RBP3

Retinol binding protein 3, interstitial
Identifiers
Symbols	RBP3 ; D10S64; D10S65; D10S66; IRBP; RBPI; RP66
External IDs	OMIM: 180290 MGI: 97878 HomoloGene: 9261 ChEMBL: 2831 GeneCards: RBP3 Gene
Gene ontology Molecular function • retinoid binding • serine-type peptidase activity • retinal binding • retinol binding Cellular component • extracellular region • extracellular space • interphotoreceptor matrix • extracellular vesicle Biological process • retinoid metabolic process • proteolysis • lipid metabolic process • transport • visual perception • phototransduction, visible light Sources: Amigo / QuickGO
RNA expression pattern
More reference expression data
Orthologs
Species	Human	Mouse
Entrez	5949	19661
Ensembl	ENSG00000265203	ENSMUSG00000041534
UniProt	P10745	P49194
RefSeq (mRNA)	NM_002900	NM_015745
RefSeq (protein)	NP_002891	NP_056560
Location (UCSC)	Chr 10: 47.35 – 47.36 Mb	Chr 14: 33.95 – 33.96 Mb
PubMed search

Retinol-binding protein 3, interstitial (RBP3), also known as IRBP is a protein that in humans is encoded by the RBP3 gene.^[1] RBP3 orthologs ^[2] have been identified in most eutherians except tenrecs and armadillos.

Function

The inter-photoreceptor retinoid-binding protein is a large glycoprotein known to bind retinoids and found primarily in the interphotoreceptor matrix of the retina between the retinal pigment epithelium and the photoreceptor cells. It is thought to transport retinoids between the retinal pigment epithelium and the photoreceptors, a critical role in the visual process.

Gene

The human IRBP gene is approximately 9.5 kbp in length and consists of four exons separated by three introns. The introns are 1.6-1.9 kbp long. The gene is transcribed by photoreceptor and retinoblastoma cells into an approximately 4.3-kilobase mRNA that is translated and processed into a glycosylated protein of 135,000 Da.

Structure

The amino acid sequence of human IRBP can be divided into four contiguous homology domains with 33-38% identity, suggesting a series of gene duplication events. In the gene, the boundaries of these domains are not defined by exon-intron junctions, as might have been expected. The first three homology domains and part of the fourth are all encoded by the first large exon, which is 3,180 base pairs long. The remainder of the fourth domain is encoded in the last three exons, which are 191, 143, and approximately 740 base pairs long, respectively.^[1]

Application

The rbp3 gene is commonly used in animals as a nuclear DNA phylogenetic marker.^[2] The exon 1 has first been used in a pioneer study to provide evidence for monophyly of Chiroptera.^[3] Then, it has been used to infer the phylogeny of placental mammal orders,^[4][5] and of the major clades of Rodentia,^[6] Macroscelidea,^[7] and Primates.^[8] RBP3 is also useful at lower taxonomic levels, e.g., in muroid rodents^[9] and Malagasy primates,^[10] at the phylogeography level in Geomys and Apodemus rodents,^[11][12] and even for carnivora species identification purposes.^[13]

Note that the RBP3 intron 1 has also been used to investigate the platyrrhine primates phylogenetics.^[14]

