Affinage

PITPNM1

Membrane-associated phosphatidylinositol transfer protein 1 · UniProt O00562

Length
1244 aa
Mass
134.8 kDa
Annotated
2026-04-28
24 papers in source corpus 17 papers cited in narrative 17 extracted findings

Mechanistic narrative

Synthesis pass · prose summary of the discoveries below

PITPNM1 (Nir2) is a multi-domain lipid transfer protein that operates principally at ER–plasma membrane contact sites to sustain phosphoinositide signaling by coupling PI(4,5)P2 consumption with phosphatidylinositol resynthesis. Its N-terminal PITP domain transfers PI from the ER to the PM while its C-terminal LNS2 domain senses phosphatidic acid (PA) at the PM and mediates counter-transport of PA back to the ER, with ER anchorage provided by an FFAT–VAP interaction and membrane stabilization by DDHD-domain dimerization; this bidirectional PI/PA exchange maintains PI(4,5)P2 homeostasis during PLC-coupled receptor signaling, phagocytosis, and angiogenesis (PMID:26028218, PMID:41129229, PMID:37376972, PMID:40010513). At the Golgi, Nir2 regulates diacylglycerol levels and protein secretion via the CDP-choline pathway (PMID:15723057), and during mitosis Cdk1-dependent phosphorylation at S382 creates a Plk1-docking site that recruits Plk1 to the cleavage furrow for cytokinesis completion, while a Rho-inhibitory domain binds GDP-RhoA to modulate actin dynamics (PMID:15125835, PMID:12077336, PMID:11909959).

Mechanistic history

Synthesis pass · year-by-year structured walk · 10 steps
  1. 2002 High

    Establishing that Nir2 is required for cytokinesis and physically associates with RhoA at the cleavage furrow answered how a lipid-transfer protein could participate in cell division, linking Nir2 to RhoA-dependent actin regulation.

    Evidence Antibody microinjection blocking cytokinesis, co-IP with RhoA, and immunolocalization to the cleavage furrow/midbody in mammalian cells

    PMID:11909959 PMID:12077336

    Open questions at the time
    • Whether the Rid domain acts catalytically on RhoA or sequesters GDP-RhoA remains unresolved
    • No structural model of the Rid–RhoA interaction
    • Physiological relevance of Rid in non-dividing cells not established beyond neurite extension
  2. 2002 Medium

    Demonstration that a phosphomimetic T59E mutation targets the PITP domain to lipid droplets revealed a phosphorylation-regulated localization switch for Nir2.

    Evidence Site-directed mutagenesis, Nile red lipid-droplet staining, and oleic acid treatment in live cells

    PMID:12225667

    Open questions at the time
    • The kinase responsible for T59 phosphorylation in vivo has not been identified
    • Functional consequence of lipid-droplet localization is unknown
    • Single-lab finding not independently replicated
  3. 2004 High

    Identification of Cdk1-mediated phosphorylation at S382 as the signal that dissociates Nir2 from the Golgi and docks Plk1 via its Polo-box domain explained how Nir2 is repositioned for cytokinesis.

    Evidence In vitro kinase assay, phospho-site mutagenesis, Plk1 PBD co-IP, and cytokinesis failure with binding-deficient mutant

    PMID:15125835

    Open questions at the time
    • Whether Nir2 lipid-transfer activity is required at the cleavage furrow or only the Plk1-scaffolding function
    • No in vivo confirmation in animal models
  4. 2005 High

    Showing that Nir2 maintains Golgi DAG levels and that its depletion blocks trans-Golgi-to-PM protein transport established Nir2 as a key regulator of Golgi lipid homeostasis and secretory trafficking.

    Evidence RNAi knockdown with Golgi DAG quantification and vesicular transport assay; rescue by CDP-choline pathway inhibition

    PMID:15723057

    Open questions at the time
    • Whether PI transfer activity or another Nir2 function controls Golgi DAG remains unclear
    • Relationship between Golgi and ER-PM contact site functions not delineated
  5. 2013 High

    Discovery that E-Syt1 facilitates Nir2 recruitment to ER-PM junctions after Ca2+ signaling, and that Nir2 replenishes PM PIP2 via its PITP activity, established the signaling-dependent mechanism by which Nir2 reaches its site of action.

