Affinage

BPNT1

3'(2'),5'-bisphosphate nucleotidase 1 · UniProt O95861

Length
308 aa
Mass
33.4 kDa
Annotated
2026-06-09
20 papers in source corpus 11 papers cited in narrative 11 extracted findings
Cross-family judge vs UniProt: Affinage preferred faithfulness: 6/6 claims corpus-supported (100%)

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

BPNT1 is a cytoplasmic lithium-sensitive phosphatase that hydrolyzes 3'-phosphoadenosine 5'-phosphate (PAP), a byproduct of cellular sulfation, to 5'-AMP, thereby detoxifying a metabolite whose accumulation impairs RNA metabolism and translation (PMID:15583009, PMID:23479625). Its enzymatic identity was established by complementation of lithium-induced PAP accumulation in yeast lacking Met22/Hal2 (PMID:15583009), and loss of Bpnt1 in mice causes up to 50-fold PAP accumulation, repressed translation, aberrant nucleolar architecture, and hepatocellular damage that are fully rescued by abolishing PAP synthesis, proving cytoplasmic PAP accumulation as the toxic mechanism (PMID:23479625). PAP toxicity is tissue-selective—affecting liver, duodenum, kidney, and specific neurons—because cytosolic sulfotransferase activity that generates PAP is itself restricted to those cells, as shown by the SSU-1-dependent vulnerability of C. elegans ASJ neurons (PMID:24309248, PMID:27397889), and BPNT1 acts genetically downstream of PAPS to clear this metabolite (PMID:41963701). Mechanistically, accumulated PAP inhibits the 5'→3' exoribonucleases XRN1/XRN2, so BPNT1 functions as a positive regulator of XRN2-dependent RNA processing and modulates a heat-stress tRNA decay pathway (PMID:27631780, PMID:40595590). Through this metabolic axis BPNT1 loss disrupts ribosome biogenesis and iron- and vitamin-B12-homeostasis gene expression: intestinal Bpnt1 loss produces iron-deficiency anemia by altering iron-handling factors in a manner partly mimicking HIF-2α loss (PMID:29507250, PMID:32019729), and biallelic loss-of-function BPNT1 mutations in humans cause vitamin-B12-dependent megaloblastic anemia via impaired ribosome biogenesis and reduced ileal cubam receptor expression (PMID:42166360). Independent of its PAP-hydrolysis role, BPNT1 in triple-negative breast cancer recruits the E3 ligase STUB1 to degrade the tumor suppressor LIMA1, promoting epithelial-mesenchymal transition and docetaxel resistance (PMID:41540000).

Mechanistic history

Synthesis pass · year-by-year structured walk · 9 steps
  1. 2004 High

    Establishing the molecular activity of human BPNT1 answered what reaction the enzyme catalyzes and why lithium perturbs it, defining the PAP-hydrolysis function.

    Evidence Heterologous expression of human BPNT1 in met22/hal2 yeast with PAP metabolite measurement and biosynthetic-gene disruption

    PMID:15583009

    Open questions at the time
    • Did not address mammalian tissue context or in vivo consequences
    • Structural basis of lithium sensitivity not resolved
  2. 2013 High

    A knockout-plus-rescue strategy in mice proved that cytoplasmic PAP accumulation, not loss of a separate enzymatic function, is the toxic consequence of BPNT1 loss.

    Evidence Bpnt1 knockout mouse with double-mutant rescue abolishing PAP synthesis, subcellular fractionation, histology, and translation analysis

    PMID:23479625 PMID:24309248

    Open questions at the time
    • Molecular link between PAP and repressed translation/nucleolar defects not yet mechanistic
    • Basis of tissue selectivity (liver/duodenum/kidney) undefined at this stage
  3. 2016 High

    C. elegans genetics explained tissue selectivity and identified XRN2 as the downstream RNA-processing target inhibited by PAP, linking BPNT1 to RNA metabolism.

    Evidence bpnt-1 loss-of-function genetics with neuron-specific rescue, SSU-1 expression analysis, and bpnt-1;paxt-1 suppressor epistasis with XRN2 activity assays

    PMID:27397889 PMID:27631780

    Open questions at the time
    • Direct biochemical inhibition of mammalian XRN2 by PAP not shown in these studies
    • Quantitative threshold of PAP required for XRN inhibition unknown
  4. 2018 High

    Tissue-specific conditional knockouts connected BPNT1/PAP to organismal iron physiology, showing intestinal PAP accumulation dysregulates iron homeostasis genes.

