bims-nucpor 2023-10-01 papers

Issue of 2023–10–01
four papers selected by
Sara Mingu, Johannes Gutenberg University

Bioinformatics. 2023 Sep 26. pii: btad587. [Epub ahead of print]

Simulating structurally variable Nuclear Pore Complexes for Microscopy.

Maria Theiss, Jean-Karim Hériché, Craig Russell, David Helekal, Alisdair Soppitt, Jonas Ries, Jan Ellenberg, Alvis Brazma, Virginie Uhlmann.

MOTIVATION: The Nuclear Pore Complex (NPC) is the only passageway for macromolecules between nucleus and cytoplasm, and an important reference standard in microscopy: it is massive and stereotypically arranged. The average architecture of NPC proteins has been resolved with pseudo-atomic precision, however observed NPC heterogeneities evidence a high degree of divergence from this average. Single Molecule Localization Microscopy (SMLM) images NPCs at protein-level resolution, whereupon image analysis software studies NPC variability. However the true picture of this variability is unknown. In quantitative image analysis experiments, it is thus difficult to distinguish intrinsically high SMLM noise from variability of the underlying structure.
RESULTS: We introduce CIR4MICS ("ceramics", Configurable, Irregular Rings FOR MICroscopy Simulations), a pipeline that synthesizes ground truth datasets of structurally variable NPCs based on architectural models of the true NPC. Users can select one or more N- or C-terminally tagged NPC proteins, and simulate a wide range of geometric variations. We also represent the NPC as a spring-model such that arbitrary deforming forces, of user-defined magnitudes, simulate irregularly shaped variations. Further, we provide annotated reference datasets of simulated human NPCs, which facilitate a side-by-side comparison with real data. To demonstrate, we synthetically replicate a geometric analysis of real NPC radii and reveal that a range of simulated variability parameters can lead to observed results. Our simulator is therefore valuable to test the capabilities of image analysis methods, as well as to inform experimentalists about the requirements of hypothesis-driven imaging studies.
AVAILABILITY: Code: https://github.com/uhlmanngroup/cir4mics. Simulated data: BioStudies S-BSST1058.
SUPPLEMENTARY INFORMATION: Supplementary data are available at.

Keywords: NPC; SMLM; Simulation

DOI: https://doi.org/10.1093/bioinformatics/btad587

Microbiol Mol Biol Rev. 2023 Sep 26. e0004822

Capsid-host interactions for HIV-1 ingress.

Sooin Jang, Alan N Engelman.

The HIV-1 capsid, composed of approximately 1,200 copies of the capsid protein, encases genomic RNA alongside viral nucleocapsid, reverse transcriptase, and integrase proteins. After cell entry, the capsid interacts with a myriad of host factors to traverse the cell cytoplasm, pass through the nuclear pore complex (NPC), and then traffic to chromosomal sites for viral DNA integration. Integration may very well require the dissolution of the capsid, but where and when this uncoating event occurs remains hotly debated. Based on size constraints, a long-prevailing view was that uncoating preceded nuclear transport, but recent research has indicated that the capsid may remain largely intact during nuclear import, with perhaps some structural remodeling required for NPC traversal. Completion of reverse transcription in the nucleus may further aid capsid uncoating. One canonical type of host factor, typified by CPSF6, leverages a Phe-Gly (FG) motif to bind capsid. Recent research has shown these peptides reside amid prion-like domains (PrLDs), which are stretches of protein sequence devoid of charged residues. Intermolecular PrLD interactions along the exterior of the capsid shell impart avid host factor binding for productive HIV-1 infection. Herein we overview capsid-host interactions implicated in HIV-1 ingress and discuss important research questions moving forward. Highlighting clinical relevance, the long-acting ultrapotent inhibitor lenacapavir, which engages the same capsid binding pocket as FG host factors, was recently approved to treat people living with HIV.