    Evidence Live-cell imaging with genetically encoded ER-PM junction markers, knockdown, and PIP2 replenishment assay

    PMID:23897088 PMID:24183667

    Open questions at the time
    • Relative contributions of E-Syt1 versus Nir1 in Nir2 recruitment not resolved
    • Whether PA binding alone is sufficient for translocation in the absence of E-Syt1
  6. 2015 High

    Reconstitution of Nir2 as a bidirectional PI/PA exchanger — transferring PI to the PM and PA back to the ER — resolved the mechanistic basis for coupling PI(4,5)P2 hydrolysis with PI resynthesis.

    Evidence Lipid transfer assays, mass spectrometry of Nir2-depleted cells, live-cell lipid sensors, PLC activation studies

    PMID:25887399 PMID:26028218

    Open questions at the time
    • Structural basis of counter-transport (how one protein simultaneously handles PI and PA) was not resolved until 2025
    • Quantitative stoichiometry of exchange in intact cells not measured
  7. 2019 Medium

    Demonstration that Nir2 replenishes PI at HCV replication organelles to sustain PI(4)P levels consumed by OSBP extended the PI/PA exchange paradigm to virus-hijacked membrane contact sites.

    Evidence Nir2 knockdown/knockout with HCV replication assays, PI(4)P sensor imaging, co-IP with VAPs

    PMID:31484747

    Open questions at the time
    • Whether other viruses exploit Nir2 in a similar manner is untested
    • Single-lab finding; independent confirmation needed
  8. 2022 Medium

    Identification of Nir1 as a constitutive ER-PM junction resident that promotes Nir2 recruitment through direct interaction revealed a hierarchical assembly mechanism among Nir family members.

    Evidence Co-IP, live-cell imaging, knockdown/rescue with PIP2 sensors

    PMID:35020418

    Open questions at the time
    • Binding interface between Nir1 and Nir2 not structurally defined
    • Single-lab finding; independent confirmation needed
  9. 2023 High

    CRISPR knockout of Nir2/3 proved that their PI/PA exchange activity is essential for PI(4,5)P2 maintenance at phagocytic cups and for successful phagosome closure, broadening the physiological scope of Nir2 beyond receptor signaling.

    Evidence CRISPR-Cas9 double KO, PI(4,5)P2 sensors, live-cell phagocytosis assays, actin imaging, re-expression rescue in macrophages

    PMID:37376972

    Open questions at the time
    • Individual contributions of Nir2 versus Nir3 to phagocytosis not fully separated
    • Whether Nir2 also contributes PA-derived signaling lipids during phagocytosis
  10. 2025 High

    Crystal structures of the LNS2 domain with PA and the FFAT–VAPB and DDHD dimer interfaces provided the first atomic-resolution framework for how Nir2 senses PA, anchors to the ER, and stabilizes membrane contacts.

    Evidence X-ray crystallography of three domain structures with mutagenesis and functional validation

    PMID:41129229

    Open questions at the time
    • Full-length Nir2 structure and mechanism of coordinated lipid counter-transport remain unresolved
    • How DDHD dimerization is regulated in vivo is unknown

Open questions

Synthesis pass · forward-looking unresolved questions
  • A unified structural and dynamic model of how Nir2 simultaneously transfers PI and PA in opposite directions across a single ER-PM contact site — and how this is coordinated with its mitotic and Golgi functions — remains unresolved.
  • No full-length structure or cryo-EM reconstruction
  • Quantitative in vivo lipid flux measurements are lacking
  • Relative physiological importance of Golgi versus ER-PM roles in tissue contexts is unknown
  • Whether Nir2 lipid-transfer and Rid/Plk1-scaffolding functions are coordinated during mitosis

Mechanism profile

Synthesis pass · controlled-vocabulary classification · explore literature graph →
Molecular activity
GO:0140104 molecular carrier activity 5 GO:0008289 lipid binding 4 GO:0098772 molecular function regulator activity 1
Localization
GO:0005783 endoplasmic reticulum 6 GO:0005886 plasma membrane 6 GO:0005794 Golgi apparatus 2 GO:0005811 lipid droplet 1 GO:0005856 cytoskeleton 1
Pathway
R-HSA-162582 Signal Transduction 5 R-HSA-1430728 Metabolism 2 R-HSA-1640170 Cell Cycle 2 R-HSA-168256 Immune System 1 R-HSA-5653656 Vesicle-mediated transport 1
Partners
ESYT1PITPNM2PITPNM3PLK1RHOAVAPAVAPB