    Evidence Whole-animal and intestine-specific Bpnt1 conditional knockout mice, iron-factor expression analysis, and genetic rescue of HFE-C282Y hemochromatosis

    PMID:29507250

    Open questions at the time
    • Mechanistic link between PAP and HIF-2α-like gene expression program not fully resolved
    • Whether iron-gene changes are transcriptional or RNA-stability driven unclear
  5. 2020 Medium

    Two orthogonal rescues defined the metabolic flux dependence of BPNT1 phenotypes and pinpointed HIF-2α as a node restoring iron-gene expression.

    Evidence Bpnt1 KO mice with dietary methionine restriction and intestinal organoids with Hif-2a overexpression

    PMID:32019729

    Open questions at the time
    • Single lab
    • Does not establish how PAP suppresses HIF-2α activity
  6. 2025 Medium

    Cell-based work extended PAP/XRN regulation to a heat-stress tRNA quality-control pathway, broadening the RNA-metabolic reach of BPNT1.

    Evidence Thumpd1 deletion in NIH/3T3 cells with tRNA decay assays, PAP measurement, and Xrn1/Xrn2 functional analysis under heat stress

    PMID:40595590

    Open questions at the time
    • Single study, abstract-level mechanism
    • Physiological relevance of mRTD beyond heat stress unclear
  7. 2026 High

    Human genetics established BPNT1 as a Mendelian disease gene and tied its loss to ribosome biogenesis and vitamin-B12 absorption, validated in mouse.

    Evidence Biallelic patient mutations with Bpnt1-null mouse model, PAP measurement, ribosome biogenesis assay, and cubam receptor expression analysis

    PMID:42166360

    Open questions at the time
    • How PAP impairs ribosome biogenesis mechanistically not fully defined
    • Causal chain from PAP to cubam downregulation unresolved
  8. 2026 Medium

    Epistasis with MESH1 placed BPNT-1 downstream of PAPS in the detoxification pathway, confirming PAP as the proximate toxic species.

    Evidence C. elegans bpnt-1 mutant with MESH1 overexpression, genetic epistasis, and PAP/PAPS metabolite measurement

    PMID:41963701

    Open questions at the time
    • Secondary finding within a MESH1-focused study
    • Generalizability to mammalian neurons not tested
  9. 2026 Medium

    A non-catalytic role emerged in cancer, where BPNT1 functions as a scaffold recruiting STUB1 to degrade LIMA1, decoupling a disease phenotype from PAP hydrolysis.

    Evidence Loss/gain-of-function in TNBC cell lines and xenografts, BPNT1-STUB1 Co-IP, LIMA1 stability and rescue assays, and docetaxel sensitivity assays

    PMID:41540000

    Open questions at the time
    • Single lab Co-IP without reciprocal/structural validation of the BPNT1-STUB1 interface
    • Whether catalytic activity contributes at all to the EMT phenotype not formally excluded

Open questions

Synthesis pass · forward-looking unresolved questions
  • It remains unresolved how PAP accumulation mechanistically converges on ribosome biogenesis and tissue-specific gene-expression programs, and whether the catalytic and STUB1-scaffolding roles operate in the same cells.
  • No structural model of PAP-mediated XRN inhibition in mammals
  • Unclear whether scaffolding and phosphatase functions are mutually exclusive or context-dependent

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0016787 hydrolase activity 2
Localization
GO:0005829 cytosol 1
Pathway
R-HSA-1430728 Metabolism 2 R-HSA-8953854 Metabolism of RNA 2
Partners
LIMA1STUB1

