bims-nucpor Biomed News
on Nuclear pore complex and nucleoporins in stress, aging and disease
Issue of 2022–03–20
eight papers selected by
Sara Mingu, Johannes Gutenberg University
  1. Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex.
  2. The nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release.
  3. The Nup2 meiotic-autonomous region relieves inhibition of Nup60 to promote progression of meiosis and sporulation in Saccharomyces cerevisiae.
  4. Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex.
  5. A perinuclear α-helix with amphipathic features in Brl1 promotes NPC assembly.
  6. Importin KPNA2 confers HIV-1 pre-integration complex nuclear import by interacting with the capsid protein.
  7. Nup98-dependent transcriptional memory is established independently of transcription.
  8. NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15INK4b.
  1. Cell Res. 2022 Mar 18.
    Cryo-EM structure of the inner ring from the Xenopus laevis nuclear pore complex.
    Gaoxingyu Huang, Xiechao Zhan, Chao Zeng, Ke Liang, Xuechen Zhu, Yanyu Zhao, Pan Wang, Qifan Wang, Qiang Zhou, Qinghua Tao, Minhao Liu, Jianlin Lei, Chuangye Yan, Yigong Shi.
      Nuclear pore complex (NPC) mediates nucleocytoplasmic shuttling. Here we present single-particle cryo-electron microscopy structure of the inner ring (IR) subunit from the Xenopus laevis NPC at an average resolution of 4.2 Å. A homo-dimer of Nup205 resides at the center of the IR subunit, flanked by two molecules of Nup188. Four molecules of Nup93 each places an extended helix into the axial groove of Nup205 or Nup188, together constituting the central scaffold. The channel nucleoporin hetero-trimer of Nup62/58/54 is anchored on the central scaffold. Six Nup155 molecules interact with the central scaffold and together with the NDC1-ALADIN hetero-dimers anchor the IR subunit to the nuclear envelope and to outer rings. The scarce inter-subunit contacts may allow sufficient latitude in conformation and diameter of the IR. Our structure reveals the molecular basis for the IR subunit assembly of a vertebrate NPC.
    DOI:  https://doi.org/10.1038/s41422-022-00633-x
  2. Nucleic Acids Res. 2022 Mar 14. pii: gkac164. [Epub ahead of print]
    The nucleoporin Gle1 activates DEAD-box protein 5 (Dbp5) by promoting ATP binding and accelerating rate limiting phosphate release.
    Shawn Gray, Wenxiang Cao, Ben Montpetit, Enrique M De La Cruz.
      The DEAD-box protein Dbp5 is essential for RNA export, which involves regulation by the nucleoporins Gle1 and Nup159 at the cytoplasmic face of the nuclear pore complex (NPC). Mechanistic understanding of how these nucleoporins regulate RNA export requires analyses of the intrinsic and activated Dbp5 ATPase cycle. Here, kinetic and equilibrium analyses of the Saccharomyces cerevisiae Gle1-activated Dbp5 ATPase cycle are presented, indicating that Gle1 and ATP, but not ADP-Pi or ADP, binding to Dbp5 are thermodynamically coupled. As a result, Gle1 binds Dbp5-ATP > 100-fold more tightly than Dbp5 in other nucleotide states and Gle1 equilibrium binding of ATP to Dbp5 increases >150-fold via slowed ATP dissociation. Second, Gle1 accelerated Dbp5 ATPase activity by increasing the rate-limiting Pi release rate constant ∼20-fold, which remains rate limiting. These data show that Gle1 activates Dbp5 by modulating ATP binding and Pi release. These Gle1 activities are expected to facilitate ATPase cycling, ensuring a pool of ATP bound Dbp5 at NPCs to engage RNA during export. This work provides a mechanism of Gle1-activation of Dbp5 and a framework to understand the joint roles of Gle1, Nup159, and other nucleoporins in regulating Dbp5 to mediate RNA export and other Dbp5 functions in gene expression.
    DOI:  https://doi.org/10.1093/nar/gkac164
  3. Genetics. 2022 Mar 18. pii: iyac045. [Epub ahead of print]
    The Nup2 meiotic-autonomous region relieves inhibition of Nup60 to promote progression of meiosis and sporulation in Saccharomyces cerevisiae.
    Kelly Komachi, Sean M Burgess.