Evidence

Reading pass · 17 per-paper findings extracted from the source corpus
Year Finding Method Journal Conf PMIDs
2025 Crystal structures of the Nir2 C-terminal LNS2 domain bound to phosphatidic acid (PA) reveal that residues S1025, T1065, K1103, and K1126 form hydrogen bonds with the phosphate headgroup of PA, conferring PA-sensing specificity; a salt bridge between E355 in Nir2 and R55 in VAPB mediates the FFAT–VAPB interaction; and the central DDHD domain forms a twofold symmetric dimer that stabilizes membrane association at ER-PM contact sites. X-ray crystallography (three crystal structures) with mutagenesis and functional validation Proceedings of the National Academy of Sciences of the United States of America High 41129229
2013 Following receptor-induced Ca2+ signaling, E-Syt1 translocates to ER-PM junctions in a Ca2+-dependent manner to enhance ER-to-PM connection, which subsequently facilitates recruitment of Nir2 to ER-PM junctions; Nir2 then replenishes PM PIP2 via its phosphatidylinositol transfer protein (PITP) activity. Genetically encoded ER-PM junction marker, live-cell imaging, knockdown with PIP2 replenishment assay, Ca2+ signaling measurements Cell reports High 24183667
2015 Nir2 functions as a bidirectional lipid exchanger at ER-PM contact sites: it transfers phosphatidylinositol (PtdIns) from the ER to the PM and transfers phosphatidic acid (PtdOH) in the reverse direction (PM to ER), coupling PI(4,5)P2 utilization with PtdIns resynthesis to maintain signaling competence; in Nir2-depleted cells, PtdOH accumulates at the PM and PtdIns synthesis is severely impaired. Lipid transfer assays, Nir2 depletion (RNAi) with lipid mass spectrometry, PLC activation studies, live-cell imaging of lipid sensors Developmental cell High 26028218
2015 Nir2 detects PIP2 hydrolysis and translocates to ER-PM junctions via binding to phosphatidic acid through its C-terminal region; ER membrane PI is required for rapid PM PIP2 replenishment; Nir2 and its homolog Nir3 differentially regulate PIP2 homeostasis—Nir2 responds to intense stimulation while Nir3 maintains resting-state PIP2 levels. PA-binding assays, dominant-negative and knockdown approaches, live-cell imaging of PIP2 sensors, ER PI depletion experiments The Journal of biological chemistry High 25887399
2005 Nir2 is a peripheral Golgi protein essential for maintaining DAG levels in the Golgi apparatus; its depletion by RNAi reduces Golgi DAG and blocks protein transport from the trans-Golgi network to the plasma membrane; inhibition of the CDP-choline pathway for phosphatidylcholine biosynthesis rescues both defects, indicating Nir2 regulates DAG homeostasis by controlling its consumption via the CDP-choline pathway. RNAi knockdown, DAG quantification in Golgi, vesicular transport assay, CDP-choline pathway inhibition rescue experiment Nature cell biology High 15723057
2004 At mitosis onset, Cdk1 phosphorylates Nir2 at multiple sites, most prominently S382, causing its dissociation from the Golgi apparatus; phospho-Nir2(pS382) localizes to the cleavage furrow and midbody during cytokinesis and serves as a docking site for the Polo box domain (PBD) of Plk1; a Nir2 mutant unable to bind Plk1 impairs cytokinesis completion. In vitro kinase assay, phospho-site mutagenesis, immunolocalization, overexpression of binding-deficient mutant, co-immunoprecipitation of Plk1 PBD Molecular cell High 15125835
2013 Nir2 translocates from the Golgi to the plasma membrane in response to growth factor stimulation; this translocation is triggered by PA formation and mediated by the C-terminal PA-binding region of Nir2; Nir2 depletion substantially reduces PM PI(4,5)P2 levels and growth factor-stimulated PI(3,4,5)P3 production, and attenuates MAPK and PI3K/AKT pathway activation. PA-binding assay (in vitro), growth factor stimulation + live imaging, RNAi knockdown with PI(4,5)P2 and PI(3,4,5)P3 sensors, signaling pathway readouts EMBO reports High 23897088
2002 Nir2 is essential for cytokinesis: microinjection of anti-Nir2 antibodies blocks cytokinesis, producing multinucleate cells; Nir2 translocates from the Golgi to the cleavage furrow and midbody during cytokinesis, colocalizes with RhoA, and associates with RhoA in mitotic cells; its N-terminal region containing a Rho-inhibitory domain (Rid) is required for cytokinesis completion. Antibody microinjection, time-lapse videomicroscopy, immunolocalization, co-immunoprecipitation with RhoA, dominant-negative overexpression Molecular and cellular biology High 12077336
