RNA and protein synthesis mechanisms

A detailed molecular picture of protein folding during active translation

This study uses a hydrogen-deuterium pulse-labeling approach to reveal structural details of nascent polypeptide folding during translation and its kinetic coupling with translation.

Ribosomal Protein bL27 Protects Translating Ribosomes from tmRNA-SmpB

This study identifies bL27's role in preventing tmRNA from interfering with protein synthesis during trans-translation in bacteria.

Distribution-Constrained Optimization for Reliable ML-Guided 5'UTR Sequence Design

This paper introduces a constrained optimization method for designing 5'UTR sequences using deep learning models, ensuring candidates stay within a trust region defined by an OOD score based on KNN distance.

RiboRep: Replicate-Aware Cross-Modal Transformers for Codon-Resolved Ribosome Density Prediction

RiboRep predicts codon-resolved ribosome density by integrating RNA sequences and ribosome occupancy signals using a cross-modal transformer framework, achieving strong performance across multiple species.

Ribosomal Architecture and rRNA Modification Landscape in the Tick-Borne Parasite Babesia divergens

This study reports cryo-EM ribosome structures and rRNA modifications in Babesia divergens, revealing novel modifications with potential therapeutic implications.

Plant DNA Designer: A Computational Framework for Multi-Objective Codon Optimisation and Synthetic Gene Design in Crop Biotechnology

Plant DNA Designer optimizes synthetic gene design for crops by balancing multiple molecular objectives, outperforming existing tools in safety and GC content while maintaining moderate CAI.

Blocked transcription-translation complexes are rescued by transcript release followed by trans-translation

The paper shows that blocked transcription-translation complexes in bacteria are rescued by transcript release and trans-translation, allowing all components to be released.

Unlocking Your Programmable and Creative RNA Sequence Designer with RDiffusion

RDiffusion is a generative transformer model for RNA sequence design that outperforms baselines in success rate and diversity, and was used to design therapeutic miRNA mimics for osteoarthritis.

Impact of Coding Region Accessibility and Uridine Chemistry on Translation in mRNA-DNA Hybrid Origami

This study investigates how folding mRNA into a six-helix bundle affects translation, finding that only the start of the coding sequence needs to be accessible, and that modifications like 5-methoxyuridine and N1-methylpseudouridine influence translation levels.

Nitro Reduction-Based RNA Control and Ultrafast Release

This paper introduces a reversible RNA modification strategy using nitro reduction to control RNA function and release, applicable across various RNA types and contexts.

Translocon Remodeling Modulates Ribosomal Frameshifting and the Maturation of the Sindbis Virus Structural Polyprotein

The paper shows that translocon remodeling affects ribosomal frameshifting and viral polyprotein maturation in alphaviruses, reducing viral fitness.

A p32 family RNA editing factor acts in mitochondrial ribosome biogenesis

The paper identifies p22, a p32 family member, as essential for mitochondrial ribosome biogenesis in Trypanosoma brucei, revealing its dual role in RNA editing and mitoribosome assembly.

A sequence-to-function model to predict T7 transcription rates and redesign T7 expression systems with lowered production of immunogenic RNA byproducts

Human SRP Subunits Coordinate Protein Targeting and mRNA Quality Control

This study investigates the roles of individual SRP subunits in mRNA protection and protein targeting, revealing distinct functions of S- and Alu-domain subunits in human SRP.

Subcellularly Resolved 3D Translatome in Mouse Oocytes and Early Embryos

The paper profiles the subcellularly resolved 3D translatome in mouse oocytes and early embryos, revealing spatially controlled translation patterns and embryo asymmetry.

23S rRNA modifications stimulate catalytic activity and prevent the formation of alternative structures

This study shows that 23S rRNA modifications enhance ribosome catalytic activity by stabilizing the peptidyl transferase center structure and preventing alternative conformations.

Unbiased screen of human transcriptome reveals an unexpected role of 3'UTRs in translation initiation

The paper identifies 3'UTR sequences that promote cap-independent translation initiation in human mRNAs, revealing a new regulatory mechanism involving translation factors.

Development of a protein synthesis network at the sarco/endoplasmic reticulum in adult cardiac myocytes

The paper examines the relationship between the ER and SR in cardiac myocytes, finding that the SR becomes the primary site of protein synthesis in adult cells, while the ER retains specialized functions.

Estimating the evolutionary fitness of specific synonymous codon changes

The paper estimates the evolutionary fitness of all synonymous codon changes in Drosophila melanogaster using polymorphism data, finding weak but significant selection on codon usage.

Dimerization and Threonine-Dependent Stabilization Govern Human YRDC Catalysis

This study elucidates the mechanism of YRDC catalysis, showing that threonine stabilizes the enzyme and dimerization is critical for function, with disease-linked mutations disrupting these processes.

Mitochondrial RNA processing promotes translation by resolving structured precursor RNAs

The paper shows that FASTKD4-dependent processing of mitochondrial RNA junctions is required for efficient CYB translation by removing RNA structures that hinder mitoribosome engagement.

Ribo-ITP expands the translatome of limited input samples

Ribo-ITP identifies thousands of translons from low-input samples, revealing their regulatory roles and impact on cell growth.

Anticodon nucleotide modifications affect translational tuning by the ribosomal CAR surface

The paper investigates how anticodon nucleotide modifications affect translational tuning via interactions at the ribosomal CAR site.

Evolution of a core ribosomal innovation in octopus

The paper identifies a unique structural break in octopus ribosomal RNA that enhances translation fidelity and supports proteomic stability through RNA editing.

Programmable Edge-to-Edge Assembly of RNA Nanostructures

This paper introduces alphaKL, a new RNA connector that enables edge-to-edge assembly of RNA nanostructures, expanding their structural design space.

Integrative Ensemble Modeling reveals RNA conformations targetable by small molecules

This study uses integrative ensemble modeling to identify RNA conformations that can be targeted by small molecules, revealing ligandable sites not visible in static structures.

Maximizing the productivity of co-transcriptional in vitro transcription

This study optimizes co-transcriptional in vitro transcription (co-IVT) to achieve high mRNA yield and quality, reducing impurities and improving production efficiency for therapeutic applications.

SQUARNA: stem maximization for accurate de novo RNA secondary structure prediction

SQUARNA improves RNA secondary structure prediction by combining stem maximization with free energy minimization, outperforming existing methods including deep learning models.

Chloroplast-encoded small subunit extensions reshape the Chlamydomonas chlororibosome

The paper determines the structure of chlororibosomes in Chlamydomonas reinhardtii, revealing an additional arm domain on the small subunit composed of chloroplast-encoded extensions.

Structural characterization of ribosome recycling and fusidic acid inhibition in Staphylococcus aureus

The paper uses cryo-EM to characterize ribosome recycling and fusidic acid inhibition in Staphylococcus aureus, revealing structural insights into the mechanism of antibiotic action.