RNA and protein synthesis mechanisms

This paper determines the structure of Toxoplasma gondii ribosomes bound to mRNA and tRNA, revealing how emetine inhibits translation by disrupting mRNA translocation.

This study shows that the antidepressant duloxetine disrupts RNA-protein interactions in both human and bacterial cells, revealing a new mechanism of drug action.

The paper identifies eIF5A as an indispensable protein in eukaryotic cells, showing that its duplicated paralogous genes act as a backup system to rescue mutations in the essential copy.

The paper integrates multi-omic data from yeast to identify translational programs during glucose starvation, revealing convergent cis-regulatory mechanisms in repressed genes.

The paper identifies neuronal stop-codon readthrough in Drosophila, showing it produces C-terminal extensions that alter protein localization.

The paper investigates ribosome clusters in neuronal RNA granules, finding they contain stalled ribosomes and unique 3D structures that avoid quality-control mechanisms.

The paper identifies a variant rRNA in Plasmodium falciparum that represses translation during host-to-vector transmission by forming a dominant-negative ribosome.

The paper introduces PCanPIE, a group I intron-based system for efficient circRNA synthesis at ambient temperatures, showing high circularization efficiency with optimized spacer sequences.

The paper investigates mitochondrial translation termination, recycling, and quality control mechanisms using Ribo-Seq and Disome-Seq, revealing roles of release factors and rescue mechanisms.

The paper develops an experimentally tuned protein-RNA score function for ROSETTA using Bayesian Optimization to improve energetic agreement with experimental data.

NUMonomer predicts nucleic acid structures directly from sequence, outperforming existing methods without auxiliary inputs.

The paper compares Boltzmann distributions of natural and random non-coding RNA, finding natural RNA are slightly more stable, except for short sequences.

This paper introduces Rho analysis to study RNA folding pathways using mutations and isolated contacts, revealing multiple folding pathways and their modulation.

This study structurally characterizes evolved ribosomes with enhanced translation kinetics, revealing how RNA structural adaptations influence translation efficiency.

The paper analyzes DMS reactivity patterns in RNA constructs to characterize 3D structural features and find correlations with hydrogen bonding and solvent accessibility.

This paper develops a looped-translation system in bacteria to synthesize ultra-large fibrous proteins, achieving molecular weights exceeding titin and enabling secretion.

This study shows that protein crowders alter RNA electrostatics and dynamics differently than PEG, challenging the use of PEG as a model for intracellular conditions.

This paper develops a programmable mRNA platform that detects specific miRNAs by converting their presence into a quantifiable protein output through miRNA-triggered ribosomal frameshifting.

This study quantifies sequence determinants of human programmed stop codon readthrough using deep mutational scanning and identifies gene-specific and context-dependent effects.

Shifu improves RNA secondary structure prediction by introducing a framework with a curated dataset, multi-axis evaluation, and compact language models that enhance accuracy and generalization.

The paper identifies translated overlapping upstream ORFs (ouORFs) in Arabidopsis, showing they repress translation more than non-overlapping uORFs and generate protein diversity.

RiboCollSensor detects ribosome collisions in living cells with high sensitivity, showing real-time kinetics and stress response dynamics.

The paper identifies novel leucine-associated reduction in protein abundance linked to 2A-like peptides from eukaryotes using a high-throughput fluorescent reporter tool.

The paper demonstrates how to use orthogonal trans-splicing ribozymes to store and report on multiple plasmid-encoded traits in microbial communities using RNA barcoding.

This study identifies conformational and electronic factors governing SAMURI ribozyme catalysis using computational methods, showing that reactivity depends on minor reactive conformations and electronic properties of cofactors.

This study optimizes DNA template design, reaction composition, and lysate genotype to extend CFPS reaction lifetime in a high-throughput format, achieving >14 h productivity and high deGFP yield.

The paper designs and validates high-affinity RNA aptamers for SARS-CoV-2 that match the binding affinity of neutralizing antibodies.

The paper develops coTFT, a live-cell imaging method to track translation and folding, showing bidirectional coupling between them.

elDORS provides an updated RNA sequence database to improve computational RNA analysis by integrating metagenomes and transcriptomes, enhancing multiple sequence alignment performance.

This paper discovers a ribozyme ligase that specifically catalyzes RNA ligation when the substrate has a 3'-phosphate group, suggesting a role in primordial RNA repair and offering new tools for RNA profiling.