bims-nucpor 2021-05-23 papers

bims-nucpor

Biomed News

on Nuclear pore complex and nucleoporins in stress, aging and disease

Issue of 2021–05–23
seven papers selected by
Sara Mingu, Johannes Gutenberg University

Mitotic checkpoint protein Mad1 is required for early Nup153 recruitment to chromatin and nuclear envelope integrity.
Karyopherin abnormalities in neurodegenerative proteinopathies.
Karyopherin enrichment at the nuclear pore complex attenuates Ran permeability.
Passive diffusion through nuclear pore complexes regulates levels of the yeast SAGA and SLIK coactivators complexes.
Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates interchromosomal movement.
ESCRT recruitment by the inner nuclear membrane protein Heh1 is regulated by Hub1-mediated alternative splicing.
Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state.

J Cell Sci. 2020 Jan 01. pii: jcs.249243. [Epub ahead of print]

Mitotic checkpoint protein Mad1 is required for early Nup153 recruitment to chromatin and nuclear envelope integrity.

Ikram Mossaid, Guillaume Chatel, Valérie Martinelli, Marcela Vaz, Birthe Fahrenkrog.

  Nucleoporin Nup153 is a multifunctional protein and mitotic checkpoint protein Mad1 a known binding partner. The functional relevance of their interaction has remained elusive. Here, we have further dissected Nup153's and Mad1's interface and functional interplay. By in situ proximity ligation assays, we found that the presence of a nuclear envelope (NE) is prerequisite for the Nup153-Mad1 association. Time-lapse microscopy revealed that depletion of Mad1 delayed recruitment of Nup153 to anaphase chromatin, which was often accompanied by a prolongation of anaphase. Furthermore, as seen by electron microscopic and three-dimensional structured illumination investigations, Nup153 and Mad1 depletion led to alterations in NE architecture, characterised by a change of membrane curvature at nuclear pore complexes (NPCs) and an expansion of the spacing between inner and outer nuclear membrane. Nup153 depletion, but not of Mad1, caused defects in interphase NPC assembly with partial displacement of cytoplasmic nucleoporins and a reduction in NPC density. Together our results suggest that Nup153 has separable roles in NE and NPC formation: in post-mitotic NE reformation in concert with Mad1 and in interphase NPC assembly, independent of Mad1.

Keywords:  Mad1; Mitotic checkpoint; Nuclear pore complex assembly; Nup153

DOI:  https://doi.org/10.1242/jcs.249243
Brain. 2021 May 21. pii: awab201. [Epub ahead of print]

Karyopherin abnormalities in neurodegenerative proteinopathies.

Terouz Pasha, Anna Zatorska, Daulet Sharipov, Boris Rogelj, Tibor Hortobágyi, Frank Hirth.

  Neurodegenerative proteinopathies are characterised by progressive cell loss that is preceded by the mislocalisation and aberrant accumulation of proteins prone to aggregation. Despite their different physiological functions, disease-related proteins like tau, alpha-synuclein, Tar DNA binding protein-43, Fused in sarcoma and mutant Huntingtin, all share low complexity regions that can mediate their liquid-liquid phase transitions. The proteins' phase transitions can range from native monomers to soluble oligomers, liquid droplets and further to irreversible, often-mislocalised aggregates that characterise the stages and severity of neurodegenerative diseases. Recent advances into the underlying pathogenic mechanisms have associated mislocalisation and aberrant accumulation of disease-related proteins with defective nucleocytoplasmic transport and its mediators called karyopherins. These studies identify karyopherin abnormalities in amyotrophic lateral sclerosis, frontotemporal dementia, Alzheimer's disease, and synucleinopathies including Parkinson's disease and dementia with Lewy bodies, that range from altered expression levels to the subcellular mislocalisation and aggregation of karyopherin alpha and beta proteins. The reported findings reveal that in addition to their classical function in nuclear import and export, karyopherins can also act as chaperones by shielding aggregation-prone proteins against misfolding, accumulation and irreversible phase-transition into insoluble aggregates. Karyopherin abnormalities can, therefore, be both the cause and consequence of protein mislocalisation and aggregate formation in degenerative proteinopathies. The resulting vicious feedback cycle of karyopherin pathology and proteinopathy identifies karyopherin abnormalities as a common denominator of onset and progression of neurodegenerative disease. Pharmacological targeting of karyopherins, already in clinical trials as therapeutic intervention targeting cancers such as glioblastoma and viral infections like COVID-19, may therefore represent a promising new avenue for disease-modifying treatments in neurodegenerative proteinopathies.

