Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast

• Published in: Molecular cell 2022-10, Vol.82 (20), p.3856-3871.e6
• Main Authors: Bensidoun, Pierre, Reiter, Taylor, Montpetit, Ben, Zenklusen, Daniel, Oeffinger, Marlene
• Format: Article
• Language: English
• Subjects: Active Transport, Cell Nucleus - physiology; basket accessory interactome; Cell Nucleus - genetics; Cell Nucleus - metabolism; Mlp1; mRNA export; mRNA processing; NPC heterogeneity; nuclear basket; nuclear compartmentalization; Nuclear Pore - genetics; Nuclear Pore - metabolism; nuclear pore complex; Nuclear Pore Complex Proteins - genetics; Nuclear Pore Complex Proteins - metabolism; nucleolus; poly(A) transcripts; Proteomics; RNA Polymerase II - genetics; RNA Polymerase II - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Saccharomycetales - genetics; Saccharomycetales - metabolism
• ISSN: 1097-2765; 1097-4164
• DOI: 10.1016/j.molcel.2022.09.019

To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly. [Display omitted] •Nuclear baskets assemble only on a subset of NPCs in budding yeast•Basket assembly requires nuclear RNA metabolism•Baskets recruit an NPC accessory interactome•Presence of a basket suggests different export dynamics for mRNAs/mRNPs Bensidoun et al. show that in budding yeast, the nuclear basket is a functionalized non-default state of the nuclear pore complex, whose formation is dependent on active nuclear mRNA metabolism and specifically 3′ end processing and polyadenylation of transcripts.