bims-nucpor Biomed News
on Nuclear pore complex and nucleoporins in stress, aging and disease
Issue of 2022–02–27
seven papers selected by
Sara Mingu, Johannes Gutenberg University
  1. The intricate roles of RCC1 in normal cells and cancer cells.
  2. Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors.
  3. Exportin Crm1 is important for Swi6 nuclear shuttling and MBF transcription activation in Saccharomyces cerevisiae.
  4. Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model.
  5. OsWRKY62 and OsWRKY76 Interact with Importin α1s for Negative Regulation of Defensive Responses in Rice Nucleus.
  6. Decoupling SARS-CoV-2 ORF6 localization and interferon antagonism.
  7. Proximity Ligation Mapping of Microcephaly Associated SMPD4 Shows Association with Components of the Nuclear Pore Membrane.
  1. Biochem Soc Trans. 2022 Feb 22. pii: BST20210861. [Epub ahead of print]
    The intricate roles of RCC1 in normal cells and cancer cells.
    Li Jing, Hang Fai Kwok.
      RCC1 (regulator of chromosome condensation 1) is a highly conserved chromatin-binding protein and the only known guanine-nucleotide exchange factor of Ran (a nuclear Ras homolog). RCC1 plays an essential role in the regulation of cell cycle-related activities such as nuclear envelope formation, nuclear pore complex and spindle assembly, and nucleocytoplasmic transport. Over the last decade, increasing evidence has emerged highlighting the potential relevance of RCC1 to carcinogenesis, especially cervical, lung, and breast cancer. In this review, we briefly discuss the roles of RCC1 in both normal and tumor cells based on articles published in recent years, followed by a brief overview of future perspectives in the field.
    Keywords:  cell cycle reguation; chromatin; chromosome condensation; tumorigenesis
    DOI:  https://doi.org/10.1042/BST20210861
  2. Cell Rep. 2022 Feb 22. pii: S2211-1247(22)00142-5. [Epub ahead of print]38(8): 110418
    Nucleoporin-93 reveals a common feature of aggressive breast cancers: robust nucleocytoplasmic transport of transcription factors.
    Nishanth Belugali Nataraj, Ashish Noronha, Joo Sang Lee, Soma Ghosh, Harsha Raj Mohan Raju, Arunachalam Sekar, Binyamin Zuckerman, Moshit Lindzen, Emilio Tarcitano, Swati Srivastava, Michael Selitrennik, Ido Livneh, Diana Drago-Garcia, Oscar Rueda, Carlos Caldas, Sima Lev, Tamar Geiger, Aaron Ciechanover, Igor Ulitsky, Rony Seger, Eytan Ruppin, Yosef Yarden.
      By establishing multi-omics pipelines, we uncover overexpression and gene copy-number alterations of nucleoporin-93 (NUP93), a nuclear pore component, in aggressive human mammary tumors. NUP93 overexpression enhances transendothelial migration and matrix invasion in vitro, along with tumor growth and metastasis in animal models. These findings are supported by analyses of two sets of naturally occurring mutations: rare oncogenic mutations and inactivating familial nephrotic syndrome mutations. Mechanistically, NUP93 binds with importins, boosts nuclear transport of importins' cargoes, such as β-catenin, and activates MYC. Likewise, NUP93 overexpression enhances the ultimate nuclear transport step shared by additional signaling pathways, including TGF-β/SMAD and EGF/ERK. The emerging addiction to nuclear transport exposes vulnerabilities of NUP93-overexpressing tumors. Congruently, myristoylated peptides corresponding to the nuclear translocation signals of SMAD and ERK can inhibit tumor growth and metastasis. Our study sheds light on an emerging hallmark of advanced tumors, which derive benefit from robust nucleocytoplasmic transport.
    Keywords:  EGF/ERK; TGF-β/SMAD; WNT/β-catenin; breast cancer; cancer hallmark; importin; metastasis; nuclear pore; nuclear transport; transcription factor
    DOI:  https://doi.org/10.1016/j.celrep.2022.110418
  3. BMC Mol Cell Biol. 2022 Feb 21. 23(1): 10
    Exportin Crm1 is important for Swi6 nuclear shuttling and MBF transcription activation in Saccharomyces cerevisiae.
    Kenneth D Belanger, William T Yewdell, Matthew F Barber, Amy N Russo, Mark A Pettit, Emily K Damuth, Naveen Hussain, Susan J Geier, Karyn G Belanger.
       BACKGROUND: Swi6 acts as a transcription factor in budding yeast, functioning in two different heterodimeric complexes, SBF and MBF, that activate the expression of distinct but overlapping sets of genes. Swi6 undergoes regulated changes in nucleocytoplasmic localization throughout the cell cycle that correlate with changes in gene expression. This study investigates how nucleocytoplasmic transport by multiple transport factors may influence specific Swi6 activities.
