Essential Genes of Human Vision
Kristy P. Myers
Abstract
Through collaborative efforts and empirical research, a link between the origins of human eye genes has been traced resulting in a phylogenetic analysis of the genes. The approach of the research was to implement the use of a tool package, TaxDome , in order to trace human eye evolutionary traits and view the taxonomic distributions of protein domains. In addition, the use of several databases resulted in evidence suggesting that the functions of many of the genes expressed in humans were similarly expressed in other organisms. Therefore, an extensive review of the functions of particular proteins led to the connection of many eye gene functions in various organisms.
1. Introduction
An opsin is a group of light-sensitive membrane-bound G protein-coupled receptors of the rhodopsin protein family found in photoreceptor cells of the retina [1]. Evidence suggests that most opsins act as pigments that activate G proteins in a light-dependent manner in both visual and nonvisual systems [2] and further supports the evolutionary link found, through our research, between the human eye gene and the rhodopsin sensory protein. Although non-animal opsins and their functions were located, there is no evidence that they are structurally related to animal opsins [2]; therefore, inferences are made as to the relationships between the functions of the opsins found in the various organisms. Ion transporting proteins were also found in animal and non-animal organisms. Their function is the same, to change the polarity of the cell, but their response mechanisms and stimuli are very different.
2. Data and Method
The goal of tracing the origins of a group of eye related genes from Homo sapiens began with the use of the TaxDome tool package. The TaxDome tool package contains several Perl scripts and one java visualization program to provide a fast overview of the taxonomic distributions of domains and a

study of protein origins [3]. The TaxDome tool package was downloaded before beginning the search for genes related to the human eye.
A group of 55 genes related to the human eye were collected using various databases such as
Ensemble, NCBI, EBI, and UniProt. Keywords such as vision, eye, blindness, optic, sensory, cornea, iris, retina, etc… were used to form the list of genes related to the human eye. Databases were used to collect accession numbers and protein descriptions for the eye genes.
The list of UniProt accession numbers were saved in Notepad in order to use the TaxDome tool and run Perl. The Notepad list of UniProt accession numbers were entered into the TaxDome folder and saved as a file. Using the TaxDome tool, a domain search was performed and a list of taxonomic distributions of domain combinations was provided.
From the taxonomic distributions of domain combinations provided, using the TaxDome tool, data showed the domain and domain combinations for the genes related to the human eye gene. A file for each UniProt accession number was created and the files were placed in the TaxDome TreeDrawer folder in order to create a taxonomic tree. By using the TreeDrawer folder located within the TaxDome tool package, a taxonomic tree for each domain was created. The information from the trees provided the origins for each of the genes related to the human eye.
3. Results and Discussion
After careful analysis of the taxonomic trees for each of the genes related to the human eye, similarities and differences among the genes became evident. In addition, the research led to the inquiry of how the human eye gene was expressed in similar genes of other organisms.
We observed the opsin gene was expressed in many of the human eye genes. The discovery influenced us to learn more about opsins and their role in the human eye. Opsins are involved in vision, mediating the conversion of a photon of light into an electrochemical signal [1]; the light absorption is observed through wavelengths. The obvious next step involved researching how the opsins of the human eye gene were similar or different in other organisms.

Using the UniProt database, we were able to research the functions of opsins in various organisms. The TaxDome tool revealed that most opsins were located in a single domain; however, the opsins were related to other eye functions in many other domains as well. By isolating one domain and narrowing our further research to the location and function of opsins, we were able to observe similarities among various organisms. The organism that we consistently observed included the Blind
Cavefish, Astyanax mexicanus, the Zebrafish, Danio rerio, the Human, Homo sapiens, and ocean bacteria, Halobacterium (genus). The origin of the opsins in one of the domains is shown in fig.1.
Figure 1: A taxonomic distribution of the origin of a human eye gene (P03999) in domain PF00001 expressing a Blue-sensitive opsin. TaxDome tool package.
The taxonomic tree allowed us to narrow our search to organisms in which there was evidence of shared proteins (as shown in red). Using UniProt, we searched for opsins, particularly blue-sensitive opsin, red-sensitive opsin and green-sensitive opsin, located in the various chosen organisms
(Zebrafish, Blind Cavefish and Human). During the search for the expression of red, blue and greensensitive opsins, the sensory rhodopsin, also evident in animals, was revealed in archaea_bacteria.
Therefore, in comparison, to look for shared genes, we searched for an organism using rhodopsin in the archaea_bacteria domain. The chart in Table 2 reveals the data.

