bims-nucpor 2022-08-28 papers

Issue of 2022‒08‒28
six papers selected by
Sara Mingu
Johannes Gutenberg University

Elife. 2022 Aug 24. pii: e78385. [Epub ahead of print]11

An amphipathic helix in Brl1 is required for nuclear pore complex biogenesis in S. cerevisiae.

Annemarie Kralt, Matthias Wojtynek, Jonas S Fischer, Arantxa Agote-Aran, Roberta Mancini, Elisa Dultz, Elad Noor, Federico Uliana, Marianna Tatarek-Nossol, Wolfram Antonin, Evgeny Onischenko, Ohad Medalia, Karsten Weis.

The nuclear pore complex (NPC) is the central portal for macromolecular exchange between the nucleus and cytoplasm. In all eukaryotes, NPCs assemble into an intact nuclear envelope (NE) during interphase, but the process of NPC biogenesis remains poorly characterized. Furthermore, little is known about how NPC assembly leads to the fusion of the outer and inner NE, and no factors have been identified that could trigger this event. Here, we characterize the transmembrane protein Brl1 as an NPC assembly factor required for NE fusion in budding yeast. Brl1 preferentially associates with NPC assembly intermediates and its depletion halts NPC biogenesis, leading to NE herniations that contain inner and outer ring nucleoporins but lack the cytoplasmic export platform. Furthermore, we identify an essential amphipathic helix in the luminal domain of Brl1 that mediates interactions with lipid bilayers. Mutations in this amphipathic helix lead to NPC assembly defects, and cryo-electron tomography analyses reveal multilayered herniations of the inner nuclear membrane with NPC-like structures at the neck, indicating a failure in NE fusion. Taken together, our results identify a role for Brl1 in NPC assembly and suggest a function of its amphipathic helix in mediating the fusion of the inner and outer nuclear membranes.

Keywords: S. cerevisiae; cell biology; membrane fusion; nuclear envelope; nuclear pore complex

DOI: https://doi.org/10.7554/eLife.78385

Front Plant Sci. 2022 ;13 998823

Editorial: Understanding the key border: Structure, function, and dynamics of the plant nuclear envelope.

David E Evans, Katja Graumann.

Keywords: LINC complex; chromosome dynamics; nuclear dynamics; nuclear envelope; nuclear pore complex; plant lamina

DOI: https://doi.org/10.3389/fpls.2022.998823

Trends Parasitol. 2022 Aug 23. pii: S1471-4922(22)00160-X. [Epub ahead of print]

Sending the message: specialized RNA export mechanisms in trypanosomes.

Samson O Obado, Michael P Rout, Mark C Field.

Export of RNA from the nucleus is essential for all eukaryotic cells and has emerged as a major step in the control of gene expression. mRNA molecules are required to complete a complex series of processing events and pass a quality control system to protect the cytoplasm from the translation of aberrant proteins. Many of these events are highly conserved across eukaryotes, reflecting their ancient origin, but significant deviation from a canonical pathway as described from animals and fungi has emerged in the trypanosomatids. With significant implications for the mechanisms that control gene expression and hence differentiation, responses to altered environments and fitness as a parasite, these deviations may also reveal additional, previously unsuspected, mRNA export pathways.

Keywords: eukaryogenesis; mRNA export; nuclear pore complex; polycistronic transcription; trans-splicing; trypanosomes

DOI: https://doi.org/10.1016/j.pt.2022.07.008

J Mol Biol. 2022 Aug 20. pii: S0022-2836(22)00407-7. [Epub ahead of print] 167798

Changes in DNA double-strand break repair during aging correlate with an increase in genomic mutations.

Aditya Mojumdar, Nicola Mair, Nancy Adam, Jennifer A Cobb.