    RESULTS: Here we show that the exportin Crm1 is important for Swi6 nuclear export and activity. Loss of a putative Crm1 NES or inhibition of Crm1 activity results in changes in nucleocytoplasmic Swi6 localization. Alteration of the Crm1 NES in Swi6 results in decreased MBF-mediated gene expression, but does not affect SBF reporter expression, suggesting that export of Swi6 by Crm1 regulates a subset of Swi6 transcription activation activity. Finally, alteration of the putative Crm1 NES in Swi6 results in cells that are larger than wild type, and this increase in cell size is exacerbated by deletion of Msn5.
    CONCLUSIONS: These data provide evidence that Swi6 has at least two different exportins, Crm1 and Msn5, each of which interacts with a distinct nuclear export signal. We identify a putative nuclear export signal for Crm1 within Swi6, and observe that export by Crm1 or Msn5 independently influences Swi6-regulated expression of a different subset of Swi6-controlled genes. These findings provide new insights into the complex regulation of Swi6 transcription activation activity and the role of nucleocytoplasmic shuttling in regulated gene expression.
    Keywords:  Exportin; Karyopherin; Nuclear shuttling; Nucleocytoplasmic transport; Swi6
    DOI:  https://doi.org/10.1186/s12860-022-00409-6
  4. Pediatr Nephrol. 2022 Feb 24.
    Exploring the relevance of NUP93 variants in steroid-resistant nephrotic syndrome using next generation sequencing and a fly kidney model.
    Agnieszka Bierzynska, Katherine Bull, Sara Miellet, Philip Dean, Chris Neal, Elizabeth Colby, Hugh J McCarthy, Shivaram Hegde, Manish D Sinha, Carmen Bugarin Diz, Kathleen Stirrups, Karyn Megy, Rutendo Mapeta, Chris Penkett, Sarah Marsh, Natalie Forrester, Maryam Afzal, Hannah Stark, Nihr BioResource, Maggie Williams, Gavin I Welsh, Ania B Koziell, Paul S Hartley, Moin A Saleem.
       BACKGROUND: Variants in genes encoding nuclear pore complex (NPC) proteins are a newly identified cause of paediatric steroid-resistant nephrotic syndrome (SRNS). Recent reports describing NUP93 variants suggest these could be a significant cause of paediatric onset SRNS. We report NUP93 cases in the UK and demonstrate in vivo functional effects of Nup93 depletion in a fly (Drosophila melanogaster) nephrocyte model.
    METHODS: Three hundred thirty-seven paediatric SRNS patients from the National cohort of patients with Nephrotic Syndrome (NephroS) were whole exome and/or whole genome sequenced. Patients were screened for over 70 genes known to be associated with Nephrotic Syndrome (NS). D. melanogaster Nup93 knockdown was achieved by RNA interference using nephrocyte-restricted drivers.
    RESULTS: Six novel homozygous and compound heterozygous NUP93 variants were detected in 3 sporadic and 2 familial paediatric onset SRNS characterised histologically by focal segmental glomerulosclerosis (FSGS) and progressing to kidney failure by 12 months from clinical diagnosis. Silencing of the two orthologs of human NUP93 expressed in D. melanogaster, Nup93-1, and Nup93-2 resulted in significant signal reduction of up to 82% in adult pericardial nephrocytes with concomitant disruption of NPC protein expression. Additionally, nephrocyte morphology was highly abnormal in Nup93-1 and Nup93-2 silenced flies surviving to adulthood.
    CONCLUSION: We expand the spectrum of NUP93 variants detected in paediatric onset SRNS and demonstrate its incidence within a national cohort. Silencing of either D. melanogaster Nup93 ortholog caused a severe nephrocyte phenotype, signaling an important role for the nucleoporin complex in podocyte biology. A higher resolution version of the Graphical abstract is available as Supplementary information.
    Keywords:  FSGS; NUP93; Nephrocyte; Podocyte; SRNS
    DOI:  https://doi.org/10.1007/s00467-022-05440-5
  5. Rice (N Y). 2022 Feb 20. 15(1): 12
    OsWRKY62 and OsWRKY76 Interact with Importin α1s for Negative Regulation of Defensive Responses in Rice Nucleus.
    Xiaohui Xu, Han Wang, Jiqin Liu, Shuying Han, Miaomiao Lin, Zejian Guo, Xujun Chen.
