IRX1 explained
Iroquois-class homeodomain protein IRX-1, also known as Iroquois homeobox protein 1, is a protein that in humans is encoded by the IRX1 gene.[1] [2] All members of the Iroquois (IRO) family of proteins share two highly conserved features, encoding both a homeodomain and a characteristic IRO sequence motif.[3] Members of this family are known to play numerous roles in early embryo patterning. IRX1 has also been shown to act as a tumor suppressor gene in several forms of cancer.[4] [5] [6] [7]
Role in development
IRX1 is a member of the Iroquois homeobox gene family. Members of this family play multiple roles during pattern formation in embryos of numerous vertebrate and invertebrate species.[8] IRO genes are thought to function early in development to define large territories, and again later in development for further patterning specification. Experimental data suggest roles for IRX1 in vertebrates may include development and patterning of lungs, limbs, heart, eyes, and nervous system.[9] [10] [11] [12] [13] [14]
Gene
Overview
IRX1 is located on the forward DNA strand (see Sense (molecular biology)) of chromosome 5, from position 3596054 - 3601403 at the 5p15.3 location. The human gene product is a 1858 base pair mRNA with 4 predicted exons in humans.[15] Promoter analysis was performed using El Dorado through the Genomatix software page.[16] The predicted promoter region spans 1040 base pairs from position 3595468 through 3595468 on the forward strand of chromosome 5.
Gene neighborhood
IRX1 is relatively isolated, with no other protein coding genes found from position 3177835 – 5070004.
Expression
Microarray and RNA seq data suggest that IRX1 is ubiquitously expressed at low levels in adult tissues, with the highest relative levels of expression occurring in the heart, adipose, kidney, and breast tissues.[17] [18] Moderate to high levels are also indicated in the lung, prostate and stomach.[19] Promoter analysis with the El Dorado program from Genomatix predicted that IRX1 expression is regulated by factors that include E2F cell cycle regulators, NRF1, and ZF5,[20] and brachyury. Expression data from human, mouse, and developing mouse brains are available though the Allen Brain Atlas.[21]
Protein
Properties and characteristics
The mature IRX1 protein has 480 amino acid residues, with a molecular mass of 49,600 daltons and an isoelectric point of 5.7. A BLAST search revealed that IRX1 contains two highly conserved domains: a homeodomain and a characteristic IRO motif of unknown function.[22] The homeodomain belongs to the TALE (three amino acid loop extension) class of homeodomains, and is characterized by the addition of three extra amino acids between the first and second helix of three alpha helices that comprise the domain.[23] The presence of this well characterized homeodomain strongly suggests that IRX1 acts as a transcription factor. This is further supported by the predicted localization of IRX1 to the nucleus.[24] The IRO motif is a region downstream of the homeodomain that is found only in members of the Iroquois-class homeodomain proteins, though its function is poorly understood. However, its similarity to an internal region of the Notch receptor protein suggests that it may be involved with protein-protein interaction. In addition to these two characteristic domains, IRX1 contains a third domain from the HARE-HTH superfamily[25] fused to the C-terminal end of the homeodomain.[26] This domain adopts a winged helix-turn-helix fold predicted to bind DNA, and is thought to play a role in recruiting effector activities to DNA. Several forms of post-translational modification are predicted, including SUMOylation, C-mannosylation, and phosphorylation, using bioinformatics tools from ExPASy.[27] Bioinformatic analysis of IRX1 with the NetPhos tool predicted 71 potential phosphorylation sites throughout the protein.[28]
Protein Interactions
Potential protein interacting partners for IRX1 were found using computational tools. The STRING database lists nine putative interacting partners supported by text mining evidence, though closer analysis of the results shows little support for most of these predicted interactions.[29] However, it is possible that one of these proteins, CDKN1A, is involved in the predicted regulation of IRX1 by E2F cell cycle regulators.
