RNA and protein synthesis mechanisms

This study investigates how pathogenic mitochondrial tRNA variants impair RNA processing by affecting 5' leader removal and downstream tRNA release.

The paper determines the structure of the ribosome stalled by the AMD1 C-tail, revealing how it traps eRF1 and ABCE1 to block translation termination.

This study identifies a molecular switch in NAC that prevents mitochondrial protein mistargeting by SRP, showing that mutations disrupt this mechanism and cause ER stress.

The paper identifies ribosome stalling as a mechanism that enhances chloroplast targeting of nuclear-encoded proteins in Arabidopsis thaliana.

The paper identifies a conformational switch in eIF5 that regulates translation initiation at AUG and non-AUG codons by stabilizing or destabilizing the initiation complex.

The paper studies how different ligands interact with the SAM-I riboswitch, revealing conformational changes and insights for RNA-targeting drug design.

The paper uses molecular dynamics simulations to study the interaction between the ribosome's A site and CAR site, revealing sequence-dependent modulation of hydrogen bonding and π-stacking interactions.

This paper introduces using Benzonase to generate ribosome footprints for Ribo-seq, simplifying the protocol and reducing time, cost, and bias.

This paper develops nine new aminoacyl-tRNA synthetase/tRNA pairs to site-specifically encode 12 histidine-like non-canonical amino acids for enzyme engineering and catalytic studies.

This study optimizes the PURE system composition using automation and active learning, achieving up to 3-fold improvements in protein yield and translation rate.

This study shows that both ATP and Mg2+ are required for high-affinity indolmycin binding to human mitochondrial TrpRS, revealing structural and thermodynamic similarities to bacterial TrpRS.

This study determines the cryo-EM structure of the RsmI-30S complex and reveals how RsmI recognizes and modifies the 16S rRNA C1402 nucleotide.

EVA is a long-context generative RNA model trained on 114 million sequences, achieving state-of-the-art performance in RNA design tasks and structural modeling.

The paper identifies SNOR, a ribosome-associated factor in S. pombe, that enables translation restart after cellular dormancy induced by glucose depletion.

The paper determines the structural ensemble-to-function relations of the B2 SINE ribozyme using RNA chemical probing, X-ray scattering, and modeling, showing cleavage site dependency on its structure and function.

The paper identifies lineage-specific tRNA sequence conservation and variation in modifying enzymes across Saccharomycotina using genomic and sequencing data.

The paper evaluates codon optimization strategies for mammalian glycoprotein production and finds that native codons are sufficient, while selective codon skewing can improve yields for some targets.

This paper analyzes the relationship between phage codon usage, infection style, and tRNA gene numbers across 154 phages infecting 7 bacterial genera, finding that virulent phages with many tRNA genes show greater codon usage divergence from their hosts.

Pro2RNA generates species-adapted mRNA coding sequences from protein sequences using a multimodal language model, outperforming existing methods in benchmark tests.

The paper uses single-molecule fluorescence microscopy to study real-time RNA folding dynamics and shows how ribosomal proteins and other factors modulate RNA conformations.

This study investigates how photosynthesis loss and horizontal gene transfer reshape organellar translation and tRNA metabolism in holoparasitic plants.

PhyloRNA provides a curated database of RNA secondary structures linked to phylogenetic classifications, enabling comparative analysis across diverse taxa.

The paper identifies Acl1 and Bcl1 as dedicated chaperones for Rpl1 by using proximity labeling and structural analysis in yeast.

ChironRNA resolves steric clashes and reconstructs missing atoms in RNA structures using an E(3)-equivariant diffusion model, achieving high precision on test data.

This study uses single-molecule fluorescence microscopy to show how stable transcription factor binding coordinates rRNA transcription and processing in bacteria.

This study shows that disrupting the Bop1-WDR12 interaction in HCT116 cells causes nucleolar stress and apoptosis without DNA damage, suggesting a non-genotoxic cancer therapy approach.

The paper presents an automated plasmid assembly pipeline using liquid handling robotics to construct and test RNA sensors efficiently.

RNAElectra is an RNA foundation model pretrained using replaced-token detection, showing strong performance across RNA regulatory tasks and supporting interpretability.

This study shows RPF2 and RPL10A regulate distinct gene translations during plant immunity and drought stress, with RPF2 overexpression enhancing growth and disease resistance while RPL10A affects ABA sensitivity and drought tolerance.