Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Structural insights into dynamics of the BMV TLS aminoacylation

ABSTRACT: We performed Biotinylated RNA pull-down coupled with mass spectrometry, which enables the identification of TLS-binding proteins. Using in vitro synthesized BMV TLS and protein extracts derived from Nicotiana tabacum L.'s leaves, mass spectrometry results demonstrated the enrichment of ribosome-associated proteins

ORGANISM(S): 'nicotiana Tabacum' Yellowing Phytoplasma

SUBMITTER: Kaiming Zhang

PROVIDER: PXD057815 | iProX | Wed Nov 13 00:00:00 GMT 2024

REPOSITORIES: iProX

ACCESS DATA

Json Xml

Publications

Structural insights into dynamics of the BMV TLS aminoacylation.

Yang Wen W Yi Ran R Yao Jing J Gao Yongxiang Y Li Shanshan S Gong Qingguo Q Zhang Kaiming K

Nature communications 20250203 1

Brome Mosaic Virus (BMV) utilizes a tRNA-like structure (TLS) within its 3' untranslated region to mimic host tRNA functions, aiding aminoacylation and viral replication. This study explores the structural dynamics of BMV TLS interacting with tyrosyl-tRNA synthetase (TyrRS) during aminoacylation. Using cryo-EM, we capture multiple states of the TLS-TyrRS complex, including unbound TLS, pre-1a, post-1a, and catalysis states, with resolutions of 4.6 Å, 3.5 Å, 3.7 Å, and 3.85 Å, respectively. These ...[more]

PMID: 39900568

Similar Datasets

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

Project description:Ribosome-footprint profiling provides genome-wide snapshots of translation, but technical challenges can confound its analysis. Here, we use improved methods to obtain ribosome-footprint profiles and mRNA abundances that more faithfully reflect gene expression in Saccharomyces cerevisiae. Our results support proposals that both the beginning of coding regions and codons matching rare tRNAs are more slowly translated. They also indicate that emergent polypeptides with as few as three basic residues within a 10-residue window tend to slow translation. With the improved mRNA measurements, the variation attributable to translational control in exponentially growing yeast was less than previously reported, and most of this variation could be predicted with a simple model that considered mRNA abundance, upstream open reading frames, cap-proximal structure and nucleotide composition, and lengths of the coding and 5'-untranslated regions. Collectively, our results provide a framework for executing and interpreting ribosome-profiling studies and reveal key features of translational control in yeast. Ribosome-footprint profiling and RNA-seq (total RNA, poly(A) selected, RiboMinus treated, or Ribo-Zero treated) from log-phase S. cerevisiae. The study includes a reanalysis of the two Samples from GSE53313. The reanalyzed data is linked to the Series record.

2016-02-10 | E-GEOD-75897 | biostudies-arrayexpress

Structural basis of ribosomal frameshifting during translation of the SARS-CoV-2 RNA genome

Project description:Programmed ribosomal frameshifting is the key event during translation of the SARS-CoV-2 RNA genome allowing synthesis of the viral RNA-dependent RNA polymerase and downstream viral proteins. Here we present the cryo-EM structure of the mammalian ribosome in the process of translating viral RNA paused in a conformation primed for frameshifting. We observe that the viral RNA adopts a pseudoknot structure lodged at the mRNA entry channel of the ribosome to generate tension in the mRNA that leads to frameshifting. The nascent viral polyprotein that is being synthesized by the ribosome paused at the frameshifting site forms distinct interactions with the ribosomal polypeptide exit tunnel. We use biochemical experiments to validate our structural observations and to reveal mechanistic and regulatory features that influence the frameshifting efficiency. Finally, a compound previously shown to reduce frameshifting is able to inhibit SARS-CoV-2 replication in infected cells, establishing coronavirus frameshifting as target for antiviral intervention.

2021-05-17 | GSE167421 | GEO

Structural Insights into tRNA Dynamics on the Ribosome.

Project description:High-resolution structures at different stages, as well as biochemical, single molecule and computational approaches have highlighted the elasticity of tRNA molecules when bound to the ribosome. It is well acknowledged that the inherent structural flexibility of the tRNA lies at the heart of the protein synthesis process. Here, we review the recent advances and describe considerations that the conformational changes of the tRNA molecules offer about the mechanisms grounded in translation.

| S-EPMC4463622 | biostudies-literature

Structural insights on the dynamics of proteasome formation.

