bims-nucpor Biomed News
on Nuclear pore complex and nucleoporins in stress, aging and disease
Issue of 2021–07–04
nine papers selected by
Sara Mingu, Johannes Gutenberg University
  1. 3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex.
  2. Recapitulation of selective nuclear import and export with a perfectly repeated 12mer GLFG peptide.
  3. Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.
  4. The Viral Capsid: A Master Key to Access the Host Nucleus.
  5. Nucleocytoplasmic Trafficking Perturbation Induced by Picornaviruses.
  6. How SARS-CoV-2 and Other Viruses Build an Invasion Route to Hijack the Host Nucleocytoplasmic Trafficking System.
  7. Mechanical Forces in Nuclear Organization.
  8. Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha.
  9. Chromatin mobility and relocation in DNA repair.
  1. Mol Biol Cell. 2021 Jun 30. mbcE20110728
    3D super-resolution fluorescence microscopy maps the variable molecular architecture of the Nuclear Pore Complex.
    Vilma Jimenez Sabinina, M Julius Hossain, Jean-Karim Hériché, Philipp Hoess, Bianca Nijmeijer, Shyamal Mosalaganti, Moritz Kueblbeck, Andrea Callegari, Anna Szymborska, Martin Beck, Jonas Ries, Jan Ellenberg.
      Nuclear pore complexes (NPCs) are large macromolecular machines that mediate the traffic between the nucleus and the cytoplasm. In vertebrates, each NPC consists of ∼1000 proteins, termed nucleoporins, and has a mass of over 100 MDa. While a pseudo-atomic static model of the central scaffold of the NPC has recently been assembled by integrating data from isolated proteins and complexes, many structural components still remain elusive due to the enormous size and flexibility of the NPC. Here, we explored the power of 3D super-resolution microscopy combined with computational classification and averaging to explore the 3D structure of the NPC in single human cells. We show that this approach can build the first integrated 3D structural map containing both central as well as peripheral NPC subunits with molecular specificity and nanoscale resolution. Our unbiased classification of over ten thousand individual NPCs indicates that the nuclear ring and the nuclear basket can adopt different conformations. Our approach opens up the exciting possibility to relate different structural states of the NPC to function in situ.
    DOI:  https://doi.org/10.1091/mbc.E20-11-0728
  2. Nat Commun. 2021 Jun 30. 12(1): 4047
    Recapitulation of selective nuclear import and export with a perfectly repeated 12mer GLFG peptide.
    Sheung Chun Ng, Thomas Güttler, Dirk Görlich.
      The permeability barrier of nuclear pore complexes (NPCs) controls nucleocytoplasmic transport. It retains inert macromolecules while allowing facilitated passage of importins and exportins, which in turn shuttle cargo into or out of cell nuclei. The barrier can be described as a condensed phase assembled from cohesive FG repeat domains. NPCs contain several distinct FG domains, each comprising variable repeats. Nevertheless, we now found that sequence heterogeneity is no fundamental requirement for barrier function. Instead, we succeeded in engineering a perfectly repeated 12mer GLFG peptide that self-assembles into a barrier of exquisite transport selectivity and fast transport kinetics. This barrier recapitulates RanGTPase-controlled importin- and exportin-mediated cargo transport and thus represents an ultimately simplified experimental model system. An alternative proline-free sequence forms an amyloid FG phase. Finally, we discovered that FG phases stain bright with 'DNA-specific' DAPI/ Hoechst probes, and that such dyes allow for a photo-induced block of nuclear transport.
    DOI:  https://doi.org/10.1038/s41467-021-24292-5
  3. Exp Mol Med. 2021 Jun 29.
    Disruption of nucleocytoplasmic trafficking as a cellular senescence driver.
    Ji-Hwan Park, Sung Jin Ryu, Byung Ju Kim, Hyun-Ji Cho, Chi Hyun Park, Hyo Jei Claudia Choi, Eun-Jin Jang, Eun Jae Yang, Jeong-A Hwang, Seung-Hwa Woo, Jun Hyung Lee, Ji Hwan Park, Kyung-Mi Choi, Young-Yon Kwon, Cheol-Koo Lee, Joon Tae Park, Sung Chun Cho, Yun-Il Lee, Sung Bae Lee, Jeong A Han, Kyung A Cho, Min-Sik Kim, Daehee Hwang, Young-Sam Lee, Sang Chul Park.
