Bioinformatic approaches for identification and characterization of olfactomedin related genes with a potential role in pathogenesis of ocular disorders.
OBJECTIVE
To identify olfactomedin domain containing proteins, which are expressed in the eye and have similarity to myocilin, to test as potential candidates for eye diseases. Most of the mutations in myocilin causing primary open angle glaucoma are located in the olfactomedin domain. In vitro experiments demonstrated interaction between optimedin and myocilin through the conserved olfactomedin domains of the proteins in rats, and it was speculated that optimedin might have a role in the pathogenesis of ocular disorders. Hence, we aimed to identify myocilin related human proteins having conserved olfactomedin domains with potential to interact between them and examine the expression patterns in the eye by bioinformatics approaches. This endeavor would have the potential to identify new candidate genes for eye diseases in general and glaucoma in particular to be tested by wet-lab experiments.


METHODS
Proteins with homology to myocilin were selected by BLASTp at the NCBI server. cDNA sequences and corresponding genomic contigs were retrieved. Pairwise BLAST was done to investigate the gene structure. The human EST database and NEIBank were searched against the selected cDNAs to look for tissue specific expression of the transcripts.


RESULTS
The study led to the identification of three groups of proteins encoded by three different genes; Noelin 1 (9q34.3), Noelin 2 (19p13.2), and Noelin 3 (1p22) encompassing 45,575 bp, 82,679 bp, and 1,93,421 bp of the genomic sequence, respectively. Genomic structures, alternate usage of exons, and molecular evolution of the Noelins were determined. Similar structures of the genes, splicing patterns and high levels of homology shed light on the relatedness and molecular evolution of this group of olfactomedin related proteins. Strikingly, however, Noelin 1 and Noelin 3 were found to be expressed as multiple splice variants while only a single spliced transcript could be identified for Noelin 2. A human EST database search suggested the expression of all three Noelin genes in the brain but only two (Noelin 1 and Noelin 2) in the eye despite experimental evidence for expression of Noelin 3 in ocular tissue. Myocilin was determined to have similar levels (60-61%) of homology with all three Noelin gene products (Noelin 1_v1, Noelin 2_v1, and Noelin 3_v1) at the conserved olfactomedin domains.


CONCLUSIONS
Mammalian Noelin 1 evolved from its precursor, followed by evolution of Noelin 3 and Noelin 2 by gene duplication events. Myocilin might have evolved from Noelin 2 by gene duplication followed by exon fusion. Noelin 1 and Noelin 2 could be tested as candidate genes for eye diseases based on their expressions in the eye and shared olfactomedin domains with Myocilin in the C-termini of the respective proteins.
Mukhopadhyay
Arijit
A
Human Genetics & Genomics Division, Indian Institute of Chemical Biology, Kolkata, India.
Talukdar
Sangita
S
Bhattacharjee
Ashima
A
Ray
Kunal
K
D000595:Amino Acid Sequence; D000818:Animals; D001483:Base Sequence; D001921:Brain / Q000378:metabolism; D019295:Computational Biology; D003598:Cytoskeletal Proteins; D018076:DNA, Complementary / Q000235:genetics; D016208:Databases, Factual; D019143:Evolution, Molecular; D016326:Extracellular Matrix Proteins / Q000235:genetics*; D005136:Eye Proteins / Q000235:genetics*; D020440:Gene Duplication; D015870:Gene Expression / Q000502:physiology; D005902:Glaucoma, Open-Angle / Q000235:genetics*; D006023:Glycoproteins / Q000235:genetics*; D006801:Humans; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000235:genetics*; D017434:Protein Structure, Tertiary; D051381:Rats; D012689:Sequence Homology, Nucleic Acid; D000099179:Myocilin
D003598:Cytoskeletal Proteins; D018076:DNA, Complementary; D016326:Extracellular Matrix Proteins; D005136:Eye Proteins; D006023:Glycoproteins; D009419:Nerve Tissue Proteins; D000099179:Myocilin; C466064:OLFM3 protein, human; C081451:olfactomedin