Project description:Molecular organization in biological systems comprises elaborately programmed processes involving metastable complex formation of biomolecules. This is exemplified by the formation of the proteasome, which is one of the largest and most complicated biological supramolecular complexes. This biomolecular machinery comprises approximately 70 subunits, including structurally homologous, but functionally distinct, ones, thereby exerting versatile proteolytic functions. In eukaryotes, proteasome formation is non-autonomous and is assisted by assembly chaperones, which transiently associate with assembly intermediates, operating as molecular matchmakers and checkpoints for the correct assembly of proteasome subunits. Accumulated data also suggest that eukaryotic proteasome formation involves scrap-and-build mechanisms. However, unlike the eukaryotic proteasome subunits, the archaeal subunits show little structural divergence and spontaneously assemble into functional machinery. Nevertheless, the archaeal genomes encode homologs of eukaryotic proteasome assembly chaperones. Recent structural and functional studies of these proteins have advanced our understanding of the evolution of molecular mechanisms involved in proteasome biogenesis. This knowledge, in turn, provides a guiding principle in designing molecular machineries using protein engineering approaches and de novo synthesis of artificial molecular systems.

| S-EPMC5899738 | biostudies-literature

Improved ribosome-footprint and mRNA measurements provide insights into dynamics and regulation of yeast translation

2016-02-10 | GSE75897 | GEO

Structural insights into intron catalysis and dynamics during splicing.

Project description:The group II intron ribonucleoprotein is an archetypal splicing system with numerous mechanistic parallels to the spliceosome, including excision of lariat introns1,2. Despite the importance of branching in RNA metabolism, structural understanding of this process has remained elusive. Here we present a comprehensive analysis of three single-particle cryogenic electron microscopy structures captured along the splicing pathway. They reveal the network of molecular interactions that specifies the branchpoint adenosine and positions key functional groups to catalyse lariat formation and coordinate exon ligation. The structures also reveal conformational rearrangements of the branch helix and the mechanism of splice site exchange that facilitate the transition from branching to ligation. These findings shed light on the evolution of splicing and highlight the conservation of structural components, catalytic mechanism and dynamical strategies retained through time in premessenger RNA splicing machines.

| S-EPMC10733145 | biostudies-literature

Structural insights into dynamics of the BMV TLS aminoacylation.

Project description:Brome Mosaic Virus (BMV) utilizes a tRNA-like structure (TLS) within its 3' untranslated region to mimic host tRNA functions, aiding aminoacylation and viral replication. This study explores the structural dynamics of BMV TLS interacting with tyrosyl-tRNA synthetase (TyrRS) during aminoacylation. Using cryo-EM, we capture multiple states of the TLS-TyrRS complex, including unbound TLS, pre-1a, post-1a, and catalysis states, with resolutions of 4.6 Å, 3.5 Å, 3.7 Å, and 3.85 Å, respectively. These structural comparisons indicate dynamic changes in both TLS and TyrRS. Upon binding, TLS undergoes dynamic rearrangements, particularly with helices B3 and E pivoting, mediated by the unpaired A36 residue, ensuring effective recognition by TyrRS. The dynamic changes also include a more compact arrangement in the catalytic center of TyrRS and the insertion of 3' CCA end into the enzyme's active site, facilitating two-steps aminoacylation. Enzymatic assays further demonstrated the functional importance of TLS-TyrRS interactions, with mutations in key residues significantly impacting aminoacylation efficiency. Furthermore, Electrophoretic Mobility Shift Assay (EMSA) demonstrated that BMV TLS binds elongation factors EF1α and EF2, suggesting a multifaceted strategy to exploit host translational machinery. These findings not only enhance our knowledge of virus-host interactions but also offer potential targets for antiviral drug development.

| S-EPMC11791061 | biostudies-literature

Insights into POT1 structural dynamics revealed by cryo-EM.

Project description:Telomeres are protein-DNA complexes that protect the ends of linear eukaryotic chromosomes. Mammalian telomeric DNA consists of 5'-(TTAGGG)n-3' double-stranded repeats, followed by up to several hundred bases of a 3' single-stranded G-rich overhang. The G-rich overhang is bound by the shelterin component POT1 which interacts with TPP1, the component involved in telomerase recruitment. A previously published crystal structure of the POT1 N-terminal half bound to the high affinity telomeric ligand 5'-TTAGGGTTAG-3' showed that the first six nucleotides, TTAGGG, are bound by the OB1 fold, while the adjacent OB2 binds the last four, TTAG. Here, we report two cryo-EM structures of full-length POT1 bound by the POT1-binding domain of TPP1. The structures differ in the relative orientation of the POT1 OB1 and OB2, suggesting that these two DNA-binding OB folds take up alternative conformations. Supporting DNA binding studies using telomeric ligands in which the OB1 and OB2 binding sites were spaced apart, show that POT1 binds with similar affinities to spaced or contiguous binding sites, suggesting plasticity in DNA binding and a role for the alternative conformations observed. A likely explanation is that the structural flexibility of POT1 enhances binding to the tandemly arranged telomeric repeats and hence increases telomere protection.

| S-EPMC8853558 | biostudies-literature

Structural characterization of ribosome variants

Project description:Structural characterization of ribosome variants

| PRJNA414663 | ENA

Ribosome profiling of polysomes from mouse brains

Project description:We performed ribosome profiling of polysomes (Poly-RIBOseq) to monitor translation of RNAs associated with polysomes in brain extracts from a mouse model Keywords: ribosome profiling, translation, polysome profiling, Poly-RIBOseq

2018-07-13 | GSE102318 | GEO

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data