RBP3

Retinol-binding protein 3, interstitial (RBP3), also known as interphotoreceptor retinoid-binding protein (IRBP), is a protein that in humans is encoded by the RBP3 gene.[5] RBP3 orthologs[6] have been identified in most eutherians except tenrecs and armadillos. A horizontal gene transfer from bacteria has been proposed to explain the evolution of the eye in chordates.[7]

RBP3
Identifiers
AliasesRBP3, D10S64, D10S65, D10S66, IRBP, RBPI, RP66, retinol binding protein 3
External IDsOMIM: 180290 MGI: 97878 HomoloGene: 9261 GeneCards: RBP3
Orthologs
SpeciesHumanMouse
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 MbChr 14: 33.68 – 33.69 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

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 (RPE) and the photoreceptor cells. It is thought to transport retinoids between the RPE and the photoreceptors, a critical role in the visual process.[8][9]

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.[5]

Application

The rbp3 gene is commonly used in animals as a nuclear DNA phylogenetic marker.[6] The exon 1 has first been used in a pioneer study to provide evidence for monophyly of Chiroptera.[10] Then, it has been used to infer the phylogeny of placental mammal orders,[11][12] and of the major clades of Rodentia,[13] Macroscelidea,[14] and Primates.[15] RBP3 is also useful at lower taxonomic levels, e.g., in muroid rodents[16] and Malagasy primates,[17] at the phylogeography level in Geomys and Apodemus rodents,[18][19] and even for carnivora species identification purposes.[20]

Note that the RBP3 intron 1 has also been used to investigate the platyrrhine primates phylogenetics.[21]

References
  1. GRCh38: Ensembl release 89: ENSG00000265203 - Ensembl, May 2017
  2. GRCm38: Ensembl release 89: ENSMUSG00000041534 - Ensembl, May 2017
  3. "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. "Entrez Gene: RBP3 retinol binding protein 3, interstitial".
  6. "OrthoMaM phylogenetic marker: RBP3 gene, exon 1".
  7. Kalluraya, Chinmay A.; Weitzel, Alexander J.; Tsu, Brian V.; Daugherty, Matthew D. (2023-04-18). "Bacterial origin of a key innovation in the evolution of the vertebrate eye". Proceedings of the National Academy of Sciences. 120 (16): e2214815120. doi:10.1073/pnas.2214815120. ISSN 0027-8424.
  8. Pennisi E (10 Apr 2023). "An ancient gene stolen from bacteria set the stage for human sight". Science. doi:10.1126/science.adi2029. Retrieved 11 Apr 2023.
  9. Kusakabe TG, Takimoto N, Jin M, Tsuda M (Oct 2009). "Evolution and the origin of the visual retinoid cycle in vertebrates". Philosophical Transactions B. 364 (1531): 2897–2910. doi:10.1098/rstb.2009.0043. PMC 2781855.
  10. 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.
  11. 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. S2CID 25865281.
  12. 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. S2CID 4398233.
  13. 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.
  14. 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.
  15. 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): 01–16. doi:10.1002/ajpa.10322. PMID 15085543.
  16. 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.
  17. 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.
  18. 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 (4): 826–836. doi:10.1644/07-mamm-a-408.1.
  19. 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. S2CID 38824060.
  20. 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. S2CID 21422211.
  21. 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
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