bims-nucpor 2024-04-21 papers

Issue of 2024–04–21
three papers selected by
Sara Mingu, Johannes Gutenberg University

Biophys J. 2024 Apr 10. pii: S0006-3495(24)00207-8. [Epub ahead of print]

Kinetic cooperativity resolves bidirectional clogging within the nuclear pore complex.

As the main gatekeeper of the nucleocytoplasmic transport in eukaryotic cells, the nuclear pore complex (NPC) faces the daunting task of facilitating the bidirectional transport of a high volume of macromolecular cargoes while ensuring the selectivity, speed, and efficiency of this process. The competition between opposing nuclear import and export fluxes passing through the same channel is expected to pose a major challenge to transport efficiency. It has been suggested that phase separation-like radial segregation of import and export fluxes within the assembly of intrinsically disordered proteins that line the NPC pore could be a mechanism for ensuring efficient bidirectional transport. We examine the impact of radial segregation on the efficiency of bidirectional transport through the NPC using a coarse-grained computational model of the NPC. We find little evidence that radial segregation improves transport efficiency. By contrast, surprisingly, we find that NTR crowding may enhance rather than impair the efficiency of bidirectional transport although it decreases the available space in the pore. We identify mechanisms of this novel crowding-induced transport cooperativity through the self-regulation of cargo density and flux in the pore. These findings explain how the functional architecture of the NPC resolves the problem of efficient bidirectional transport, and provide inspiration for the alleviation of clogging in artificial selective nanopores.

DOI: https://doi.org/10.1016/j.bpj.2024.03.027

Nat Struct Mol Biol. 2024 Apr 17.

DNA double-strand break-capturing nuclear envelope tubules drive DNA repair.

Mitra Shokrollahi, Mia Stanic, Anisha Hundal, Janet N Y Chan, Defne Urman, Chris A Jordan, Anne Hakem, Roderic Espin, Jun Hao, Rehna Krishnan, Philipp G Maass, Brendan C Dickson, Manoor P Hande, Miquel A Pujana, Razqallah Hakem, Karim Mekhail.

Current models suggest that DNA double-strand breaks (DSBs) can move to the nuclear periphery for repair. It is unclear to what extent human DSBs display such repositioning. Here we show that the human nuclear envelope localizes to DSBs in a manner depending on DNA damage response (DDR) kinases and cytoplasmic microtubules acetylated by α-tubulin acetyltransferase-1 (ATAT1). These factors collaborate with the linker of nucleoskeleton and cytoskeleton complex (LINC), nuclear pore complex (NPC) protein NUP153, nuclear lamina and kinesins KIF5B and KIF13B to generate DSB-capturing nuclear envelope tubules (dsbNETs). dsbNETs are partly supported by nuclear actin filaments and the circadian factor PER1 and reversed by kinesin KIFC3. Although dsbNETs promote repair and survival, they are also co-opted during poly(ADP-ribose) polymerase (PARP) inhibition to restrain BRCA1-deficient breast cancer cells and are hyper-induced in cells expressing the aging-linked lamin A mutant progerin. In summary, our results advance understanding of nuclear structure-function relationships, uncover a nuclear-cytoplasmic DDR and identify dsbNETs as critical factors in genome organization and stability.

DOI: https://doi.org/10.1038/s41594-024-01286-7

PLoS One. 2024 ;19(4): e0297738

Size-dependent steady state saturation limit in biomolecular transport through nuclear membranes.

P K Shakhi, M M Bijeesh, J Hareesh, Toby Joseph, P Nandakumar, Geetha K Varier.

The nucleus preserves the genomic DNA of eukaryotic organisms and maintains the integrity of the cell by regulating the transport of molecules across the nuclear membrane. It is hitherto assumed that small molecules having a size below the passive permeability limit are allowed to diffuse freely to the nucleus while the transport of larger molecules is regulated via an active mechanism involving energy. Here we report on the kinetics of nuclear import and export of dextran molecules having a size below the passive permeability limit. The studies carried out using time-lapse confocal fluorescence microscopy show a clear deviation from the passive diffusion model. In particular, it is observed that the steady-state concentration of dextran molecules inside the nucleus is consistently less than the concentration outside, in contradiction to the predictions of the passive diffusion model. Detailed analysis and modeling of the transport show that the nuclear export rates significantly differ from the import rates, and the difference in rates is dependent on the size of the molecules. The nuclear export rates are further confirmed by an independent experimental study where we observe the diffusion of dextran molecules from the nucleus directly. Our experiments and transport model would suggest that the nucleus actively rejects exogenous macromolecules even below the passive permeability limit. This result can have a significant impact on biomedical research, especially in areas related to targeted drug delivery and gene therapy.

DOI: https://doi.org/10.1371/journal.pone.0297738