RNA and protein synthesis mechanisms

This paper develops two codon optimization tools using classical and AI methods, showing they outperform existing tools in protein expression.

The paper develops a two-step in vitro evolution method to improve translational proteins and identifies mutations that enhance translation activity.

The paper determines high-resolution structures of NediV IRES-mediated translation initiation complexes and their transition to elongation, revealing structural changes and interactions during viral translation.

The paper introduces IRES-TrAPPr, a method to quantify CDI and IRES activity, revealing that viral IRESes from warm-blooded hosts are more structurally stable and many DNA-based IRES candidates have negligible activity.

This paper identifies RNA elements in the 3'UTR that enhance translation efficiency across multiple systems.

The paper identifies a dynamic A-minor switch in RNA structures using NMR and cryo-EM, showing RNA dynamics influence function and revealing a new therapeutic target.

RiboPipe imputes codon-resolution Ribo-seq coverage for low-coverage transcripts using a unified framework that improves accuracy and efficiency.

This paper develops a peptidomimetic inhibitor of eIF4E that suppresses cap-dependent translation in cancer and neurodevelopmental disorders, showing efficacy in cell and animal models.

The paper introduces RNAprecis, an algorithm that predicts detailed RNA conformations from low-resolution experimental data, showing improved performance on outlier cases.

This study shows that the Gcn1-Gcn20 complex inhibits RQC initiation during transient ribosome collisions, preventing unnecessary protein degradation.

This study identifies IFRD1 as a ribosome-salvaging factor that stabilizes non-translating 80S ribosomes during ER stress, preventing degradation and cell death.

This study shows that Reh1 is required for the degradation of 25S rRNA with mutations in the catalytic center, but not for other defective rRNAs.

The paper develops a cysteine-free UTag system for live-cell single-mRNA translation tracking, showing improved thermostability and performance comparable to existing systems.

The paper investigates the translational expression and intracellular behavior of the microprotein SEP53BP1, identifying its Golgi targeting tag and lack of impact on proteasome activity.

The study shows that the 20 genetically-encoded amino acids are non-randomly distributed in functionally-relevant chemical properties like HOMO-LUMO gaps, expanding previous theories on amino acid alphabet design.

This study shows queuosine modification enhances phage resistance and biofilm formation in Shewanella glacialimarina by altering translation efficiency and promoting mutagenesis.

The paper identifies RNA binding proteins and cis-regulatory elements that control translation in human effector T cells through multi-omics and machine learning analysis.

This study shows that queuosine modification in Shewanella glacialimarina is essential for cold-active growth, as its deficiency leads to cold sensitivity and metabolic changes.

The paper quantifies the conformational dynamics of the ribosomal tunnel constriction in E. coli, showing its flexibility and response to nascent polypeptides.

The paper identifies a novel sense-to-sense codon reassignment in Acidimicrobiales bacteria where ACA specifies aspartate instead of threonine.

This study investigates how ionic conditions and structural flexibility affect RNA folding by comparing cryo-EM and XRD structures of the SARS-CoV-2 frameshifting stimulatory element.

The paper introduces RNAFOLBO, a continual learning framework that improves RNA secondary-structure prediction by mitigating family effects and catastrophic forgetting.

This study designs functional exoribonuclease-resistant RNAs using a mechanics-aware approach, achieving wild-type efficiency without sequence similarity to known xrRNAs.

The paper identifies stop codon reassignment of UGA to tryptophan in the Actinomycetota phylum, expanding known bacterial lineages with this genetic code plasticity.

The paper analyzes how medically important antimicrobials bind to the 30S ribosomal subunit of Borrelia burgdorferi using structural analogy and computational methods to predict binding free energy.

This paper shows that eIF3F and PDCD4 interact to regulate IRES-mediated translation of Bcl-xL mRNA, with implications for glioblastoma pathophysiology.

The paper identifies a conserved four-codon dORF in the 3'UTR of MAP3K10 regulated by an RNA G-quadruplex, which modulates MAP3K10 expression.

The paper analyzes codon usage patterns in pancreatic cancer to show how oncogenic gene expression is systematically optimized through GC content, preferred codons, and cost-effective amino acids.

The paper identifies RNF25 as a ribosome collision response pathway that competes with GCN2 in amino acid starvation, resolving stalls independently of GCN2 activation.

This study identifies how F. tularensis regulates its bS21 paralogs, showing that bS21-2 is autogenously repressed and its mRNA stability is modulated, impacting virulence.