2002 Nir2 contains a Rho-inhibitory domain (Rid) with sequence homology to formin-homology Rho-binding sites; Rid preferentially binds the inactive GDP-bound form of RhoA, inhibits Rho-mediated stress fiber formation and LPA-induced RhoA activation; microinjection of anti-Nir2 antibodies into neuronal cells attenuates neurite extension, whereas Nir2 overexpression attenuates Rho-mediated neurite retraction. Biochemical GTPase-binding assays, stress fiber and actin staining, antibody microinjection, overexpression in neuronal cells Molecular and cellular biology Medium 11909959
2002 A T59E mutation in the PI-transfer domain of Nir2 targets the protein to lipid droplets; the PI-transfer domain alone (T59E) is sufficient for lipid droplet targeting; oleic acid treatment induces wild-type Nir2 (but not T59A) translocation to lipid droplets; this targeting is attributed to enhanced threonine phosphorylation at position 59. Site-directed mutagenesis, Nile red lipid droplet staining, live-cell imaging, oleic acid treatment, phosphorylation analysis Current biology Medium 12225667
2016 Nir2 localizes to ER-PM contact zones via interaction of its FFAT domain with ER-bound VAP-A and VAP-B; following PLC activation, Nir2 also binds the PM via interaction of its C-terminal domains with DAG and PtdOH; VAP-B mutations linked to familial ALS cause VAP-B aggregation and impair its binding to Nir2. Co-immunoprecipitation, lipid-binding assays, live-cell imaging, dominant-negative mutant analysis Biochemical Society transactions Medium 26862206
2019 Nir2 acts as an effector of VAMP-associated proteins (VAPA and VAPB) to support HCV replication; Nir2 replenishes phosphoinositides (PI) at the HCV replication organelle to maintain elevated PI(4)P levels consumed by OSBP, completing a PI/PA exchange cycle between the ER and the viral replication organelle. Nir2 knockdown/knockout with HCV replication assays, PI(4)P sensor imaging, co-immunoprecipitation with VAPs Journal of virology Medium 31484747
2023 PITPNM1 (Nir2) and PITPNM2 (Nir3) accumulate on ER cisternae juxtaposed to phagocytic cups and maintain PI(4,5)P2 homeostasis at phagocytic cups; CRISPR-Cas9 double knockout of Nir2/3 decreases PM PI(4,5)P2, reduces actin ring density at particle capture sites, stalls phagocytosis at the cup stage, and causes repetitive abortive phagosome closure events. CRISPR-Cas9 knockout, PI(4,5)P2 sensors, live-cell imaging, phagocytosis assays, actin imaging, re-expression rescue Journal of cell science High 37376972
2022 Nir1 constitutively localizes at ER-PM junctions and promotes Nir2 recruitment to ER-PM junctions during receptor-mediated signaling via a direct protein–protein interaction between Nir1 and a region between the FFAT motif and the DDHD domain of Nir2, thereby facilitating efficient PM PIP2 replenishment. Live-cell imaging, biochemical co-immunoprecipitation, knockdown/rescue experiments, PIP2 sensor measurements Molecular biology of the cell Medium 35020418
2025 Nir2 knockdown in HUVECs inhibits angiogenic tube formation, reduces cell viability, proliferation and migration, diminishes actin stress fibers, and decreases AKT and ERK signaling upon VEGF stimulus; co-immunoprecipitation and co-localization confirmed that Nir2 interacts with VAPA at membrane contact sites. siRNA knockdown, angiogenesis tube formation assay, proliferation/migration assays, shRNA-resistant rescue, co-immunoprecipitation, proximity ligation Biochimica et biophysica acta. Molecular cell research Medium 40010513
2014 Nir2 enhances epithelial-mesenchymal transition (EMT) in mammary epithelial and breast cancer cells; Nir2 depletion attenuates growth factor-induced cell migration and invasion; effects on EMT are mediated through the PI3K/AKT and ERK1/2 pathways; Nir2 depletion inhibits lung metastasis in animal models. shRNA knockdown, EMT marker quantification, migration/invasion assays, PI3K/AKT and ERK pathway readouts, in vivo metastasis model Journal of cell science Medium 25179602
2013 Pitpnm1 is expressed in inner hair cells of the organ of Corti from late embryonic stages to adulthood and transiently in outer hair cells postnatally, but Pitpnm1 null mice show no hearing defects, indicating functional redundancy with Pitpnm2 and Pitpnm3. In situ hybridization/expression analysis, Pitpnm1 knockout mouse audiometry (ABR) Neuroscience Medium 23820044