      During meiosis, chromosomes undergo dramatic changes in structural organization, nuclear positioning, and motion. Although the nuclear pore complex has been shown to affect genome organization and function in vegetative cells, its role in meiotic chromosome dynamics has remained largely unexplored. Recent work in the budding yeast Saccharomyces cerevisiae demonstrated that the mobile nucleoporin Nup2 is required for normal progression through meiosis I prophase and sporulation in strains where telomere-led chromosome movement has been compromised. The meiotic autonomous region (MAR), a short fragment of Nup2 responsible for its role in meiosis, was shown to localize to the nuclear envelope via Nup60 and to bind to meiotic chromosomes. To understand the relative contribution these two activities have on MAR function, we first carried out a screen for MAR mutants defective in sporulation and found that all the mutations disrupt interaction with both Nup60 and meiotic chromosomes. Moreover, nup60 mutants phenocopy nup2 mutants, exhibiting similar nuclear division kinetics, sporulation efficiencies, and genetic interactions with mutations that affect the telomere bouquet. Although full-length Nup60 requires Nup2 for function, removal of Nup60's C-terminus allows Nup60 to bind meiotic chromosomes and promote sporulation without Nup2. In contrast, binding of the MAR to meiotic chromosomes is completely dependent on Nup60. Our findings uncover an inhibitory function for the Nup60 C-terminus and suggest that Nup60 mediates recruitment of meiotic chromosomes to the nuclear envelope, while Nup2 plays a secondary role counteracting the inhibitory function in Nup60's C-terminus.
    Keywords:   Saccharomyces cerevisiae ; LINC complex; Ndj1; Nup2; Nup60; budding yeast; meiosis; meiotic chromosomes; nuclear pore complex; sporulation
    DOI:  https://doi.org/10.1093/genetics/iyac045
  4. Cell Res. 2022 Mar 18.
    Near-atomic structure of the inner ring of the Saccharomyces cerevisiae nuclear pore complex.
    Zongqiang Li, Shuaijiabin Chen, Liang Zhao, Guoqiang Huang, Xiong Pi, Shan Sun, Peiyi Wang, Sen-Fang Sui.
      Nuclear pore complexes (NPCs) mediate bidirectional nucleocytoplasmic transport of substances in eukaryotic cells. However, the accurate molecular arrangement of NPCs remains enigmatic owing to their huge size and highly dynamic nature. Here we determined the structure of the asymmetric unit of the inner ring (IR monomer) at 3.73 Å resolution by single-particle cryo-electron microscopy, and created an atomic model of the intact IR consisting of 192 molecules of 8 nucleoporins. In each IR monomer, the Z-shaped Nup188-Nup192 complex in the middle layer is sandwiched by two approximately parallel rhomboidal structures in the inner and outer layers, while Nup188, Nup192 and Nic96 link all subunits to constitute a relatively stable IR monomer. In contrast, the intact IR is assembled by loose and instable interactions between IR monomers. These structures, together with previously reported structural information of IR, reveal two distinct interaction modes between IR monomers and extensive flexible connections in IR assembly, providing a structural basis for the stability and malleability of IR.
    DOI:  https://doi.org/10.1038/s41422-022-00632-y
  5. Mol Biol Cell. 2022 Mar 16. mbcE21120616
    A perinuclear α-helix with amphipathic features in Brl1 promotes NPC assembly.
    Jlenia Vitale, Azqa Khan, Annett Neuner, Elmar Schiebel.
      How nuclear pore complexes (NPC) assemble in the intact nuclear envelope (NE) is only rudimentarily understood. Nucleoporins accumulate at the inner NE (INM), deform this membrane towards the outer nuclear membrane (ONM) and eventually INM and ONM fuse by an unclear mechanism. In budding yeast, the integral membrane protein Brl1 that transiently associates with NPC assembly intermediates is involved in INM/ONM fusion during NPC assembly but leaving the molecular mechanism open. AlphaFold predictions indicate that Brl1-like proteins carry as common motifs an α-helix with amphipathic features (AαH) and a disulfide-stabilized anti-parallel helix bundle (DAH) in the perinuclear space. Mutants with defective AαH (brl1F391E, brl1F391P, brl1L402E) impair the essential function of BRL1. Overexpression of brl1F391E promotes formation of INM and ONM enclosed petal-like structures that carry nucleoporins at their base suggesting that they are derived from an NPC assembly attempt with failed INM/ONM fusion. Accordingly, brl1F391E expression triggers mis-localisation of Nup159 and Nup42 and to a lesser extent Nsp1 that localize on the cytoplasmic face of the NPC. The DAH also contributes to the function of Brl1 and AαH has functions independent of DAH. We propose that AαH and DAH in Brl1 promote INM/ONM fusion during NPC assembly.
    DOI:  https://doi.org/10.1091/mbc.E21-12-0616
  6. Antiviral Res. 2022 Mar 14. pii: S0166-3542(22)00057-2. [Epub ahead of print] 105289
    Importin KPNA2 confers HIV-1 pre-integration complex nuclear import by interacting with the capsid protein.
    Yanhui Song, Hongguang Zhang, Yinmiao Wang, Jin Guo, Shengjie Tang, Lu Wang, Ke Peng, Chun-Sheng Dong.