Conservation
Orthologs
IRX1 has a high degree of conservation across vertebrate and invertebrate species. The entire protein is more fully conserved through vertebrate species, while only the homeodomain and IRO motif are conserved in more distant homologs.Homologous sequences were found in species as distantly related to humans as the pig roundworm Ascaris suum, from the family Ascarididae, using BLAST and the ALIGN tool through the San Diego Super Computer Biology Workbench. The following is a table describing the evolutionary conservation of IRX1.
| Organism Common Name | Divergence from Humans (MYA) [30] | NCBI Protein Accession Number | Sequence Identity | Protein Length | Common Gene Name |
---|
| Humans | -- | NP_077313 | 100% | 480 | IRX-1 |
Pongo abelii[31] | Sumatran Orangutan | 15.7 | XP_002815448 | 99% | 480 | IRX-1 |
Bos taurus[32] | Cattle | 94.2 | XP_002696496 | 92.3% | 476 | IRX-1 |
Mus musculus[33] | House Mouse | 92.3 | NP_034703 | 91.5% | 480 | IRX-1 |
Rattus norvegicus[34] | Brown rat | 92.3 | NP_001100801 | 90.4% | 480 | IRX-1 |
Gallus gallus[35] | Red Junglefowl | 296 | NP_001025509 | 72.9% | 467 | IRX-1 |
Xenopus tropicalis[36] | Western clawed frog | 371.2 | NP_001188351 | 68% | 467 | IRX-1 |
Latimeria chalumnae[37] | West Indian Ocean coelacanth | 441.9 | XP_006002089 | 65.1% | 460 | Irx-1-A-like isoform X1 |
Danio rerio[38] | Zebrafish | 400.1 | NP_997067 | 61.1% | 426 | Irx-1 isoform 1 |
Taeniopygia guttata[39] | Zebra finch | 296 | XP_002189063 | 59.7% | 400 | Irx-1-A-like |
Astyanax mexicanus[40] | Mexican tetra | 400.1 | XP_007254591.1 | 58% | 450 | IRX-1 |
Ophiophagus hannah[41] | King cobra | 296 | ETE68928 | 54.5% | 387 | Irx-1-A partial |
Ovis aries[42] | Sheep | 94.2 | XP_004017207 | 43.3% | 260 | IRX-1 |
Condylura cristata[43] | Star-nosed mole | 94.2 | XP_004678440 | 41.7% | 342 | IRX-1 |
Branchiostoma floridae[44] | Lancelet | 713.2 | ACF10237.1 | 35.5% | 461 | Iroquois A isoform 1 |
Strongylocentrotus purpuratus[45] | Purple sea urchin | 742.9 | NP_001123285 | 31.7% | 605 | Iroquois homeobox A |
Ascaris suum[46] | Pig roundworm | 937.5 | F1KXE6 | 29% | 444 | IRX-1 |
Caenorhabditis elegans[47] | Nematode roundworm | 937.5 | NP_492533.2 | 28.6% | 377 | IRX-1 |
Drosophila melanogaster[48] | Fruit fly | 782.7 | NP_524045 | 27% | 717 | Araucan isoform A |
|
Paralogs
IRX1 is one of six members of the Iroquois-class homeodomain proteins found in humans: IRX2, IRX3, IRX4, IRX5, and IRX6. IRX1, IRX2, and IRX4 are found on human chromosome 5, and their orientation corresponds to that of IRX3, IRX5, and IRX6 found on human chromosome 16. It is thought that the genomic organization of IRO genes in conserved gene clusters allows for coregulation and enhancer sharing during development.
Further reading
- Lam CY, Tam PO, Fan DS, Fan BJ, Wang DY, Lee CW, Pang CP, Lam DS . A genome-wide scan maps a novel high myopia locus to 5p15 . Investigative Ophthalmology & Visual Science . 49 . 9 . 3768–3778 . September 2008 . 18421076 . 10.1167/iovs.07-1126 .
- Cirulli ET, Kasperaviciūte D, Attix DK, Need AC, Ge D, Gibson G, Goldstein DB . Common genetic variation and performance on standardized cognitive tests . European Journal of Human Genetics . 18 . 7 . 815–820 . July 2010 . 20125193 . 2987367 . 10.1038/ejhg.2010.2 .
- Trynka G, Zhernakova A, Romanos J, Franke L, Hunt KA, Turner G, Bruinenberg M, Heap GA, Platteel M, Ryan AW, de Kovel C, Holmes GK, Howdle PD, Walters JR, Sanders DS, Mulder CJ, Mearin ML, Verbeek WH, Trimble V, Stevens FM, Kelleher D, Barisani D, Bardella MT, McManus R, van Heel DA, Wijmenga C . Coeliac disease-associated risk variants in TNFAIP3 and REL implicate altered NF-kappaB signalling . Gut . 58 . 8 . 1078–1083 . August 2009 . 19240061 . 10.1136/gut.2008.169052 . 17111427 .