References

1. "Entrez Gene: RBP3 retinol binding protein 3, interstitial".
2. "OrthoMaM phylogenetic marker: RBP3 gene, exon 1".
3. Stanhope MJ, Czelusniak J, Si JS, Nickerson J, Goodman M (Jun 1992). "A molecular perspective on mammalian evolution from the gene encoding interphotoreceptor retinoid binding protein, with convincing evidence for bat monophyly". Molecular Phylogenetics and Evolution 1 (2): 148–60. doi:10.1016/1055-7903(92)90026-D. PMID 1342928.
4. Stanhope MJ, Smith MR, Waddell VG, Porter CA, Shivji MS, Goodman M (Aug 1996). "Mammalian evolution and the interphotoreceptor retinoid binding protein (IRBP) gene: convincing evidence for several superordinal clades". Journal of Molecular Evolution 43 (2): 83–92. doi:10.1007/BF02337352. PMID 8660440.
5. Madsen O, Scally M, Douady CJ, Kao DJ, DeBry RW, Adkins R, Amrine HM, Stanhope MJ, de Jong WW, Springer MS (Feb 2001). "Parallel adaptive radiations in two major clades of placental mammals". Nature 409 (6820): 610–4. doi:10.1038/35054544. PMID 11214318.
6. Huchon D, Madsen O, Sibbald MJ, Ament K, Stanhope MJ, Catzeflis F, de Jong WW, Douzery EJ (Jul 2002). "Rodent phylogeny and a timescale for the evolution of Glires: evidence from an extensive taxon sampling using three nuclear genes". Molecular Biology and Evolution 19 (7): 1053–65. doi:10.1093/oxfordjournals.molbev.a004164. PMID 12082125.
7. Douady CJ, Catzeflis F, Raman J, Springer MS, Stanhope MJ (Jul 2003). "The Sahara as a vicariant agent, and the role of Miocene climatic events, in the diversification of the mammalian order Macroscelidea (elephant shrews)". Proceedings of the National Academy of Sciences of the United States of America 100 (14): 8325–30. doi:10.1073/pnas.0832467100. PMC 166228. PMID 12821774.
8. Poux C, Douzery EJ (May 2004). "Primate phylogeny, evolutionary rate variations, and divergence times: a contribution from the nuclear gene IRBP". American Journal of Physical Anthropology 124 (1): 1–16. doi:10.1002/ajpa.10322. PMID 15085543.
9. Jansa SA, Weksler M (Apr 2004). "Phylogeny of muroid rodents: relationships within and among major lineages as determined by IRBP gene sequences". Molecular Phylogenetics and Evolution 31 (1): 256–76. doi:10.1016/j.ympev.2003.07.002. PMID 15019624.
10. Horvath JE, Weisrock DW, Embry SL, Fiorentino I, Balhoff JP, Kappeler P, Wray GA, Willard HF, Yoder AD (Mar 2008). "Development and application of a phylogenomic toolkit: resolving the evolutionary history of Madagascar's lemurs". Genome Research 18 (3): 489–99. doi:10.1101/gr.7265208. PMC 2259113. PMID 18245770.
11. Genoways HH, Hamilton MJ, Bell DM, Chambers RR, Bradley RD (2008). "Hybrid zones, genetic isolation, and systematics of pocket gophers (genus Geomys) in Nebraska". J. Mammal 89: 826–836. doi:10.1644/07-mamm-a-408.1.
12. Tomozawa M, Suzuki H (Mar 2008). "A trend of central versus peripheral structuring in mitochondrial and nuclear gene sequences of the Japanese wood mouse, Apodemus speciosus". Zoological Science 25 (3): 273–85. doi:10.2108/zsj.25.273. PMID 18393564.
13. Oliveira R, Castro D, Godinho R, Luikart G, Alves PC (June 2009). "Species identification using a small nuclear gene: application to sympatric wild carnivores from South-western Europe". Conserv. Genet. 11 (3): 1023–1032. doi:10.1007/s10592-009-9947-4.
14. Schneider H, Sampaio I, Harada ML, Barroso CM, Schneider MP, Czelusniak J, Goodman M (Jun 1996). "Molecular phylogeny of the New World monkeys (Platyrrhini, primates) based on two unlinked nuclear genes: IRBP intron 1 and epsilon-globin sequences". American Journal of Physical Anthropology 100 (2): 153–79. doi:10.1002/(SICI)1096-8644(199606)100:2<153::AID-AJPA1>3.0.CO;2-Z. PMID 8771309.

