Affinage

YBX3

Y-box-binding protein 3 · UniProt P16989

Length
372 aa
Mass
40.1 kDa
Annotated
2026-04-28
100 papers in source corpus 31 papers cited in narrative 31 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

YBX3 (also known as ZONAB/DbpA/CSDA) is a cold shock domain-containing protein that functions as both a transcription factor and an mRNA stability factor, coupling cell density sensing at tight junctions to the control of proliferation, differentiation, and amino acid metabolism. At tight junctions, YBX3 is sequestered by ZO-1/ZO-2 and regulated by competing interactions with CDK4, RalA, GEF-H1/RhoA, Apg-2, and symplekin; release from this junctional pool permits nuclear translocation, where YBX3 activates proliferative gene promoters (cyclin D1, PCNA) and represses differentiation-associated targets (megalin, cubilin, AML1, claudin-5, occludin) (PMID:12566432, PMID:16508013, PMID:19328795, PMID:20133480, PMID:26106824). As an RNA-binding protein, YBX3 directly binds and stabilizes mRNAs encoding amino acid transporters (SLC7A5, SLC3A2, SLC1A5) and metabolic regulators (Pparg), thereby maintaining intracellular amino acid pools and supporting processes including brown adipose thermogenesis and skeletal muscle differentiation (PMID:31189097, PMID:38159852, PMID:39481849). In vivo, tissue-specific loss of Ybx3 impairs brown fat thermogenesis and exacerbates diet-induced obesity, while in kidney it reduces fibrotic remodeling, underscoring context-dependent roles in metabolic homeostasis and tissue injury (PMID:39481849, PMID:37408260).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 1991 Medium

    Establishing the fundamental DNA-binding specificity of YBX3 resolved whether this cold shock domain protein preferentially recognized damaged versus intact DNA, revealing broad nucleic acid binding capacity with enhanced affinity for depurinated substrates.

    Evidence EMSA and competition assays with double-stranded, single-stranded, and abasic DNA substrates

    PMID:1923758

    Open questions at the time
    • No in vivo relevance to DNA repair demonstrated
    • Structural basis for depurinated DNA preference unknown
  2. 1997 Medium

    Discovery that YBX3 represses stress-induced grp78 transcription and activates the thymidine kinase promoter established its dual role as a context-dependent transcriptional activator and repressor.

    Evidence Reporter assays, EMSA, and Southwestern blots on grp78 and htk promoters; functional antagonism with YY1

    PMID:8972186 PMID:9419421

    Open questions at the time
    • No ChIP confirmation of endogenous promoter occupancy
    • Mechanisms determining activator versus repressor function unresolved
  3. 2003 High

    The finding that ZO-1 sequesters YBX3/ZONAB at tight junctions and that nuclear YBX3 controls CDK4 levels and cell proliferation established the paradigm of junctional retention as a mechanism coupling cell density to proliferative signaling.

    Evidence Co-immunoprecipitation, antisense/RNAi knockdown, ZO-1 overexpression with proliferation and cell density readouts in MDCK cells

    PMID:12566432

    Open questions at the time
    • Direct structural basis of ZO-1–ZONAB interaction debated; later work showed full-length ZO-1 does not directly bind ZONAB in vitro
    • Contribution of ZO-2/ZO-3 redundancy not yet appreciated
  4. 2006 High

    Identification of cyclin D1 and PCNA as direct transcriptional targets via ChIP, and discovery of symplekin as a nuclear co-factor and Apg-2 as a ZO-1 competitor, built a multi-component regulatory circuit explaining how YBX3 integrates junctional signals into G1/S progression.

    Evidence ChIP, reporter assays, RNAi, recombinant protein reconstitution in MCF-10A, MDCK, and Eph4 cells

    PMID:16407410 PMID:16508013 PMID:17158914

    Open questions at the time
    • No genome-wide target map at this stage
    • How symplekin modulates YBX3 DNA-binding specificity unknown
  5. 2009 High

    Demonstration that GEF-H1/RhoA signaling drives ZONAB nuclear translocation and that the symplekin/ZONAB complex represses AML1 and KLF4 to inhibit goblet cell differentiation extended the model from proliferation control to lineage decisions in intestinal epithelium.

    Evidence Co-IP, reporter assays, ChIP, EMSA, RNAi in epithelial and intestinal cell systems

    PMID:19328795 PMID:19730435

    Open questions at the time
    • In vivo intestinal phenotype of Ybx3 loss not examined
    • Whether GEF-H1 and symplekin pathways converge on the same ZONAB pool unclear
  6. 2010 High

    Extension to kidney proximal tubule cells and retinal pigment epithelium demonstrated that YBX3 represses differentiation markers (megalin, cubilin) and promotes EMT-like changes in vivo, generalizing its role beyond simple cell lines.

