Nuclear mRNPs are compact particles packaged with a network of proteins promoting RNA–RNA interactions

Abstract

Messenger RNAs (mRNAs) are at the center of the central dogma of molecular biology. In eukaryotic cells, these long ribonucleic acid polymers do not exist as naked transcripts; rather, they associate with mRNA-binding proteins to form messenger ribonucleoprotein (mRNP) complexes. Recently, global proteomic and transcriptomic studies have provided comprehensive inventories of mRNP components. However, knowledge of the molecular features of distinct mRNP populations has remained elusive. We purified endogenous nuclear mRNPs fromSaccharomyces cerevisiaeby harnessing the mRNP biogenesis factors THO and Sub2 in biochemical procedures optimized to preserve the integrity of these transient ribonucleoprotein assemblies. We found that these mRNPs are compact particles that contain multiple copies of Yra1, an essential protein with RNA-annealing properties. To investigate their molecular and architectural organization, we used a combination of proteomics, RNA sequencing, cryo-electron microscopy, cross-linking mass spectrometry, structural models, and biochemical assays. Our findings indicate that yeast nuclear mRNPs are packaged around an intricate network of interconnected proteins capable of promoting RNA–RNA interactions via their positively charged intrinsically disordered regions. The evolutionary conservation of the major mRNA-packaging factor (yeast Yra1 and Aly/REF in metazoans) points toward a general paradigm governing nuclear mRNP packaging.

A molecular switch orchestrates the nuclear export of human messenger RNA

“…Nuclear mRNPs form compact globules (Skoglund et al, 1986; Pacheco-Fiallos et al, 2023; Bonneau et al, 2023) decorated with TREX complexes on their surface (Pacheco-Fiallos et al, 2023) (Fig. 1a).…”

“… ABSTRACTThe nuclear export of messenger RNA (mRNA) is a key step in eukaryotic gene expression (Köhler and Hurt, 2007). Despite recent insights into the packaging of newly transcribed mRNAs into ribonucleoprotein complexes (mRNPs) (Pacheco-Fiallos et al, 2023; Bonneau et al, 2023), the subsequent events that govern mRNA export are poorly understood. Here, we elucidate the molecular basis of human mRNA export licensing, which involves the remodeling of mRNP-bound transcription-export complexes (TREX), the formation of export-competent mRNPs, the docking of mRNPs at the nuclear pore complex (NPC), and the release of mRNPs at the NPC to initiate export.…”

A paradigm for regulation at the effector interface with RNA-binding proteins

“…Predictions were generated with AlphaFold-Multimer 29,30 version 2.3.2 following a published approach 31 and using a computing cluster with these key settings: --db_preset=full_dbs --max_template_date=2020-05-14 --models_to_relax=best -- model_preset=multimer --num_multimer_predictions_per_model=5 The resulting predicted models were aligned in PyMOL v2.5.4 to assess prediction convergence, and this software was used to prepare all structural figures. For UNK, the IDR segment, the C-terminal region, or the full-length sequences were provided.…”

“…Predictions were generated with AlphaFold-Multimer 29,30 version 2.3.2 following a published approach 31 and using a computing cluster with these key settings:…”

“…We then used AlphaFold employing the rigorous approach proposed by Conti and coworkers to generate structure predictions of UNKIDR in complex with the NOT9 module (Figures 4D-4G) [29][30][31] . Interestingly, these predictions suggested that a segment of UNKIDR folds into a helix (residues 507-537; henceforth SLiM 1) that binds across the CNOT9 concave surface (Figures 4D and 4E), which serves as a protein-protein interaction site for several other factors 32 , whereas the sole tryptophan residue within UNKIDR, W622, inserts into either of the defined tryptophan (W)-binding pockets on the convex surface of CNOT9 (Figures 4F and 4G).…”