Evidence

Reading pass · 11 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2004 Human BPNT1 (bisphosphate 3'-nucleotidase) dephosphorylates 3'-phosphoadenosine 5'-phosphate (PAP); lithium inhibits this enzymatic activity, causing >80-fold accumulation of PAP in yeast, and heterologous expression of human BPNT1 rescues lithium-induced growth inhibition in yeast cells lacking Met22/Hal2. Yeast complementation assay, heterologous expression of human BPNT1 in met22/hal2 mutant yeast, PAP metabolite measurement, genetic disruption of PAP biosynthetic genes (met3, met14) The Journal of biological chemistry High 15583009
2013 Bpnt1 localizes to the cytoplasm (distinct from Golgi-resident gPAPP) and its loss in mice causes PAP accumulation (up to 50-fold in liver), repressed translation, aberrant nucleolar architecture, hypoproteinemia, hepatocellular damage, and death; all phenotypes are rescued by a double mutant abolishing PAP synthesis, establishing that cytoplasmic PAP accumulation is the toxic mechanism. Bpnt1 knockout mouse, double-mutant rescue (Bpnt1 KO × PAPS synthesis KO), subcellular fractionation/localization, metabolite quantification, histology, protein synthesis analysis Proceedings of the National Academy of Sciences of the United States of America High 23479625
2013 Although Bpnt1 protein is widely expressed in mice, tissue-specific PAP accumulation and dysmorphic nucleoli upon Bpnt1 loss occur selectively in liver, duodenum, and kidneys, indicating tissue-specific susceptibility to loss of cytoplasmic PAP hydrolysis. Immunohistochemistry/western blot for Bpnt1 protein expression, PAP metabolite measurement across tissues, nucleolar morphology analysis in wild-type and Bpnt1−/− mice Advances in biological regulation Medium 24309248
2016 In C. elegans, loss of BPNT-1 causes selective dysfunction of ASJ chemosensory neurons and behavioral defects (dauer exit and pathogen avoidance); acute lithium treatment phenocopies this via BPNT-1 inhibition, and the selectivity is explained by restricted expression of the cytosolic sulfotransferase SSU-1 in ASJ neurons, which drives neuron-specific PAP production. C. elegans bpnt-1 loss-of-function genetics, behavioral assays (dauer exit, pathogen avoidance), neuron-specific rescue experiments, lithium treatment with reversibility assay, tissue-specific expression analysis of SSU-1 Current biology : CB High 27397889
2016 BPNT-1 promotes XRN2 (exoribonuclease) activity in C. elegans by hydrolyzing PAP, an endogenous XRN inhibitor; loss of bpnt-1 suppresses lethality caused by paxt-1 deletion through XRN2 autoregulation, placing BPNT-1 as a positive regulator of XRN2-dependent RNA processing. C. elegans double-mutant epistasis (bpnt-1; paxt-1), unbiased genetic suppressor screen, XRN2 activity assays, transcript-level analysis of xrn-2 autoregulation PLoS genetics Medium 27631780
2018 Intestinal Bpnt1 loss in mice leads to iron-deficiency anemia by causing PAP accumulation that alters expression of key iron homeostasis factors (involved in dietary iron reduction, import, and transport), partially mimicking loss of HIF-2α; intestine-specific Bpnt1 knockout rescues hepatic iron overload in HFE-C282Y hemochromatosis mice. Whole-animal and intestine-specific Bpnt1 conditional knockout mice, iron homeostasis factor expression analysis, genetic rescue experiments, PAP metabolite measurement Proceedings of the National Academy of Sciences of the United States of America High 29507250
2020 Iron-deficiency anemia caused by Bpnt1 loss is rescued by dietary methionine restriction (which reduces sulfur assimilation flux and PAP production) or by overproduction of HIF-2α (which restores iron homeostatic gene expression in intestinal organoids), defining two independent rescue mechanisms for BPNT1 deficiency. Bpnt1 KO mice with dietary methionine restriction, intestinal organoids with Hif-2a overexpression, iron homeostasis gene expression analysis Advances in biological regulation Medium 32019729
2025 Bpnt1 (together with Bpnt2) controls intracellular PAP levels to regulate a mammalian rapid tRNA decay (mRTD) pathway; PAP accumulation upon Bpnt1/Bpnt2 activity reduction promotes degradation of tRNALeu(CAG) by Xrn1/Xrn2-mediated 5'→3' exonuclease digestion under heat stress. Deletion of Thumpd1 in NIH/3T3 cells, tRNA decay assays, PAP level measurement, Xrn1/Xrn2 functional analysis, heat stress experiments Nature communications Medium 40595590
2026 Biallelic loss-of-function BPNT1 mutations in humans cause PAP accumulation, impaired ribosome biogenesis, and reduced ileal expression of the cubam receptor complex (required for vitamin B12 absorption), resulting in vitamin B12-dependent megaloblastic anemia. Human patient genetics (biallelic mutations), Bpnt1-null mouse model, PAP metabolite measurement, ribosome biogenesis assay, cubam receptor expression analysis Blood High 42166360
2026 BPNT1 promotes triple-negative breast cancer progression and docetaxel resistance by recruiting the E3 ubiquitin ligase STUB1 to induce proteasomal degradation of tumor suppressor LIMA1, thereby promoting epithelial-mesenchymal transition; re-expression of LIMA1 partially attenuates BPNT1-driven EMT. Loss- and gain-of-function assays in TNBC cell lines and xenograft mouse models, Co-IP (BPNT1-STUB1 interaction), LIMA1 protein stability assays, rescue by LIMA1 re-expression, docetaxel sensitivity assays Cell death & disease Medium 41540000
2026 In C. elegans lacking bpnt-1, neurotoxic PAP accumulation is alleviated by overexpression of MESH1 (a PAPS phosphatase), which reduces upstream PAPS levels and thereby decreases sulfotransferase-driven PAP production, providing genetic evidence that BPNT-1 acts downstream of PAPS to detoxify PAP. C. elegans bpnt-1 mutant, MESH1 overexpression, genetic epistasis, PAP/PAPS metabolite measurement Nature chemical biology Medium 41963701