Further reading

• Fong SL, Fong WB, Morris TA, Kedzie KM, Bridges CD (Mar 1990). "Characterization and comparative structural features of the gene for human interstitial retinol-binding protein". The Journal of Biological Chemistry 265 (7): 3648–53. PMID 2303470.
• Albini A, Toffenetti J, Zhu Z, Chader GJ, Noonan DM (Sep 1990). "Hypomethylation of the interphotoreceptor retinoid-binding protein (IRBP) promotor and first exon is linked to expression of the gene". Nucleic Acids Research 18 (17): 5181–7. doi:10.1093/nar/18.17.5181. PMC 332140. PMID 2402443.
• Liou GI, Ma DP, Yang YW, Geng L, Zhu C, Baehr W (May 1989). "Human interstitial retinoid-binding protein. Gene structure and primary structure". The Journal of Biological Chemistry 264 (14): 8200–6. PMID 2542268.
• Si JS, Borst DE, Redmond TM, Nickerson JM (Aug 1989). "Cloning of cDNAs encoding human interphotoreceptor retinoid-binding protein (IRBP) and comparison with bovine IRBP sequences". Gene 80 (1): 99–108. doi:10.1016/0378-1119(89)90254-0. PMID 2792773.
• Nakamura Y, Lathrop M, Bragg T, Leppert M, O'Connell P, Jones C, Lalouel JM, White R (Nov 1988). "An extended genetic linkage map of markers for human chromosome 10". Genomics 3 (4): 389–92. doi:10.1016/0888-7543(88)90133-4. PMID 2907505.
• Fong SL, Bridges CD (Oct 1988). "Internal quadruplication in the structure of human interstitial retinol-binding protein deduced from its cloned cDNA". The Journal of Biological Chemistry 263 (30): 15330–4. PMID 3170584.
• Liou GI, Fong SL, Gosden J, van Tuinen P, Ledbetter DH, Christie S, Rout D, Bhattacharya S, Cook RG, Li Y (Jul 1987). "Human interstitial retinol-binding protein (IRBP): cloning, partial sequence, and chromosomal localization". Somatic Cell and Molecular Genetics 13 (4): 315–23. doi:10.1007/BF01534925. PMID 3455009.
• Fong SL, Cook RG, Alvarez RA, Liou GI, Landers RA, Bridges CD (Sep 1986). "N-terminal sequence homologies in interstitial retinol-binding proteins from 10 vertebrate species". FEBS Letters 205 (2): 309–12. doi:10.1016/0014-5793(86)80918-8. PMID 3743780.
• Redmond TM, Wiggert B, Robey FA, Chader GJ (Nov 1986). "Interspecies conservation of structure of interphotoreceptor retinoid-binding protein. Similarities and differences as adjudged by peptide mapping and N-terminal sequencing". The Biochemical Journal 240 (1): 19–26. doi:10.1042/bj2400019. PMC 1147370. PMID 3827838.
• Chen Y, Houghton LA, Brenna JT, Noy N (Aug 1996). "Docosahexaenoic acid modulates the interactions of the interphotoreceptor retinoid-binding protein with 11-cis-retinal". The Journal of Biological Chemistry 271 (34): 20507–15. doi:10.1074/jbc.271.34.20507. PMID 8702792.
• Shaw NS, Noy N (Feb 2001). "Interphotoreceptor retinoid-binding protein contains three retinoid binding sites". Experimental Eye Research 72 (2): 183–90. doi:10.1006/exer.2000.0945. PMID 11161734.
• Foltz DR, Nye JS (Aug 2001). "Hyperphosphorylation and association with RBP of the intracellular domain of Notch1". Biochemical and Biophysical Research Communications 286 (3): 484–92. doi:10.1006/bbrc.2001.5421. PMID 11511084.
• Howard OM, Dong HF, Su SB, Caspi RR, Chen X, Plotz P, Oppenheim JJ (Jun 2005). "Autoantigens signal through chemokine receptors: uveitis antigens induce CXCR3- and CXCR5-expressing lymphocytes and immature dendritic cells to migrate". Blood 105 (11): 4207–14. doi:10.1182/blood-2004-07-2697. PMC 1895027. PMID 15713799.

External links

• GeneReviews/NCBI/NIH/UW entry on Retinitis Pigmentosa Overview
• "Overview of the coding DNA and protein sequence alignments of the RBP3 marker". OrthoMaM – a biological database of orthologous mammalian markers. The rbp3 evolutionary marker can be found, together with the corresponding gene phylogeny