circadian entrainment in mammals have led to the discovery that melanopsin-expressing ipRGCs project directly into the superchiasmatic nucleus, the region of the brain known to regulate circadian rhythms (Hattar et al. 2002). Additionally, circadian activity rhythms in melanopsin-deficient mice (opn4-/-) are less affected by light, a result that is more pronounced under certain lighting conditions (Panda et al. 2002)
The zebrafish melanopsin gene transcript
Without daily entrainment by light, the mammalian circadian clock tends to "free-run" on a period which is different from the 24 hour day:night cycle. Mammals without eyes do not show circadian entrainment, that is, their circadian rhythms start to free-run even when subjected to normal light:dark cycles. This is evidence that they eye is the organ which entrains circadian rhythms. Interestingly, photoadaptation occurs normally in mammals whose eyes that are intact but have complete loss of rods and cones. This is the first line of evidence to suggest that a novel, non-rod, non-cone opsin mediates photoadaptation in mammals (see Nayak et al. 2007 for historical review). Efforts to elucidate the pathways regulating circadian entrainment in mammals have led to the discovery that melanopsin-expressing ipRGCs project directly into the superchiasmatic nucleus, the region of the brain known to regulate circadian rhythms (Hattar et al. 2002). Additionally, circadian activity rhythms in melanopsin-deficient mice (opn4-/-) are less affected by light, a result that is more pronounced under certain lighting conditions (Panda et al. 2002)
The zebrafish melanopsin gene transcript
Size: 1.6 kb
Tissue: adult retina
Nucleotide Sequence:
Tissue: adult retina
Nucleotide Sequence:
CAACACGAAAACATCAACCTGCTCAGCATGAGCCATCACTCTTCATGGAGAGGGCATCACTGTGCCCCTG
GAGACATCAACTGCACCGCAGGCTTTAAGGAATCTTTGGGAAGCAGAAACTACAAGTTGCTCCATGTGCC
TGTCCATGGGCCAACCCACAGCCACCACCATGATCCTCCACACCCTTTCCCCACCGTGGATGTTCCGGAT
CATGCCCACTACATCATCGGCTCTGTTATCTTAATAGTCGGCATCACCGGAGTGATTGGAAATGCACTGG
TGGTCTATGTATTCTGCCGGAGCCGTACTCTTCGCACCGCTGGAAACATGTTTATAGTGAACCTAGCTGT
GGCTGATTTCTTAATGTCCGTCACCCAGTCTCCTGTGTTCTTTGCTGCAAGTTTACACAGGCGATGGGTA
TTTGGCGAGCGTCCTTGCGAGCTCTACGCCTTCTGCGGTGCCCTCTTTGGAATCTGCTCCATGATGACTT
TGACCGCCATCGCTGCTGATCGTTGTCTCGCCATAACTCAGCCTCTCGCCCTAGTAAGCAGAGTTAGCCG
ACGCAAAGCTGGAGCTGTGTTTGTCGTTGTGTGGCTCTACTCCCTGGGTTGGAGCCTTCCGCCTTTCTTT
GGCTGGAGTGCTTATGTCCCTGAGGGGCTTCAGACGTCTTGTTCTTGGGATTACATGACCTTCACCCCAT
CGGTGCGTGCGTACACCATCCTCCTCTTTGTTTTTGTATTCTTCATCCCACTAGGCATTATAGGCAGCTG
CTACTTCGCAATTTTTCAAACAATCCGAGCAGCGGGGAAGGAAATTCGAGAGCTGGATTGCGGGGAAACG
CACAAGGTGTATGAACGCATGCAGAACGAATGGAAGATGGCGAAAGTCGCTCTTGTAGTCATTTTGCTTT
TTATTATATCCTGGTCGCCCTATTCTGTGGTGGCTCTCACCGCTACGGCTGGTTATTCCCATTTCCTGAC
TCCCTATATGAATTCAGTACCTGCTGTGATTGCCAAGGCTTCAGCCATCCATAATCCAATCATCTACGCC
ATTACGCATCCAAAGTATCGTGTGGCTATCGCCCGTTACATTCCGGTACTTCGTCCCATCTTGCGTGTGA
AAGAGAAGGACCTTCGTTCCTCTTTTAGCTCTGGCAGTGTTAGTTCTCGTCGTCCAACCCTCACCAGTCA
TCAGTGCTCTTTGGGGGTTAGCATGGGCAATGCTGCACGAGCTAATGGCCGCTGGGGGAAGACGCGATTG
TCTTCTGCCTCTGATAGTGATTCTTGCTGGACTGAGAGTGAGGCTGATGGTTCCAGTGTCAGTTCCCTGA
CCTTCGGTCGTCGTGTTTCCACAGAAATCTCTACAGATACTGTCATTCTCTCACCTGGATCAAGTGTTAG
CAATGCTAGTGGGCAGAAATCTGAGAGGGCACACAAAGTTGTAAGTGTACCAGTGCCGTCTATTACTTTT
