RNA and protein synthesis mechanisms

The paper uses cryo-electron tomography to visualize bacterial translation processes in Mycoplasma pneumoniae, revealing structural coordination between transcription, translation, and membrane attachment.

This study investigates how herpesvirus ubiquitin deconjugases counteract ribosomal quality control responses during translational stress, revealing differences in their effectiveness across virus types.

This study identifies Hib, a new family of ribosome hibernation factors in Archaea, showing its role in preserving ribosomes during stress and revealing its structural and functional mechanisms.

The paper shows that virus propagation can occur through low-level host protein variants caused by gene-expression errors, using bacteriophage T7 and thioredoxin as a model.

This study uses single-molecule techniques to analyze tRNA selection during eukaryotic translation, revealing faster near-cognate sampling and a negative correlation between near-cognate concentration and tRNA accommodation efficiency.

This paper develops a chemical probing strategy using preQ1 and its riboswitch RNA to study RNA-small molecule interactions in living bacteria, mapping binding sites through mutational profiling.

The paper identifies alanine's role in linking trans-translation to WhiB7-mediated antibiotic resistance and recalcitrance in Mycobacterium smegmatis.

This study investigates how RNA structure and sequence context influence RAN translation initiation in C9orf72 repeats, revealing a kinetic bottleneck in initiation at near-cognate start codons.

This study investigates the substrate specificity of the PEARL BhaBCAla, showing it can use non-cognate amino acids and tRNAs for peptide extension, with efficiency depending on both amino acid and tRNA features.

RNAcomp2D provides a web tool to run multiple RNA secondary structure prediction methods and compare their results visually.

STONE improves RNA structure analysis by integrating mutation and stop signals from a single experiment, enhancing coverage and accuracy in single-cell data.

This study designs a covalent small molecule targeting unpaired guanines in a riboswitch, showing it modulates riboswitch function in a cellular reporter system.

The paper investigates the structural and mechanistic details of translation initiation on the enterovirus Type 1 IRES using cryo-electron microscopy, revealing key RNA-RNA interactions critical for viral replication.

This study characterizes the effects of three small-molecule inhibitors on MtbRNAP transcription elongation using optical tweezers, revealing distinct inhibition mechanisms and synergistic effects.

RNAtranslator generates RNA sequences that bind to specific proteins by treating RNA design as a sequence-to-sequence translation task, producing novel and high-affinity sequences.

This paper introduces NA-MPNN, a unified deep learning model for nucleic acid inverse folding, which outperforms existing methods in RNA sequence design and protein-DNA specificity prediction.

The paper identifies and characterizes ribosomal frameshifting sites across organisms, showing their prevalence and evolutionary tuning to mitigate harmful effects.

The paper shows heat shock increases silent ribosomes and reorganizes mRNA turnover in yeast by prioritizing heat-shock protein synthesis over ribosome biogenesis.

The paper identifies primate-specific motifs in human rRNAs and 45S spacers that are also found in nervous system genes linked to disorders like autism and schizophrenia.

This paper introduces CaCoFold-R3D, a method that jointly predicts RNA 3D motifs and secondary structure using evolutionary information, demonstrating its effectiveness for RNA structure prediction.

This paper introduces a generative diffusion model for de novo design of RNA and nucleoprotein complexes, validated experimentally with SHAPE-seq and electron microscopy.

This study enhances mRNA translation efficiency by engineering Kozak repeats in the 5'-UTR, showing improved expression in both cell culture and mice.

This paper introduces a theoretical framework for co-translational condensation (CTC), showing how polysomes drive the formation of biomolecular condensates through protein synthesis.

This study uses RCP-seq to analyze translation initiation dynamics in mouse brain tissues, revealing SSU poising and uORF effects on translational efficiency.

The paper presents a platform for biosynthesizing aromatic noncanonical amino acids in E. coli and incorporating them into proteins using orthogonal translation systems.

This study examines the Central Dogma in Arabidopsis thaliana, showing that codon frequencies and mRNA levels are better predictors of protein expression than methylation, tRNA, or ribosome-associated transcripts.

This study shows that BCAA starvation causes codon-specific ribosome stalling, affecting translational dynamics and protein output in mammalian cells.

This study reveals how tetracyclines target the bacterial ribosome using cryo-EM structures, showing species-specific interactions and a new mechanism for antibiotic action.

This study identifies PARP10 as essential for stress granule initiation, showing it regulates assembly kinetics and modifies G3BP1 to influence SG composition.

This study uses cell-free systems to characterize RNA circuits for programmable protein expression, logic, and biosensing, revealing design principles applicable across different environments.