Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Fast and global reorganization of the chloroplast protein biogenesis network during heat acclimation

ABSTRACT: Heat waves caused by global warming severely challenge photosynthesis and hence plant biomass production, but the mechanisms of its adjustment, repair and biogenesis during heat acclimation are elusive. We provide a global and time-resolved insight, how these processes are modulated during heat acclimation in chloroplasts, revealing profound modulation of protein biogenesis. Ribosome profiling with Chlamydomonas reinhardtii showed early translational downregulation during synthesis of photosynthesis core antenna proteins, a response that is conserved in Nicotiana tabacum. Our data suggest that these early effects may be caused by reduced translocation of ribosomes synthesizing thylakoid proteins, and that later heat acclimation alleviates these effects. Analysis of the proteinaceous interactome of plastid ribosomes demonstrates widespread remodeling of ribosome-associated processes that could be responsible for the early translational impacts and subsequent acclimation responses. The role of chlorophyll metabolism, protein targeting, and assembly of photosystem complexes as co-translational bottlenecks during heat acclimation are discussed.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Chlamydomonas Reinhardtii

TISSUE(S): Cell Culture

SUBMITTER: Markus Räschle

LAB HEAD: Zuzana Storchova

PROVIDER: PXD024949 | Pride | 2022-01-06

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Similar Datasets

The proteomic inventory reveals the chloroplast ribosome as nexus within a diverse protein network

Project description:In plant cells, chloroplast gene expression is predominantly controlled through regulation of translation. Fine-tuning of protein synthesis is vital for plant development, acclimation to environmental challenges and for the assembly of major protein complexes such as the photosynthesis machinery. However, little is known about the degree and nature of the regulatory network, mainly due to challenges associated with the specific isolation of chloroplast ribosomes under conditions that also retain weak or transient interactions. Here, we established a ribosome affinity purification method, which enabled us to map the global interaction network of chloroplast ribosomes. Endogenously tagging a protein of the large or small subunit revealed not only interactors of the holo complex, but also preferential interactors of the two subunits. This includes known canonical regulatory proteins as well as several new proteins belonging to the categories of protein and RNA regulation, photosystem biogenesis, redox control and plastidic metabolism. By further characterizing identified proteins, we provide the first evidence for the existence of a co-translational N-acetyltransferase process in chloroplasts. Our dataset establishes the chloroplast ribosome as nexus in a highly choreographed, spatially interconnected protein network and reveals its wide-ranging regulatory potential during gene expression.

2021-01-04 | PXD020377 | Pride

The proteomic inventory reveals the chloroplast ribosome as nexus within a diverse protein network - Effect of Crosslinking

Project description:In plant cells, chloroplast gene expression is predominantly controlled through regulationof translation. Fine-tuning of protein synthesis is vital for plant development, acclimation to environmental challenges and for the assembly of major protein complexes such as the photosynthesis machinery. However, little is known about the degree and nature of the regulatory network, mainly due to challenges associated with the specific isolation of chloroplast ribosomes under conditions that also retain weak or transient interactions. Here, we established a ribosome affinity purification method, which enabled us to map the global interaction network of chloroplast ribosomes. Endogenously tagging a protein of the large or small subunit revealed not only interactors of the holo complex, but also preferential interactors of the two subunits. This includes known canonical regulatory proteins as well as several new proteins belonging to the categories of protein and RNA regulation, photosystem biogenesis, redox control and plastidic metabolism. By further characterizing identified proteins, we provide the first evidence for the existence of a co-translational N-acetyltransferase process in chloroplasts. Our dataset establishes the chloroplast ribosome as nexus in a highly choreographed, spatially interconnected protein network and reveals its wide-ranging regulatory potential during gene expression.

2020-11-23 | PXD022210 | Pride

Heat acclimation memory: Does the de-acclimated transcriptome reveal epigenetic processes of transcriptional regulation?

2014-03-31 | GSE43404 | GEO

Metabolomics Adaptation of Juvenile Pacific Abalone Haliotis discus hannai to Heat Stress

Project description:We compared two groups of abalones (from the same population) with different temperature acclimation history, through their survival at acute heat treatment and metabolites changes. The results indicated significantly higher survival for the high temperature acclimation group. Both groups experienced mitochondrial homeostasis break down during heat treatment, while the higher temperature acclimation group accumulated more metabolites beneficial to metabolic homeostasis, including various dipeptides, antioxidants, and neuroprotective substances.

2020-01-30 | ST001324 | MetabolomicsWorkbench

Difference in gene expression between WT (Col-0) and atxrn4-3 mutant under non-stress and heat stress condition

Project description:Arabidopsis 5’-3’ exoribonuclease, AtXRN4, a homolog of yeast Xrn1p, functions in degradation of uncapped RNAs after de-capping step. While Xrn1p-dependent on plant XRN4’s targets for degradation is still limited. For understanding biological function of AtXRN4, we tested survivability of atxrn4 mutants under heat stress. Our results showed that atxrn4 mutants increased survival rate under short-term degradation is a main mRNA decay in yeast, knowledge heat stress compared with WT plants. Our microarray and mRNA decay assay showed that loss of AtXRN4 function caused reduction of mRNA degradation of heat shock factor A2 (HSFA2) and ethylene response factor 1 (ERF1). HSFA2 has been known as a key regulator in heat acclimation, was found as a target for AtXRN4 for degradation at non-stress condition. Heat stress applied on atxrn4-3 hsfa2 double mutant severely lacked heat tolerance phenotype of atxrn4 mutant. These results suggest that AtXRN4-mediated mRNA degradation linked to suppress heat acclimation. In the study here, 2 week-old WT and atxrn4-3 mutant plants were exposure to non-stress (22oC) and heat-stress (37oC, 1 h). Custom microarray was applied to acquire expression profile of 32788 Arabidopsis genes. 3 biological repeats of WT (non-stress), WT(heat stress), atxrn4-3 (non-stress) and atxrn4-3 (heat stress) were used for microarray analysis

