RNA and protein synthesis mechanisms

This study identifies unmodified EF-P variants from Rhodomicrobium vannielii that restore function in E. coli lacking EF-P modifications, revealing design principles for polyproline synthesis.

This study identifies Dbp10/DDX54's role in forming the peptidyl transferase center during 60S ribosome biogenesis using cryo-EM.

This study identifies two distinct B12 riboswitches in M. tuberculosis that regulate different operons through unique structural and regulatory mechanisms.

This study identifies RimP as a ribosome assembly factor in Salmonella that contributes to streptomycin resistance and motility impairment.

The paper uses cryo-EM and structure prediction to analyze new configurations of the ribosome-translocon complex, revealing dynamic interactions during protein biogenesis.

The paper identifies TAOK2β as a regulator of translational elongation and shows its disruption leads to increased protein synthesis in an ASD mouse model.

The paper introduces BASH MaP and DAGGER to identify alternative tertiary structures of RNA, revealing conformational dynamics in vitro and in cells.

This study identifies how ABCF proteins in E. coli alleviate noncanonical translations caused by specific nascent peptide sequences.

This paper introduces a language model for 5' UTRs that improves predictions of translation efficiency and mRNA expression, and validates novel 5' UTR designs through wet-lab experiments.

This paper introduces eaDCA, a sparse generative model for RNA families that efficiently predicts functional sequences and mutation effects, showing comparable performance to complex methods with fewer parameters.

This paper benchmarks nine RNA 3D structure prediction methods using the RNA-Puzzles dataset and provides an online dashboard for their predictions.

The paper investigates how downstream RNA structures influence non-AUG translation initiation in eukaryotes and identifies genome-wide alternative initiation sites in humans.

The paper identifies sequence motifs that trigger co-translational mRNA decay in yeast using a massively parallel reporter assay and shows their predictive power for endogenous sequences.

The paper maps temperature-dependent conformational free energy landscapes of homopolymeric RNAs using simulations and deep learning, revealing base-specific phase separation propensities.

The paper identifies novel bacterial arrest peptides associated with protein localization machinery through domain-wide searches and phylogenetic analysis, revealing their widespread distribution and evolutionary significance.

The paper shows that salt concentration affects RNA self-association rates and yields through changes in free energy gaps, with implications for repeat RNA aggregation.

This study shows ribosomes in E. coli are not entirely excluded from the nucleoid, with some located in a central void, suggesting dynamic localization for efficient translation.

This study identifies a direct interaction between eIF4G and the 40S ribosomal subunit, independent of eIF3, and shows that the eIF4G-RBD enhances translation without requiring m7G cap or mRNA tethering.

This paper identifies a novel pathway for mnm5s2U synthesis in Gram-positive bacteria, revealing alternative biosynthetic mechanisms involving the MnmL enzyme.

comradesOO is an R package for analyzing RNA structure data from COMRADES experiments, providing tools for processing, clustering, and comparing RNA structures and interactions.

The paper introduces RNA3DB, a dataset of structured RNAs designed for training and benchmarking deep learning models, with non-redundant sequence and structure splits to improve generalization.

This study investigates how pseudoknot base pairing affects cotranscriptional structural switching in fluoride riboswitches, showing a critical wobble base pair is essential for function across different temperatures.

This study investigates the conformational dynamics of the guanidine-IV riboswitch using single-molecule techniques, revealing its ligand-response mechanism and transcriptional sensitivity.

The paper identifies a stem-loop and modified adenines in the uORF2/ATF4 overlap that regulate ATF4 translation under stress, revealing a more complex mechanism than previously thought.

This study identifies sequence and structural features in the JUN 5' UTR that regulate translation, showing the involvement of eIF4A and multiple start codons.

The paper maps tRNA modifications and their synthesis genes in two Bartonella species, identifying gene reductions linked to reductive evolution.

This paper demonstrates that dried cell-free protein synthesis reactions can withstand harsh conditions during polymer casting, enabling the creation of functional materials with spatially patterned genetic capabilities.

The paper presents high-resolution cryo-EM structures of wheat ribosomes and identifies unique features compared to other eukaryotes.

The paper validates a cell-free protein synthesis platform in microgravity by testing biosensors for small molecules and RNA sequences aboard the International Space Station.

Riboformer predicts context-dependent translation dynamics using deep learning, correcting artifacts and identifying sequence motifs affecting ribosome stalling.