Y box binding protein 1

YBX1
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 1H95
Identifiers
Aliases	YBX1 , BP-8, CSDA2, CSDB, DBPB, MDR-NF1, NSEP-1, NSEP1, YB-1, YB1, CBF-A, EFI-A, Y-box binding protein 1
External IDs	OMIM: 154030; MGI: 99146; HomoloGene: 88707; GeneCards: YBX1; OMA:YBX1 - orthologs
Gene location (Human) Chr. Chromosome 1 (human) [1] Band 1p34.2 Start 42,682,418 bp [1] End 42,703,805 bp [1]
Gene location (Mouse) Chr. Chromosome 4 (mouse) [2] Band 4|4 D2.1 Start 119,135,178 bp [2] End 119,151,801 bp [2]
RNA expression pattern Bgee Human Mouse (ortholog) Top expressed in left testis right testis ganglionic eminence ventricular zone Achilles tendon gastrocnemius muscle muscle of thigh skeletal muscle tissue left ventricle stromal cell of endometrium Top expressed in Ileal epithelium primitive streak tail of embryo abdominal wall medial ganglionic eminence endothelial cell of lymphatic vessel seminiferous tubule choroid plexus of fourth ventricle migratory enteric neural crest cell maxillary prominence More reference expression data BioGPS n/a
Gene ontology Molecular function DNA binding DNA-binding transcription factor activity DNA-binding transcription activator activity, RNA polymerase II-specific RNA polymerase II cis-regulatory region sequence-specific DNA binding protein binding RNA binding nucleic acid binding GTPase binding double-stranded DNA binding single-stranded DNA binding chromatin binding DNA-binding transcription factor activity, RNA polymerase II-specific Cellular component cytoplasm CRD-mediated mRNA stability complex nuclear membrane intracellular membrane-bounded organelle U12-type spliceosomal complex nucleoplasm extracellular region cytoplasmic stress granule extracellular exosome nucleus histone pre-mRNA 3'end processing complex cytosol ribonucleoprotein complex Biological process CRD-mediated mRNA stabilization mRNA splicing, via spliceosome regulation of transcription, DNA-templated mRNA processing transcription by RNA polymerase II protein localization to cytoplasmic stress granule transcription, DNA-templated positive regulation of cell division positive regulation of transcription by RNA polymerase II in utero embryonic development RNA splicing negative regulation of striated muscle cell differentiation negative regulation of transcription by RNA polymerase II Notch signaling pathway cellular response to interleukin-7 Sources:Amigo / QuickGO
Orthologs Species Human Mouse Entrez 4904 22608 Ensembl ENSG00000065978 ENSMUSG00000028639 UniProt P67809 P62960 RefSeq (mRNA) NM_004559 NM_011732 RefSeq (protein) NP_004550 NP_035862 Location (UCSC) Chr 1: 42.68 – 42.7 Mb Chr 4: 119.14 – 119.15 Mb PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse

Y box binding protein 1 also known as Y-box transcription factor or nuclease-sensitive element-binding protein 1 is a protein that in humans is encoded by the YBX1 gene. ^[5] YBX1 is an RNA binding protein ^[6] that stabilises messenger RNAs modified with N6-methyladenosine. ^[7]

Clinical significance

YBX1 is a potential drug target in cancer therapy. ^[8] YB-1 helps the replication of adenovirus type 5, a commonly used vector in gene therapy. ^[8] Thus, YB-1 can cause an "oncolytic" effect in YB-1 positive cancer cells treated with adenoviruses.