    Evidence ChIP, reporter assays, overexpression/knockdown in OK cells, lentiviral manipulation in mouse RPE

    PMID:20133480 PMID:21209887

    Open questions at the time
    • Genetic loss-of-function in kidney epithelium not performed at this stage
    • Downstream effectors of EMT phenotype not fully mapped
  7. 2014 High

    Findings that ZO-1, ZO-2, and ZO-3 redundantly stabilize ZONAB at junctions (with proteasomal degradation upon combined depletion) and that CFTR signals through ZO-1 to regulate ZONAB localization refined the junctional retention model and linked it to cystic fibrosis pathophysiology.

    Evidence Combined ZO-protein depletion, MG132 rescue, in vitro binding, CFTR KO mice and 3D culture

    PMID:24986862 PMID:25107366

    Open questions at the time
    • Identity of E3 ligase targeting ZONAB for proteasomal degradation unknown
    • Whether CFTR–ZO-1–ZONAB axis operates in human CF lung tissue not tested
  8. 2019 High

    iCLIP mapping and multi-omics integration revealed that YBX3 functions as an mRNA stability factor for amino acid transporter mRNAs (SLC7A5, SLC3A2), fundamentally expanding its role from transcription factor to post-transcriptional regulator of cellular metabolism.

    Evidence iCLIP, integrated proteomics and transcriptomics, mRNA stability assays upon YBX3 depletion

    PMID:31189097

    Open questions at the time
    • Structural basis for mRNA target selectivity unresolved
    • Relative contribution of transcriptional versus post-transcriptional roles in the same cell type not quantified
  9. 2023 High

    Multiple studies established that non-coding RNAs (circSERPINE2, lncRNA BLACAT3) regulate YBX3 localization and activity, that YBX3 stabilizes SLC1A5 mRNA in muscle, and that Ybx3-deficient mice are protected from renal fibrosis — collectively demonstrating tissue-specific in vivo functions and RNA-mediated regulation.

    Evidence RNA pulldown/MS, RIP, 3ʹ UTR reporters, ChIP, Ybx3 KO mice with UUO model, skeletal muscle differentiation assays

    PMID:37408260 PMID:37612524 PMID:37831180 PMID:38159852

    Open questions at the time
    • Global landscape of regulatory RNAs controlling YBX3 unknown
    • Whether fibrosis role is transcriptional or post-transcriptional not distinguished
  10. 2024 High

    BAT-specific Ybx3 manipulation demonstrated that YBX3-mediated stabilization of Slc3a2 and Pparg mRNAs drives BCAA catabolism and thermogenesis, directly linking YBX3 mRNA stabilization to systemic metabolic control.

    Evidence AAV-mediated BAT-specific KD/OE in mice, transcriptomics, mRNA stability assays, metabolic phenotyping

    PMID:39481849

    Open questions at the time
    • Whether YBX3 also controls thermogenesis through transcriptional targets not excluded
    • Mechanism by which YBX3 is regulated in response to cold or dietary cues unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • Key open questions include: the structural basis for YBX3's dual DNA/RNA-binding target selectivity; the identity of the E3 ligase mediating its proteasomal turnover upon loss of junctional anchoring; how its transcriptional and mRNA-stabilizing functions are coordinated in the same cell; and the full scope of its in vivo metabolic roles across tissues.
  • No high-resolution structure of YBX3 bound to mRNA or DNA target
  • E3 ligase for ZONAB degradation unidentified
  • No systematic in vivo comparison of transcriptional versus post-transcriptional contributions

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140110 transcription regulator activity 8 GO:0003677 DNA binding 7 GO:0003723 RNA binding 4 GO:0098772 molecular function regulator activity 2
Localization
GO:0005634 nucleus 10 GO:0005886 plasma membrane 4 GO:0005829 cytosol 3
Pathway
R-HSA-74160 Gene expression (Transcription) 7 R-HSA-1640170 Cell Cycle 4 R-HSA-8953854 Metabolism of RNA 4 R-HSA-1500931 Cell-Cell communication 3 R-HSA-162582 Signal Transduction 3 R-HSA-382551 Transport of small molecules 3
Partners
ARHGEF2CDK4HSPA4RALASYMPKTJP1TJP2YBX1
Complex memberships
CHK2/YBX1/YBX3 hubsymplekin/ZONAB complex

