Interphotoreceptor retinoid-binding protein gene structure in tetrapods and teleost fish.
OBJECTIVE
The interphotoreceptor retinoid-binding protein (IRBP) gene possesses an unusual structure, encoding multiple Repeats, each consisting of about 300 amino acids. Our goals were to gain insight into the function of IRBP, and to test the current model for the evolution of IRBP, in which Repeats were replicated from a simpler ancestral gene.


METHODS
We employed a bioinformatics approach to analyze IRBP loci in recently completed or near-complete genome sequences of several vertebrates and nonvertebrate chordates. IRBP gene expression in zebrafish was evaluated by reverse transcriptase PCR (RT-PCR) and in situ mRNA hybridizations with gene-specific probes.


RESULTS
Patterns of exons and introns in the IRBP genes of tetrapods were highly similar, as were predicted amino acid sequences and Repeat structures. IRBP gene structure in teleost fish was more variable, and we report a new gene structure for two species, the Japanese puffer fish (Takifugu rubripes) and the zebrafish (Danio rerio). These teleost genomes contain a two-gene IRBP locus arranged head-to-tail in which the first gene, Gene 1, is intronless and contains a single large exon encoding three complete Repeats. It is followed by a second gene, Gene 2, which corresponds to the previously reported gene consisting of two Repeats spread across four exons and three introns. Each of the two zebrafish genes is transcribed. Gene 2 is expressed in the photoreceptors and RPE, and Gene 1 is expressed in the inner nuclear layer and weakly in the ganglion cell layer.


CONCLUSIONS
The tetrapod IRBP gene structure is highly conserved while the teleost fish gene structure was a surprise: It appears to be a two-gene locus with distinct Repeat organization in each open reading frame. This gene structure and gene expression data are consistent with possible neofunctionalization or sub-function partitioning of Gene 1 and Gene 2 in the zebrafish. We suggest that the two-gene locus in teleost fish arose as a consequence of either the known whole genome duplication or single gene tandem duplication.
Nickerson
John M
JM
Ophthalmology Department, Emory University, Atlanta, GA 30322, USA. litjn@emory.edu
Frey
Ruth A
RA
Ciavatta
Vincent T
VT
Stenkamp
Deborah L
DL
D000818:Animals; D001001:Anura / Q000235:genetics*; D001483:Base Sequence; D002645:Chickens / Q000235:genetics*; D043344:Chordata / Q000235:genetics; D002874:Chromosome Mapping; D017124:Conserved Sequence; D005091:Exons; D005136:Eye Proteins / Q000235:genetics* / Q000378:metabolism; D005399:Fishes / Q000235:genetics*; D006801:Humans; D007438:Introns; D008322:Mammals / Q000235:genetics*; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D010786:Photoreceptor Cells / Q000378:metabolism; D010857:Pigment Epithelium of Eye / Q000378:metabolism; D011487:Protein Conformation; D012091:Repetitive Sequences, Nucleic Acid; D012165:Retinal Ganglion Cells / Q000378:metabolism; D012177:Retinol-Binding Proteins / Q000235:genetics* / Q000378:metabolism; D023721:Tetraodontiformes; D015027:Zebrafish; D000099214:Retinol-Binding Proteins, Interstitial
D005136:Eye Proteins; D012177:Retinol-Binding Proteins; D000099214:Retinol-Binding Proteins, Interstitial