DNA repair

The mitochondria of human cells possess a repair pathway for DNA base pair mismatches that is distinct from the DNA mismatch repair pathway of the nucleus. ^[9] This mitochondrial pathway includes participation of Y box binding protein 1 (designated YB-1 or YBX1), that likely acts in the mismatch binding and recognition steps of mismatch repair. ^[9]

Interactions

Y box binding protein 1 has been shown to interact with:

• ANKRD2, ^[10]
• CTCF, ^[11]
• P53, ^{[10] [12]}
• PCNA, ^[13]
• RBBP6, ^[14] and
• SFRS9. ^[15]

References

1. GRCh38: Ensembl release 89: ENSG00000065978 – Ensembl, May 2017
2. GRCm38: Ensembl release 89: ENSMUSG00000028639 – 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. EntrezGene 4904 YBX1 Y-box binding protein 1
6. Kwon E, Todorova K, Wang J, Horos R, Lee KK, Neel VA, et al. (April 2018). "The RNA-binding protein YBX1 regulates epidermal progenitors at a posttranscriptional level". Nature Communications. 9 (1) 1734. Bibcode:2018NatCo...9.1734K. doi:10.1038/s41467-018-04092-0. PMC   5928080 . PMID   29712925.
7. Feng M, Xie X, Han G, Zhang T, Li Y, Li Y, et al. (July 2021). "YBX1 is required for maintaining myeloid leukemia cell survival by regulating BCL2 stability in an m6A-dependent manner". Blood. 138 (1): 71–85. doi:10.1182/blood.2020009676. PMC   8667054 . PMID   33763698.
8. Lage H, Surowiak P, Holm PS (November 2008). "[YB-1 as a potential target in cancer therapy]". Der Pathologe (in German). 29 (Suppl 2): 187–190. doi: 10.1007/s00292-008-1030-2 . PMID   18773210.
9. deSouza-Pinto NC, Mason PA, Hashiguchi K, Weissman L, Tian J, Guay D, et al. (2009). "Novel DNA mismatch-repair activity involving YB-1 in human mitochondria". DNA Repair (Amst). 8 (6): 704–19. doi:10.1016/j.dnarep.2009.01.021. PMC   2693314 . PMID   19272840.
10. Kojic S, Medeot E, Guccione E, Krmac H, Zara I, Martinelli V, et al. (May 2004). "The Ankrd2 protein, a link between the sarcomere and the nucleus in skeletal muscle". Journal of Molecular Biology. 339 (2): 313–325. doi:10.1016/j.jmb.2004.03.071. PMID   15136035.
11. Chernukhin IV, Shamsuddin S, Robinson AF, Carne AF, Paul A, El-Kady AI, et al. (September 2000). "Physical and functional interaction between two pluripotent proteins, the Y-box DNA/RNA-binding factor, YB-1, and the multivalent zinc finger factor, CTCF". The Journal of Biological Chemistry. 275 (38): 29915–29921. doi: 10.1074/jbc.M001538200 . PMID   10906122.
12. Okamoto T, Izumi H, Imamura T, Takano H, Ise T, Uchiumi T, et al. (December 2000). "Direct interaction of p53 with the Y-box binding protein, YB-1: a mechanism for regulation of human gene expression". Oncogene. 19 (54): 6194–6202. doi: 10.1038/sj.onc.1204029 . PMID   11175333.
13. Ise T, Nagatani G, Imamura T, Kato K, Takano H, Nomoto M, et al. (January 1999). "Transcription factor Y-box binding protein 1 binds preferentially to cisplatin-modified DNA and interacts with proliferating cell nuclear antigen". Cancer Research. 59 (2): 342–346. PMID   9927044.
14. Chibi M, Meyer M, Skepu A, G Rees DJ, Moolman-Smook JC, Pugh DJ (December 2008). "RBBP6 interacts with multifunctional protein YB-1 through its RING finger domain, leading to ubiquitination and proteosomal degradation of YB-1". Journal of Molecular Biology. 384 (4): 908–916. doi:10.1016/j.jmb.2008.09.060. PMID   18851979.
15. Raffetseder U, Frye B, Rauen T, Jürchott K, Royer HD, Jansen PL, et al. (May 2003). "Splicing factor SRp30c interaction with Y-box protein-1 confers nuclear YB-1 shuttling and alternative splice site selection". The Journal of Biological Chemistry. 278 (20): 18241–18248. doi: 10.1074/jbc.M212518200 . PMID   12604611.