2015-07-14 | E-GEOD-66369 | biostudies-arrayexpress

RNA-sequencing of preoptic area leptin receptor-expressing neurons from heat acclimated LepRCreHTB mice

Project description:This experiment intended to look for the transcriptome changes that happen in neuronal cells from the preoptic area of the hypothalamus expressing leptin receptors during heat acclimation conditions. 3 groups of animals were used; long-term heat-acclimated animals constantly exposed to 36˚C for 28-35 days, short-term heat-acclimated animals constantly exposed to 36˚C for 5 days, and non-habituated (non-acclimated) animals which were not exposed to heat. The animal line used was LepRCreHTB.

2024-05-06 | E-MTAB-14029 | biostudies-arrayexpress

Extensive translation of small Open Reading Frames revealed by Poly-Ribo-Seq

Project description:We present a genome-wide assessment of small open reading frames (smORF) translation by ribosomal profiling of polysomal fractions in Drosophila S2 cell. In this way, mRNAs bound by multiple ribosomes and hence actively translated can be isolated and distinguished from mRNAs bound by sporadic, putatively non-productive single ribosomes or ribosomal subunits. Ribosomal profiling of large and small polysomal fractions in Drosophila S2 cells to assess translation of smORFs

2014-09-11 | E-GEOD-60384 | biostudies-arrayexpress

Heat acclimation memory: Does the de-acclimated transcriptome reveal epigenetic processes of transcriptional regulation?

Project description:Heat acclimation (AC) allows its faster re-induction following its decline. Constitutively preserved euchromatin state in hsp70 promoter during acclimation decline/regain pushed forward the hypothesis that acclimation decline is a period of M-bM-^@M-^\dormant memoryM-bM-^@M-^] involving molecular program including epigenetic controlled transcriptional regulation leading to heat acclimation mediated cytoprotective memory. We used microarray to uncover hallmark pathways in the induction of heat-acclimation-mediated memory, focusing on markers of epigenetic processes. Rats subjected to heat acclimation, deacclimation, reacclimation and untreated controls were used. We showed here that (i) AC2d provides the molecular switch for acclimation (ii) AC30 heart demonstrates qualitative adaptations (iii) specific molecular program encompassing up/down regulated gene during DeAC, of which epigenetic markers such as class A histones, chromatin modifiers and microRNA suggest epigenetic transcriptional regulation linked to acclimation memory (iv) constitutive upregulation of MAPK P38 module and targets as well as jak/stat and AKT associated pathways during DeAC imply its major role in this process. Noteworthy are players such as poly-(ADP-ribose)polymerase-1 (PARP1) and linker histones (histones H1 cluster in this process).

2014-03-31 | E-GEOD-43404 | biostudies-arrayexpress

Identification of protein-RNA interactions in Drosophila using RIP-Seq

Project description:The goal of these experiments is to identify RNAs bound by individual RNA-binding proteins. Drosophila S2R+ cells were transiently transfected with vectors encoding the indicated HA-tagged RNA-binding proteins, or without an insert as a control. Expression was induced with CuSO4, whole cell lysates were prepared and protein-RNA complexes were isolated by immunoprecipitation with HA immunoaffinity resin. RNA was then isolated from the immunoprecipitated material, and RNA-Seq libraries were prepared and sequenced. Sequence reads were aligned to the D. melanogaster reference genome Dm3 using TopHat and expression levels were quantitated using cufflinks. This work was funded as part of the modENCODE project by NHGRI. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf At least two biological replicates were performed for each protein studied. In addition, control experiments were performed in which cells were transfected with the same vector lacking an open reading frame.

2012-05-05 | E-GEOD-37756 | biostudies-arrayexpress

Cardiac and Soleus muscles following exposure of rats to heat acclimation and exercise training

Project description:The processes of adaptation to environmental heat and aerobic exercise training improve efficiency in various body systems and bring about acclimatory homeostasis. In order to examine the global genomic responses of the soleus and heart following exposure of rats to these stressors, nylon cDNA Atlas Array was used. Male rats were exposed to one of the following stressors: heat acclimation, aerobic training (treadmill), and combined heat acclimation and aerobic training for short (2, 3 days) and long (1 mo) time period. The study comprised seven experimental groups: Controls-untreated. Heat acclimated groups (2dac, Acc)â exposure to environmental heat at 34C for 2 or 30 days. Exercise groups (3dex, Ex)â graduated training protocol under normothermic conditions for 3 and 30 days at 24C. Exercise training and heat acclimation â (3dexac, ExAc)- exposed to both environmental heat and aerobic exercise as above. The Series data tables appended below: 1) Heart - normalized log2 ratio of geomeans defined as treatment/control 2) Soleus - normalized log2 ratio of geomeans defined as treatment/control 21 samples, 3 pool each, of: 1)Â Control untreated rats 2)Â Long-term heat acclimated rats 3)Â Long-term aerobic-exercised trained rats. 4)Â Rats exposed to long-term heat acclimation and exercise training. 5)Â Short term heat acclimated rats. 6)Â Short term aerobic exercised trained rats 7)Â Rats exposed to short-term heat acclimation and exercise training.

2010-05-27 | E-GEOD-7799 | biostudies-arrayexpress

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

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