RNA and protein synthesis mechanisms

This study shows that the Prp protease cleaves the N-terminal extension of ribosomal protein L27 in S. pneumoniae, and that this cleavage is essential for viability, though the extension itself is not required.

TISCalling identifies and ranks translational initiation sites in plants and viruses using machine learning and statistical analysis, providing prediction scores and web tools for visualization.

The paper examines rRNA transcription and abundance in normal and leukemic hematopoiesis, finding cell-type-specific variations and functional roles in myeloid differentiation.

This paper describes the creation of a synthetic Escherichia coli strain with a 57-codon genetic code by recoding 105 codons in a 4 Mb synthetic genome.

The paper identifies NVL as a target for cancer therapy, showing that its inhibition by MM17 and MM927 suppresses tumor growth through ribosome biogenesis disruption.

This paper uses {lambda}-dynamics to predict RNA binding preferences of human Pumilio, including modified RNAs, showing high accuracy compared to experimental data.

This study identifies a distinct tRNase module in rabbit SAMD9 that retains antiviral activity despite structural differences from human SAMD9.

The paper shows that ribosome biogenesis factors and pre-rRNA processing enzymes are present in distal neuronal compartments, suggesting local ribosome maturation occurs in dendrites.

The paper shows that 40S ribosomal subunits scan mRNA via one-dimensional diffusion rather than helicase-driven translocation in yeast.

This paper shows that a simple probabilistic model with few parameters can learn RNA base-pairing rules from RNA sequences alone, without structural or alignment data.

This paper develops a DNA scaffold method for 5' labeling of SARS-CoV-2 RNA pseudoknots to study their conformational dynamics using smFRET.

This study investigates how eIF1 and eIF5 dynamically regulate translation start site fidelity through single-molecule analysis and cell experiments.

ARTEM identifies RNA and DNA tertiary motifs by searching structural databases, revealing new kink-turn variants and their functional implications.

The paper combines experimental and computational methods to model how uORFs regulate translation, identifying key features and interactions that influence their repressive activity.

This study uses single-molecule tracking in E. coli to show that the longer IF2 isoform interacts with NusA, linking transcription and translation initiation and affecting growth adaptation.

The paper predicts translation efficiency (TE) of mRNA in mammalian cells using a deep learning model trained on ribosomal profiling data across multiple cell types.

The paper maps RNA secondary structure ensembles in living E. coli cells, identifying conserved structural elements and cold shock-responsive RNA thermometers.

The paper analyzes ribosome profiling data to show translation efficiency covariation (TEC) is conserved across human and mouse cells, revealing gene functions not evident from RNA or protein co-expression.

The paper uses structural biology and computational methods to design MSI-1 mutants that alter RNA binding selectivity, validated by NMR and SPR experiments.

This paper introduces AlignmentFold and AlignmentPartition to improve RNA secondary structure prediction using fixed alignments and new thermodynamic parameters, achieving accuracy comparable to existing tools.

The paper investigates neomycin's binding to human ribosomes using Cryo-EM and functional assays, revealing structural binding patterns that differ from cellular observations.

RNALens improves 5' UTR modeling by integrating genomic context and thermodynamics, achieving better performance in predicting mRNA expression and translation efficiency across cell types.

TransCodon is a Transformer-based model that predicts optimal synonymous codons by integrating species-specific information, 5'UTRs, and RNA structure, improving translational efficiency in heterologous hosts.

The paper uses anti-sense oligonucleotides to disrupt RNA interactions in bacterial ribosome assembly, revealing intermediate structures and domain consolidation during RNP formation.

This study improves the potency of N1-methylpseudouridine-modified self-amplifying RNA by identifying mutations that enhance RNA synthesis and antigen expression.

The paper screens translation-enhancing peptides (TEPs) in E. coli and develops a machine learning model to predict their activity, showing strong correlation with experimental results.

The paper identifies divergent ribosomal RNA sequences in the PTC of archaea and determines their structure, revealing sequence variation and a novel hibernation factor.

This study investigates the molecular interactions of eIF2β with eIF5, eIF2B, and 5MP1 using crystallography and NMR, revealing binding sites and regulatory roles of CK2 phosphorylation.

This study identifies phosphorylation sites in LeishIF4E1 and shows that phosphorylation modulates its protein and transcript interactions, extending its role beyond translation initiation.

The paper examines the distribution of rRNA gene copies in prokaryotic genomes, finding that normalized range varies with copy number, phylum, and genomic features, suggesting different mechanisms in bacteria and archaea.