Further reading

• Kolluri R, Torrey TA, Kinniburgh AJ (January 1992). "A CT promoter element binding protein: definition of a double-strand and a novel single-strand DNA binding motif". Nucleic Acids Research. 20 (1): 111–116. doi:10.1093/nar/20.1.111. PMC   5356827 . PMID   1738588.
• Kolluri R, Kinniburgh AJ (September 1991). "Full length cDNA sequence encoding a nuclease-sensitive element DNA binding protein". Nucleic Acids Research. 19 (17): 4771. doi:10.1093/nar/19.17.4771. PMC   328725 . PMID   1891370.
• Sakura H, Maekawa T, Imamoto F, Yasuda K, Ishii S (December 1988). "Two human genes isolated by a novel method encode DNA-binding proteins containing a common region of homology". Gene. 73 (2): 499–507. doi:10.1016/0378-1119(88)90514-8. PMID   2977358.
• Didier DK, Schiffenbauer J, Woulfe SL, Zacheis M, Schwartz BD (October 1988). "Characterization of the cDNA encoding a protein binding to the major histocompatibility complex class II Y box". Proceedings of the National Academy of Sciences of the United States of America. 85 (19): 7322–7326. Bibcode:1988PNAS...85.7322D. doi: 10.1073/pnas.85.19.7322 . PMC   282178 . PMID   3174636.
• Kudo S, Mattei MG, Fukuda M (July 1995). "Characterization of the gene for dbpA, a family member of the nucleic-acid-binding proteins containing a cold-shock domain". European Journal of Biochemistry. 231 (1): 72–82. doi:10.1111/j.1432-1033.1995.tb20672.x. PMID   7628487.
• Lloberas J, Maki RA, Celada A (September 1995). "Repression of major histocompatibility complex I-A beta gene expression by dbpA and dbpB (mYB-1) proteins". Molecular and Cellular Biology. 15 (9): 5092–5099. doi:10.1128/mcb.15.9.5092. PMC   230756 . PMID   7651426.
• Chen NN, Chang CF, Gallia GL, Kerr DA, Johnson EM, Krachmarov CP, et al. (February 1995). "Cooperative action of cellular proteins YB-1 and Pur alpha with the tumor antigen of the human JC polyomavirus determines their interaction with the viral lytic control element". Proceedings of the National Academy of Sciences of the United States of America. 92 (4): 1087–1091. Bibcode:1995PNAS...92.1087C. doi: 10.1073/pnas.92.4.1087 . PMC   42642 . PMID   7862639.
• Horwitz EM, Maloney KA, Ley TJ (May 1994). "A human protein containing a "cold shock" domain binds specifically to H-DNA upstream from the human gamma-globin genes". The Journal of Biological Chemistry. 269 (19): 14130–14139. doi: 10.1016/S0021-9258(17)36764-9 . PMID   8188694.
• Kashanchi F, Duvall JF, Dittmer J, Mireskandari A, Reid RL, Gitlin SD, et al. (January 1994). "Involvement of transcription factor YB-1 in human T-cell lymphotropic virus type I basal gene expression". Journal of Virology. 68 (1): 561–565. doi:10.1128/JVI.68.1.561-565.1994. PMC   236322 . PMID   8254772.
• Makino Y, Ohga T, Toh S, Koike K, Okumura K, Wada M, et al. (May 1996). "Structural and functional analysis of the human Y-box binding protein (YB-1) gene promoter". Nucleic Acids Research. 24 (10): 1873–1878. doi:10.1093/nar/24.10.1873. PMC   145870 . PMID   8657568.
• Funke B, Zuleger B, Benavente R, Schuster T, Goller M, Stévenin J, et al. (October 1996). "The mouse poly(C)-binding protein exists in multiple isoforms and interacts with several RNA-binding proteins". Nucleic Acids Research. 24 (19): 3821–3828. doi:10.1093/nar/24.19.3821. PMC   146158 . PMID   8871564.
