Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Unexpected role of a truncated ribosome-associated chloroplast trigger factor homolog serving ribosome biogenesis in plants - Data set 1 (Global proteome of wt and tig2 mutants)

ABSTRACT: Molecular chaperones are essential throughout a protein's life and act already during protein synthesis. Bacteria and chloroplasts of plant cells share the ribosome-associated chaperone trigger factor (Tig1 in plastids), facilitating maturation of emerging nascent polypeptides. While typical trigger factor chaperones employ three domains for their task, we identified a truncated form, Tig2, containing just the ribosome binding domain. Tig2 is predominantly found within higher-evolved photosynthetic species and appears to have acquired an entirely different tasks than co-translational folding. Tig2 deletion results in remarkable leaf developmental defects of cold-exposed Arabidopsis thaliana plants. Our data indicate that Tig2 functions during ribosome assembly, specifically promoting the hidden break formation within the 23S rRNA, the final step of chloroplast ribosome biogenesis. We hypothesize that Tig2 binding to the tunnel-exit surface serves protecting this sensitive surface during ribosome assembly, illustrating a fascinating concept of how similar chaperone domains have evolved for different molecular tasks.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Arabidopsis Thaliana (mouse-ear Cress)

TISSUE(S): Cell Culture

SUBMITTER: Markus Räschle

LAB HEAD: Markus Räschle

PROVIDER: PXD057252 | Pride | 2024-12-09

REPOSITORIES: pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	20220104_HF1_MaRa_SA_P0142_01.raw	Raw
	20220104_HF1_MaRa_SA_P0142_02.raw	Raw
	20220104_HF1_MaRa_SA_P0142_03.raw	Raw
	20220104_HF1_MaRa_SA_P0142_04.raw	Raw
	20220104_HF1_MaRa_SA_P0142_05.raw	Raw

Items per page:

1 - 5 of 50

Similar Datasets

Unexpected role of a truncated ribosome-associated chloroplast trigger factor homolog serving ribosome biogenesis in plants - Data set 2: Analysis of sedimented ribosomes

Project description:Molecular chaperones are essential throughout a protein's life and act already during protein synthesis. Bacteria and chloroplasts of plant cells share the ribosome-associated chaperone trigger factor (Tig1 in plastids), facilitating maturation of emerging nascent polypeptides. While typical trigger factor chaperones employ three domains for their task, we identified a truncated form, Tig2, containing just the ribosome binding domain. Tig2 is predominantly found within higher-evolved photosynthetic species and appears to have acquired an entirely different tasks than co-translational folding. Tig2 deletion results in remarkable leaf developmental defects of cold-exposed Arabidopsis thaliana plants. Our data indicate that Tig2 functions during ribosome assembly, specifically promoting the hidden break formation within the 23S rRNA, the final step of chloroplast ribosome biogenesis. We hypothesize that Tig2 binding to the tunnel-exit surface serves protecting this sensitive surface during ribosome assembly, illustrating a fascinating concept of how similar chaperone domains have evolved for different molecular tasks.

2024-12-09 | PXD057264 | Pride

Mechanism of chaperone coordination during cotranslational protein folding in bacteria

Project description:Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally-distinct classes of chaperones promote de novo folding, suggesting that their activity is coordinated at the ribosome. Here we use biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We find that chaperone binding is disfavoured close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor subsequently recognises compact folding intermediates exposing extensive non-native surface and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates, and recruits DnaK to solvent-accessible sites in a sequence non-specific manner. Neither Trigger factor, DnaJ nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to create a protected space for protein maturation that extends well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.

2024-07-03 | PXD048638 | Pride

Mechanism of chaperone coordination during cotranslational protein folding in bacteria

2024-07-03 | PXD048645 | Pride

Mechanism of chaperone coordination during cotranslational protein folding in bacteria

2024-07-03 | PXD048642 | Pride

Mechanism of chaperone coordination during cotranslational protein folding in bacteria

Project description:Protein folding is assisted by molecular chaperones that bind nascent polypeptides during mRNA translation. Several structurally-distinct classes of chaperone promote de novo folding, suggesting that their activities are coordinated at the ribosome. We used biochemical reconstitution and structural proteomics to explore the molecular basis for cotranslational chaperone action in bacteria. We found that chaperone binding is disfavoured close to the ribosome, allowing folding to precede chaperone recruitment. Trigger factor recognises compact folding intermediates exposing extensive unfolded surface and dictates DnaJ access to nascent chains. DnaJ uses a large surface to bind structurally diverse intermediates, and recruits DnaK to sequence-diverse solvent-accessible sites. Neither Trigger factor, DnaJ nor DnaK destabilize cotranslational folding intermediates. Instead, the chaperones collaborate to protect incipient structure in the nascent polypeptide well beyond the ribosome exit tunnel. Our findings show how the chaperone network selects and modulates cotranslational folding intermediates.