GAAACGGATGCAGCAGACGGGGAATCTCTGTCTGATGGGAAGGCTTTGCTTGGAGGGAACTAAAGAAATG
ATACTGCACTTCGTTTGATTCTAATTTCCTTAGTAGTAGAAACAGTAGTACTATTAATAGTAGTACTATT
ATTTTTGATTCTGAATATATAATCTTATATTTTTCTTCACTCTGCACGTTGTAAGTAA
TGTCCATGGGCCAACCCACAGCCACCACCATGATCCTCCACACCCTTTCCCCACCGTGGATGTTCCGGAT
CATGCCCACTACATCATCGGCTCTGTTATCTTAATAGTCGGCATCACCGGAGTGATTGGAAATGCACTGG
TGGTCTATGTATTCTGCCGGAGCCGTACTCTTCGCACCGCTGGAAACATGTTTATAGTGAACCTAGCTGT
GGCTGATTTCTTAATGTCCGTCACCCAGTCTCCTGTGTTCTTTGCTGCAAGTTTACACAGGCGATGGGTA
TTTGGCGAGCGTCCTTGCGAGCTCTACGCCTTCTGCGGTGCCCTCTTTGGAATCTGCTCCATGATGACTT
TGACCGCCATCGCTGCTGATCGTTGTCTCGCCATAACTCAGCCTCTCGCCCTAGTAAGCAGAGTTAGCCG
ACGCAAAGCTGGAGCTGTGTTTGTCGTTGTGTGGCTCTACTCCCTGGGTTGGAGCCTTCCGCCTTTCTTT
GGCTGGAGTGCTTATGTCCCTGAGGGGCTTCAGACGTCTTGTTCTTGGGATTACATGACCTTCACCCCAT
CGGTGCGTGCGTACACCATCCTCCTCTTTGTTTTTGTATTCTTCATCCCACTAGGCATTATAGGCAGCTG
CTACTTCGCAATTTTTCAAACAATCCGAGCAGCGGGGAAGGAAATTCGAGAGCTGGATTGCGGGGAAACG
CACAAGGTGTATGAACGCATGCAGAACGAATGGAAGATGGCGAAAGTCGCTCTTGTAGTCATTTTGCTTT
TTATTATATCCTGGTCGCCCTATTCTGTGGTGGCTCTCACCGCTACGGCTGGTTATTCCCATTTCCTGAC
TCCCTATATGAATTCAGTACCTGCTGTGATTGCCAAGGCTTCAGCCATCCATAATCCAATCATCTACGCC
ATTACGCATCCAAAGTATCGTGTGGCTATCGCCCGTTACATTCCGGTACTTCGTCCCATCTTGCGTGTGA
AAGAGAAGGACCTTCGTTCCTCTTTTAGCTCTGGCAGTGTTAGTTCTCGTCGTCCAACCCTCACCAGTCA
TCAGTGCTCTTTGGGGGTTAGCATGGGCAATGCTGCACGAGCTAATGGCCGCTGGGGGAAGACGCGATTG
TCTTCTGCCTCTGATAGTGATTCTTGCTGGACTGAGAGTGAGGCTGATGGTTCCAGTGTCAGTTCCCTGA
CCTTCGGTCGTCGTGTTTCCACAGAAATCTCTACAGATACTGTCATTCTCTCACCTGGATCAAGTGTTAG
CAATGCTAGTGGGCAGAAATCTGAGAGGGCACACAAAGTTGTAAGTGTACCAGTGCCGTCTATTACTTTT
GAAACGGATGCAGCAGACGGGGAATCTCTGTCTGATGGGAAGGCTTTGCTTGGAGGGAACTAAAGAAATG
ATACTGCACTTCGTTTGATTCTAATTTCCTTAGTAGTAGAAACAGTAGTACTATTAATAGTAGTACTATT
ATTTTTGATTCTGAATATATAATCTTATATTTTTCTTCACTCTGCACGTTGTAAGTAA
BLAST results
When zebrafish melanopsin mRNA (AY078161.1) is BLASTed against the NCBI database (10/30/07), the most similar sequence results are other zebrafish entries including ESTs, and predicted coding regions from BAC clone libraries, presumably data from genome sequencing projects. Refer to the tree at left to see how melanopsin from other interesting taxa is related to zebrafish melanopsin. As expected, the closest relatives are other teleosts roach (Rutilus rutilus; a cyprinid) and cod (Gadus morhua). Next closest related species include a lizard (Podarcis sicula), frog (Xenopus laevis), and chicken (Gallus gallus). Also listed are marsupials (Sminthopsis, opposum) and mammals (mole rat, Russian dwarf hamster, mouse, rat, cow, horse, and dog.
Messenger RNA Expression Patterns
When zebrafish melanopsin mRNA (AY078161.1) is BLASTed against the NCBI database (10/30/07), the most similar sequence results are other zebrafish entries including ESTs, and predicted coding regions from BAC clone libraries, presumably data from genome sequencing projects. Refer to the tree at left to see how melanopsin from other interesting taxa is related to zebrafish melanopsin. As expected, the closest relatives are other teleosts roach (Rutilus rutilus; a cyprinid) and cod (Gadus morhua). Next closest related species include a lizard (Podarcis sicula), frog (Xenopus laevis), and chicken (Gallus gallus). Also listed are marsupials (Sminthopsis, opposum) and mammals (mole rat, Russian dwarf hamster, mouse, rat, cow, horse, and dog.