Evidence

Reading pass · 31 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2003 ZONAB (YBX3) associates with CDK4, and its nuclear localization (regulated by the tight junction protein ZO-1) controls nuclear CDK4 levels and epithelial cell proliferation and cell density. Co-immunoprecipitation, antisense/RNAi knockdown, ZO-1 overexpression with proliferation and cell density readouts in MDCK cells The Journal of cell biology High 12566432
2006 ZONAB (YBX3) directly regulates transcription of PCNA and cyclin D1 by binding to responsive elements in their promoters, thereby promoting G1/S-phase progression and epithelial cell differentiation. cDNA microarray screening, chromatin immunoprecipitation (ChIP), reporter gene assays, RNAi knockdown and overexpression in MCF-10A and MDCK cells Molecular and cellular biology High 16508013
1997 Human YBX3 (dbpA) binds to the lower strand of the grp78 core promoter stress-inducible change region (SICR) and represses stress-induced grp78 promoter activity; dbpA interacts with YY1 and antagonizes YY1-mediated transcriptional activation. Expression library screening, gel shift assays, cotransfection reporter assays, Southwestern blot Molecular and cellular biology Medium 8972186
1991 YBX3/dbpA binds to double-stranded, single-stranded, and abasic (depurinated) DNA, with preferential binding to depurinated DNA, and the extent of specificity is influenced by Mg2+. Phage expression library screening, electrophoretic mobility shift assays (EMSA), DNA binding competition assays Nucleic acids research Medium 1923758
1995 Human YBX3/dbpA gene encodes a protein localized both in the cytoplasm and nucleus (particularly at the perinuclear region), contains a cold shock domain encoded by exons 2–5, and has an alternative exon 6; the gene is located on chromosome 12p13.1. Immunofluorescence, Northern blot, in situ hybridization, genomic cloning and sequencing European journal of biochemistry Medium 7628487
1997 YBX3/dbpA overexpression stimulates human thymidine kinase (htk) promoter activity through the proximal CCAAT element (TKC1) in a serum-inducible manner. Recombinant protein binding assays, cell transfection reporter assays Cell growth & differentiation Medium 9419421
1999 A C-terminal 172 amino acid domain of YBX3/dbpA binds to CDK5 and strongly inhibits p35-activated CDK5 kinase activity, as well as CDK4/cyclin D1 activity; it does not interact with CDK2. Yeast two-hybrid screening of HeLa cDNA library, in vitro kinase inhibition assays FEBS letters Medium 10100871
2004 RalA (a Ras superfamily GTPase) interacts with ZONAB/YBX3 in a GTP-dependent manner; this interaction increases with epithelial cell density and relieves ZONAB-mediated transcriptional repression; oncogenic Ras alleviates ZONAB repression via RalA. Reverse Ras recruitment system (yeast), co-immunoprecipitation, reporter gene assays, cell density experiments The EMBO journal High 15592429
2004 YBX3/dbpA transcription is positively regulated by E2F1 through a sequence resembling an E2F binding site (-8 to -1) in the promoter region. E2F1 overexpression, promoter deletion and mutation analysis, luciferase reporter assays Biochemical and biophysical research communications Medium 15313206
2006 ZONAB/YBX3 forms a complex with the RNA processing factor symplekin in the nucleus of epithelial cells; this complex can be reconstituted with recombinant proteins; symplekin depletion reduces nuclear ZONAB accumulation and transcriptional activity, cyclin D1 expression, and proliferation. Co-immunoprecipitation, recombinant protein reconstitution, RNAi knockdown, reporter gene assays Journal of cell science High 17158914
2006 The heat-shock protein Apg-2 binds to the SH3 domain of ZO-1 and competes with ZONAB/YBX3 for ZO-1 binding, thereby modulating ZONAB transcriptional activity and G1/S phase progression in epithelial cells. Expression library screening, co-immunoprecipitation, in vitro competition binding assays, reporter gene assays, regulated knockdown Molecular biology of the cell High 16407410