Keywords:  karyopherin; neurodegeneration; nucleocytoplasmic transport; phase transition; protein aggregation

DOI:  https://doi.org/10.1093/brain/awab201
J Cell Sci. 2020 Jan 01. pii: jcs.238121. [Epub ahead of print]

Karyopherin enrichment at the nuclear pore complex attenuates Ran permeability.

Suncica Barbato, Larisa E Kapinos, Chantal Rencurel, Roderick Y H Lim.

  Ran is a small GTPase whose nucleotide-bound forms cycle through nuclear pore complexes (NPCs) to direct nucleocytoplasmic transport (NCT). Generally, Ran guanosine triphosphate (GTP) binds cargo-carrying karyopherin receptors (Kaps) in the nucleus and liberates them in the cytoplasm following hydrolysis to Ran guanosine diphosphate (GDP). This generates a remarkably steep Ran gradient across the nuclear envelope that sustains compartment-specific cargo delivery and accumulation. However, because NPCs are permeable to small molecules of comparable size, it is unclear how an uncontrolled mixing of RanGTP and RanGDP is prevented. Here, we find that an NPC-enriched pool of Kapβ1 selectively mediates Ran diffusion across the pore, but not passive molecules of similar size (e.g. GFP). This is due to binding interactions with Kapβ1, which is stronger for RanGTP, but weaker for RanGDP. On this basis, the RanGDP importer, nuclear transport factor 2 (NTF2), facilitates the release of RanGDP from Kapβ1 following GTP hydrolysis. Accordingly, the enrichment of Kapβ1 at NPCs may function as a retention mechanism that preserves the sharp transition of RanGTP and RanGDP in the nucleus and cytoplasm, respectively.

Keywords:  Karyopherins; Nuclear pore complex; Nucleocytoplasmic transport; RanGTP

DOI:  https://doi.org/10.1242/jcs.238121
J Cell Sci. 2020 Jan 01. pii: jcs.237156. [Epub ahead of print]

Passive diffusion through nuclear pore complexes regulates levels of the yeast SAGA and SLIK coactivators complexes.

Tadashi Makio, Richard W Wozniak.

  Nuclear pore complexes (NPCs) control gene expression by regulating the bi-directional exchange of proteins and RNAs between nuclear and cytoplasmic compartments, including access of transcriptional regulators to the nucleoplasm. Here we show that the yeast nucleoporin Nup170, in addition to binding and silencing subtelomeric genes, supports transcription of genes regulated by the SAGA transcriptional activator. Specifically, we show that less SAGA complex is bound to target genes in the absence Nup170. Consistent with this observation, levels of the SAGA complex are decreased in cells lacking Nup170, while SAGA-related SLIK complexes are increased. This change in the ratio of SAGA to SLIK complexes is due to increased nuclear activity of Pep4, a protease responsible for production of the SLIK complex. Further analyses of various nucleoporin mutants revealed that the increased nuclear entry of Pep4 observed in the nup170Δ mutant likely occurs as consequence of an increase in the sieving limits of the NPC diffusion channel. On the basis of these results, we propose that changes in passive diffusion rates represents a mechanism for regulating SAGA/SLIK complex-mediated transcriptional events.

Keywords:  Nuclear pore complex; Nuclear transport; Nup170; Passive diffusion; SAGA/SLIK complex; Yeast

DOI:  https://doi.org/10.1242/jcs.237156
Elife. 2021 May 18. pii: e66238. [Epub ahead of print]10

Random sub-diffusion and capture of genes by the nuclear pore reduces dynamics and coordinates interchromosomal movement.

Michael Chas Sumner, Steven B Torrisi, Donna G Brickner, Jason H Brickner.