      Background OsWRKY62 and OsWRKY76, two close members of WRKY transcription factors, function together as transcriptional repressors. OsWRKY62 is predominantly localized in the cytosol. What are the regulatory factors for OsWRKY62 nuclear translocation? Results In this study, we characterized the interaction of OsWRKY62 and OsWRKY76 with rice importin, OsIMα1a and OsIMα1b, for nuclear translocation. Chimeric OsWRKY62.1-GFP, which is predominantly localized in the cytoplasm, was translocated to the nucleus of Nicotiana benthamiana leaf cells in the presence of OsIMα1a or OsIMαΔIBB1a lacking the auto-inhibitory importin β-binding domain. OsIMαΔIBB1a interacted with the WRKY domain of OsWRKY62.1, which has specific bipartite positively charged concatenated amino acids functioning as a nuclear localization signal (NLS). Similarly, we found that OsIMαΔIBB1a interacted with the AvrPib effector of rice blast fungus Magnaporthe oryzae, which contains a scattered distribution of positively charged amino acids. Furthermore, we identified a nuclear export signal (NES) in OsWRKY62.1 that inhibited nuclear transportation. Overexpression of OsIMα1a or OsIMα1b enhanced resistance to M. oryzae, whereas knockout mutants decreased resistance to the pathogen. However, overexpressing both OsIMα1a and OsWRKY62.1 were slightly more susceptible to M. oryzae than OsWRKY62.1 alone. Ectopic overexpression of OsWRKY62.1-NES fused gene compromised the enhanced susceptibility of OsWRKY62.1 to M. oryzae. Conclusion These results revealed the existence of NLS and NES in OsWRKY62. OsWRKY62, OsWRKY76, and AvrPib effector translocate to nucleus in association with importin α1s through new types of nuclear localization signals for negatively regulating defense responses.
    Keywords:  AvrPib; Importin α; Magnaporthe oryzae; Nuclear localization signal; Oryza sativa; WRKY
    DOI:  https://doi.org/10.1186/s12284-022-00558-4
  6. J Cell Sci. 2022 Feb 21. pii: jcs.259666. [Epub ahead of print]
    Decoupling SARS-CoV-2 ORF6 localization and interferon antagonism.
    Hoi Tong Wong, Victoria Cheung, Daniel J Salamango.
      Like many pathogenic viruses, SARS-CoV-2 must overcome interferon (IFN)-mediated host defenses for infection establishment. To achieve this, SARS-CoV-2 deploys overlapping mechanisms to antagonize IFN production and signaling. The strongest IFN antagonist is the accessory protein ORF6, which localizes to multiple membranous compartments, including the nuclear envelope, where it directly binds nuclear pore components Nup98-Rae1 to inhibit nuclear translocation of activated STAT1/IRF3 transcription factors. However, this direct cause-and-effect relationship between ORF6 localization and IFN antagonism has yet to be explored experimentally. Here, we use extensive mutagenesis studies to define the structural determinants required for steady-state localization and demonstrate that mis-localized ORF6 variants still potently inhibit nuclear trafficking and IFN signaling. Additionally, expression of a peptide that mimics the ORF6/Nup98 interaction domain robustly blocked nuclear trafficking. Furthermore, pharmacologic and mutational approaches combined to suggest that ORF6 is likely a peripheral-membrane protein, opposed to being a transmembrane protein as previously speculated. Thus, ORF6 localization and IFN antagonism are independent activities, which raises the possibility that ORF6 may have additional functions within membrane networks to enhance virus replication.
    Keywords:  COVID-19; Importin-alpha; Innate immune suppression; Peripheral membrane protein; Subcellular localization
    DOI:  https://doi.org/10.1242/jcs.259666
  7. Cells. 2022 Feb 15. pii: 674. [Epub ahead of print]11(4):
    Proximity Ligation Mapping of Microcephaly Associated SMPD4 Shows Association with Components of the Nuclear Pore Membrane.
    Alexandra C A Piët, Marco Post, Dick Dekkers, Jeroen A A Demmers, Maarten Fornerod.
      SMPD4 is a neutral sphingomyelinase implicated in a specific type of congenital microcephaly. Although not intensively studied, SMPD4 deficiency has also been found to cause cell division defects. This suggests a role for SMPD4 in cell-cycle and differentiation. In order to explore this role, we used proximity ligation to identify the partners of SMPD4 in vivo in HEK293T cells. We found that these partners localize near the endoplasmic reticulum (ER) and the nuclear membrane. Using mass spectrometry, we could identify these partners and discovered that SMPD4 is closely associated with several nucleoporins, including NUP35, a nucleoporin directly involved in pore membrane curvature and pore insertion. This suggests that SMPD4 may play a role in this process.
    Keywords:  NUP35; SMPD4; n-smnase-3; nuclear pore membrane; sphingomyelinase
    DOI:  https://doi.org/10.3390/cells11040674
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