2009 ZONAB/YBX3 associates with GEF-H1/Lfc at tight junctions; GEF-H1 overexpression drives ZONAB nuclear accumulation and transcriptional activation; RhoA signaling via GEF-H1 is required for ZONAB-dependent cyclin D1 promoter activity and expression. Co-immunoprecipitation, nuclear fractionation, reporter gene assays, RNAi knockdown EMBO reports High 19730435
2009 The symplekin/ZONAB (YBX3) complex represses AML1/Runx1 transcription; ZONAB binds to the AML1 gene promoter and represses KLF4 expression, thereby inhibiting intestinal goblet cell differentiation. RNAi knockdown, reporter gene assays, electrophoretic mobility shift assay (EMSA), chromatin immunoprecipitation (ChIP) Gastroenterology High 19328795
2010 ZONAB/YBX3 overexpression promotes proliferation and represses differentiation (megalin/cubilin expression, brush border, primary cilium) of proximal tubule cells; ZONAB binds to megalin and cubilin promoters as shown by ChIP and reporter assays. Overexpression, RNAi knockdown, ChIP, reporter gene assays, immunofluorescence in OK cells and mouse kidney Journal of the American Society of Nephrology High 20133480
2007 Accumulation of phosphatidylethanol (produced by phospholipase D from ethanol) disrupts claudin-1/ZO-1 association and induces nuclear translocation of ZONAB/YBX3, which mediates increased intestinal cell density. Phosphatidylethanol treatment, claudin-1 endocytosis assays, co-immunoprecipitation, nuclear fractionation, ZONAB knockdown, in vivo mouse colon analysis Molecular cancer research Medium 18025260
2014 CFTR interacts with ZO-1 via its PDZ-binding domain, and CFTR inhibition/knockdown induces nuclear translocation of ZONAB/YBX3, leading to upregulation of CCND1 and downregulation of ErbB2 transcription and impaired tubulogenesis. Co-immunoprecipitation, knockdown, 3D epithelial culture model, in vivo cftr-/- and cftrΔF508 mouse analysis Journal of cell science High 25107366
2014 ZO proteins (ZO-1, ZO-2, ZO-3) redundantly control the junctional retention and stability of ZONAB/YBX3; depletion of ZO-1 and ZO-2 together (but not individually) causes ZONAB cytoplasmic mislocalization and reduced expression rescued by proteasome inhibitor MG132; full-length ZO-1 does not directly interact with ZONAB in vitro. Depletion of individual and multiple ZO proteins by RNAi, ZO-1 KO Eph4 cells, in vitro binding assays, MG132 rescue, immunofluorescence The Journal of biological chemistry High 24986862
2010 Overexpression of ZONAB/YBX3 or knockdown of ZO-1 in retinal pigment epithelium (RPE) increases proliferation and induces an EMT-like phenotype in vivo, demonstrating that ZO-1 and ZONAB regulate RPE homeostasis. Lentiviral-mediated overexpression and knockdown in vivo, electron microscopy, fluorescein angiography, EMT marker expression PloS one Medium 21209887
2015 Bradykinin increases BTB permeability via NOS/NO signaling, which promotes ZONAB/YBX3 nuclear translocation; nuclear ZONAB then directly binds promoters of claudin-5 and occludin (verified by ChIP), downregulating their expression. NOS inhibitor treatment, ZONAB overexpression, ChIP assay, BTB permeability assay Biochemical and biophysical research communications Medium 26106824
2018 Hypoxia-inducible HIF1α induces miR-191, which suppresses ZONAB/YBX3 expression; miR-191 overexpression promotes G0/G1 arrest and apoptosis, effects abrogated by ZONAB overexpression, placing ZONAB downstream of HIF1α/miR-191 in hepatic IRI. miR-191 KO mice (CRISPR/Cas9), miR-191 overexpression/inhibition, ZONAB overexpression rescue, ChIP of HIF1α on miR-191 promoter, hepatic IRI mouse model Cell death and differentiation High 29769640
2005 YBX3/dbpA binds to DNase I hypersensitive site sequences at -250 bp in the MUC1 promoter and upregulates MUC1 promoter activity via this element in COS-7 cells. Expression library screening, EMSA, Southwestern blot, UV cross-linking, transient reporter gene assay Experimental cell research Medium 15893750
