RNA and protein synthesis mechanisms

The paper determines in situ structures of Pf80S ribosomes in Plasmodium falciparum-infected erythrocytes, identifies a bifurcation in translation elongation, and links perturbations to inhibitor effects on ribosome interactions.

The paper analyzes >12,000 bacterial genomes to study the conservation and evolution of the programmed ribosomal frameshift in prfB, finding it was present in the last common ancestor of bacteria and linked to stop codon usage.

The paper analyzes RNA secondary structures to determine if they show signs of positive selection, finding they are mostly random but shaped by developmental bias.

This study identifies bottromycin's mechanism of action as selectively trapping EF-Tu/glycyl-tRNA complex on the ribosome, inhibiting translation at glycine codons.

The paper investigates the translational activation mechanisms of COX1 mRNA in yeast mitochondria, revealing that Pet309 and Mss51 interact with the mitoribosome independently of active translation.

This study identifies staged translational remodeling in mouse cortex after ischemic stroke, showing changes in codon usage, ribosome occupancy, and frame-disruption events not captured by transcriptomics.

The paper shows co-translational ribosome pairing enables the formation of coiled-coil homodimers from misfolding-prone subunits through chaperone-like interactions between nascent chains.

This study compares stress granule formation and composition during MHV and SFV infections, revealing virus-specific differences in their proteomes, kinetics, and RNA content.

The paper develops an empirical kinetic model of E. coli tRNA synthetases to study tRNA charging dynamics and their impact on translational efficiency.

The paper identifies ITAF45 as a host factor essential for picornavirus Type II IRES-mediated translation, showing its role in multiple viruses and suggesting it as an antiviral target.

This study investigates how bacteriophage MS2 coat proteins selectively package viral RNA over host RNA, finding that selectivity arises from collective interactions rather than a single stem-loop.

The paper investigates codon usage bias and its relationship with protein expression in Trypanosoma cruzi by integrating tRNA sequencing and transcriptomic data.

The paper determines the structure of a plant-virus xrRNA and shows it forms a pseudoknot that confers exoribonuclease resistance, revealing a conserved mechanism across diverse viruses.

The paper investigates the multi-layered repression system controlling C9ORF72 translation and identifies strategies to rescue loss-of-function in disease.

RESM improves RNA sequence-structure-function prediction by transferring knowledge from protein language models, outperforming existing models in multiple tasks.

The paper improves generative models for biological sequences by integrating experimental feedback, increasing functional sequence generation from 6.7% to 63.7% in ribozyme design.

The paper develops substitution models that account for changes in the coding alphabet size over time, finding support for a reduced ancient alphabet in old proteins and rejecting it in young ones.

The paper identifies NEPRO and C18ORF21 as constitutive subunits of metazoan RNase MRP, clarifying its composition and RNA binding specificity.

The paper introduces HomRank, a ranking method for RNA 3D structure assessment that improves accuracy over existing methods on benchmark datasets.

This study shows that RNA structural flexibility influences its ion atmosphere, with unstructured RNAs having diffuse ion clouds that extend further than folded RNAs.

The paper reports cryo-EM structures of the MnmE-MnmG complex in different oligomeric states, revealing conformational changes and a mechanism for substrate and cofactor transfer during tRNA modification.

This study investigates the role of divalent metal ions in catalysis by 3'-5' RNA polymerases, revealing distinct metal dependencies and providing direct evidence of ATP and NTP presence in the active site.

This paper introduces structRFM, a structure-guided RNA foundation model that improves RNA function prediction and structural inference through pre-training on sequence-structure pairs.

The paper develops a semi-automated Ribo-Seq and Disome-Seq platform to analyze translation status across many samples, identifying factors regulating translation and revealing links between stop codon readthrough and mitochondrial translation deficiency in COVID-19.

The paper uses protein language models to uncover evolutionary constraints on synonymous codon choice in yeast by combining sequence analysis with experimental validation.

This paper introduces a new coarse-grained RNA model compatible with Martini 3, showing improved accuracy and stability for simulating RNA and RNA-protein complexes.

This paper introduces RAPPL, a rapid, simple, and cost-effective method for isolating ribosomes and translational machinery, demonstrating its utility in functional and structural studies across various species and sample types.

The paper identifies NAC's role in promoting co-translational folding by interacting with nascent chains at the ribosomal tunnel exit, expanding its known functions in protein biogenesis.

This paper identifies Ashwin as a nuclear import factor for the tRNA ligase complex and shows that FAM98 paralogs determine its subcellular localization for tRNA biogenesis and UPR.

This study investigates the in vitro interaction between eIF4E and Dcp2, showing that eIF4E does not interfere with Dcp2's decapping activity and may even enhance its RNA binding affinity.