bims-nucpor 2023-01-29 papers

Issue of 2023‒01‒29
five papers selected by
Sara Mingu
Johannes Gutenberg University

J Cell Biol. 2023 Feb 06. pii: e202301044. [Epub ahead of print]222(2):

How to unravel a basket: NPC reorganization during meiosis.

Annemiek C Veldsink, Liesbeth M Veenhoff.

While our understanding of the nuclear pore complex (NPC) structure is progressing spectacularly, the organizational principles of its nuclear basket remain elusive. In this issue, King et al. (2022. J. Cell Biol.https://doi.org/10.1083/jcb.202204039) provide new insights into the mechanisms that govern nuclear basket reorganization during meiosis.

DOI: https://doi.org/10.1083/jcb.202301044

J Mol Biol. 2023 Jan 20. pii: S0022-2836(23)00028-1. [Epub ahead of print] 167972

Interactions between FUS and the C-terminal domain of Nup62 are sufficient for their co-phase separation into amorphous assemblies.

Meenakshi Sundaram Kumar, Karly M Stallworth, Anastasia C Murthy, Su Min Lim, Nan Li, Aastha Jain, James B Munro, Nicolas L Fawzi, Clotilde Lagier-Tourenne, Daryl A Bosco.

Deficient nucleocytoplasmic transport is emerging as a pathogenic feature of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), including in ALS caused by mutations in Fused in Sarcoma (FUS). Recently, both wild-type and ALS-linked mutant FUS were shown to directly interact with the phenylalanine-glycine (FG)-rich nucleoporin 62 (Nup62) protein, where FUS WT/ Nup62 interactions were enriched within the nucleus but ALS-linked mutant FUS/ Nup62 interactions were enriched within the cytoplasm of cells. Nup62 is a central channel Nup that has a prominent role in forming the selectivity filter within the nuclear pore complex and in regulating effective nucleocytoplasmic transport. Under conditions where FUS phase separates into liquid droplets in vitro, the addition of Nup62 caused the synergetic formation of amorphous assemblies containing both FUS and Nup62. Here, we examined the molecular determinants of this process using recombinant FUS and Nup62 proteins and biochemical approaches. We demonstrate that the structured C-terminal domain of Nup62 containing an alpha-helical coiled-coil region plays a dominant role in binding FUS and is sufficient for inducing the formation of FUS/Nup62 amorphous assemblies. In contrast, the natively unstructured, F/G repeat-rich N-terminal domain Nup62 modestly contributed to FUS/Nup62 phase separation behavior. Expression of individual Nup62 domain constructs in human cells confirmed that the Nup62 C-terminal domain is essential for localization of the protein to the nuclear envelope. Our results raise the possibility that interactions between FUS and the C-terminal domain of Nup62 can influence the function of Nup62 under physiological and/or pathological conditions.

Keywords: amyotrophic lateral sclerosis (ALS) (Lou Gehrig disease); fused in sarcoma (FUS); nucleocytoplasmic transport; nucleoporin 62 (Nup62); phase separation

DOI: https://doi.org/10.1016/j.jmb.2023.167972

J Biol Chem. 2023 Jan 20. pii: S0021-9258(23)00064-9. [Epub ahead of print] 102932

Transportin 1 is a major nuclear import receptor of the nitric oxide synthase interacting protein.

Marius Pörschke, Inés Rodríguez-González, Iwan Parfentev, Henning Urlaub, Ralph H Kehlenbach.

