RNA and protein synthesis mechanisms

This study identifies structural and evolutionary mechanisms underlying the diversification of viral IRESs through accretion and recombination.

This study identifies NudC as a novel regulator of ribosome biogenesis and homeostasis in Drosophila polyploid cells, independent of its known role in dynein regulation.

The paper reports crystal structures of dopamine-binding RNA aptamers to show how they recognize ligands while maintaining scaffold integrity through metal-mediated interactions and local remodeling.

The paper develops a regression-based model to predict mRNA and protein abundance using codon weights derived from transcriptomic data, validated across multiple species.

This study shows that an A2062U mutation in 23S rRNA improves ribosome activity for translating sequences with challenging monomers like proline and β2-hydroxy acids.

The paper analyzes translatome and translation dynamics in RiboCancer cell lines to show that Rps15 mutations disrupt tRNA accommodation, affecting translation efficiency and transcriptional regulation in CLL.

LinearCapR computes per-nucleotide structural-context probabilities for RNA in linear time without span limits, outperforming existing methods on long-range structures and large RNAs.

This study uses cryo-EM to show doxycycline binds to the ribosome exit tunnel in C. burnetii and E. coli, revealing new mechanisms of ribosome inhibition.

The paper introduces i-POPFLEX, a modular cell-free protein synthesis system that improves protein yield and reduces costs compared to commercial kits.

The paper compares mitochondrial and chloroplast proteomes across two flowering plant species to understand how gene loss and transfer affect organellar translation machinery.

The paper identifies and structures MpTACO1, a dual-targeted protein in plants, showing its role in enhancing translation of mitochondrial and plastid-encoded proteins.

This study investigates whether genomic language models have learned RNA thermodynamics by analyzing their pairwise dependencies using the categorical Jacobian operation and comparing them to biophysical models.

The paper experimentally validates the self-cleavage activity of 855 hairpin ribozymes using high-throughput sequencing, showing most are efficient despite rare nucleotides at conserved positions.

This paper develops a low-input polysome profiling protocol for human postmortem brain tissue and adapts it for neuronal cell lines and mouse brain.

This paper introduces a fluorescence-based microscale platform to study bacterial translation initiation, revealing the dissociation constant of streptomycin and the effect of antimicrobial peptides.

The paper uses a mechanistic model to explain the bell-shaped protein production profile in the PURE system, showing that excess EF-Tu sequesters tRNAfMet, and confirms this by experimental validation.

This study uses single-molecule FRET to observe intersubunit rotation in yeast ribosomes and links it to tRNA transitions and elongation factor actions.

This study identifies 17 rRNA methyltransferases in Bacillus subtilis, revealing their roles in ribosome function and antibiotic sensitivity through genetic and biochemical analyses.

This study shows that eukaryotic tRNA ligases repair RNA breaks in ribosomes and other RNPs, restoring translational activity and maintaining transcriptome integrity.

The paper uses quantitative phase imaging to measure B cell mass growth and finds an offset exponential model explains mass accumulation, indicating constant degradation during activation.

The paper shows EF-G1, not EF-G2, is the canonical ribosome recycling factor in mycobacteria, with structural evidence explaining EF-G2's lack of recycling activity.

CoSTAR aligns RNA structures by focusing on stems rather than nucleotides, improving alignment of pseudoknotted structures and enabling efficient comparisons across RNA families.

The paper shows eIF4E3 enables efficient translation of viral mRNAs with short 5' UTRs, unlike the canonical eIF4E1, and identifies this as a mechanism used by viruses like VSV to bypass host translation suppression.

The paper identifies missplicing as a common issue in heterologous gene expression and develops a splice-aware optimization algorithm to improve transgene performance.

The paper introduces a cost-effective reverse transcriptase, MarathonRT, and compares its performance with commercial enzymes for tRNA sequencing library preparation.

This study identifies nanometer-scale RNA-protein clusters (RPCs) formed by eIF4A with cofactors eIF4B and eIF4G, showing their role in enhancing helicase activity through multivalent RNA interactions.

The paper develops an orthogonal initiation system for efficient N-terminal noncanonical amino acid incorporation in cell-free translation without disrupting the native methionine pathway.

The paper investigates the evolutionary loss of prfB autoregulation in Pseudomonas fluorescens SBW25, finding that compensatory mutations enable this loss without significant fitness cost.