Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Strigolactones positively regulate HY5-dependent autophagy and the degradation of ubiquitinated proteins in response to cold stress in tomato

ABSTRACT: Autophagy, involved in protein degradation and amino acid recycling, plays a key role in plant development and stress responses. However, the relationship between autophagy and phytohormones is unclear. We used diverse methods, including CRISPR/Cas9, UPLC-MS/MS, chromatin immunoprecipitation, electrophoretic mobility shift assays, and dual-luciferase assays to explore the molecular mechanism of strigolactones in regulating autophagy and the degradation of ubiquitinated proteins under cold stress in tomato. We show that cold stress induced the accumulation of ubiquitinated proteins. Mutants deficient in strigolactone biosynthesis were more sensitive to cold stress with a higher accumulation of ubiquitinated proteins, while treatment with the synthetic strigolactone analog GR245DS enhanced cold tolerance in tomato, with a higher accumulation of autophagosomes and transcripts of autophagy-related genes (ATGs), and a lower accumulation of ubiquitinated proteins. Meanwhile, cold stress induced ELONGATED HYPOCOTYL 5 (HY5) accumulation, which was triggered by strigolactones. HY5 further trans-activated ATG18a promoter, resulting in autophagy formation. Mutation of ATG18a compromised strigolactone-induced cold tolerance, followed by a decreased formation of autophagosomes and an increased accumulation of ubiquitinated proteins. These findings reveal that strigolactones positively regulate autophagy in an HY5-dependent manner and promote the degradation of ubiquitinated proteins under cold conditions in tomato.

INSTRUMENT(S): Orbitrap Eclipse

ORGANISM(S): Solanum Lycopersicum

TISSUE(S): Leaf

SUBMITTER: Cheng Chi

LAB HEAD: Jie Zhou

PROVIDER: PXD052107 | Pride | 2024-08-01

REPOSITORIES: Pride

ACCESS DATA

Json Xml

Dataset's files

Source:

			Action	DRS
	230827-P-Total-C1-C12.msf	Msf
	230827-P-WTLT-C10-1.msf	Msf
	230827-P-WTLT-C10-1.raw	Raw
	230827-P-WTLT-C11-1.msf	Msf
	230827-P-WTLT-C11-1.raw	Raw

Items per page:

1 - 5 of 25

Similar Datasets

Proteomes and Ubiquitylome Analyses of Maize Endoplasmic Reticulum Under Heat Stress

Project description:High temperature severely affects plant growth and threatens crop production. Heat causes accumulation of misfolded proteins in the ER and triggers heat shock response (HSR) in cytosol and unfolded protein response (UPR) in the ER. Excessive misfolded proteins further undergo degradation through ER associated degradation (ERAD). Although much work had been done on plant heat stress response, regulation of ER-localized proteins has not been well studied so far. We isolated the microsome fraction from heat treated and untreated maize seedlings and performed proteomics and ubtiquitylome analyses. 8306 proteins are detected by proteomics and 1675 and 708 proteins are significantly upregulated and downregulated respectively. Global ubiquitination analysis discovers 1780 proteins with at least one ubiquitination site in each protein. Motif analysis reveals that alanine and glycine are preferred at the upstream and downstream of the ubiquitinated lysine. ERAD components are found to be hyper-ubiquitinated after heat treatment, implying the feedback regulation of ERAD activity through protein degradation.

2023-05-10 | PXD039418 | Pride

RNA-seq; comparison of root and shoot transcriptome between WT and strigolactone-insensitive mutant (hvd14.d), barley; three-week-old seedlings

Project description:Identification of strigolactone-dependent genes in barley. Comparison of two organs (shoot and root) allowed to identify tissue specific genes remains under control of strigolactones in barley

2024-07-26 | E-MTAB-13641 | biostudies-arrayexpress

TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato

Project description:The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth and development. It is increasingly evident that TOR also has a significant impact on plant stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that the inhibition of SlTOR transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. Furthermore, a widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition. This disruption led to the accumulation of two important defense metabolites: salicylic acid (SA) and putrescine (Put). Subsequent gain- and loss-of-function analyses validated the crucial roles of salicylic acid and putrescine in enhancing tomato cold tolerance. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.

2024-12-19 | GSE266850 | GEO

Ubiquitin remnant analysis in melanoma post inhibition of Usp9x

Project description:Assay the ubiquitinated protein remmants post depletion or inhibition of the deubiquitinase Usp9x in melanoma cells.