Messenger RNA Expression Patterns
In the zebrafish, melanopsin mRNA is detected mainly in the retina and brain, shown in the figure at right taken from NCBI's UniGene Expression Profiler. A recently described paralog in the zebrafish is weakly expressed in the pineal gland (Bellingham et al. 2002).
The table below lists tissues where mRNA for the two zebrafish melanopsin paralogs has been detected compared to other vertebrate species (Bellingham et al. 2006).
Gene structure
Melanopsin is found on chromosome 2 of the zebrafish genome. It has no exons. The figure to the right shows the location of the opn4l locus within its BAC contig on chromosome two, its adjacent untranslated regions (UTRs), and neighboring genes. The 5' UTR is 117 base pairs long, the 3' UTR is 1.6 kb long.
Figure taken from Ensembl Zebrafish TransView
Protein structure
Putative Melanopsin Protein Sequence:
MSHHSSWRGHHCAPGDINCTAGFKESLGSRNYKLLHVPVHGPTH
SHHHDPPHPFPTVDVPDHAHYIIGSVILIVGITGVIGNALVVYVFCRSRTLRTAGNMF
IVNLAVADFLMSVTQSPVFFAASLHRRWVFGERPCELYAFCGALFGICSMMTLTAIAA
DRCLAITQPLALVSRVSRRKAGAVFVVVWLYSLGWSLPPFFGWSAYVPEGLQTSCSWD
YMTFTPSVRAYTILLFVFVFFIPLGIIGSCYFAIFQTIRAAGKEIRELDCGETHKVYE
RMQNEWKMAKVALVVILLFIISWSPYSVVALTATAGYSHFLTPYMNSVPAVIAKASAI
HNPIIYAITHPKYRVAIARYIPVLRPILRVKEKDLRSSFSSGSVSSRRPTLTSHQCSL
GVSMGNAARANGRWGKTRLSSASDSDSCWTESEADGSSVSSLTFGRRVSTEISTDTVI
LSPGSSVSNASGQKSERAHKVVSVPVPSITFETDAADGESLSDGKALLGGN
Certain domains of the melanopsin protein (and nucleotide sequence) are similar in sequence to those found in rhodopsin, prostanoid receptor, peropsin, oxytocin receptor, and opsins in general. This information is shown schematically in the figure at right taken from Ensemble ProtView.
The putative 3D crystal structure for melanopsin is depicted at left (Hermann et al. 2005 ). The orange areas are mainly alpha-helices of the transmembrane domains. The green represents loop regions. The yellow area represents the chromophore binding region.
Other sites with interesting information about zebrafish melanopsin:
NCBI (sequence data for melanopsin gene, mRNA, orthologs, paralogs, and protein)
ZFIN (this page has links to more information about how melanopsin fits into the opsins and the GPCR superfamily of proteins)
Ensembl (this page contains information about genomic location, orthologs, paralogs, and protein structure)
References:
Bellingham, J., Whitmore, D., Philp, A. R., Wells, D. J., Foster, R. G. (2002) Zebrafish melanopsin: Isolation, tissue localization and phylogenetic position. Brain Res. Mol. Brain Res. 107, 128-136.
Bellingham, J., Chaurasia, S. S., Melyan, Z., Liu, C., Cameron, A. M, Tarttelin, E. E., Iuvone, P. M., Hankins, M. W., Tosini, G., Lucas, R. J. (2006) Evolution of melanopsin photoreceptors: discovery and characterization of a new melanopsin in nonmammalian vertebrates.
Drivenes, O., Soviknes, A. M., Ebbesson, L. O. E., Fjose, A., Seo H.-C. , Helvik, J. V. (2003) Isolation and characterization of two teleost melanopsin genes and their differential expression within the inner retina and brain. J. Comp. Neurol. 456, 84-93.
Hattar, S., Liao, H. W., Takao, M., Berson, D. M., and Yau, K. W. (2002) Melanopsin-containing retinal ganglion cells: architecture , projections, and intrinsic photosensitivity. Science 295, 1065-1070.
Nayak, S. K., Jegla, T., and Panda, S. (2007) Role of a novel photopigment, melanopsin, in behavioral adaptation to light. Cell Mol. Life Sci. 64, 144-154.
Hermann, R., Poppe, L., Boden, C., Maurer, J., Weber, S., Lerchi, A. (2004) Predicted 3D-structure of melanopsin, the non-rod, non-cone photopigment of the mammalian circadian cloack, from Djungarian hamsters (Phodopus sungorus). Neurosci. Lett. 376, 76-80.
Panda, S. Sato, T. K., Castrucci, A. M., Rollag, M. D., DeGrip, W. J., Hogenesch, J. B., Provencio, I., and Kay, S. A. (2002) Melanopsin (Opn4) requirement for normal light-induced circadian phase shifting. Science 298, 2213-2216.