      Senescent cells exhibit a reduced response to intrinsic and extrinsic stimuli. This diminished reaction may be explained by the disrupted transmission of nuclear signals. However, this hypothesis requires more evidence before it can be accepted as a mechanism of cellular senescence. A proteomic analysis of the cytoplasmic and nuclear fractions obtained from young and senescent cells revealed disruption of nucleocytoplasmic trafficking (NCT) as an essential feature of replicative senescence (RS) at the global level. Blocking NCT either chemically or genetically induced the acquisition of an RS-like senescence phenotype, named nuclear barrier-induced senescence (NBIS). A transcriptome analysis revealed that, among various types of cellular senescence, NBIS exhibited a gene expression pattern most similar to that of RS. Core proteomic and transcriptomic patterns common to both RS and NBIS included upregulation of the endocytosis-lysosome network and downregulation of NCT in senescent cells, patterns also observed in an aging yeast model. These results imply coordinated aging-dependent reduction in the transmission of extrinsic signals to the nucleus and in the nucleus-to-cytoplasm supply of proteins/RNAs. We further showed that the aging-associated decrease in Sp1 transcription factor expression was critical for the downregulation of NCT. Our results suggest that NBIS is a modality of cellular senescence that may represent the nature of physiological aging in eukaryotes.
    DOI:  https://doi.org/10.1038/s12276-021-00643-6
  4. Viruses. 2021 Jun 20. pii: 1178. [Epub ahead of print]13(6):
    The Viral Capsid: A Master Key to Access the Host Nucleus.
    Guillermo Blanco-Rodriguez, Francesca Di Nunzio.
      Viruses are pathogens that have evolved to hijack the cellular machinery to replicate themselves and spread to new cells. During the course of evolution, viruses developed different strategies to overcome the cellular defenses and create new progeny. Among them, some RNA and many DNA viruses require access to the nucleus to replicate their genome. In non-dividing cells, viruses can only access the nucleus through the nuclear pore complex (NPC). Therefore, viruses have developed strategies to usurp the nuclear transport machinery and gain access to the nucleus. The majority of these viruses use the capsid to manipulate the nuclear import machinery. However, the particular tactics employed by each virus to reach the host chromatin compartment are very different. Nevertheless, they all require some degree of capsid remodeling. Recent notions on the interplay between the viral capsid and cellular factors shine new light on the quest for the nuclear entry step and for the fate of these viruses. In this review, we describe the main components and function of nuclear transport machinery. Next, we discuss selected examples of RNA and DNA viruses (HBV, HSV, adenovirus, and HIV) that remodel their capsid as part of their strategies to access the nucleus and to replicate.
    Keywords:  host–viral interactions; viral nuclear entry; viral replication
    DOI:  https://doi.org/10.3390/v13061178
  5. Viruses. 2021 Jun 23. pii: 1210. [Epub ahead of print]13(7):
    Nucleocytoplasmic Trafficking Perturbation Induced by Picornaviruses.
    Belén Lizcano-Perret, Thomas Michiels.
      Picornaviruses are positive-stranded RNA viruses. Even though replication and translation of their genome take place in the cytoplasm, these viruses evolved different strategies to disturb nucleocytoplasmic trafficking of host proteins and RNA. The major targets of picornavirus are the phenylalanine-glycine (FG)-nucleoporins, which form a mesh in the central channel of the nuclear pore complex through which protein cargos and karyopherins are actively transported in both directions. Interestingly, while enteroviruses use the proteolytic activity of their 2A protein to degrade FG-nucleoporins, cardioviruses act by triggering phosphorylation of these proteins by cellular kinases. By targeting the nuclear pore complex, picornaviruses recruit nuclear proteins to the cytoplasm, where they increase viral genome translation and replication; they affect nuclear translocation of cytoplasmic proteins such as transcription factors that induce innate immune responses and retain host mRNA in the nucleus thereby preventing cell emergency responses and likely making the ribosomal machinery available for translation of viral RNAs.
    Keywords:  2A protease; 3C protease; RAN GTPase; karyopherin; leader (L) protein; nuclear pore complex; nucleoporins; picornavirus
    DOI:  https://doi.org/10.3390/v13071210
  6. Cells. 2021 Jun 07. pii: 1424. [Epub ahead of print]10(6):
    How SARS-CoV-2 and Other Viruses Build an Invasion Route to Hijack the Host Nucleocytoplasmic Trafficking System.
    Elma Sakinatus Sajidah, Keesiang Lim, Richard W Wong.
      The host nucleocytoplasmic trafficking system is often hijacked by viruses to accomplish their replication and to suppress the host immune response. Viruses encode many factors that interact with the host nuclear transport receptors (NTRs) and the nucleoporins of the nuclear pore complex (NPC) to access the host nucleus. In this review, we discuss the viral factors and the host factors involved in the nuclear import and export of viral components. As nucleocytoplasmic shuttling is vital for the replication of many viruses, we also review several drugs that target the host nuclear transport machinery and discuss their feasibility for use in antiviral treatment.