Table 1. Chart containing data collected from various organisms that show the function of opsins.
Organism/Species
Halobacterium (genus)
“ocean bacterium”
Blind Cave Fish
Astyanax mexicanus
Zebrafish
Danio rerio
Human
Homo sapiens
Zebrafish
Danio rerio
Blind Cave Fish
Astyanax mexicanus
Human
Homo sapiens
Blind Cave Fish
Astyanax mexicanus
Zebrafish
Danio rerio
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Accession
ID
P33743
P22331
Q8AYM8
PO4001
P26367
Q02962
O43186
Q02846
1
Protein name:
Sensory rhodopsin-
Green-sensitive opsin
Green-sensitive opsin
Green-sensitive opsin paired box protein
PAX6 paired box protein
PAX2 cone/rod homeobox protein
Retinal guanylyl
Function
Involved in the control of phototaxis.
Mediates both photoattractant (in the red) and photophobic (near UV) responses. Seems to activate a methylaccepting protein Photoreceptor for green-red and UV light.
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Q8AYN0 Red-sensitive opsin Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
P22332
P04000
Red-sensitive opsin Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Red-sensitive opsin Visual pigments are the light-absorbing
P51472
Q9W6A8
Blue-sensitive opsin
Blue-sensitive opsin molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
P03999 Blue-sensitive opsin
Visual pigments are the light-absorbing molecules that mediate vision. They consist of an apoprotein, opsis, covalently linked to cis-retinal.
Functions in the morphogenesis of the eye, nose, central nervous system and pancreas.
Plays a critical role in the development of the kindneys, urogenital tract, eyes, and central nervous system.
Maintains photoreceptors, including opsins.
Recovery of dark state after
Domain
Archaea
Chordata
Chordata
Chordata/Mammalia
Chordata
Chordata
Chordata/Mammalia
Chordata
Chordata
Chordata/Mammalia
Eukaryota
Eukaryota
Eukaryota
Metazoa

Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens
Human
Homo sapiens cyclase 1 precursor phototransduction.
Q9Y2V3 retinal homeobox protein Rx
P29973 cGMP-gated cation channel alpha 1
Regulates initial specification of retinal cells.
Depolarizes rod photoreceptors.
O60721 Sodium/potassium/ calcium exchanger
1
Regulates Ca/K/Na during dark and light signals.
Generates light evoked e- signals in S,
M, LW opsins.
Q9NQW8 Cyclic nucleotidegated cation channel beta 3
O75106 Retina-specific copper amine oxidase precursor
P43080 Guanylyl cyclaseactivating protein 1
Modulates signal transmission in the retina.
Ca exchanger, recovery of rods after light exposure.
Metazoa
Bacteria
Archaea_Bacteria
Bacteria
Archaea_Bacteria
Archaea_Bacteria
The functions of the opsins among the organisms were highly similar. When using the EBI sequence alignment tool to blast the proteins, the results of any two organisms sharing the same opsins came back highly similar (see Figure 3).
Length: 357
# Identity: 313/357 (87.7%)
# Similarity: 335/357 (93.8%)
# Gaps: 1/357 ( 0.3%)
# Score: 1728.0
Figure 2: The results of using the EBI tool to compare 2 sequences (red-sensitive opsin of Zebrafish and red-sensitive opsin of Blind Cavefish). The region of similarity between the two sequences is high
(93.8%).
As stated earlier, there is a lack of evidence that reveals a relationship between the non-animal opsin (example: Halobacterium ) and animal opsin. The research revealed that opsins in the form of bacteriorhodopsin are used by archaea, most notably halobacteria. The bacteriorhodopsin is a photosynthetic pigment used by halobacteria to capture light energy and uses it to move protons across the membrane out of the cell resulting in chemical energy [1].
In comparison to opsin coding genes, ion transport coding genes, such as CNGA1 and
SLC24A1 have a much wider and more diverse evolutionary origin. Ion transporting proteins can be found in many archaea, with domain combinations similar to those in eukaryotes, Figure 3. The functions of these ion transporting proteins are well understood but not the focus of our current research. Research has shown that archaea-organisms do not have eyes, but further research reveals

