RNA and protein synthesis mechanisms

RNArank assesses RNA 3D structure model quality using deep learning and intermediate 2D maps, outperforming existing methods in benchmark tests.

The paper evaluates six mechanistic models of SAM-II riboswitch folding under varying SAM and magnesium concentrations, finding one model accurately predicts experimental data and reveals the most efficient mechanism.

This study examines how HCMV and SARS-CoV-2 affect the human tRNA pool and finds HCMV alters tRNA expression and modifications, while SARS-CoV-2 does not, with implications for viral codon usage and host-virus interactions.

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.

The paper shows that the ribosome coordinates folding and assembly of a complex protein to enable efficient biogenesis.

ColiFormer improves E. coli gene expression by balancing multiple codon optimization objectives using a transformer model, outperforming existing methods in CAI, tAI, and cis-regulatory element reduction.

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 that 2'-O-methylation alters ribozyme active site geometries and reaction mechanisms, challenging assumptions about its role in stabilizing pre-catalytic conformations.

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 identifies Sni445 as a novel factor that recruits snR4 and snR45 snoRNPs to 90S pre-ribosomes, enabling Kre33-mediated acetylation of 18S rRNA.

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

The paper develops a mathematical model of translation incorporating tRNA dynamics and re-charging to show that codon usage optimizes protein synthesis depending on tRNA availability.

The paper shows that New1 prevents ribosomal collisions and subsequent mRNA degradation in yeast by no-go decay, protecting essential genes from downregulation.

This study identifies TlyA as an rRNA methyltransferase critical for ribosome assembly in B. subtilis, showing its role in cold sensitivity and antibiotic resistance.

The paper implements a Ribo-BiFC method in plant systems using split mVenus to visualize translational rate and study translation dynamics in Arabidopsis thaliana.

ADAM-tRNA-seq improves demultiplexing and mapping accuracy in direct tRNA sequencing by addressing sequence similarity and multimapping issues.

This paper evaluates deep learning methods for RNA secondary structure prediction, highlights generalization challenges, and discusses integration with traditional methods.

The paper shows how mimiviruses create a subcellular environment to overcome codon-tRNA mismatch by localizing viral mRNAs and proteins at the periphery of a viral factory.

The paper compares ribosome structures of naked mole-rats, tuco-tucos, and guinea pigs, finding fragmented 28S rRNA in the former with potential links to high translational fidelity.

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 mixed-material models and dynamic programming algorithms for analyzing equilibrium base-pairing properties of nucleic acid systems containing RNA, DNA, and 2'OMe-RNA strands.

This paper demonstrates codon compression of the Chlamydomonas chloroplast genome to 51 codons without affecting chloroplast function or photosynthetic growth.

The paper evaluates codon usage bias in humans, showing its association with biological processes, protein structure, and tRNA abundance, while disentangling mutational pressure from translational selection.

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

Dosa covalently bars proteins for high-throughput biochemical analysis by linking variants to RNA barcodes via a methyltransferase, enabling assessment of protein function through direct biochemical assays.

The paper uses molecular dynamics simulations to study RsmZ-RsmE interactions, revealing how RNA structure and linker regions affect binding affinities and informing the design of synthetic sRNAs.

PARSEbp improves RNA structure scoring by integrating pairwise agreement and base pairing consistency, outperforming existing methods on CASP16 targets.