2019 YBX3 directly binds the mRNAs of SLC7A5 and SLC3A2 amino acid transporter genes and stabilizes these mRNAs, maintaining intracellular amino acid levels; YBX3 depletion specifically reduces SLC7A5/SLC3A2 substrates. YBX3 depletion with integrated proteomics and transcriptomics, iCLIP RNA binding site mapping, mRNA stability assays Cell reports High 31189097
2023 The lncRNA BLACAT3 recruits YBX3 to shuttle into the nucleus where it synergistically enhances NCF2 transcription, activating downstream NF-κB signaling to promote bladder cancer angiogenesis and hematogenous metastasis. RNA sequencing, mass spectrometry, functional assays, animal models, m6A microarray Oncogene Medium 37612524
2023 CircSERPINE2 interacts with YBX3 via the CCAUC motif, increasing the affinity of YBX3 for ZO-1 and sequestering YBX3 in the cytoplasm; this inhibits YBX3 binding to the PCNA promoter, ultimately affecting p21 ubiquitin-mediated degradation and promoting mesenchymal stem cell senescence. RNA pulldown followed by mass spectrometry, siRNA knockdown, overexpression, ChIP, co-immunoprecipitation, in vivo intra-articular injection Cellular and molecular life sciences High 37831180
2010 YBX3/CSDA overexpression in squamous cell carcinoma cells directly represses production of VEGF-A and VEGF-C by binding to hypoxia response elements (HRE) and serum response elements (SRE) in their promoters, inhibiting tumor angiogenesis and lymph node metastasis. YBX3/CSDA overexpression via plasmid transfection, VEGF-A/C measurement, in vivo tumor and metastasis assays Clinical & experimental metastasis Medium 20623179
2012 YBX3/CSDA physically interacts with Egr1 mRNA via a CSD element in its 3' UTR, and siRNA-mediated reduction of CSDA attenuates GnRH-regulated LHB reporter activity, establishing a posttranscriptional regulatory role for YBX3 in gonadotroph cells. RNA immunoprecipitation, siRNA knockdown, reporter gene assays with 3'UTR CSD element, transient expression studies Biology of reproduction Medium 22053098
2020 YBX3 interacts with the influenza A virus ribonucleoprotein (vRNP) complex; YBX3 overexpression inhibits vRNA synthesis and viral protein expression, while YBX3 knockdown increases virus growth, augments nuclear NP accumulation and primary transcription. Strep-tag affinity purification and mass spectrometry, overexpression, RNAi knockdown, vRNA synthesis measurement The Journal of general virology Medium 32553055
2023 YBX3 directly binds and stabilizes SLC1A5 mRNA via its 3' UTR in mouse skeletal muscle cells; YBX3 depletion specifically reduces SLC1A5 amino acid transporter substrates, reduces proliferation, and impairs differentiation of skeletal muscle cells. RIP (RNA immunoprecipitation), 3' UTR reporter assays, YBX3 depletion, amino acid measurement, proliferation and differentiation assays The Journal of biological chemistry High 38159852
2024 YBX3 stabilizes Slc3a2 and Pparg mRNAs in brown adipocytes, facilitating branched-chain amino acid (BCAA) influx and catabolism; BAT-specific Ybx3 loss dampens thermogenesis and worsens diet-induced obesity in mice, while overexpression is protective. AAV-mediated BAT-specific KD/OE, transcriptome analysis, mitochondrial stress test, in vitro KD/OE, mRNA stability analysis Molecular metabolism High 39481849
2023 YBX3 (DbpA) expression is induced in activated renal fibroblasts during obstructive nephropathy; Ybx3-deficient mice have reduced immune cell infiltration and extracellular matrix deposition in obstructed kidneys, establishing a role for YBX3 in renal fibrosis. UUO mouse model, Ybx3 KO mice, RNAseq, histological analysis of fibrosis and immune infiltration Cells Medium 37408260
2025 CHK2 (CHEK2), YBX1, and YBX3 form a regulatory hub in glioma cells; these proteins reciprocally regulate each other's expression and collectively repress pro-inflammatory gene transcription; ChIP-seq confirmed common inflammatory gene targets; targeting this hub with YBX1 inhibitor SU056 degrades the complex and enhances antigen presentation. Immunoprecipitation/mass spectrometry, phosphoproteomics, single-gene KO/OE, RNA-seq, ChIP-seq, pharmacological inhibition bioRxivpreprint Medium 40161682