2017-02-20 | PXD005417 | Pride

Strigolactone analogs induce apoptosis through activation of p38 and the stress response pathway in cancer cell lines and in conditionally reprogrammed primary prostate cancer cells

Project description:Strigolactones are a novel class of plant hormones produced in roots and regulate shoot and root development. We have previously shown that synthetic strigolactone analogues potently inhibit growth of breast cancer cells and breast cancer stem cells. Here we show that strigolactone analogues inhibit the growth and survival of an array of cancer-derived cell lines representing solid and non-solid cancer cells including: prostate, colon, lung, melanoma, osteosarcoma and leukemic cell lines, while normal cells were minimally affected. Furthermore, we tested the response of patient-matched conditionally reprogrammed normal and prostate cancer cells. The tumor cells exhibited significantly higher sensitivity to the two most potent SL analogues with increased apoptosis compared to their normal counterpart cells. Treatment of cancer cells with strigolactone analogues was hallmarked by increased expression and activity of genes involved in stress signaling, cell cycle arrest and apoptosis. All five strigolactone analogues induced G2/M cell cycle arrest, accompanied with a decrease in the expression level of cyclin B1. Apoptosis was marked by increased percentages of cells in the sub-G1 fraction and was confirmed by Annexin V staining. In conditionally reprogramed matched tumor and normal prostate cells, the cleavage of PARP1 confirmed the specific increase in apoptosis of tumor cells. In summary, Strigolactone analogues are promising candidates for anticancer therapy by their ability to specifically induce cell cycle arrest, cellular stress and apoptosis in tumor cells with minimal effects on growth and survival of normal cells. There are duplicate samples for each condition. U2OS cells were treated with 2 different strigolactone analogues: ST362 or MEB55 at the concentration of 5 ppm for either 6 hr or 24 hr.Control samples were those treated with vehicle only .

2014-02-10 | E-GEOD-54820 | biostudies-arrayexpress

Proteome and Ubiquitome Changes during Rose Petal Senescence

Project description:Petal senescence involves numerous programmed changes in biological and biochemical processes. Ubiquitination plays a critical role in protein degradation, a hallmark of organ senescence. Therefore, we investigated changes in the proteome and ubiquitome of senescing rose (Rosa hybrida) petals to better understand their involvement in petal senescence. Of 3859 proteins quantified in senescing petals, 1198 were up-regulated and 726 were down-regulated during senescence. We identified 2208 ubiquitinated sites including 384 with increased ubiquitination in 298 proteins and 1035 with decreased ubiquitination in 674 proteins. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses revealed that proteins related to peptidases in proteolysis and autophagy pathways were enriched in the proteome, suggesting that protein degradation and autophagy play important roles in petal senescence. In addition, many transporter proteins accumulated in senescing petals, and several transport processes were enriched in the ubiquitome, indicating that transport of substances is associated with petal senescence and regulated by ubiquitination. Moreover, several components of the brassinosteroid (BR) biosynthesis and signaling pathways were significantly altered at the protein and ubiquitination levels, implying that BR plays important roles in petal senescence. Our data provide a comprehensive view of rose petal senescence at the posttranslational level.

2020-05-27 | PXD016490 | Pride

The response of the root proteome to the synthetic strigolactone GR24 in Arabidopsis

Project description:Strigolactones are plant metabolites that act as phytohormones and rhizosphere signals. Whereas most research on unraveling the action mechanisms of strigolactones is focused on plant shoots, we investigated proteome adaptation during strigolactone signaling in the roots of Arabidopsis thaliana. Through large-scale, time-resolved, and quantitative proteomics, the impact of the strigolactone analog rac-GR24 was elucidated on the root proteome of the wild type and the signaling mutant more axillary growth 2 (max2). Our study revealed a clear MAX2-dependent rac-GR24 response: an increase in abundance of enzymes involved in flavonol biosynthesis, which was reduced in the max2-1 mutant. Mass spectrometry-driven metabolite profiling and thin-layer chromatography experiments demonstrated that these changes in protein expression lead to the accumulation of specific flavonols. Moreover, quantitative RT-PCR revealed that the flavonol-related protein expression profile was caused by rac-GR24--induced changes in transcript levels of the corresponding genes. This induction of flavonol production was shown to be activated by the two pure enantiomers that together make up rac-GR24. Finally, our data provide much needed clues concerning the multiple roles played by MAX2 in the roots and a comprehensive view of the rac-GR24--induced response in the root proteome.

2022-02-28 | PXD004269 | Pride

The response of the root proteome to the synthetic strigolactone GR24 in Arabidopsis

2016-06-20 | PXD003879 | Pride

Dissecting ubiquitylation and DNA damage response pathways in the yeast Saccharomyces cerevisiae using a proteome-wide approach

Project description:The proper function of DNA damage response pathways (DDR) is essential to protect eukaryotic cells from the accumulation of DNA damage and genome instability, a major cause of cancer and other diseases in humans. Ubiquitylation orchestrates the regulation of DDR events.Blaszczak et al. use quantitative proteomics and a reporter system based on the NanoLuc luciferase to study ubiquitylation and protein abundance changes upon genotoxic stress in yeast. The authors point out proteins that may be regulated by ubiquitylation during the DDR.

2023-12-13 | PXD043291 | Pride

Combined analysis of ATAC-Seq and RNA-Seq reveal a potential role of WRKY34 in tomato response to cold stress [ATAC]

Project description:To further clarify the differences in the potential regulatory mechanisms of cold tolerance between wild and cultivated tomatoes, we subjected cold-sensitive cultivated tomato (Solanum lycopersicum) Ailsa Craig (AC) and cold-tolerant wild tomato (S. habrochaites) LA1777 to cold stress for 6 h, and performed ATAC-Seq and RNA-Seq, respectively.

2024-02-23 | GSE254893 | 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