The nitric oxide synthase interacting protein (NOSIP), an E3-ubiquitin ligase, is involved in various processes like neuronal development, craniofacial development, granulopoiesis, mitogenic signaling, apoptosis and cell proliferation. The best characterized function of NOSIP is the regulation of eNOS (endothelial nitric oxide synthase) activity by translocating the membrane-bound enzyme to the cytoskeleton, specifically in the G2 phase of the cell cycle. For this, NOSIP itself has to be translocated from its prominent localization, the nucleus, to the cytoplasm. Nuclear import of NOSIP was suggested to be mediated by the canonical transport receptors importin α/β. Recently, we found NOSIP in a proteomic screen as a potential importin 13 cargo. Here, we describe the nuclear shuttling characteristics of NOSIP in living cells and in vitro and show that it does not interact directly with importin α. Instead, it formed stable complexes with several importins (-β, -7, -β/7, -13, and transportin 1) and was also imported into the nucleus in digitonin-permeabilized cells by these factors. In living HeLa cells, transportin 1 seems to be the major nuclear import receptor for NOSIP. A detailed analysis of the NOSIP-transportin 1 interaction revealed a high affinity and an unusual binding mode, involving the N-terminal half of transportin 1. In contrast to nuclear import, nuclear export of NOSIP seems to occur mostly by passive diffusion. Thus, our results uncover additional layers in the larger process of eNOS regulation.

Keywords: NOSIP; TNPO1; eNOS; importin α/β; nuclear transport; transportin 1

DOI: https://doi.org/10.1016/j.jbc.2023.102932

Nat Methods. 2023 Jan 23.

Convolutional networks for supervised mining of molecular patterns within cellular context.

Irene de Teresa-Trueba, Sara K Goetz, Alexander Mattausch, Frosina Stojanovska, Christian E Zimmerli, Mauricio Toro-Nahuelpan, Dorothy W C Cheng, Fergus Tollervey, Constantin Pape, Martin Beck, Alba Diz-Muñoz, Anna Kreshuk, Julia Mahamid, Judith B Zaugg.

Cryo-electron tomograms capture a wealth of structural information on the molecular constituents of cells and tissues. We present DeePiCt (deep picker in context), an open-source deep-learning framework for supervised segmentation and macromolecular complex localization in cryo-electron tomography. To train and benchmark DeePiCt on experimental data, we comprehensively annotated 20 tomograms of Schizosaccharomyces pombe for ribosomes, fatty acid synthases, membranes, nuclear pore complexes, organelles, and cytosol. By comparing DeePiCt to state-of-the-art approaches on this dataset, we show its unique ability to identify low-abundance and low-density complexes. We use DeePiCt to study compositionally distinct subpopulations of cellular ribosomes, with emphasis on their contextual association with mitochondria and the endoplasmic reticulum. Finally, applying pre-trained networks to a HeLa cell tomogram demonstrates that DeePiCt achieves high-quality predictions in unseen datasets from different biological species in a matter of minutes. The comprehensively annotated experimental data and pre-trained networks are provided for immediate use by the community.

DOI: https://doi.org/10.1038/s41592-022-01746-2

iScience. 2023 Jan 20. 26(1): 105906

Characterization of cell-to-cell variation in nuclear transport rates and identification of its sources.

Durrieu Lucía, Bush Alan, Grande Alicia, Johansson Rikard, Janzén David, Andrea Katz, Gunnar Cedersund, Colman-Lerner Alejandro.

Nuclear transport is an essential part of eukaryotic cell function. Here, we present scFRAP, a model-assisted fluorescent recovery after photobleaching (FRAP)- based method to determine nuclear import and export rates independently in individual live cells. To overcome the inherent noise of single-cell measurements, we performed sequential FRAPs on the same cell. We found large cell-to-cell variation in transport rates within isogenic yeast populations. For passive transport, the variability in NPC number might explain most of the variability. Using this approach, we studied mother-daughter cell asymmetry in the active nuclear shuttling of the transcription factor Ace2, which is specifically concentrated in daughter cell nuclei in early G1. Rather than reduced export in the daughter cell, as previously hypothesized, we found that this asymmetry is mainly due to an increased import in daughters. These results shed light on cell-to-cell variation in cellular dynamics and its sources.

Keywords: Biological sciences; Cell biology; Mathematical biosciences

DOI: https://doi.org/10.1016/j.isci.2022.105906