Source papers

Stage 0 corpus · 100 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2003 The ZO-1-associated Y-box factor ZONAB regulates epithelial cell proliferation and cell density. The Journal of cell biology 311 12566432
2001 Expression of Borrelia burgdorferi OspC and DbpA is controlled by a RpoN-RpoS regulatory pathway. Proceedings of the National Academy of Sciences of the United States of America 293 11675503
2004 CsdA, a cold-shock RNA helicase from Escherichia coli, is involved in the biogenesis of 50S ribosomal subunit. Nucleic acids research 202 15148362
2006 Regulation of PCNA and cyclin D1 expression and epithelial morphogenesis by the ZO-1-regulated transcription factor ZONAB/DbpA. Molecular and cellular biology 181 16508013
2004 Physical and functional interactions among RNase E, polynucleotide phosphorylase and the cold-shock protein, CsdA: evidence for a 'cold shock degradosome'. Molecular microbiology 156 15554978
1993 DbpA: a DEAD box protein specifically activated by 23s rRNA. The EMBO journal 139 8253085
2001 Escherichia coli DbpA is an RNA helicase that requires hairpin 92 of 23S rRNA. The EMBO journal 125 11574482
1998 Active and passive immunity against Borrelia burgdorferi decorin binding protein A (DbpA) protects against infection. Infection and immunity 116 9573101
1991 DNA binding properties of YB-1 and dbpA: binding to double-stranded, single-stranded, and abasic site containing DNAs. Nucleic acids research 113 1923758
2014 CFTR interacts with ZO-1 to regulate tight junction assembly and epithelial differentiation through the ZONAB pathway. Journal of cell science 106 25107366
2007 The ATPase cycle mechanism of the DEAD-box rRNA helicase, DbpA. Journal of molecular biology 102 18237742
2010 The tight junction associated signalling proteins ZO-1 and ZONAB regulate retinal pigment epithelium homeostasis in mice. PloS one 98 21209887
2005 Analysis of the heteromeric CsdA-CsdE cysteine desulfurase, assisting Fe-S cluster biogenesis in Escherichia coli. The Journal of biological chemistry 95 15901727
2010 ZONAB promotes proliferation and represses differentiation of proximal tubule epithelial cells. Journal of the American Society of Nephrology : JASN 94 20133480
2005 Expression of zonula occludens-1 (ZO-1) and the transcription factor ZO-1-associated nucleic acid-binding protein (ZONAB)-MsY3 in glial cells and colocalization at oligodendrocyte and astrocyte gap junctions in mouse brain. The European journal of neuroscience 89 16045494
2000 Decorin-binding protein A (DbpA) of Borrelia burgdorferi is not protective when immunized mice are challenged via tick infestation and correlates with the lack of DbpA expression by B. burgdorferi in ticks. Infection and immunity 87 10899883
2002 Effects of ribosomal proteins S1, S2 and the DeaD/CsdA DEAD-box helicase on translation of leaderless and canonical mRNAs in Escherichia coli. Molecular microbiology 86 12068815
2001 The Escherichia coli DEAD protein DbpA recognizes a small RNA hairpin in 23S rRNA. RNA (New York, N.Y.) 86 11350034
2004 RalA interacts with ZONAB in a cell density-dependent manner and regulates its transcriptional activity. The EMBO journal 85 15592429
2010 Pathway of ATP utilization and duplex rRNA unwinding by the DEAD-box helicase, DbpA. Proceedings of the National Academy of Sciences of the United States of America 77 20160110
1995 The "DEAD box" protein DbpA interacts specifically with the peptidyltransferase center in 23S rRNA. Proceedings of the National Academy of Sciences of the United States of America 72 8524828
1998 Kinetic analysis of the RNA-dependent adenosinetriphosphatase activity of DbpA, an Escherichia coli DEAD protein specific for 23S ribosomal RNA. Biochemistry 71 9836593
1997 Suppression of grp78 core promoter element-mediated stress induction by the dbpA and dbpB (YB-1) cold shock domain proteins. Molecular and cellular biology 63 8972186
2002 Cooperative binding of ATP and RNA substrates to the DEAD/H protein DbpA. Biochemistry 62 11888286
2019 The RNA-Binding Protein YBX3 Controls Amino Acid Levels by Regulating SLC mRNA Abundance. Cell reports 60 31189097
2009 A dominant negative mutant of the E. coli RNA helicase DbpA blocks assembly of the 50S ribosomal subunit. Nucleic acids research 60 19734347
2007 Complementation analysis of the cold-sensitive phenotype of the Escherichia coli csdA deletion strain. Journal of bacteriology 60 17557820
2006 Functional interaction between the ZO-1-interacting transcription factor ZONAB/DbpA and the RNA processing factor symplekin. Journal of cell science 57 17158914
2011 Allelic variation of the Lyme disease spirochete adhesin DbpA influences spirochetal binding to decorin, dermatan sulfate, and mammalian cells. Infection and immunity 54 21708995
2008 Ribosome assembly in Escherichia coli strains lacking the RNA helicase DeaD/CsdA or DbpA. The FEBS journal 54 18565105
2003 Significant improvement of the recombinant Borrelia-specific immunoglobulin G immunoblot test by addition of VlsE and a DbpA homologue derived from Borrelia garinii for diagnosis of early neuroborreliosis. Journal of clinical microbiology 54 12624072
2009 The CsdA cysteine desulphurase promotes Fe/S biogenesis by recruiting Suf components and participates to a new sulphur transfer pathway by recruiting CsdL (ex-YgdL), a ubiquitin-modifying-like protein. Molecular microbiology 52 20054882
