RNA and protein synthesis mechanisms

This study identifies a pivotal aa-tRNA pivoting mechanism in human translation that enhances fidelity by navigating the constrained ribosomal accommodation corridor.

NucleicBERT is a self-supervised masked-language model for RNA that learns contextual representations without alignments or evolutionary data, outperforming existing models in structural and functional tasks.

This study shows that polysomes and mRNA organization control cytoplasmic biophysical properties by affecting diffusivity through translation inhibition and mRNA condensation.

The paper traces the evolutionary divergence of ribosomal drug-binding residues across eukaryotic clades to assess similarities and differences with humans and bacteria.

The paper tracks ribozyme population dynamics during in vitro selection using high-throughput sequencing data, revealing early convergence on catalytic strategies.

The paper improves orthogonal translation in yeast by enhancing a pyrrolysyl-tRNA synthetase system and identifies ribosomal protein deletions that increase non-canonical amino acid incorporation.

The paper analyzes tRNA gene variation across 17 closely related mouse strains to understand evolutionary dynamics and identifies conserved and strain-specific tRNA features.

The paper analyzes codon usage bias in WRKY genes of Musa acuminata to understand evolutionary patterns and resistance mechanisms.

This study identifies DKC1-mediated pseudouridylation of rRNA as essential for sustaining IRES-dependent translation and ATF4-driven metabolic adaptation in neuroblastoma.

The paper investigates the role of Mettl15 and Mettl17 in mitoribosome assembly, revealing their cooperative mechanism in transitioning from early to late stages of small subunit formation.

This study shows that the C-terminal lobe of calmodulin can fully activate eEF-2K independently of Ca2+ and external CaM, revealing a unique activation mechanism.

GEMORNA generates mRNA sequences with enhanced translation capacity and stability, showing significant improvements in expression levels and therapeutic applications.

The paper studies cotranslational folding and autoproteolytic processing of HIV-1 protease during viral particle assembly.

This paper develops a competitive binding HTS assay to identify small molecule ligands for bacterial PreQ1 riboswitches, discovering 4 hits with activity against multiple riboswitches and one showing translation inhibition.

The paper shows that mitotic arrest in cancer cells enhances uORF/uoORF translation, leading to increased immunopeptide presentation and T-cell mediated killing.

The paper uses cryo-electron tomography to reveal structural insights into ribosome hibernation in microsporidian spores, showing ribosome dimers arranged in ordered arrays around the polar tube.

This study develops a tRNA array method to simultaneously express all 21 tRNAs in vitro, supporting translation and genetic code engineering.

RNAJog optimizes RNA sequences for multiple objectives using autoregressive reinforcement learning, achieving faster performance and improved vaccine design outcomes.

The paper shows that purine bias in bacterial genes prevents premature transcription termination by evading Rho-dependent termination, leading to biased codon usage in species with runaway transcription.

The paper reveals a temporal control mechanism driven by coupled ribosomes that enables the formation of intertwined protein dimers by bypassing closed monomeric states.

This study identifies Levipalatum texanum as a eukaryote lacking tRNA introns and the tRNA splicing endonuclease, revealing adaptations to this loss.

ProtRNA transfers knowledge from protein language models to RNA using cross-modality transfer learning, achieving comparable or better performance with less data and parameters.

This paper introduces a method to simultaneously measure tRNA sequence, modification, and aminoacylation using nanopore sequencing and machine learning.

This paper presents a method for high-yield, low magnesium flexizyme reactions in a water-ice eutectic phase, improving product stability and reducing Mg(II) carryover.

The paper determines cryo-EM structures of E. histolytica ribosomes, revealing unique features like an RNA triple helix and co-evolved rRNA expansion segments.

This study identifies suitable tRNA sources for cell-free protein synthesis by evaluating tRNA pools from different E. coli strains and V. natriegens, finding that A19 tRNAs are most effective for in vitro translation.

This study investigates how RNase A and RNase 1 cleave pseudouridine and its derivatives, finding that UpA is cleaved more efficiently than {Psi}pA or m1{Psi}pA.

ARCADE enables flexible, controllable codon design using activation engineering from genomic language models to steer biological metrics like Codon Adaptation Index and GC content.

The paper analyzes >12,000 bacterial genomes to study the conservation and evolution of the programmed ribosomal frameshift in prfB, finding it was present in the last common ancestor of bacteria and linked to stop codon usage.

The paper analyzes RNA secondary structures to determine if they show signs of positive selection, finding they are mostly random but shaped by developmental bias.