id: MODULE:karyopherin_nuclear_protein_import title: Karyopherin-mediated nuclear protein import description: >- Signal-dependent import of a protein cargo from the cytosol into the nucleus through the nuclear pore complex, driven by the Ran GTPase gradient. A karyopherin carrier recognizes the cargo in the cytosol, either through an importin-alpha adaptor that binds a classical nuclear localization signal and bridges it to importin-beta1, or directly through an importin-beta-family carrier (importin-beta1, importin-7, importin-8). The carrier-cargo complex moves through the pore by transient contacts with FG-repeat nucleoporins. In the nucleus, RanGTP (kept high by the chromatin-bound exchange factor RCC1) binds the carrier and releases the cargo into the nucleoplasm. Carriers return to the cytosol, importin-alpha by the RanGTP-dependent exporter CSE1L, and cytosolic RanGAP1 with RanBP1 hydrolyses the exported RanGTP; NTF2 returns RanGDP to the nucleus. The module is cargo-neutral so that signalling modules can include it wherever a transcription factor activated in the cytosol must reach its nuclear targets (STATs, SMADs). status: DRAFT scope: ABSTRACT evidence: - source_id: PMID:17287812 title: Molecular mechanism of the nuclear protein import cycle. statement: Review of the karyopherin import cycle as a spatially organized cycle of cargo, carrier and Ran GTPase interactions. supporting_text: >- The nuclear import of proteins through nuclear pore complexes (NPCs) illustrates how a complex biological function can be generated by a spatially and temporally organized cycle of interactions between cargoes, carriers and the Ran GTPase. - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: >- Establishes the importin-alpha/beta route, RanGTP-driven release in the nucleus, CSE1L (CAS)-mediated return of importin-alpha, and its cytosolic release by RanBP1 and RanGAP1. supporting_text: >- NLS proteins are transported into the nucleus by the importin alpha/beta heterodimer. notes: >- Written for reuse by module_ref from signalling modules, to make explicit the step that GO-CAM models leave implicit when a cytosolic kinase directly activates a transcription factor whose activity is placed in the nucleus (see projects/GOCAM_COMPARTMENTS.md). Which carrier route a cargo uses is a property of the cargo, recorded in the including module: STAT1 uses the importin-alpha5 (KPNA1) route and STAT3 importin-alpha3 (KPNA4); activated SMAD3 binds importin-beta1 directly, and activated SMADs are imported by importin-7/8. The nuclear pore itself is not re-modelled here; the translocation step names FG-nucleoporins only as the surface the carrier moves along. No member of this module has a gene review yet, so the annotons are grounded by UniProt accession and literature only. module: id: karyopherin_nuclear_protein_import label: Karyopherin-mediated nuclear protein import module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: protein import into nucleus term: id: GO:0006606 label: protein import into nucleus context: taxa: - preferred_term: Eukaryota term: id: NCBITaxon:2759 label: Eukaryota cellular_components: - preferred_term: cytosol term: id: GO:0005829 label: cytosol - preferred_term: nuclear envelope term: id: GO:0005635 label: nuclear envelope - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm parts: - order: 1 role: cargo recognition by a karyopherin carrier in the cytosol node: id: cargo_recognition label: Cargo recognition by a karyopherin carrier module_type: TRANSPORT_STEP description: >- The cargo is bound in the cytosol by an import carrier, either via an importin-alpha adaptor and importin-beta1, or directly by an importin-beta-family carrier. Which route is used depends on the cargo. variant_sets: - id: carrier_route label: Carrier route axis: how the cargo is recognized by the import carrier selection: ONE_OR_MORE variants: - id: importin_alpha_beta_route label: Importin-alpha/importin-beta1 route module_type: TRANSPORT_STEP description: >- An importin-alpha adaptor binds the cargo's nuclear localization signal and importin-beta1, which carries the trimeric complex through the pore. Used by tyrosine-phosphorylated STAT1 (importin-alpha5/KPNA1) and STAT3 (importin-alpha3/KPNA4). annotons: - id: importin_alpha_adaptor label: Importin-alpha cargo adaptor participant: selector_type: FAMILY family: preferred_term: importin-alpha family description: >- Armadillo-repeat adaptors that bind classical nuclear localization signals and importin-beta1. No PANTHER id is asserted; the family is identified by its members. Members differ in cargo: KPNA2 (Rch1) is a general cNLS adaptor but does not import STAT1, which uses KPNA1 (NPI-1). representative_members: - preferred_term: KPNA1 term: id: UniProtKB:P52294 label: Importin subunit alpha-5 - preferred_term: KPNA4 term: id: UniProtKB:O00629 label: Importin subunit alpha-3 - preferred_term: KPNA2 term: id: UniProtKB:P52292 label: Importin subunit alpha-1 function: preferred_term: nuclear import signal receptor activity term: id: GO:0061608 label: nuclear import signal receptor activity processes: - preferred_term: protein import into nucleus term: id: GO:0006606 label: protein import into nucleus locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: Recognizes the cargo's nuclear localization signal and links it to importin-beta1. evidence: - source_id: PMID:9384585 title: Extracellular signal-dependent nuclear import of Stat1 is mediated by nuclear pore-targeting complex formation with NPI-1, but not Rch1. statement: Tyrosine-phosphorylated STAT1 is imported by importin-beta1 through the NPI-1 (importin-alpha5) adaptor family. supporting_text: >- Tyrosine-phosphorylated Stat1 associated with the beta subunit (a 97 kDa component) of the nuclear pore-targeting complex via the NPI-1 family, but not the Rch1 family, of alpha subunit - source_id: PMID:15919823 title: STAT3 nuclear import is independent of tyrosine phosphorylation and mediated by importin-alpha3. statement: STAT3 is recognized by importin-alpha3 through a coiled-coil region. supporting_text: >- this region is critical for its recognition by specific import carrier importin-alpha3 - id: importin_beta1_alpha_route label: Importin-beta1 carrier (with importin-alpha) participant: selector_type: GENE_PRODUCT gene_product: preferred_term: KPNB1 term: id: UniProtKB:Q14974 label: Importin subunit beta-1 function: preferred_term: nuclear import signal receptor activity term: id: GO:0061608 label: nuclear import signal receptor activity processes: - preferred_term: protein import into nucleus term: id: GO:0006606 label: protein import into nucleus locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: Binds the importin-alpha/cargo complex and mediates its translocation through the pore. evidence: - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: Importin-alpha binds the NLS while importin-beta mediates translocation. supporting_text: >- Importin alpha binds the NLS, while importin beta mediates translocation through the nuclear pore complex. - id: direct_importin_beta_route label: Direct importin-beta-family route module_type: TRANSPORT_STEP description: >- An importin-beta-family carrier binds the cargo without an importin-alpha adaptor. Receptor-activated SMAD3 binds importin-beta1 through its N-terminal domain, and activated SMAD1 and SMAD2/3 are imported by importin-7 and importin-8. annotons: - id: importin_beta_direct_carrier label: Importin-beta-family direct carrier participant: selector_type: FAMILY family: preferred_term: importin-beta (karyopherin-beta) family carriers description: >- HEAT-repeat Ran-binding carriers that bind cargo directly. No PANTHER id is asserted; the family is identified by its members. representative_members: - preferred_term: KPNB1 term: id: UniProtKB:Q14974 label: Importin subunit beta-1 - preferred_term: IPO7 term: id: UniProtKB:O95373 label: Importin-7 - preferred_term: IPO8 term: id: UniProtKB:O15397 label: Importin-8 function: preferred_term: nuclear import signal receptor activity term: id: GO:0061608 label: nuclear import signal receptor activity processes: - preferred_term: protein import into nucleus term: id: GO:0006606 label: protein import into nucleus locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: Binds the cargo directly and carries it through the pore. evidence: - source_id: PMID:11294908 title: Transforming growth factor-beta induces nuclear import of Smad3 in an importin-beta1 and Ran-dependent manner. statement: Receptor-activated SMAD3 binds importin-beta1 directly; importin-beta1, Ran and NTF2 suffice for its import. supporting_text: >- Importin-beta1, Ran, and p10/NTF2 are sufficient to mediate import of activated Smad3. - source_id: PMID:17785517 title: Msk is required for nuclear import of TGF-{beta}/BMP-activated Smads. statement: Importin-7 and importin-8 are required for nuclear accumulation of BMP-activated SMAD1 and TGF-beta-activated SMAD2/3. supporting_text: >- knockdown of importin 7 and 8 (Imp7 and 8), the mammalian orthologues of Msk, markedly impaired nuclear accumulation of Smad1 in response to BMP2 and of Smad2/3 in response to TGF-beta. - order: 2 role: translocation through the nuclear pore node: id: pore_translocation label: Translocation through the nuclear pore module_type: TRANSPORT_STEP description: >- The carrier-cargo complex passes through the central channel of the nuclear pore complex by transient contacts with FG-repeat nucleoporins. NUP153, on the nuclear basket, is named as a representative FG-nucleoporin; the pore complex as a whole is not modelled here. annotons: - id: fg_nucleoporin label: FG-repeat nucleoporin participant: selector_type: FAMILY family: preferred_term: FG-repeat nucleoporins description: Nucleoporins whose FG repeats form the permeability barrier that karyopherins traverse. representative_members: - preferred_term: NUP153 term: id: UniProtKB:P49790 label: Nuclear pore complex protein Nup153 function: preferred_term: structural constituent of nuclear pore term: id: GO:0017056 label: structural constituent of nuclear pore locations: - preferred_term: nuclear envelope term: id: GO:0005635 label: nuclear envelope role_description: Provides the FG-repeat surface along which the carrier-cargo complex moves. - order: 3 role: RanGTP-dependent cargo release in the nucleus node: id: rangtp_cargo_release label: RanGTP-dependent cargo release module_type: TRANSPORT_STEP description: >- Nuclear RanGTP binds importin-beta and releases the cargo (and importin-alpha) into the nucleoplasm. RCC1, bound to chromatin, charges Ran with GTP and so keeps RanGTP high in the nucleus. annotons: - id: ran_gtpase label: Ran GTPase participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RAN term: id: UniProtKB:P62826 label: GTP-binding nuclear protein Ran function: preferred_term: GTPase activity term: id: GO:0003924 label: GTPase activity processes: - preferred_term: protein import into nucleus term: id: GO:0006606 label: protein import into nucleus locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: In its GTP-bound form binds importin-beta in the nucleus and displaces the cargo. evidence: - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: Nuclear RanGTP binds importin-beta and displaces importin-alpha with its cargo. supporting_text: >- RanGTP, whose predicted concentration is high in the nucleus and low in the cytoplasm, binds importin beta and displaces importin alpha. - source_id: PMID:11294908 title: Transforming growth factor-beta induces nuclear import of Smad3 in an importin-beta1 and Ran-dependent manner. statement: Ran releases activated SMAD3 from importin-beta1. supporting_text: >- Nuclear import of Smad3 in vivo requires the action of the Ran GTPase, which mediates release of Smad3 from the complex with importin-beta1. - id: rcc1_ran_gef label: RCC1 Ran guanine-nucleotide exchange factor participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RCC1 term: id: UniProtKB:P18754 label: Regulator of chromosome condensation function: preferred_term: guanyl-nucleotide exchange factor activity term: id: GO:0005085 label: guanyl-nucleotide exchange factor activity locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: Chromatin-bound exchange factor that loads Ran with GTP, maintaining the nuclear RanGTP pool. evidence: - source_id: PMID:1944575 title: Catalysis of guanine nucleotide exchange on Ran by the mitotic regulator RCC1. statement: RCC1 is a nuclear, chromatin-bound protein that catalyses guanine nucleotide exchange on Ran. supporting_text: >- Here we show that RCC1 specifically catalyses the exchange of guanine nucleotides on the Ran protein - order: 4 role: carrier return and Ran gradient maintenance node: id: carrier_recycling label: Carrier return and Ran gradient maintenance module_type: TRANSPORT_STEP description: >- Carriers return to the cytosol for another round. Importin-alpha is exported by CSE1L in a complex with RanGTP; in the cytosol RanBP1 and RanGAP1 release it and convert RanGTP to RanGDP, which NTF2 carries back into the nucleus. annotons: - id: rangap1_cytosolic_gap label: RanGAP1 cytosolic Ran GTPase-activating protein participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RANGAP1 term: id: UniProtKB:P46060 