2006 The heat-shock protein Apg-2 binds to the tight junction protein ZO-1 and regulates transcriptional activity of ZONAB. Molecular biology of the cell 51 16407410
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 51 7628487
2018 Hypoxia-induced microRNA-191 contributes to hepatic ischemia/reperfusion injury through the ZONAB/Cyclin D1 axis. Cell death and differentiation 47 29769640
2001 Visualization of unwinding activity of duplex RNA by DbpA, a DEAD box helicase, at single-molecule resolution by atomic force microscopy. Proceedings of the National Academy of Sciences of the United States of America 47 11296244
2009 The Y-box factor ZONAB/DbpA associates with GEF-H1/Lfc and mediates Rho-stimulated transcription. EMBO reports 46 19730435
2008 Ablation of Cx47 in transgenic mice leads to the loss of MUPP1, ZONAB and multiple connexins at oligodendrocyte-astrocyte gap junctions. The European journal of neuroscience 46 18973575
1999 Interaction of the Escherichia coli DEAD box protein DbpA with 23 S ribosomal RNA. Journal of molecular biology 44 10525403
2007 Mutation of the arginine finger in the active site of Escherichia coli DbpA abolishes ATPase and helicase activity and confers a dominant slow growth phenotype. Nucleic acids research 41 17986459
2005 Equilibrium and kinetic analysis of nucleotide binding to the DEAD-box RNA helicase DbpA. Biochemistry 40 15654752
1997 Positive and negative regulation of the human thymidine kinase promoter mediated by CCAAT binding transcription factors NF-Y/CBF, dbpA, and CDP/cut. Cell growth & differentiation : the molecular biology journal of the American Association for Cancer Research 40 9419421
2013 Structural changes during cysteine desulfurase CsdA and sulfur acceptor CsdE interactions provide insight into the trans-persulfuration. The Journal of biological chemistry 38 23913692
2023 M6A-mediated-upregulation of lncRNA BLACAT3 promotes bladder cancer angiogenesis and hematogenous metastasis through YBX3 nuclear shuttling and enhancing NCF2 transcription. Oncogene 37 37612524
2004 Transcription of dbpA, a Y box binding protein, is positively regulated by E2F1: implications in hepatocarcinogenesis. Biochemical and biophysical research communications 37 15313206
2003 Diagnosis of Lyme neuroborreliosis with antibodies to recombinant proteins DbpA, BBK32, and OspC, and VlsE IR6 peptide. Journal of neurology 37 14648148
2007 Mutational analysis of the Escherichia coli DEAD box protein CsdA. Journal of bacteriology 36 17259309
2006 Molecular analysis of decorin-binding protein A (DbpA) reveals five major groups among European Borrelia burgdorferi sensu lato strains with impact for the development of serological assays and indicates lateral gene transfer of the dbpA gene. International journal of medical microbiology : IJMM 36 16530482
2009 The symplekin/ZONAB complex inhibits intestinal cell differentiation by the repression of AML1/Runx1. Gastroenterology 34 19328795
2014 ZO proteins redundantly regulate the transcription factor DbpA/ZONAB. The Journal of biological chemistry 33 24986862
2010 Requirement of the CsdA DEAD-box helicase for low temperature riboregulation of rpoS mRNA. RNA biology 32 21045550
2007 Phosphatidylethanol accumulation promotes intestinal hyperplasia by inducing ZONAB-mediated cell density increase in response to chronic ethanol exposure. Molecular cancer research : MCR 31 18025260
2004 Interaction of Escherichia coli DbpA with 23S rRNA in different functional states of the enzyme. Nucleic acids research 30 15173385
2005 Escherichia coli DbpA is a 3' --> 5' RNA helicase. Biochemistry 28 15910005
1997 Characterization of DbpA, an Escherichia coli DEAD box protein with ATP independent RNA unwinding activity. Nucleic acids research 27 9016593
2014 Identification of lysine residues in the Borrelia burgdorferi DbpA adhesin required for murine infection. Infection and immunity 26 24842928
2015 Bradykinin increased the permeability of BTB via NOS/NO/ZONAB-mediating down-regulation of claudin-5 and occludin. Biochemical and biophysical research communications 24 26106824
2021 Notoginsenoside R1 attenuates breast cancer progression by targeting CCND2 and YBX3. Chinese medical journal 23 33480613
2021 YBX3 Mediates the Metastasis of Nasopharyngeal Carcinoma via PI3K/AKT Signaling. Frontiers in oncology 23 33816248
2012 Escherichia coli cold-shock gene profiles in response to over-expression/deletion of CsdA, RNase R and PNPase and relevance to low-temperature RNA metabolism. Genes to cells : devoted to molecular & cellular mechanisms 23 22957931
2002 Somatic mutation and SNP in the promoter of dbpA and human hepatocarcinogenesis. International journal of oncology 22 12239625
2017 Insights into the Structure of Dimeric RNA Helicase CsdA and Indispensable Role of Its C-Terminal Regions. Structure (London, England : 1993) 21 29107486
2002 The RNA helicase DbpA exhibits a markedly different conformation in the ADP-bound state when compared with the ATP- or RNA-bound states. The Journal of biological chemistry 21 12324462
2009 Upregulation of human DNA binding protein A (dbpA) in gastric cancer cells. Acta pharmacologica Sinica 20 19749785
2021 Structural basis for the activation of the DEAD-box RNA helicase DbpA by the nascent ribosome. Proceedings of the National Academy of Sciences of the United States of America 19 34453003
1999 DNA binding protein dbpA binds Cdk5 and inhibits its activity. FEBS letters 19 10100871