that they use proteins with the same domains as vertebrate eyes to transport cations into and out of their cells. (Figure 3)
Figure 3. Protein domain distribution for the gene SLC24A1, an Ca2+/Na+/K+ ion exchanger.
When using EBI to compare protein sequences in the SLC24A1 gene, we find many organisms who express the proteins with a 30% or better sequence similarity (Table 3). This may sound slight, but consider the PAX6_MOUSE gene, which can activate the expression of eyes in D. melanogaster with a sequence similarity value of 33.4%.
The Drosophila gene eyeless (ey) encodes a transcription factor with both a paired domain and a homeodomain. It is homologous to the mouse Small eye (Pax-6) gene and to the Aniridia gene in humans.By targeted expression of the ey complementary
DNA in various imaginal disc primordia of Drosophila, ectopic eye structures were induced on the wings, the legs, and on the antennae. The ectopic eyes appeared morphologically normal and consisted of groups of fully differentiated ommatidia with a complete set of photoreceptor cells. [4]

Table 3. A comparison of the gene and the percentage identity, similarity and gap from different organisms who share the ion transport family with H. sapiens.
Gene ID
SLC24A11
NCKX1_BOVIN
NCKX1_CHICK
NCKX2_CHICK
NICKX_DROME
NCKX3_MOUSE
Q1RPT9_CAEEL
O97801_MACMU
NCKX6_MOUSE
Organism
Homo sapiens
Bos taurus
Gallus gallus
Gallus gallus
Drosophila melanogaster
Mus musculus
Caenorhabditis elegans
Macaca mulatta
Mus musculus
% ID
100
65.8
37.9
33.8
30
20.9
13.5
13.3
13
% Similarity % Gap
100 0
73.6
43.7
12.2
44.6
40.6
41.8
32.4
22.7
23.5
21.6
44.4
32.6
47.2
55.5
54.9
59.7
Q8TLL5_METAC Methanosarcina acetivorans 8.3 16 73.1
After running the TaxDome tool, and finding the proteins’ domains origins, patterns and combinations, two of these genes were selected for further study. One gene, PAX6 is only expressed in higher order Eukaryotes, while the other gene, SLC24A1 is expressed in all classification domains.
In Table 3 , you can see the protein families that make up the gene and the various functions they serve in the listed organism.
Table 3 . gene Pfam
This gene has only been found in
Eukaryota, however, it has protein
PAX6 domains that are shared in other organisms.
PF00046
PF00292 organism function
H. sapiens 402 different homeobox proteins with this domain
M. musculus 559 different homeobox proteins with this domain
D. melanogaster 196 different homeobox proteins with this domain
D. rerio
B. taurus
402 different homeobox proteins with this domain
54 different homeobox proteins with this domain
G. gallus
M. mulatta
164 different homeobox proteins with this domain
18 different homeobox proteins with this domain
4 species use this protein as a possible transposase insertion sequence Proteobacteria
H. sapiens
M. musculus
43 different paired box proteins
45 different paired box proteins
D. melanogaster 28 paired box proteins
D. rerio 23 different paired box proteins and transcription

factors
B. taurus
G. gallus
7 paired box transcription factors
9 paired box proteins
M. mulatta 1 paired box protein
PAX6 serves as a transcription factor in the development of the eye, nose, central nervous system and pancreas. [5] PAX6 function is very clearly understood, and it will cause the expression of an eye in any gene into which it is inserted. This gene uses PF00046, which is part of a homeobox protein group that has a wide range of gene regulating functions, but its main purpose is coding for morphogenesis.
[1]
3. Summary:
Through the implementation of TaxDome, a link between the origins of human eye genes was traced resulting in a phylogenetic analysis of the genes. The research revealed taxonomic distributions of protein domains which allowed for further research involving the origins of the genes. The use of several databases also led to evidence suggesting that the functions of many of the genes expressed in humans were similarly expressed in other organisms. The study revealed that the functions of particular proteins led to the connection of many eye gene functions in various organisms.
ACKNOWLEDGEMENTS
This research was supported by the National Science Foundation (NSF) and the University of
Georgia under the supervision of Ying Xu, Ph.D., Department of Biochemistry and Molecular Biology.
Thanks to Qi Liu for the TaxDome tool package. Also, Dr. Phuongan Dam and Dr. Fenglou Mao collaborated and assisted with the application of the materials and the databases used in the research.