• Koike K, Uchiumi T, Ohga T, Toh S, Wada M, Kohno K, et al. (November 1997). "Nuclear translocation of the Y-box binding protein by ultraviolet irradiation". FEBS Letters. 417 (3): 390–394. Bibcode:1997FEBSL.417..390K. doi: 10.1016/S0014-5793(97)01296-9 . PMID   9409758. S2CID   24656107.
• Toh S, Nakamura T, Ohga T, Koike K, Uchiumi T, Wada M, et al. (January 1998). "Genomic organization of the human Y-box protein (YB-1) gene". Gene. 206 (1): 93–97. doi:10.1016/S0378-1119(97)00570-2. PMID   9461420.
• Sawaya BE, Khalili K, Amini S (February 1998). "Transcription of the human immunodeficiency virus type 1 (HIV-1) promoter in central nervous system cells: effect of YB-1 on expression of the HIV-1 long terminal repeat". The Journal of General Virology. 79. 79 (2): 239–246. doi: 10.1099/0022-1317-79-2-239 . PMID   9472608.
• Mertens PR, Alfonso-Jaume MA, Steinmann K, Lovett DH (December 1998). "A synergistic interaction of transcription factors AP2 and YB-1 regulates gelatinase A enhancer-dependent transcription". The Journal of Biological Chemistry. 273 (49): 32957–32965. doi: 10.1074/jbc.273.49.32957 . PMID   9830047.
• Ise T, Nagatani G, Imamura T, Kato K, Takano H, Nomoto M, et al. (January 1999). "Transcription factor Y-box binding protein 1 binds preferentially to cisplatin-modified DNA and interacts with proliferating cell nuclear antigen". Cancer Research. 59 (2): 342–346. PMID   9927044.
• Safak M, Gallia GL, Khalili K (April 1999). "Reciprocal interaction between two cellular proteins, Puralpha and YB-1, modulates transcriptional activity of JCVCY in glial cells". Molecular and Cellular Biology. 19 (4): 2712–2723. doi:10.1128/mcb.19.4.2712. PMC   84064 . PMID   10082537.
• Kelm RJ, Cogan JG, Elder PK, Strauch AR, Getz MJ (May 1999). "Molecular interactions between single-stranded DNA-binding proteins associated with an essential MCAT element in the mouse smooth muscle alpha-actin promoter". The Journal of Biological Chemistry. 274 (20): 14238–14245. doi: 10.1074/jbc.274.20.14238 . PMID   10318844.
• Safak M, Gallia GL, Ansari SA, Khalili K (December 1999). "Physical and functional interaction between the Y-box binding protein YB-1 and human polyomavirus JC virus large T antigen". Journal of Virology. 73 (12): 10146–10157. doi:10.1128/JVI.73.12.10146-10157.1999. PMC   113067 . PMID   10559330.
• Ansari SA, Safak M, Gallia GL, Sawaya BE, Amini S, Khalili K (October 1999). "Interaction of YB-1 with human immunodeficiency virus type 1 Tat and TAR RNA modulates viral promoter activity". The Journal of General Virology. 80. 80 (10): 2629–2638. doi: 10.1099/0022-1317-80-10-2629 . PMID   10573156.
• Basaki Y, Hosoi F, Oda Y, Fotovati A, Maruyama Y, Oie S, et al. (April 2007). "Akt-dependent nuclear localization of Y-box-binding protein 1 in acquisition of malignant characteristics by human ovarian cancer cells". Oncogene. 26 (19): 2736–2746. doi: 10.1038/sj.onc.1210084 . PMID   17072343.

External links

• YBX1+protein,+human at the U.S. National Library of Medicine Medical Subject Headings (MeSH)

This article incorporates text from the United States National Library of Medicine, which is in the public domain.