2024-07-03 | PXD048623 | Pride

Selective ribosome profiling reveals the co-translational chaperone action of trigger factor in vivo

Project description:As nascent polypeptides exit ribosomes, they are engaged by a series of processing, targeting and folding factors. Here we present a selective ribosome profiling strategy that enables global monitoring of when these factors engage polypeptides in the complex cellular environment. Studies of the Escherichia coli chaperone Trigger Factor (TF) reveal that, while TF can interact with many polypeptides, Î²-barrel outer membrane proteins are the most prominent substrates. Loss of TF leads to broad outer membrane defects and premature, cotranslational protein translocation. While in vitro studies suggested that TF is prebound to ribosomes waiting for polypeptides to emerge from the exit channel, we find that in vivo TF engages ribosomes only after ~100 amino acids are translated. Moreover, excess TF interferes with cotranslational removal of the N-terminal formyl methionine. Our studies support a triaging model in which proper protein biogenesis relies on the fine-tuned, sequential engagement of processing, targeting ad folding factors. Examination of translation in the Gram-negative bacterium Escherichia coli, as well as an analysis of the interactions between nascent chains and the molecular chaperone Trigger Factor.

2011-12-09 | E-GEOD-33671 | biostudies-arrayexpress

Bacterial RF3 Senses Chaperone Function in Co-translational Folding

Project description:Molecular chaperones assist in protein folding by interacting with nascent polypeptide chains (NCs) during translation, but whether the ribosome can sense chaperone defects and abort translation of misfolding NCs has not been explored. Here we used quantitative proteomics in E. coli to investigate the ribosome-associated chaperone network and the consequences of its dysfunction. Trigger factor and the DnaK (Hsp70) system are the major NC-binding chaperones. HtpG (Hsp90), GroEL and ClpB contribute increasingly, when DnaK is deficient. Surprisingly, misfolding of NCs due to defects in co-translational chaperone function or amino acid analog incorporation, results in recruitment of the non-canonical release factor RF3 to the ribosome. RF3 then cooperates with RF2 in mediating premature chain termination of a subset of abundant NCs, allowing their efficient degradation. This function of RF3 reduces the accumulation of misfolded proteins. It is critical for proteostasis maintenance and cell growth under conditions of limited chaperone availability.

2022-12-09 | PXD025219 | Pride

Bacterial RF3 Senses Chaperone Function in Co-translational Folding

2021-05-28 | PXD022239 | Pride

RNA coimmunoprecipitations

Project description:Nascent polypeptides emerging from the ribosome during biogenesis can interact with many chaperones and protein homeostasis factors. The high sensitivity of RNA identification can be used to identify substrates of specific cotranslationally acting chaperones. Protein A-tagged (TAP-tag) chaperones associated with translating ribosomes were immunopurified by binding to magnetic IgG beads, washed, and chaperone complexes were eluted with TEV protease treatment. Immunopurified RNAs and total cell extract RNAs were isolated, reverse transcribed, coupled to Cy5 and Cy3 dyes, respectively, and comparatively hybridized to DNA microarrays Set of arrays that are part of repeated experiments

2013-04-05 | E-GEOD-45794 | biostudies-arrayexpress

Study of ribosome dynamics of rpl3[W255C] and its interactions with ribosome-associated chaperones

Project description:Proteostasis is a fundamental network of cellular pathways that ensures the optimal concentration and composition of correctly folded proteins within cells in normal and stress conditions. Among key components of this network are the molecular chaperones, which mediate protein folding but also act as modulators of protein synthesis. We have reported on a functional link between translation and de novo folding of proteins in the yeast Saccharomyces cerevisiae by uncovering a specific synthetic-lethal interaction between apparent unrelated mutant variants, the uL3[W255C] variant of the ribosomal protein uL3 and the null mutants of Zuo1 and Ssz1. Zuo1 and Ssz1 are components of the chaperone system named as ribosome-associated complex. Here, we performed a genome-wide analysis of ribosome dynamics by 5PSeq (Pelechano et al. 2015 PMID 26046441) in strains harbouring either wild-type uL3 or mutant uL3[W255C] in the presence or absence of Zuo1 or Ssz1. This method allows the study of ribosome dynamics, by sequencing 5’ phosphorylated mRNA co-translational degradation intermediates. Our results indicate that the rpl3[W255C] mutant is slightly impaired in translation elongation, defect that is significantly enhanced when combined with the deprivation of either Zuo1 or Ssz1.

2020-11-25 | GSE114899 | 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