RNA and protein synthesis mechanisms

This paper expands the genetic code of C. elegans to incorporate two non-canonical amino acids using orthogonal tRNA-synthetase pairs and photocaged amino acids, enabling optical control of gene expression.

This study identifies the Archaeal Ribosome regulatory Complex (ARC) as a dual-factor complex that modulates ribosome hibernation in response to energy status.

This paper identifies a cytoplasmic role for NRMT1 in regulating translation by interacting with ribosomal subunits and affecting mRNA selection in C2C12 mouse myoblasts.

Struct2SeQ uses deep Q-learning to design RNA sequences that fold into target structures and match SHAPE reactivity constraints, outperforming humans and existing methods.

The paper shows hidden stop codons promote mRNA decay by causing ribosomal frameshifting in fungi and human cells, disrupting circadian rhythms and stabilizing mRNAs with nonoptimal codons.

The paper investigates how amino acid limitation affects translation by analyzing ribosome stalling and the role of RQC pathways and RNF14 in response to arginine depletion.

The paper shows that decreased tRNA abundance reduces translation elongation during mitosis, leading to reduced protein synthesis.

The paper identifies an IRES-mediated cap-independent translation mechanism for NbRabGAP1 during BaMV infection, facilitated by NbPAB8 binding to a purine-rich R-motif in the 5' UTR.

The paper develops mRNAbow, a system for generating low-toxicity mRNAs for multiplexed fluorescent imaging in diverse cellular and organismal systems.

This study characterizes RlaP family nucleotidyltransferases from Pseudomonas species, showing they repair damaged RNAs by adding nucleotides and are essential for RNA function restoration.

This study shows linear mRNAs can undergo backward translation in vitro, producing signals comparable to forward translation, and demonstrates the potential of backward translation in synthetic biology.

The paper identifies missing steps in mitochondrial translation initiation in plants using cryogenic electron microscopy.

The paper describes a Kaggle competition for RNA 3D structure prediction, showing that template-based methods can outperform deep learning approaches.

The paper shows that nascent polypeptide feedback triggers ribosomal frameshifting and transcript decay through specific motifs and splicing events.

This paper introduces OPENER, an engineered eRF1 variant that suppresses nonsense mutations and enables nonstandard amino acid incorporation, showing therapeutic benefits in a Duchenne muscular dystrophy model.

The paper introduces mRNA-GPT, a generative mRNA language model trained on sequences from bacteria, eukaryotes, and archaea, showing improved translation efficiency and stability in mRNA design.

This study investigates how two structurally similar ligands, 4EGI-1 and i4EG-BiP, regulate eIF4E through distinct binding modes, revealing that frontal binding promotes 4E-BP1 over eIF4G interaction.

This study develops an orthogonal translation initiation system using an i-tRNA-AAC mutant and evaluates its physiological impact through fluorescence assays, proteomics, and tRNA sequencing.

This study identifies montanine as a potent antiviral compound that inhibits RNA viruses by targeting translational elongation and GCN1-related stress responses.

This study shows that codon usage changes with longevity in mammals, with some codons favoring optimal translation and others slowing translation to aid protein folding, contributing to proteostasis and reduced aging.

The paper demonstrates that the PURE cell-free system can be reconstituted from non-ribosomal proteins synthesized by the system itself.

The paper identifies translational repression of 5' TOP mRNAs in exhausted human CD8+ T cells despite elevated mTOR activity.

The paper introduces an efficient RNA folding model that accurately simulates RNA hairpin unfolding and reproduces experimental thermodynamic properties.

The paper introduces cfRNA-ICL, a model trained on synthetic data generated from a biologically grounded SCM, showing improved performance in cancer classification tasks compared to generic models.

This study identifies VARS1 as a driver of prostate cancer progression by altering codon usage in translation, showing that targeting VARS1 can suppress tumor growth through dietary valine restriction or inhibitors.

This study uses nanopore sequencing to identify operon-specific ribosome remodeling in Staphylococcus aureus resistant to naphthyridone antibiotics.

The paper analyzes ribosome profiling and RNA-seq data to show that translation efficiency in yeast changes during heat shock, differing from bacterial responses.

This study identifies tRNA halves and fragments (tsRNAs) in Escherichia coli, showing their association with 30S ribosomal subunits and cytosol, and their generation during translation arrest.

This paper introduces gRNAde, an RNA language model for inverse design of RNA structure and function, achieving success rates comparable to human experts in designing pseudoknotted RNAs.

The paper introduces SPARP-seq, a method combining poly(A) assessment and ribosome profiling to show poly(A) tail shortening is a hallmark of active translation in human cells.