2005 Hydrodynamic characterization of the DEAD-box RNA helicase DbpA. Journal of molecular biology 18 16325852
2022 Identification and verification of YBX3 and its regulatory gene HEIH as an oncogenic system: A multidimensional analysis in colon cancer. Frontiers in immunology 17 36059530
2011 Requirement for RNA helicase CsdA for growth of Yersinia pseudotuberculosis IP32953 at low temperatures. Applied and environmental microbiology 17 22156424
2016 Time course of large ribosomal subunit assembly in E. coli cells overexpressing a helicase inactive DbpA protein. RNA (New York, N.Y.) 16 27194011
2023 Silencing circSERPINE2 restrains mesenchymal stem cell senescence via the YBX3/PCNA/p21 axis. Cellular and molecular life sciences : CMLS 15 37831180
2011 Probing conformational variations at the ATPase site of the RNA helicase DbpA by high-field electron-nuclear double resonance spectroscopy. Journal of the American Chemical Society 15 21819147
2010 Cold shock domain protein A (CSDA) overexpression inhibits tumor growth and lymph node metastasis in a mouse model of squamous cell carcinoma. Clinical & experimental metastasis 15 20623179
2017 DbpA is a region-specific RNA helicase. Biopolymers 13 27813083
2013 Characterization of the kinetics of RNA annealing and strand displacement activities of the E. coli DEAD-box helicase CsdA. RNA biology 12 23291905
2023 Structural basis for RNA-duplex unwinding by the DEAD-box helicase DbpA. RNA (New York, N.Y.) 9 37221012
2023 Fungal secondary metabolism is governed by an RNA-binding protein CsdA/RsdA complex. Nature communications 9 37963872
2019 Modulation of Contact Inhibition by ZO-1/ZONAB Gene Transfer-A New Strategy to Increase the Endothelial Cell Density of Corneal Grafts. Investigative ophthalmology & visual science 9 31335954
2016 The DbpA catalytic core unwinds double-helix substrates by directly loading on them. RNA (New York, N.Y.) 9 26755693
2011 Escherichia coli cold shock protein CsdA effects an increase in septation and the resultant formation of coccobacilli at low temperature. Archives of microbiology 9 21359956
2005 MZF-1 and DbpA interact with DNase I hypersensitive sites that correlate with expression of the human MUC1 mucin gene. Experimental cell research 9 15893750
2023 The YBX3 RNA-binding protein posttranscriptionally controls SLC1A5 mRNA in proliferating and differentiating skeletal muscle cells. The Journal of biological chemistry 8 38159852
2020 Y-Box-Binding Protein 3 (YBX3) Restricts Influenza A Virus by Interacting with Viral Ribonucleoprotein Complex and Imparing its Function. The Journal of general virology 8 32553055
2017 Kinetics and Thermodynamics of DbpA Protein's C-Terminal Domain Interaction with RNA. ACS omega 8 29214235
2022 RNA Post-Transcriptional Modifications in Two Large Subunit Intermediates Populated in E. coli Cells Expressing Helicase Inactive R331A DbpA. Biochemistry 7 35481783
2018 Decreased ZONAB expression promotes excessive transdifferentiation of alveolar epithelial cells in hyperoxia-induced bronchopulmonary dysplasia. International journal of molecular medicine 7 29393348
2024 RNA-binding protein YBX3 promotes PPARγ-SLC3A2 mediated BCAA metabolism fueling brown adipogenesis and thermogenesis. Molecular metabolism 5 39481849
2020 DNA sequence-specific ligands. XVIII. Synthesis, physico-chemical properties; genetic, virological, and biochemical studies of fluorescent dimeric bisbenzimidazoles DBPA(n). Bioorganic & medicinal chemistry 5 32089391
2015 Functional csdA is needed for effective adaptation and initiation of growth of Clostridium botulinum ATCC 3502 at suboptimal temperature. International journal of food microbiology 5 26057109
2012 Cold-shock-domain protein A (CSDA) contributes posttranscriptionally to gonadotropin-releasing hormone-regulated expression of Egr1 and indirectly to Lhb. Biology of reproduction 5 22053098
2018 Bradykinin potentially stimulates cell proliferation in rabbit corneal endothelial cells through the ZO‑1/ZONAB pathway. International journal of molecular medicine 4 29568941
2013 Stopping power and CSDA range calculations for incident electrons and positrons in breast and brain tissues. Radiation and environmental biophysics 4 23334249
2026 YBX1&YBX3 as novel targets to potentiate immune checkpoint blockade response in gliomas. Neuro-oncology 3 41025501
2023 Cold Shock Domain Protein DbpA Orchestrates Tubular Cell Damage and Interstitial Fibrosis in Inflammatory Kidney Disease. Cells 3 37408260
2023 Identification of RNA-binding protein YBX3 as an oncogene in clear cell renal cell carcinoma. Functional & integrative genomics 3 37418046
2022 A novel 27-bp indel in the intron region of the YBX3 gene is associated with growth traits in chickens. British poultry science 3 35382648
2012 Up-regulation of dbpA mRNA in hepatocellular carcinoma associated with metabolic syndrome. Hepatology international 3 26201636
2025 Targeting CHEK2-YBX1&YBX3 regulatory hub to potentiate immune checkpoint blockade response in gliomas. bioRxiv : the preprint server for biology 2 40161682
2022 Serological Analysis Identifies Consequential B Cell Epitopes on the Flexible Linker and C-Terminus of Decorin Binding Protein A (DbpA) from Borrelia burgdorferi. mSphere 2 35876530
2020 Assignment of the Ile, Leu, Val, Met and Ala methyl group resonances of the DEAD-box RNA helicase DbpA from E. coli. Biomolecular NMR assignments 2 33277687