Source papers

Stage 0 corpus · 24 papers · ranked by NIH iCite citations
Year Title Journal Citations PMID
2013 Feedback regulation of receptor-induced Ca2+ signaling mediated by E-Syt1 and Nir2 at endoplasmic reticulum-plasma membrane junctions. Cell reports 295 24183667
2015 Phosphatidylinositol-Phosphatidic Acid Exchange by Nir2 at ER-PM Contact Sites Maintains Phosphoinositide Signaling Competence. Developmental cell 197 26028218
2005 Maintenance of the diacylglycerol level in the Golgi apparatus by the Nir2 protein is critical for Golgi secretory function. Nature cell biology 146 15723057
2015 Phosphatidylinositol 4,5-Bisphosphate Homeostasis Regulated by Nir2 and Nir3 Proteins at Endoplasmic Reticulum-Plasma Membrane Junctions. The Journal of biological chemistry 115 25887399
2013 The phosphatidylinositol-transfer protein Nir2 binds phosphatidic acid and positively regulates phosphoinositide signalling. EMBO reports 112 23897088
2004 Mitotic phosphorylation of the peripheral Golgi protein Nir2 by Cdk1 provides a docking mechanism for Plk1 and affects cytokinesis completion. Molecular cell 77 15125835
2012 Rd9 is a naturally occurring mouse model of a common form of retinitis pigmentosa caused by mutations in RPGR-ORF15. PloS one 72 22563472
2002 Targeting of Nir2 to lipid droplets is regulated by a specific threonine residue within its PI-transfer domain. Current biology : CB 47 12225667
2002 Nir2, a human homolog of Drosophila melanogaster retinal degeneration B protein, is essential for cytokinesis. Molecular and cellular biology 39 12077336
2019 Nir2 Is an Effector of VAPs Necessary for Efficient Hepatitis C Virus Replication and Phosphatidylinositol 4-Phosphate Enrichment at the Viral Replication Organelle. Journal of virology 30 31484747
2016 Phosphatidylinositol and phosphatidic acid transport between the ER and plasma membrane during PLC activation requires the Nir2 protein. Biochemical Society transactions 30 26862206
2014 The lipid-transfer protein Nir2 enhances epithelial-mesenchymal transition and facilitates breast cancer metastasis. Journal of cell science 30 25179602
2020 Inhibition of miR-490-5p Promotes Human Adipose-Derived Stem Cells Chondrogenesis and Protects Chondrocytes via the PITPNM1/PI3K/AKT Axis. Frontiers in cell and developmental biology 22 33240879
2002 Nir2, a novel regulator of cell morphogenesis. Molecular and cellular biology 19 11909959
2022 Nir1 constitutively localizes at ER-PM junctions and promotes Nir2 recruitment for PIP2 homeostasis. Molecular biology of the cell 18 35020418
2018 Toxicology and Pharmacology of an AAV Vector Expressing Codon-Optimized RPGR in RPGR-Deficient Rd9 Mice. Human gene therapy. Clinical development 17 30280954
2016 Transforming Growth Factor Beta-Induced Factor 2-Linked X (TGIF2LX) Regulates Two Morphogenesis Genes, Nir1 and Nir2 in Human Colorectal. Acta medica Iranica 17 27309477
1977 Inhibition of transformation and transfection in Haemophilus influenzae Rd9 by lysogeny. Journal of bacteriology 17 299746
2019 Retinal Phenotype in the rd9 Mutant Mouse, a Model of X-Linked RP. Frontiers in neuroscience 16 31607844
2013 Pitpnm1 is expressed in hair cells during development but is not required for hearing. Neuroscience 11 23820044
2023 The lipid transfer proteins Nir2 and Nir3 sustain phosphoinositide signaling and actin dynamics during phagocytosis. Journal of cell science 7 37376972
2021 Attenuation of PITPNM1 Signaling Cascade Can Inhibit Breast Cancer Progression. Biomolecules 6 34572478
2025 The role of Nir2, a lipid-transfer protein, in regulating endothelial cell functions. Biochimica et biophysica acta. Molecular cell research 2 40010513
2025 Nir2 crystal structures reveal a phosphatidic acid-sensing mechanism at ER-PM contact sites. Proceedings of the National Academy of Sciences of the United States of America 2 41129229