RNA and protein synthesis mechanisms

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 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.

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

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 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 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 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 shows that substituting ribonucleotides with deoxyribonucleotides in mRNA improves translation efficiency and therapeutic potential in vivo.

Ribo-LENS detects RNA small-molecule binding sites using a geometric deep-learning framework, outperforming existing methods and enabling efficient virtual screening.

The paper uses single-cell analysis to show YbeX and YbeY have distinct roles in ribosome biogenesis in E. coli, with YbeX causing heterogeneous pre-rRNA processing and YbeY affecting 16S rRNA maturation.

The paper quantifies reverse-complement symmetry in codon usage across taxa and shows it is not fully explained by compositional constraints.

The paper demonstrates that community-designed riboregulators outperform canonical designs and identifies structural features that influence translational activation.

The paper shows that amino acid stress shifts c-myc translation from AUG-initiated to CUG-initiated isoforms via ribosome stalling and queue formation.

This paper reprograms a protein ligase into a functional aminoacyl-tRNA synthetase, enabling the incorporation of non-canonical amino acids and post-translational modifications into proteins.

The paper systematically engineers and analyzes intrinsic terminators in bacteria, finding that an adenosine upstream of the terminator hairpin improves protein production and reduces read-through.

This study identifies that RsmF activity in E. coli depends on prior modification of 16S rRNA helix 44 by RsmE and RsmH, revealing an order of operations for ribosome biogenesis modifications.

The paper shows viral infection represses host genes with codon usage similar to viruses, supporting multiple hypotheses about tRNA competition during infection.

The paper investigates the conformational landscape of a SMN2 splice-site defect using molecular dynamics simulations and shows that solvation models significantly affect the equilibrium between different conformations.

This paper develops a cell-free platform linking metabolic activity to protein synthesis under resource scarcity, demonstrating how metabolic control can influence gene expression in synthetic cells.