bims-nucpor 2023-07-30 papers

Issue of 2023–07–30
four papers selected by
Sara Mingu, Johannes Gutenberg University

Nucleus. 2023 12;14(1): 2240139

A survey of the specificity and mechanism of 1,6 hexanediol-induced disruption of nuclear transport.

Elizabeth C Riquelme Barrientos, Tegan A Otto, Sara N Mouton, Anton Steen, Liesbeth M Veenhoff.

Selective transport through the nuclear pore complex (NPC) depends on the dynamic binding of FG-repeat containing nucleoporins, the FG-nups, with each other and with Karyopherins (Kaps). Here, we assessed the specificity and mechanism by which the aliphatic alcohol 1,6-hexanediol (1,6HD) disrupts the permeability barrier of NPCs in live baker's yeast cells. After a 10-minute exposure to 5% 1,6HD, no notable changes were observed in cell growth, cytosolic pH and ATP levels, or the appearance of organelles. However, effects on the cytoskeleton and Hsp104 were noted. 1,6HD clearly affected the NPC permeability barrier, allowing passive nuclear entry of a 177kDa reporter protein that is normally confined to the cytosol. Moreover, multiple Kaps were displaced from NPCs, and the displacement of Kap122-GFP correlated with the observed passive permeability changes. 1,6HD thus temporarily permeates NPCs, and in line with Kap-centric models, the mechanism includes the release of numerous Kaps from the NPCs.

Keywords: 1,6-hexanediol; Karyopherin; Nuclear pore complex; Nuclear transport receptors; aliphatic alcohol; baker’s yeast; liquid-liquid phase separation; nuclear transport

DOI: https://doi.org/10.1080/19491034.2023.2240139

J Biomol Struct Dyn. 2023 Jul 28. 1-12

Identification of novel nuclear pore complex associated proteins in esophageal carcinoma by an integrated bioinformatics analysis.

Parisa Mohamadynejad, Mehdi Moghanibashi, Kambiz Bagheri.

Nucleoporins (NUPs) are components of the nuclear pore complex (NPC) that participate in the nucleocytoplasmic transport of macromolecules as well as in many essential processes that may be led to carcinogenesis. We selected three expression profile microarray datasets from GEO and as well as TCGA data to identify differentially expressed NUPs genes in esophageal carcinoma. Our findings indicated that NUP133, NUP37, NUP43, NUP50, GLE1 and NDC1 are overexpressed in esophageal carcinoma, among which NUP50 and GLE1genes are reported for the first time in esophageal carcinoma. All identified NUPs were also associated with distant metastasis.Communicated by Ramaswamy H. Sarma.

Keywords: Esophageal Carcinoma; GEO; GLE1; NUP50; Nuclear Pore Complex; TCGA

DOI: https://doi.org/10.1080/07391102.2023.2240414

Chem Biomed Eng. 2023 Jul 24. 1(4): 356-371

Application of Super-resolution SPEED Microscopy in the Study of Cellular Dynamics.

Wenlan Yu, Coby Rush, Mark Tingey, Samuel Junod, Weidong Yang.

Super-resolution imaging techniques have broken the diffraction-limited resolution of light microscopy. However, acquiring three-dimensional (3D) super-resolution information about structures and dynamic processes in live cells at high speed remains challenging. Recently, the development of high-speed single-point edge-excitation subdiffraction (SPEED) microscopy, along with its 2D-to-3D transformation algorithm, provides a practical and effective approach to achieving 3D subdiffraction-limit information in subcellular structures and organelles with rotational symmetry. One of the major benefits of SPEED microscopy is that it does not rely on complex optical components and can be implemented on a standard, inverted epifluorescence microscope, simplifying the process of sample preparation and the expertise requirement. SPEED microscopy is specifically designed to obtain 2D spatial locations of individual immobile or moving fluorescent molecules inside submicrometer biological channels or cavities at high spatiotemporal resolution. The collected data are then subjected to postlocalization 2D-to-3D transformation to obtain 3D super-resolution structural and dynamic information. In recent years, SPEED microscopy has provided significant insights into nucleocytoplasmic transport across the nuclear pore complex (NPC) and cytoplasm-cilium trafficking through the ciliary transition zone. This Review focuses on the applications of SPEED microscopy in studying the structure and function of nuclear pores.

DOI: https://doi.org/10.1021/cbmi.3c00036

Biomolecules. 2023 Jul 14. pii: 1127. [Epub ahead of print]13(7):

Dissecting the Nuclear Import of the Ribosomal Protein Rps2 (uS5).

Andreas Steiner, Sébastien Favre, Maximilian Mack, Annika Hausharter, Benjamin Pillet, Jutta Hafner, Valentin Mitterer, Dieter Kressler, Brigitte Pertschy, Ingrid Zierler.

The ribosome is assembled in a complex process mainly taking place in the nucleus. Consequently, newly synthesized ribosomal proteins have to travel from the cytoplasm into the nucleus, where they are incorporated into nascent ribosomal subunits. In this study, we set out to investigate the mechanism mediating nuclear import of the small subunit ribosomal protein Rps2. We demonstrate that an internal region in Rps2, ranging from amino acids 76 to 145, is sufficient to target a 3xyEGFP reporter to the nucleus. The importin-β Pse1 interacts with this Rps2 region and is involved in its import, with Rps2 residues arginine 95, arginine 97, and lysine 99 being important determinants for both Pse1 binding and nuclear localization. Moreover, our data reveal a second import mechanism involving the N-terminal region of Rps2, which depends on the presence of basic residues within amino acids 10 to 28. This Rps2 segment overlaps with the binding site of the dedicated chaperone Tsr4; however, the nuclear import of Rps2 via the internal as well as the N-terminal nuclear-targeting element does not depend on Tsr4. Taken together, our study has unveiled hitherto undescribed nuclear import signals, showcasing the versatility of the mechanisms coordinating the nuclear import of ribosomal proteins.

Keywords: Kap121; Pse1; Rps2; dedicated chaperone; importin; nuclear import; ribosomal protein; ribosome assembly; uS5; yeast

DOI: https://doi.org/10.3390/biom13071127