A double -strand break (DSB) is one of the most deleterious forms of DNA damage. In eukaryotic cells, two main repair pathways have evolved to repair DSBs, homologous recombination (HR) and non-homologous end-joining (NHEJ). HR is the predominant pathway of repair in the unicellular eukaryotic organism, S. cerevisiae. However, during replicative aging the relative use of HR and NHEJ shifts in favor of end-joining repair. By monitoring repair events in the HO-DSB system, we find that early in replicative aging there is a decrease in the association of long-range resection factors, Dna2-Sgs1 and Exo1 at the break site and a decrease in DNA resection. Subsequently, as aging progressed, the recovery of Ku70 at DSBs decreased and the break site associated with the nuclear pore complex at the nuclear periphery, which is the location where DSB repair occurs through alternative pathways that are more mutagenic. End-bridging remained intact as HR and NHEJ declined, but eventually it too became disrupted in cells at advanced replicative age. In all, our work provides insight into the molecular changes in DSB repair pathway during replicative aging. HR first declined, resulting in a transient increase in the NHEJ. However, with increased cellular divisions, Ku70 recovery at DSBs and NHEJ subsequently declined. In wild type cells of advanced replicative age, there was a high frequency of repair products with genomic deletions and microhomologies at the break junction, events not observed in young cells which repaired primarily by HR.

Keywords: DNA end resection; DSB repair; alt-repair; homologous recombination (HR); non-homologous end-joining (NHEJ); nuclear localization; replicative aging

DOI: https://doi.org/10.1016/j.jmb.2022.167798

ACS Chem Neurosci. 2022 Aug 24.

Mislocalization of Nup62 Contributes to TDP-43 Proteinopathy in ALS/FTLD.

Niharika Nag, Timir Tripathi.

The nucleocytoplasmic transport (NCT) is impaired in C9-ALS/FTLD, a common genetically caused form of ALS and FTLD. The NCT is regulated by proteins called FG-nucleoporins (FG-Nups), with domains enriched in phenylalanine-glycine repeats. However, the relationship between FG-Nups and TDP-43, an RBP found to be mislocalized in ALS/FTLD patients, has not been defined. A recent study found that a critical protein, FG-Nup62, is mislocalized both in vivo and in vitro in diseased states. The mislocalized Nup62 was colocalized with TDP-43 in cytoplasmic inclusions and promoted its liquid-to-solid transition. The work highlights the involvement of Nup62 in the pathogenesis of ALS/FTLD and the interaction between Nup62 and TDP-43.

Keywords: ALS/FTLD; FG-Nups; Nucleocytoplasmic transport; Nup62; TDP-43; TDP-43 condensates; amyotrophic lateral sclerosis; proteinopathy

DOI: https://doi.org/10.1021/acschemneuro.2c00480

Life Sci Alliance. 2022 Oct;pii: e202201431. [Epub ahead of print]5(10):

Binding stoichiometry and structural model of the HIV-1 Rev/importin β complex.

Didier Spittler, Rose-Laure Indorato, Elisabetta Boeri Erba, Elise Delaforge, Luca Signor, Simon J Harris, Isabel Garcia-Saez, Andrés Palencia, Frank Gabel, Martin Blackledge, Marjolaine Noirclerc-Savoye, Carlo Petosa.

HIV-1 Rev mediates the nuclear export of intron-containing viral RNA transcripts and is essential for viral replication. Rev is imported into the nucleus by the host protein importin β (Impβ), but how Rev associates with Impβ is poorly understood. Here, we report biochemical, mutational, and biophysical studies of the Impβ/Rev complex. We show that Impβ binds two Rev monomers through independent binding sites, in contrast to the 1:1 binding stoichiometry observed for most Impβ cargos. Peptide scanning data and charge-reversal mutations identify the N-terminal tip of Rev helix α2 within Rev's arginine-rich motif (ARM) as a primary Impβ-binding epitope. Cross-linking mass spectrometry and compensatory mutagenesis data combined with molecular docking simulations suggest a structural model in which one Rev monomer binds to the C-terminal half of Impβ with Rev helix α2 roughly parallel to the HEAT-repeat superhelical axis, whereas the other monomer binds to the N-terminal half. These findings shed light on the molecular basis of Rev recognition by Impβ and highlight an atypical binding behavior that distinguishes Rev from canonical cellular Impβ cargos.

DOI: https://doi.org/10.26508/lsa.202201431