Keywords: CPSF6; FG domain; HIV; NUP153; capsid; lenacapavir; liquid-liquid phase separation; mixed-charge domain; nuclear import; prion-like domain; speckle-associated domain; trafficking

DOI: https://doi.org/10.1128/mmbr.00048-22

Life (Basel). 2023 Aug 22. pii: 1791. [Epub ahead of print]13(9):

Nucleoporin Nup358 Downregulation Tunes the Neuronal Excitability in Mouse Cortical Neurons.

Vladimir A Martínez-Rojas, Francesca Pischedda, Isabel Romero-Maldonado, Bouchra Khalaf, Giovanni Piccoli, Paolo Macchi, Carlo Musio.

Nucleoporins (NUPs) are proteins that comprise the nuclear pore complexes (NPCs). The NPC spans the nuclear envelope of a cell and provides a channel through which RNA and proteins move between the nucleus and the cytoplasm and vice versa. NUP and NPC disruptions have a great impact on the pathophysiology of neurodegenerative diseases (NDDs). Although the downregulation of Nup358 leads to a reduction in the scaffold protein ankyrin-G at the axon initial segment (AIS) of mature neurons, the function of Nup358 in the cytoplasm of neurons remains elusive. To investigate whether Nup358 plays any role in neuronal activity, we downregulated Nup358 in non-pathological mouse cortical neurons and measured their active and passive bioelectrical properties. We identified that Nup358 downregulation is able to produce significant modifications of cell-membrane excitability via voltage-gated sodium channel kinetics. Our findings suggest that Nup358 contributes to neuronal excitability through a functional stabilization of the electrical properties of the neuronal membrane. Hypotheses will be discussed regarding the alteration of this active regulation as putatively occurring in the pathophysiology of NDDs.

Keywords: ion channels; membrane excitability; neurodegenerative disease; neuronal activity; nucleoporins; patch-clamp; voltage-gated sodium channels

DOI: https://doi.org/10.3390/life13091791

J Clin Med. 2023 Sep 07. pii: 5810. [Epub ahead of print]12(18):

Steroid-Resistant Nephrotic Syndrome Caused by NUP93 Pathogenic Variants.

Anna Wasilewska, Agnieszka Rybi-Szuminska, Pawel Dubiela.

BACKGROUND: Although steroid therapy is a standard of care for nephrotic syndrome treatment, 15-20% of patients do not respond to it. Finding the genetic background is possible in >10% of steroid-resistant nephrotic syndrome (SRNS) cases. Variants in genes encoding nuclear pore complex proteins are a novel cause of paediatric steroid-resistant nephrotic syndrome (SRNS). Recent studies suggest NUP93 variants to be a significant cause of paediatric onset SRNS. The clinical data on certain variants and disease history are still very limited.
METHODS AND RESULTS: We report the SRNS case of a 12-year-old boy with two detected NUP93 variants, which are pathogenic and possibly pathogenic. The onset of the disease was early and severe. The patient was admitted to the paediatric nephrology department due to nephrotic-range proteinuria and hypoalbuminemia with a long medical history of steroid and non-steroid immunosuppressive treatment. The genetic panel targeting 50 genes, clinically relevant for nephrotic syndrome, was performed. The only gene which was found to be affected by mutations, namely c.2326C>T and c.1162C>T, respectively, was NUP93. Conclusions: NUP93 variants are rarely identified as causes of SRNS. Clinical data are of utmost importance to establish the standard of care for SRNS patients suffering from this genetic disfunction. This is the first case of a heterozygous patient with the c.2326C>T and c.1162C>T variants and confirmed clinical history of the SRNS described so far. Our data suggest the clinical relevance of the c.1162C>T variant.

Keywords: NUP93; SRNS; new pathogenic variant; nuclear pore complex proteins; paediatric nephrology; steroid-resistant nephrotic syndrome

DOI: https://doi.org/10.3390/jcm12185810