  Hundreds of genes interact with the yeast nuclear pore complex (NPC), localizing at the nuclear periphery and clustering with co-regulated genes. Dynamic tracking of peripheral genes shows that they cycle on and off the NPC and that interaction with the NPC slows their sub-diffusive movement. Furthermore, NPC-dependent inter-chromosomal clustering leads to coordinated movement of pairs of loci separated by hundreds of nanometers. We developed Fractional Brownian Motion simulations for chromosomal loci in the nucleoplasm and interacting with NPCs. These simulations predict the rate and nature of random sub-diffusion during repositioning from nucleoplasm to periphery and match measurements from two different experimental models, arguing that recruitment to the nuclear periphery is due to random sub-diffusion and transient capture by NPCs. Finally, the simulations do not lead to inter-chromosomal clustering or coordinated movement, suggesting that interaction with the NPC is necessary, but not sufficient, to cause clustering.

Keywords:  S. cerevisiae; cell biology; chromosomes; gene expression

DOI:  https://doi.org/10.7554/eLife.66238
J Cell Sci. 2020 Jan 01. pii: jcs.250688. [Epub ahead of print]

ESCRT recruitment by the inner nuclear membrane protein Heh1 is regulated by Hub1-mediated alternative splicing.

Matías Capella, Lucía Martín Caballero, Boris Pfander, Sigurd Braun, Stefan Jentsch.

  Misassembled nuclear pore complexes (NPCs) are removed by sealing off the surrounding nuclear envelope (NE), which is conducted by the ESCRT (endosomal sorting complexes required for transport) machinery. Recruitment of ESCRT proteins to the NE is mediated by the interaction between the ESCRT member Chm7 and the inner nuclear membrane protein Heh1, which belongs to the conserved LEM family. Increased ESCRT recruitment results in excessive membrane scission at damage sites but its regulation remains poorly understood. Here, we show that Hub1-mediated alternative splicing of HEH1 pre-mRNA, resulting into its shorter form Heh1-S, is critical for the integrity of the NE in Saccharomyces cerevisiae. ESCRT-III mutants lacking Hub1 or Heh1-S display severe growth defects and accumulate improperly assembled NPCs. This depends on the interaction of Chm7 with the conserved MSC domain only present in the longer variant Heh1-L. Heh1 variants assemble into heterodimers and we demonstrate that a unique splice segment in Heh1-S suppresses growth defects associated with uncontrolled interaction between Heh1-L and Chm7. Together, our findings reveal that Hub1-mediated splicing generates Heh1-S to regulate ESCRT recruitment to the nuclear envelope.

Keywords:  ESCRT; LEM domain; Nuclear envelope surveillance; Nuclear pore complex; Splicing

DOI:  https://doi.org/10.1242/jcs.250688
Mol Biol Cell. 2021 May 19. mbcE20090584

Heh2/Man1 may be an evolutionarily conserved sensor of NPC assembly state.

Sapan Borah, David J Thaller, Zhanna Hakhverdyan, Elisa C Rodriguez, Anthony W Isenhour, Michael P Rout, Megan C King, C Patrick Lusk.

Integral membrane proteins of the Lap2-emerin-MAN1 (LEM) family have emerged as important components of the inner nuclear membrane (INM) required for the functional and physical integrity of the nuclear envelope. However, like many INM proteins, there is limited understanding of the biochemical interaction networks that enable LEM protein function. Here, we show that Heh2/Man1 can interact with major scaffold components of the nuclear pore complex (NPC), specifically the inner ring complex (IRC), in evolutionarily distant yeasts. Although an N-terminal domain is required for Heh2 targeting to the INM, we demonstrate that stable interactions with the NPC are mediated by a C-terminal winged helix (WH) domain, thus decoupling INM targeting and NPC binding. Inhibiting Heh2's interactions with the NPC by deletion of the Heh2 WH domain leads to NPC clustering. Interestingly, Heh2's association with NPCs can also be disrupted by knocking out several outer ring nucleoporins. Thus, Heh2's association with NPCs depends on the structural integrity of both major NPC scaffold complexes. We propose a model in which Heh2 acts as a sensor of NPC assembly state, which may be important for NPC quality control mechanisms and the segregation of NPCs during cell division.

DOI: https://doi.org/10.1091/mbc.E20-09-0584