Source papers

Stage 0 corpus · 20 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2004 Alteration of lithium pharmacology through manipulation of phosphoadenosine phosphate metabolism. The Journal of biological chemistry 30 15583009
2013 Role for cytoplasmic nucleotide hydrolysis in hepatic function and protein synthesis. Proceedings of the National Academy of Sciences of the United States of America 20 23479625
2016 Inhibition of Lithium-Sensitive Phosphatase BPNT-1 Causes Selective Neuronal Dysfunction in C. elegans. Current biology : CB 19 27397889
2018 Glycerophosphatidylcholine PC(36:1) absence and 3'-phosphoadenylate (pAp) accumulation are hallmarks of the human glioma metabolome. Scientific reports 13 30283018
2016 XRN2 Autoregulation and Control of Polycistronic Gene Expresssion in Caenorhabditis elegans. PLoS genetics 13 27631780
2019 RAPID COMMUNICATION: Multi-breed validation study unraveled genomic regions associated with puberty traits segregating across tropically adapted breeds1. Journal of animal science 12 30997484
2018 Modulation of intestinal sulfur assimilation metabolism regulates iron homeostasis. Proceedings of the National Academy of Sciences of the United States of America 12 29507250
2015 Subpath analysis of each subtype of head and neck cancer based on the regulatory relationship between miRNAs and biological pathways. Oncology reports 12 26239836
2015 Hyperoxia-Induced Protein Alterations in Renal Rat Tissue: A Quantitative Proteomic Approach to Identify Hyperoxia-Induced Effects in Cellular Signaling Pathways. Disease markers 10 26106253
2022 Proteomic analysis of rat colonic mucosa following acupuncture treatment for irritable bowel syndrome with diarrhea. PloS one 8 36094925
2022 Proteomic analysis of urinary extracellular vesicles of kidney transplant recipients with BKV viruria and viremia: A pilot study. Frontiers in medicine 7 36465937
2021 Circular RNA erythrocyte membrane protein band 4.1 assuages ultraviolet irradiation-induced apoptosis of lens epithelial cells by stimulating 5'-bisphosphate nucleotidase 1 in a miR-24-3p-dependent manner. Bioengineered 7 34652259
2013 Tissue-specific regulation of 3'-nucleotide hydrolysis and nucleolar architecture. Advances in biological regulation 7 24309248
2020 Modulation of sulfur assimilation metabolic toxicity overcomes anemia and hemochromatosis in mice. Advances in biological regulation 5 32019729
2025 Mammalian tRNA acetylation determines translation efficiency and tRNA quality control. Nature communications 3 40595590
2024 CircRNA HLCS regulates lens epithelial cell apoptosis via miR-338-3p/BPNT1 axis. International ophthalmology 3 38493427
2026 Bisphosphate nucleotidase 1 promotes progression and docetaxel resistance in triple-negative breast cancer via STUB1-mediated destabilization of LIMA1. Cell death & disease 0 41540000
2026 MESH1 functions as a metazoan PAPS phosphatase to regulate sulfation. Nature chemical biology 0 41963701
2026 Proteomic Signatures of Protected APOE-ε4 Carriers Reveal Causal Pathways Associated with Delayed Alzheimer's Disease Onset. medRxiv : the preprint server for health sciences 0 42094129
2026 Biallelic loss-of-function mutations in BPNT1 cause vitamin B12-dependent megaloblastic anemia. Blood 0 42166360

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