bims-nucpor 2021-09-12 papers

bims-nucpor

Biomed News

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

Issue of 2021‒09‒12
six papers selected by
Sara Mingu
Johannes Gutenberg University

Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS.
Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore.
Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans.
C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers.
Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the BDF2 mRNA.
High-Resolution Microscopy to Learn the Nuclear Organization of the Living Yeast Cells.

Int J Mol Sci. 2021 Aug 26. pii: 9217. [Epub ahead of print]22(17):

Measuring and Interpreting Nuclear Transport in Neurodegenerative Disease-The Example of C9orf72 ALS.

Marije F W Semmelink, Anton Steen, Liesbeth M Veenhoff.

  Transport from and into the nucleus is essential to all eukaryotic life and occurs through the nuclear pore complex (NPC). There are a multitude of data supporting a role for nuclear transport in neurodegenerative diseases, but actual transport assays in disease models have provided diverse outcomes. In this review, we summarize how nuclear transport works, which transport assays are available, and what matters complicate the interpretation of their results. Taking a specific type of ALS caused by mutations in C9orf72 as an example, we illustrate these complications, and discuss how the current data do not firmly answer whether the kinetics of nucleocytoplasmic transport are altered. Answering this open question has far-reaching implications, because a positive answer would imply that widespread mislocalization of proteins occurs, far beyond the reported mislocalization of transport reporters, and specific proteins such as FUS, or TDP43, and thus presents a challenge for future research.

Keywords:  C9orf72; amyotrophic lateral sclerosis (ALS); nuclear pore complex; nuclear transport; nuclear transport receptor

DOI:  https://doi.org/10.3390/ijms22179217
Proc Natl Acad Sci U S A. 2021 Sep 14. pii: e2015621118. [Epub ahead of print]118(37):

Distinct roles of nuclear basket proteins in directing the passage of mRNA through the nuclear pore.

Yichen Li, Vasilisa Aksenova, Mark Tingey, Jingjie Yu, Ping Ma, Alexei Arnaoutov, Shane Chen, Mary Dasso, Weidong Yang.

  The in vivo characterization of the exact copy number and the specific function of each composite protein within the nuclear pore complex (NPC) remains both desirable and challenging. Through the implementation of live-cell high-speed super-resolution single-molecule microscopy, we first quantified the native copies of nuclear basket (BSK) proteins (Nup153, Nup50, and Tpr) prior to knocking them down in a highly specific manner via an auxin-inducible degron strategy. Second, we determined the specific roles that BSK proteins play in the nuclear export kinetics of model messenger RNA (mRNA) substrates. Finally, the three-dimensional (3D) nuclear export routes of these mRNA substrates through native NPCs in the absence of specific BSK proteins were obtained and further validated via postlocalization computational simulations. We found that these BSK proteins possess the stoichiometric ratio of 1:1:1 and play distinct roles in the nuclear export of mRNAs within live cells. The absence of Tpr from the NPC predominantly reduces the probability of nuclear mRNAs entering the NPC for export. Complete depletion of Nup153 and Nup50 results in an mRNA nuclear export efficiency decrease of approximately four folds. mRNAs can gain their maximum successful export efficiency as the copy number of Nup153 increased from zero to only half the full complement natively within the NPC. Lastly, the absence of Tpr or Nup153 seems to alter the 3D export routes of mRNAs as they pass through the NPC. However, the removal of Nup50 alone has almost no impact upon mRNA export route and kinetics.

Keywords:  3D super-resolution microscopy; NPC stoichiometry; nucleocytoplasmic transport

DOI:  https://doi.org/10.1073/pnas.2015621118
Hum Mol Genet. 2021 Sep 07. pii: ddab248. [Epub ahead of print]

Pathogenic variants in nucleoporin TPR (translocated promoter region, nuclear basket protein) cause severe intellectual disability in humans.

Nicole J Van Bergen, Katrina M Bell, Kirsty Carey, Russell Gear, Sean Massey, Edward K Murrell, Lyndon Gallacher, Kate Pope, Paul J Lockhart, Andrew Kornberg, Lynn Pais, Marzena Walkiewicz, Cas Simons, , Vihandha O Wickramasinghe, Susan M White, John Christodoulou.

The nuclear pore complex (NPC) is a multi-protein complex that regulates the trafficking of macromolecules between the nucleus and cytoplasm. Genetic variants in components of the NPC have been shown to cause a range of neurological disorders, including intellectual disability and microcephaly. Translocated promoter region, nuclear basket protein (TPR) is a critical scaffolding element of the nuclear facing interior of the NPC. Here we present two siblings with biallelic variants in TPR who present with a phenotype of microcephaly, ataxia and severe intellectual disability. The variants result in a premature truncation variant, and a splice variant leading to a 12-amino acid deletion respectively. Functional analyses in patient fibroblasts demonstrate significantly reduced TPR levels, and decreased TPR-containing NPC density. A compensatory increase in total NPC levels was observed, and decreased global RNA intensity in the nucleus. The discovery of variants that partly disable TPR function provide valuable insight into this essential protein in human disease, and our findings suggest that TPR variants are the cause of the siblings' neurological disorder.