- Bonaldo MF, Lennon G, Soares MB . Normalization and subtraction: two approaches to facilitate gene discovery . Genome Research . 6 . 9 . 791–806 . September 1996 . 8889548 . 10.1101/gr.6.9.791 . free .
- Lewis MT, Ross S, Strickland PA, Snyder CJ, Daniel CW . Regulated expression patterns of IRX-2, an Iroquois-class homeobox gene, in the human breast . Cell and Tissue Research . 296 . 3 . 549–554 . June 1999 . 10370142 . 10.1007/s004410051316 . 37046813 .
- Bennett KL, Karpenko M, Lin MT, Claus R, Arab K, Dyckhoff G, Plinkert P, Herpel E, Smiraglia D, Plass C . Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma . Cancer Research . 68 . 12 . 4494–4499 . June 2008 . 18559491 . 10.1158/0008-5472.CAN-07-6509 . free .
Notes and References
- Web site: Entrez Gene: iroquois homeobox 1 .
- Ogura K, Matsumoto K, Kuroiwa A, Isobe T, Otoguro T, Jurecic V, Baldini A, Matsuda Y, Ogura T . Cloning and chromosome mapping of human and chicken Iroquois (IRX) genes . Cytogenetics and Cell Genetics . 92 . 3–4 . 320–325 . 2001 . 11435706 . 10.1159/000056921 . 46509502 .
- Cavodeassi F, Modolell J, Gómez-Skarmeta JL . The Iroquois family of genes: from body building to neural patterning . Development . 128 . 15 . 2847–2855 . August 2001 . 11532909 . 10.1242/dev.128.15.2847 . free . 10261/198505 .
- Bennett KL, Karpenko M, Lin MT, Claus R, Arab K, Dyckhoff G, Plinkert P, Herpel E, Smiraglia D, Plass C . Frequently methylated tumor suppressor genes in head and neck squamous cell carcinoma . Cancer Research . 68 . 12 . 4494–4499 . June 2008 . 18559491 . 10.1158/0008-5472.CAN-07-6509 . free .
- Marcinkiewicz KM, Gudas LJ . Altered epigenetic regulation of homeobox genes in human oral squamous cell carcinoma cells . Experimental Cell Research . 320 . 1 . 128–143 . January 2014 . 24076275 . 3880227 . 10.1016/j.yexcr.2013.09.011 .
- Guo X, Liu W, Pan Y, Ni P, Ji J, Guo L, Zhang J, Wu J, Jiang J, Chen X, Cai Q, Li J, Zhang J, Gu Q, Liu B, Zhu Z, Yu Y . Homeobox gene IRX1 is a tumor suppressor gene in gastric carcinoma . Oncogene . 29 . 27 . 3908–3920 . July 2010 . 20440264 . 10.1038/onc.2010.143 . 6638457 .
- Park SH, Kim SK, Choe JY, Moon Y, An S, Park MJ, Kim DS . Hypermethylation of EBF3 and IRX1 genes in synovial fibroblasts of patients with rheumatoid arthritis . Molecules and Cells . 35 . 4 . 298–304 . April 2013 . 23456299 . 3887890 . 10.1007/s10059-013-2302-0 .
- Kerner P, Ikmi A, Coen D, Vervoort M . Evolutionary history of the iroquois/Irx genes in metazoans . BMC Evolutionary Biology . 9 . 74 . 74 . April 2009 . 19368711 . 2674049 . 10.1186/1471-2148-9-74 . free . 2009BMCEE...9...74K .
- Choy SW, Cheng CW, Lee ST, Li VW, Hui MN, Hui CC, Liu D, Cheng SH . A cascade of irx1a and irx2a controls shh expression during retinogenesis . Developmental Dynamics . 239 . 12 . 3204–3214 . December 2010 . 21046643 . 10.1002/dvdy.22462 . 38099649 . free .
