Y-box-binding protein 1 (YBX1)
The protein contains 324 amino acids for an estimated molecular weight of 35924 Da.
DNA- and RNA-binding protein involved in various processes, such as translational repression, RNA stabilization, mRNA splicing, DNA repair and transcription regulation (PubMed:8188694, PubMed:10817758, PubMed:11698476, PubMed:14718551, PubMed:18809583, PubMed:31358969). Predominantly acts as a RNA-binding protein: binds preferentially to the 5'-[CU]CUGCG-3' RNA motif and specifically recognizes mRNA transcripts modified by C5-methylcytosine (m5C) (PubMed:19561594, PubMed:31358969). Promotes mRNA stabilization: acts by binding to m5C-containing mRNAs and recruiting the mRNA stability maintainer ELAVL1, thereby preventing mRNA decay (PubMed:10817758, PubMed:11698476, PubMed:31358969). Component of the CRD-mediated complex that promotes MYC mRNA stability (PubMed:19029303). Contributes to the regulation of translation by modulating the interaction between the mRNA and eukaryotic initiation factors (By similarity). Plays a key role in RNA composition of extracellular exosomes by defining the sorting of small non-coding RNAs, such as tRNAs, Y RNAs, Vault RNAs and miRNAs (PubMed:27559612, PubMed:29073095). Probably sorts RNAs in exosomes by recognizing and binding C5-methylcytosine (m5C)-containing RNAs (PubMed:28341602, PubMed:29073095). Acts as a key effector of epidermal progenitors by preventing epidermal progenitor senescence: acts by regulating the translation of a senescence-associated subset of cytokine mRNAs, possibly by binding to m5C-containing mRNAs (PubMed:29712925). (updated: Oct. 16, 2019)
Protein identification was indicated in the following studies:
- Goodman and co-workers. (2013) The proteomics and interactomics of human erythrocytes. Exp Biol Med (Maywood) 238(5), 509-518.
- Lange and co-workers. (2014) Annotating N termini for the human proteome project: N termini and Nα-acetylation status differentiate stable cleaved protein species from degradation remnants in the human erythrocyte proteome. J Proteome Res. 13(4), 2028-2044.
- Hegedűs and co-workers. (2015) Inconsistencies in the red blood cell membrane proteome analysis: generation of a database for research and diagnostic applications. Database (Oxford) 1-8.
- Wilson and co-workers. (2016) Comparison of the Proteome of Adult and Cord Erythroid Cells, and Changes in the Proteome Following Reticulocyte Maturation. Mol Cell Proteomics. 15(6), 1938-1946.
- Bryk and co-workers. (2017) Quantitative Analysis of Human Red Blood Cell Proteome. J Proteome Res. 16(8), 2752-2761.
- Chu and co-workers. (2018) Quantitative mass spectrometry of human reticulocytes reveal proteome-wide modifications during maturation. Br J Haematol. 180(1), 118-133.
Methods
The following articles were analysed to gather the proteome content of erythrocytes.
The gene or protein list provided in the studies were processed using the ID mapping API of Uniprot in September 2018. The number of proteins identified and mapped without ambiguity in these studies is indicated below.
Only Swiss-Prot entries (reviewed) were considered for protein evidence assignation.
| Publication | Identification 1 | Uniprot mapping 2 | Not mapped / Obsolete | TrEMBL | Swiss-Prot |
|---|---|---|---|---|---|
| Goodman (2013) | 2289 (gene list) | 2278 | 53 | 20599 | 2269 |
| Lange (2014) | 1234 | 1234 | 7 | 28 | 1224 |
| Hegedus (2015) | 2638 | 2622 | 0 | 235 | 2387 |
| Wilson (2016) | 1658 | 1528 | 170 | 291 | 1068 |
| d'Alessandro (2017) | 1826 | 1817 | 2 | 0 | 1815 |
| Bryk (2017) | 2090 | 2060 | 10 | 108 | 1942 |
| Chu (2018) | 1853 | 1804 | 55 | 362 | 1387 |
1 as available in the article and/or in supplementary material
2 uniprot mapping returns all protein isoforms as one entry
The compilation of older studies can be retrieved from the Red Blood Cell Collection database.
The data and differentiation stages presented below come from the proteomic study and analysis performed by our partners of the GReX consortium, more details are available in their published work.