DOI: https://doi.org/10.1093/hmg/ddab248
Nat Commun. 2021 Sep 06. 12(1): 5301

C9orf72-derived arginine-rich poly-dipeptides impede phase modifiers.

Hitoki Nanaura, Honoka Kawamukai, Ayano Fujiwara, Takeru Uehara, Yuichiro Aiba, Mari Nakanishi, Tomo Shiota, Masaki Hibino, Pattama Wiriyasermkul, Sotaro Kikuchi, Riko Nagata, Masaya Matsubayashi, Yoichi Shinkai, Tatsuya Niwa, Taro Mannen, Naritaka Morikawa, Naohiko Iguchi, Takao Kiriyama, Ken Morishima, Rintaro Inoue, Masaaki Sugiyama, Takashi Oda, Noriyuki Kodera, Sachiko Toma-Fukai, Mamoru Sato, Hideki Taguchi, Shushi Nagamori, Osami Shoji, Koichiro Ishimori, Hiroyoshi Matsumura, Kazuma Sugie, Tomohide Saio, Takuya Yoshizawa, Eiichiro Mori.

Nuclear import receptors (NIRs) not only transport RNA-binding proteins (RBPs) but also modify phase transitions of RBPs by recognizing nuclear localization signals (NLSs). Toxic arginine-rich poly-dipeptides from C9orf72 interact with NIRs and cause nucleocytoplasmic transport deficit. However, the molecular basis for the toxicity of arginine-rich poly-dipeptides toward NIRs function as phase modifiers of RBPs remains unidentified. Here we show that arginine-rich poly-dipeptides impede the ability of NIRs to modify phase transitions of RBPs. Isothermal titration calorimetry and size-exclusion chromatography revealed that proline:arginine (PR) poly-dipeptides tightly bind karyopherin-β2 (Kapβ2) at 1:1 ratio. The nuclear magnetic resonances of Kapβ2 perturbed by PR poly-dipeptides partially overlapped with those perturbed by the designed NLS peptide, suggesting that PR poly-dipeptides target the NLS binding site of Kapβ2. The findings offer mechanistic insights into how phase transitions of RBPs are disabled in C9orf72-related neurodegeneration.

DOI: https://doi.org/10.1038/s41467-021-25560-0
RNA. 2021 Sep 08. pii: rna.078880.121. [Epub ahead of print]

Stress-induced inhibition of mRNA export triggers RNase III-mediated decay of the BDF2 mRNA.

Charles Wang, Keaton W Barr, Dean Neutel, Kevin Roy, Yanru Liu, Guillaume Chanfreau.

  The expression of bromodomain-containing proteins that regulate chromatin structure and accessibility must be tightly controlled to ensure the appropriate regulation of gene expression. In the yeast S. cerevisiae, Bromodomain Factor 2 (BDF2) expression is extensively regulated post-transcriptionally during stress by RNase III-mediated decay (RMD), which is triggered by cleavage of the BDF2 mRNA in the nucleus by the RNase III homologue Rnt1p. Previous studies have shown that RMD-mediated down-regulation of BDF2 is hyper-activated in osmotic stress conditions, yet the mechanisms driving the enhanced nuclear cleavage of BDF2 RNA under these conditions remain unknown. Here, we show that RMD hyper-activation can be detected in multiple stress conditions that inhibit mRNA export, and that Rnt1p remains primarily localized in the nucleus during salt stress. We show that globally inhibiting mRNA nuclear export by anchoring away mRNA biogenesis or export factors out of the nucleus can recapitulate RMD hyper-activation in the absence of stress. RMD hyperactivation requires Rnt1p nuclear localization but does not depend on the BDF2 gene endogenous promoter, and its efficiency is affected by the structure of the stem-loop cleaved by Rnt1p. Because multiple stress conditions have been shown to mediate global inhibition of mRNA export, our results suggest that the hyperactivation of RMD is primarily the result of the increased nuclear retention of the BDF2 mRNA during stress.

Keywords:  Bromodomain; RNase III; Rnt1p; Stress; mRNA export

DOI:  https://doi.org/10.1261/rna.078880.121
Stem Cells Int. 2021 ;2021 9951114

High-Resolution Microscopy to Learn the Nuclear Organization of the Living Yeast Cells.

Renjie Wang, Aiwen Huang, Yan Wang, Pengxin Mei, He Zhu, Qianqian Chen, Sankui Xu.

The spatial organization of the nucleus is a key determinant in all genome activities. However, the accurate measurement of the nuclear organization is still technically challenging. Here, the technology NucQuant we created previously was utilized to detect the variation of the nuclear organization, including the heterogeneity of the nuclear geometry, the change of the NPC distribution along different cell cycle stages during interphase, and the organization of the nucleolus. The results confirmed that not only the growth rate and the NPC distribution are influenced by the carbon source; the nuclear shape is also impacted by the carbon source. The nuclei lost their spherical geometry gradually when the cell was cultured from the most to a less favorable carbon source. We also discovered that the nucleolus prefers to locate at the nuclear periphery, which was called the "genes poor region," especially when the cells entered quiescence. Furthermore, the distribution of the NPC along the different stages during the interphase was analyzed. We proposed that with the growth of the cell, the nucleus would grow from the surface of the NE flanking the nucleolus firstly.

DOI: https://doi.org/10.1155/2021/9951114