      For human immunodeficiency virus 1 (HIV-1) to infect non-dividing cells, pre-integration complex (PIC) must be transported into the nucleus within the replication cycle. We previously reported that the karyopherin β1 (KPNB1)-nucleoporin Pom121 pathway, related to the downstream process of PIC nuclear import, mediates efficient HIV-1 PIC nuclear import. Further, our earlier RNA transcriptome sequencing revealed that karyopherin α2 (KPNA2) was among the differentially expressed importin family members during monocyte to macrophage differentiation. Although PIC transport into the nucleus in HIV-1 has been widely studied, much remains to be understood about it. In this study, we confirmed our previous RNA sequencing results and found that HIV-1 replication was significantly lower in 293T cells with siRNA-mediated KPNA2 knockdown and higher in KPNA2-upregulated cells. Quantitative PCR indicated that viral replication was impaired during cDNA nuclear import. The N-terminal of the capsid protein p24 interacted with KPNA2, and KPNB1 participated in KPNA2-mediated PIC nuclear import. Disruption of the capsid-KPNA2 binding by overexpression of full-length p24 or p24 N-terminal impaired the PIC nuclear import. These results indicate that KPNA2 is an important upstream adaptor of the KPNB1-Pom121 axis, thereby mediating HIV-1 PIC nuclear transportation. KPNA2 is thus a potential target for HIV-1 antiviral treatment.
    Keywords:  HIV-1; KPNA2; Nuclear import; Viral replication
    DOI:  https://doi.org/10.1016/j.antiviral.2022.105289
  7. Elife. 2022 Mar 15. pii: e63404. [Epub ahead of print]11
    Nup98-dependent transcriptional memory is established independently of transcription.
    Pau Pascual-Garcia, Shawn C Little, Maya Capelson.
      Cellular ability to mount an enhanced transcriptional response upon repeated exposure to external cues is termed transcriptional memory, which can be maintained epigenetically through cell divisions and can depend on a nuclear pore component Nup98. The majority of mechanistic knowledge on transcriptional memory has been derived from bulk molecular assays. To gain additional perspective on the mechanism and contribution of Nup98 to memory, we used single-molecule RNA FISH (smFISH) to examine the dynamics of transcription in Drosophila cells upon repeated exposure to the steroid hormone ecdysone. We combined smFISH with mathematical modeling and found that upon hormone exposure, cells rapidly activate a low-level transcriptional response, but simultaneously begin a slow transition into a specialized memory state characterized by a high rate of expression. Strikingly, our modeling predicted that this transition between non-memory and memory states is independent of the transcription stemming from initial activation. We confirmed this prediction experimentally by showing that inhibiting transcription during initial ecdysone exposure did not interfere with memory establishment. Together, our findings reveal that Nup98's role in transcriptional memory is to stabilize the forward rate of conversion from low to high expressing state, and that induced genes engage in two separate behaviors - transcription itself and the establishment of epigenetically propagated transcriptional memory.
    Keywords:  D. melanogaster; Nup98; chromosomes; epigenetic; gene expression; nuclear pore; transcription; transcriptional memory
    DOI:  https://doi.org/10.7554/eLife.63404
  8. Dig Liver Dis. 2022 Mar 11. pii: S1590-8658(22)00199-2. [Epub ahead of print]
    NUP153 promotes HCC cells proliferation via c-Myc-mediated downregulation of P15INK4b.
    Caiqin Gan, Kezhi Zhou, Mengting Li, Jian Shang, Lan Liu, Qiu Zhao.
       BACKGROUND AND AIM: Nucleoporin NUP153 (NUP153) is involved in the regulation of nuclear transportation, mitosis, and tumor progression in various cancer cells. we aimed to investigate the roles of NUP153 in hepatocellular carcinoma (HCC).
    METHODS: NUP153 expression level and its relationship with clinical prognosis were analyzed based on The Cancer Genome Atlas (TCGA). Quantitative real-time PCR (qRT-PCR), Western Blot (WB), and Immunohistochemistry (IHC) were used to assess NUP153 expression in tissues and cell lines. Loss-of-function experiments were implemented for exploring the roles of NUP153 in HCC cells. Ultimately, how NUP153 exerted biological functions was plumbed by performing rescue assays in HCC.
    RESULTS: NUP153 expressed highly in HCC tissues and cell lines. Silencing NUP153 inhibited cellular multiplication, G1/S transition, migration, and triggered cytoskeletal rearrangement of Huh7 and HepG2 cells. Knockdown NUP153 caused up-regulation of mRNA and protein levels of P15, and siRNA deprivation of P15 partially reversed the function of low-level NUP153 in HCC. Meanwhile, silencing NUP153 caused down-regulation of mRNA and protein levels of c-Myc. Furthermore, the up-regulation of P15 and cell G1/S phase arrest induced by silencing NUP153 were partially reversed by overexpression of c-Myc.
    CONCLUSIONS: NUP153 increases the proliferation ability of cells via the c-Myc/P15 axis in HCC.
    Keywords:  G1 cell cycle arrest; Hepatocellular carcinoma; NUP153; P15(INK4b)
    DOI:  https://doi.org/10.1016/j.dld.2022.02.008
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