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Biological Process
Cellular response to interleukin-7
CRD-mediated mRNA stabilization
Embryonic morphogenesis
Epidermis development
Gene expression
In utero embryonic development
MiRNA transport
MRNA splicing, via spliceosome
MRNA stabilization
Negative regulation of cellular senescence
Negative regulation of striated muscle cell differentiation
Negative regulation of transcription by RNA polymerase II
Negative regulation of translation
Notch receptor processing, ligand-dependent
Notch signaling pathway
Positive regulation of cell division
Positive regulation of transcription by RNA polymerase II
Protein localization to cytoplasmic stress granule
Regulation of gene expression
Regulation of transcription, DNA-templated
RNA splicing
RNA transport
Transcription by RNA polymerase II
TRNA transport
Cellular Component
CRD-mediated mRNA stability complex
Cytoplasm
Cytoplasmic stress granule
Cytosol
Extracellular exosome
Extracellular region
Histone pre-mRNA 3'end processing complex
Intracellular membrane-bounded organelle
Intracellular ribonucleoprotein complex
Messenger ribonucleoprotein complex
Nuclear membrane
Nucleoplasm
Nucleus
Ribonucleoprotein complex
U12-type spliceosomal complex
Molecular Function
C5-methylcytidine-containing RNA binding
Chromatin binding
DNA binding
DNA-binding transcription activator activity, RNA polymerase II-specific
DNA-binding transcription factor activity
DNA-binding transcription factor activity, RNA polymerase II-specific
Double-stranded DNA binding
GTPase binding
MiRNA binding
MRNA binding
Nucleic acid binding
Poly(A) RNA binding
Proximal promoter DNA-binding transcription activator activity, RNA polymerase II-specific
RNA binding
RNA polymerase II cis-regulatory region sequence-specific DNA binding
Sequence-specific double-stranded DNA binding
Single-stranded DNA binding
The reference OMIM entry for this protein is 154030
Nuclease-sensitive element-binding protein 1; nsep1
Major histocompatibility complex, class ii, y box-binding protein 1; yb1
Ybx1
Dna-binding protein b; dbpb
CLONING
The expression of HLA class II genes is regulated by a series of cis-acting elements and transacting factors. Several cis-acting elements have been identified and have been termed the Z box, X box, Y box, octamer, and TATA box. The Y box contains an inverted CCAAT box. Didier et al. (1988) isolated a cDNA encoding a Y box-binding protein designated YB1, or NSEP1. YB1 binding has an absolute requirement for the CCAAT box and relative specificity for the Y box. It has a molecular mass of 35,414 and contains 18% basic residues and putative nuclear localization signals. Didier et al. (1988) found an inverse correlation of YB1 and HLA-DR(beta) mRNA levels, suggesting that YB1 is a negative regulatory factor. By screening a human placenta cDNA expression library with DNA fragments containing either the human epidermal growth factor receptor (EGFR; 131550) enhancer or the human c-erbB2 (164870) promoter, Sakura et al. (1988) isolated cDNAs encoding DBPA (603437) and DBPB (NSEP1). The deduced DBPA and DBPB proteins share a central region in which 100 of 109 amino acids are identical between the 2 proteins. Northern blot analysis of HeLa cell RNA detected a 2.3-kb DBPB transcript. Spitkovsky et al. (1992) cloned cDNAs encoding YB1 by screening a HeLa cell cDNA expression library with an oligonucleotide containing a YB1 recognition site from the human papillomavirus type 18 enhancer. They stated that the sequences of their cDNAs are identical to the sequence of DBPB (Sakura et al., 1988) and nearly identical to the sequence of the YB1 cDNA isolated by Didier et al. (1988). Northern blot analysis of RNAs from a 24-week-old human fetus showed differential expression of the YB1 gene. Immunoblot analysis of HeLa cell and fibroblast extracts using antibodies against a YB1 synthetic peptide identified a 42-kD nuclear protein. Using an oligonucleotide containing the NSE of the MYC gene (190080) gene as probe, Kolluri and Kinniburgh (1991) cloned NSEP1 from a HeLa cell cDNA expression library. The deduced 322-amino acid protein contains 4 putative DNA-binding domains, 3 of which are rich in basic amino acids. Two of these basic regions, basic-1 and basic-2, form the double-strand DNA-binding domain of the protein. NSEP1 also has a pro/ser/thr-rich domain and an asp/glu/gln-rich domain, both of which are reminiscent of activation domains. It also contains an octapeptide single-strand DNA-binding motif that shares weak homology with the ribonucleoprotein consensus sequence of RNA-binding proteins. Kudo et al. (1995) isolated human cDNAs encoding DBPA and DBPB by screening for proteins that bind to the human leukosialin (182160) promoter. Northern blot analysis of human tissues detected the highest DBPB expression levels in skeletal muscle and heart. The authors isolated several DBPB processed pseudogenes and determined that they map to many different chromosomes. Coles et al. (1996) isolated human DBPA and DBPB cDNAs by screening for proteins that are able to bind to the repressor element in the human GMCSF (138960) promoter. The deduced 324-amino acid DBPB protein contains a central cold-shock domain (CSD), which is a highly conserved, approximately 100-amino acid domain with similarity to bacterial cold-shock proteins. Overexpression of DBPB led to repression of the GMCSF promoter.GENE FUNCTION
Fukada and Tonks (2003) found that overexpression of Yb1 in Rat1 cells resulted in increased Ptp1b (176885) expression. Depletion o ... More on the omim web site
Oct. 27, 2019: Protein entry updated
Automatic update: Entry updated from uniprot information.
Feb. 2, 2018: Protein entry updated
Automatic update: Uniprot description updated
Dec. 19, 2017: Protein entry updated
Automatic update: Uniprot description updated
Nov. 23, 2017: Protein entry updated
Automatic update: Uniprot description updated
June 20, 2017: Protein entry updated
Automatic update: comparative model was added.
March 16, 2016: Protein entry updated
Automatic update: OMIM entry 154030 was added.
Jan. 24, 2016: Protein entry updated
Automatic update: model status changed