- Cheng CW, Yan CH, Choy SW, Hui MN, Hui CC, Cheng SH . Zebrafish homologue irx1a is required for the differentiation of serotonergic neurons . Developmental Dynamics . 236 . 9 . 2661–2667 . September 2007 . 17685478 . 10.1002/dvdy.21272 . 142831 . free .
- Becker MB, Zülch A, Bosse A, Gruss P . Irx1 and Irx2 expression in early lung development . Mechanisms of Development . 106 . 1–2 . 155–158 . August 2001 . 11472847 . 10.1016/S0925-4773(01)00412-9 . 16857354 .
- Bosse A, Zülch A, Becker MB, Torres M, Gómez-Skarmeta JL, Modolell J, Gruss P . Identification of the vertebrate Iroquois homeobox gene family with overlapping expression during early development of the nervous system . Mechanisms of Development . 69 . 1–2 . 169–181 . December 1997 . 9486539 . 10.1016/S0925-4773(97)00165-2 . free . 9655500 . 11858/00-001M-0000-0012-FE9F-5 .
- Christoffels VM, Keijser AG, Houweling AC, Clout DE, Moorman AF . Patterning the embryonic heart: identification of five mouse Iroquois homeobox genes in the developing heart . Developmental Biology . 224 . 2 . 263–274 . August 2000 . 10926765 . 10.1006/dbio.2000.9801 . free .
- Díaz-Hernández ME, Bustamante M, Galván-Hernández CI, Chimal-Monroy J . Irx1 and Irx2 are coordinately expressed and regulated by retinoic acid, TGFβ and FGF signaling during chick hindlimb development . PLOS ONE . 8 . 3 . e58549 . March 11, 2013 . 23505533 . 3594311 . 10.1371/journal.pone.0058549 . 2013PLoSO...858549D . free .
- Web site: NCBI Nucleotide: IRX1 . May 17, 2014.
- Web site: El Dorado . May 17, 2014 . Genomatix .
- Web site: BioGPS: IRX1 . 17 May 2014.
- Web site: GeneCards: IRX1 . 17 May 2014.
- Web site: GEO Profile: IRX1 . May 17, 2014.
- Numoto M, Yokoro K, Koshi J . ZF5, which is a Kruppel-type transcriptional repressor, requires the zinc finger domain for self-association . Biochemical and Biophysical Research Communications . 256 . 3 . 573–578 . March 1999 . 10080939 . 10.1006/bbrc.1999.0375 .
- Web site: Allen Brain Atlas . May 17, 2014.
- Web site: IRX1 Analysis . 8 May 2014 . Biology Workbench . San Diego Supercomputing Center- University of California San Diego.
- Bürglin TR . Analysis of TALE superclass homeobox genes (MEIS, PBC, KNOX, Iroquois, TGIF) reveals a novel domain conserved between plants and animals . Nucleic Acids Research . 25 . 21 . 4173–4180 . November 1997 . 9336443 . 147054 . 10.1093/nar/25.21.4173 .
- Web site: Expasy: Psort . 18 May 2014.
- Aravind L, Iyer LM . The HARE-HTH and associated domains: novel modules in the coordination of epigenetic DNA and protein modifications . Cell Cycle . 11 . 1 . 119–131 . January 2012 . 22186017 . 3272235 . 10.4161/cc.11.1.18475 .
- Web site: NCBI Protein: IRX1 . 18 May 2014.
- Web site: ExPASy: Bioinformatics Resource Portal . 18 May 2014.
- Web site: NetPhos . 18 May 2014.
- Web site: STRING Database . 5 May 2014.
- Web site: Time Tree .
- Web site: NCBI Nucleotide: XP_002815448 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_002696496 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_034703 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_001100801 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_001025509 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_001188351 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_006002089 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_997067 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_002189063 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_007254591.1 . 18 May 2014.
- Web site: NCBI Nucleotide: ETE68928 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_004017207 . 18 May 2014.
- Web site: NCBI Nucleotide: XP_004678440 . 18 May 2014.
- Web site: NCBI Nucleotide: ACF10237.1 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_001123285 . 18 May 2014.
- Web site: UniProt: F1KXE6 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_492533.2 . 18 May 2014.
- Web site: NCBI Nucleotide: NP_524045 . 18 May 2014.