RNA and protein synthesis mechanisms

The paper constructs non-standard genetic codes in vitro and shows that mutational robustness of reporter proteins remains similar despite changes in genetic code, supporting the error minimization theory.

The paper identifies genes near tRNAs in fungal genomes that are enriched in proteasome regulation, ion transport, and rRNA, suggesting local co-regulation of protein synthesis and quality control.

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 identifies benzoxaboroles as selective binders of eIF4E, revealing stereoselective interactions and structural insights into their binding mechanism.

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.

The paper investigates how the Kozak sequence is recognized during eukaryotic translation initiation using cryo-EM structures, revealing an induced-fit mechanism involving conformational changes in mRNA, rRNA, and initiation factors.

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.

RAFTER quantifies mRNA translation by labeling efficiently translated RNAs with an RNA editing enzyme and releasing factor, showing correlation with Ribo-seq and Polysome-seq but with a simpler workflow enabling single-cell analysis.

The paper profiles terminating ribosomes to show sequence-dependent pausing at stop codons and its impact on translation fidelity and protein diversity.

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 study characterizes the ribosomal exit tunnel's functional complexity across species using molecular dynamics simulations, revealing dynamic changes and lineage-specific features.

This study uses a noncanonical amino acid to label stress granule and TDP-43 proteins with minimal disruption, showing accurate localization and dynamics in live cells.

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.

The paper examines changes in chloroplast ribosomes during evolution from cyanobacteria to land plants, identifying structural features and protein modifications.

The paper shows that CodonBERT and ESM-2 embeddings encode synonymous codon information through a shared geometric relationship across species.

The paper quantifies amino acid substitution rates in E. coli, finding no significant differences in overall translation error rates among ribosomal variants but unique mistranslation profiles.

This paper identifies FDA-approved drugs that modulate SARS-CoV-2 -1 PRF by altering RNA pseudoknot folding dynamics, demonstrating a strategy for targeting structured RNAs.

The paper presents cryo-EM structures of the naked mole-rat ribosome, revealing a stabilized split 28S rRNA and its structural context.

This study identifies eIF3d as essential for cholesterol biosynthesis required for KSHV lytic replication, showing its role in supporting translation of cholesterol-related host mRNAs.

This study shows that GIGYF2/4EHP-mediated translational repression helps maintain cellular homeostasis after ionizing radiation by preserving proteostasis and cell viability.

The paper uses optogenetic stimulation and Ribo-seq in Drosophila to show that neuronal activity triggers two phases of translation: one for synaptic factors and another for ribosomal proteins, regulated by TOP motifs and La-related protein.

The paper shows short RNAs can form complex structures like icosahedrons and filaments, expanding the known RNA quaternary structures and supporting RNA-based self-assembly in an RNA world.

seq2ribo predicts ribosome location profiles from RNA sequences using a hybrid simulation and machine learning approach, achieving high correlation with experimental data.