label: Ran GTPase-activating protein 1 function: preferred_term: GTPase activator activity term: id: GO:0005096 label: GTPase activator activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: Stimulates GTP hydrolysis on exported Ran, keeping cytosolic RanGTP low. evidence: - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: RanBP1 and RanGAP1 release importin-alpha from the CSE1L/RanGTP export complex in the cytosol. supporting_text: >- Importin alpha is released from this complex in the cytoplasm by the combined action of RanBP1 and RanGAP1. - id: ranbp1_ran_binding_cofactor label: RanBP1 cofactor of RanGAP1 participant: selector_type: GENE_PRODUCT gene_product: preferred_term: RANBP1 term: id: UniProtKB:P43487 label: Ran-specific GTPase-activating protein locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: >- Acts with RanGAP1 in the cytosol to release importin-alpha from the CSE1L/RanGTP export complex and allow GTP hydrolysis on Ran. evidence: - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: RanBP1 and RanGAP1 together release importin-alpha from the export complex in the cytoplasm. supporting_text: >- Importin alpha is released from this complex in the cytoplasm by the combined action of RanBP1 and RanGAP1. - id: nutf2_rangdp_import label: NTF2 RanGDP import carrier participant: selector_type: GENE_PRODUCT gene_product: preferred_term: NUTF2 term: id: UniProtKB:P61970 label: Nuclear transport factor 2 function: preferred_term: nucleocytoplasmic carrier activity term: id: GO:0140142 label: nucleocytoplasmic carrier activity locations: - preferred_term: cytosol term: id: GO:0005829 label: cytosol role_description: Binds RanGDP in the cytosol and returns it to the nucleus, where RCC1 recharges it. evidence: - source_id: PMID:11294908 title: Transforming growth factor-beta induces nuclear import of Smad3 in an importin-beta1 and Ran-dependent manner. statement: NTF2 is one of the minimal factors needed to reconstitute import of activated SMAD3. supporting_text: >- Importin-beta1, Ran, and p10/NTF2 are sufficient to mediate import of activated Smad3. - order: 5 role: importin-alpha re-export optional: true notes: Needed only for the importin-alpha/beta route; cargoes carried directly by an importin-beta-family carrier do not use it. node: id: importin_alpha_reexport label: Importin-alpha re-export by CSE1L module_type: TRANSPORT_STEP description: CSE1L binds cargo-free importin-alpha together with RanGTP and exports it to the cytosol. annotons: - id: cse1l_importin_alpha_exporter label: CSE1L importin-alpha exporter participant: selector_type: GENE_PRODUCT gene_product: preferred_term: CSE1L term: id: UniProtKB:P55060 label: Exportin-2 function: preferred_term: nuclear export signal receptor activity term: id: GO:0005049 label: nuclear export signal receptor activity processes: - preferred_term: protein export from nucleus term: id: GO:0006611 label: protein export from nucleus locations: - preferred_term: nucleoplasm term: id: GO:0005654 label: nucleoplasm role_description: Binds cargo-free importin-alpha with RanGTP in the nucleus and returns it to the cytosol, leaving the cargo behind. evidence: - source_id: PMID:9323134 title: Export of importin alpha from the nucleus is mediated by a specific nuclear transport factor. statement: CSE1L (CAS) mediates RanGTP-dependent re-export of cargo-free importin-alpha. supporting_text: >- CAS binds strongly to importin alpha only in the presence of RanGTP, forming an importin alpha/CAS/RanGTP complex. connections: - source: cargo_recognition target: pore_translocation connection_type: PRECEDES description: The carrier-cargo complex formed in the cytosol enters the pore. - source: pore_translocation target: rangtp_cargo_release connection_type: PRECEDES description: On reaching the nucleus the complex meets RanGTP, which releases the cargo. - source: rangtp_cargo_release target: carrier_recycling connection_type: PRECEDES description: The RanGTP-bound carrier returns to the cytosol, where RanGAP1 hydrolyses the GTP. - source: rangtp_cargo_release target: importin_alpha_reexport connection_type: PRECEDES description: Released importin-alpha is exported by CSE1L with RanGTP. - source: carrier_recycling target: rangtp_cargo_release connection_type: PROVIDES_INPUT_FOR description: NTF2 returns RanGDP to the nucleus, where RCC1 recharges it, sustaining the RanGTP gradient that drives release.