RNA and protein synthesis mechanisms

The paper demonstrates that bulk signals from processive enzyme reactions can be decomposed to reveal hidden information about individual reaction steps, using mRNA translation as a case study.

The paper shows that cytoplasmic lncRNAs in yeast are translated, affecting their abundance and post-transcriptional regulation through mechanisms involving NMD and ribosome binding.

This study identifies a mechanism by which RSV sequesters eIF4F initiation complex components into bi-phasic inclusion bodies to facilitate viral mRNA translation.

AutoRNC generates atomic models of ribosome-nascent chain complexes by sampling dipeptide conformations from RCSB, matching experimental data and enabling hypothesis generation for protein folding studies.

This study investigates RNA structure in Candida pathogens using genome-wide probing, revealing structural conservation, SNP impacts, and conserved hairpin features in lncRNAs.

The paper investigates sequence, structure, and functional features of SINE-derived RNAs in SINEUP non-coding RNAs, showing their role in post-transcriptional gene regulation through interactions with RBPs and ribosomal RNAs.

The paper shows that specific codon usage patterns affect host fitness and gene expression, introducing a coding scheme called CHI to optimize multi-gene expression systems.

The paper identifies theta ribozymes in gut phages that associate with suppressor tRNAs, suggesting a role in regulating phage assembly through RNA-based mechanisms.

The paper develops a mechanistic model to examine how ribosome composition affects growth rate, finding that RNA instability and protein protection influence optimal ribosome composition.

This study introduces a method to assemble ssRNA structures using hierarchical chain growth, showing agreement with experimental data and improving accuracy with Bayesian refinement.

This study identifies small RNAs from mitochondrial recombination sites in T. gondii that are integrated into mitoribosomes, suggesting a dual role for mitochondrial sequences as both mRNA and rRNA.

This study identifies how antiviral resistance mutations in Enterovirus-A71 alter RNA structure and interactions, revealing mechanisms of DMA-135 action and viral resistance.

This study identifies YfmR as a translation factor essential for preventing ribosome stalling and cell death in B. subtilis when EF-P is absent.

This study identifies Nsp1's role in enhancing SARS-CoV-2 translation by interacting with EIF1A, leading to reduced viral titers when EIF1A is depleted.

This paper develops cell-free transcription-translation systems in three soil Pseudomonads, demonstrating their ability to characterize and engineer biological parts without genome integration.

The paper shows that puromycylated peptides remain in neuronal ribosomes in a hybrid state, revealing a distinct conformation and stalling mechanism in neurons.

The paper optimizes DNA codons in Ebola virus genes to improve expression, resulting in higher codon adaptation index and GC content without producing truncated proteins.

The paper identifies that Mucorales fungi use a sealing-only tRNA ligase, implying that targeting sealing activity could lead to broader-spectrum antifungals.

The paper develops a model to predict alternative translation initiation sites in plants, revealing conserved cis-regulatory codes across eukaryotes and viruses.

This paper shows that mutations in ribosomal protein genes suppress temperature sensitivity in S. pombe tRNA modification mutants by reducing ribosome concentrations, thereby decreasing tRNA demand and GAAC activation.

RNAvigate provides a Python library for efficiently exploring RNA chemical probing datasets through automated parsing and visualization of diverse structural and functional data.

This paper describes a dual-selection system using T7 phage to evolve functional theophylline riboswitches by alternating selection pressures in ON and OFF states.

The paper describes the structure of a human 48S initiation complex, revealing a second eIF4A helicase at the mRNA entry site that unwinds secondary structure downstream of the scanning complex.

This study investigates eIF4F complex function and structure in human cancers, finding frequent gene amplifications and revealing structural mechanisms for cap-dependent and cap-independent translation initiation.

RNAdvisor benchmarks RNA structural model quality by integrating metrics and scoring functions to evaluate 3D structure predictions.

This paper reports the cryo-EM structure of the mycobacterial 70S ribosome complexed with RafH, revealing unique mechanisms of ribosome hibernation in mycobacteria.

This study uses Rec-Seq to show Ded1 promotes 48S PIC formation on mRNAs with long 5UTRs and that eIF4A is required for PIC assembly on all mRNAs.

The paper examines RQC gene expression and phenotypes across human tissues, finding widespread expression and mild effects of RQC silencing, with TCF25 showing mRNA-protein discordance due to proteasomal degradation.

The paper shows that GADD34, an Integrated Stress Response effector, is used by neurons to enhance eIF2-dependent translation in response to BDNF stimulation.

The paper describes the design and characterization of mini-PTC 1.1, a minimal ribosomal PTC RNA optimized through community science and RNA structural analysis.