    Keywords:  Dengue virus; Ebola virus; Epstein-Barr virus; HS-AFM; Hepatitis B virus; Human Immunodeficiency virus; Human Papillomavirus; Influenza A; SARS-CoV-2; antiviral drug; clinical trial; exportin; importins; nuclear transport inhibitor; nucleoporins; viral nuclear export; viral nuclear import
    DOI:  https://doi.org/10.3390/cells10061424
  7. Cold Spring Harb Perspect Biol. 2021 Jun 29. pii: a039685. [Epub ahead of print]
    Mechanical Forces in Nuclear Organization.
    Yekaterina A Miroshnikova, Sara A Wickström.
      Cells generate and sense mechanical forces that trigger biochemical signals to elicit cellular responses that control cell fate changes. Mechanical forces also physically distort neighboring cells and the surrounding connective tissue, which propagate mechanochemical signals over long distances to guide tissue patterning, organogenesis, and adult tissue homeostasis. As the largest and stiffest organelle, the nucleus is particularly sensitive to mechanical force and deformation. Nuclear responses to mechanical force include adaptations in chromatin architecture and transcriptional activity that trigger changes in cell state. These force-driven changes also influence the mechanical properties of chromatin and nuclei themselves to prevent aberrant alterations in nuclear shape and help maintain genome integrity. This review will discuss principles of nuclear mechanotransduction and chromatin mechanics and their role in DNA damage and cell fate regulation.
    DOI:  https://doi.org/10.1101/cshperspect.a039685
  8. Biochem J. 2021 Jun 25. pii: BCJ20210401. [Epub ahead of print]
    Structural and calorimetric studies reveal specific determinants for the binding of a high-affinity NLS to mammalian importin-alpha.
    Hamine C Oliveira, Taina D da Silva, Guilherme H Salvador, Ivan R Moraes, Cintia A Fukuda, Andrea Coelho Barros, Marcos Roberto de Mattos Fontes.
      The classical nuclear import pathway is mediated by importin (Impα and Impβ), which recognizes the cargo protein by its Nuclear Localization Sequence (NLS). NLSs have been extensively studied resulting in different proposed consensus; however, recent studies showed that exceptions may occur. This mechanism may be also dependent on specific characteristics of different Impα. Aiming to better understand the importance of specific residues from consensus and adjacent regions of NLSs, we studied different mutations of a high affinity NLS complexed to Impα by crystallography and calorimetry. We showed that although the consensus sequence allows Lys or Arg residues at the second residue of a monopartite sequence, the presence of Arg is very important to its binding in major and minor sites of Impα. Mutations in the N or C-terminus (position P1 or P6) of the NLS drastically reduces their affinity to the receptor, which is corroborated by the loss of hydrogen bonds and hydrophobic interactions. Surprisingly, a mutation in the far N-terminus of the NLS led to an increase in the affinity for both binding sites, corroborated by the structure with an additional hydrogen bond. The binding of NLSs to the human variant Impα1 revealed that these are similar to those found in structures presented here. For human variant Impα3 the bindings are only relevant for the major site. This study increases understanding of specific issues sparsely addressed in previous studies that are important to the task of predicting NLSs, which will be relevant in the eventual design of synthetic NLSs.
    Keywords:  Nuclear Localization Sequence; X-ray crystallography; importin; isothermal titration calorimetry; nucleocytoplasmatic transport
    DOI:  https://doi.org/10.1042/BCJ20210401
  9. Trends Cell Biol. 2021 Jun 26. pii: S0962-8924(21)00118-5. [Epub ahead of print]
    Chromatin mobility and relocation in DNA repair.
    Noa Lamm, Samuel Rogers, Anthony J Cesare.
      The nucleus is a dynamic environment containing chromatin, membraneless organelles, and specialized molecular structures at the nuclear membrane. Within the spectrum of DNA repair activities are observations of increased mobility of damaged chromatin and the displacement of DNA lesions to specific nuclear environments. Here, we focus on the role that nuclear-specific filamentous actin plays in mobilizing damaged chromatin in response to DNA double-strand breaks and replication stress. We also examine nuclear pore complexes and promyelocytic leukemia-nuclear bodies as specialized platforms for homology-directed repair. The literature suggests an emerging model where specific types of DNA lesions are subjected to nuclear-derived forces that mobilize damaged chromatin and promote interaction with repair hubs to facilitate specialized repair reactions.
    Keywords:  alternative lengthening of telomeres; chromatin mobility; homology directed repair; nuclear actin; nuclear pore complex
    DOI:  https://doi.org/10.1016/j.tcb.2021.06.002
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