Dataset Information

Label-free quantitative proteomic analysis reveals the physiological and biochemical responses of Arabidopsis thaliana to cinnamon essential oil

ABSTRACT: The increasing use of synthetic chemical herbicides has resulted in environmental, human and animal health issues. This has also led to the development of herbicide resistance in weed populations. The use of essential oils (EOs) can contribute to the development of effective, eco-friendly and nature-based alternatives to these chemical products due to their phytotoxicity and multisite action. Our study aimed to evaluate the proteomic response of Arabidopsis thaliana (A. thaliana) leaves to application of a cinnamon essential oil (CEO) emulsion. The results showed that the application of CEO emulsion at a concentration of 6% severely impacted the proteomic profile of A. thaliana, especially for membrane proteins and those involved in the photosynthesis process. In fact, the analysis of principal components and the regression analysis with limma revealed significant differences in protein expression between nontreated leaves and those sprayed with CEO. Interestingly, 40 proteins were identified and listed as the most differentially accumulated proteins in the leaves of A. thaliana. It decreased the expression of all the proteins associated with catabolism and anabolism processes while simultaneously increasing the expression level of proteins involved in the response to oxidative stress. Overall, these findings allowed us to obtain a global view of the proteome response to CEO, opening promising perspectives for the development of natural herbicides, especially given the low probability of developing resistant weed populations.

INSTRUMENT(S): Synapt MS

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

TISSUE(S): Plant Cell, Leaf

SUBMITTER: Sofiene Ben kaab

LAB HEAD: Sofiene Ben Kaab

PROVIDER: PXD056647 | Pride | 2025-05-07

REPOSITORIES: Pride

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Label free quantitative proteomic analysis reveals the physiological and biochemical responses of Arabidopsis thaliana to cinnamon essential oil.

Kaab Sofiene Ben SB Martin Manon M Degand Hervé H Foncoux Bérénice B Morsomme Pierre P Jijakli M Haissam MH

Scientific reports 20250220 1

The increasing use of synthetic chemical herbicides has resulted in environmental, human and animal health issues. This has also led to the development of herbicide resistance in weed populations. The use of essential oils (EOs) can contribute to the development of effective, eco-friendly and nature-based alternatives to these chemical products due to their phytotoxicity and multisite action. Our study aimed to evaluate the proteomic response of Arabidopsis thaliana (A. thaliana) leaves to the a ...[more]

PMID: 39979395

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Project description:Background The interaction of proteins with RNA in the cell is crucial to orchestrate all steps of RNA pro-cessing. RNA interactome capture (RIC) techniques have been implemented to catalogue RNA binding proteins in the cell. In RIC, RNA-protein complexes are stabilized by UV crosslinking in vivo. Polyadenylated RNAs and associated proteins are pulled down from cell lysates using oli-go(dT) beads and the RNA binding proteome is identified by quantitative mass spectrometry. However, insights into the RNA-binding proteome of a single RNA that would yield mechanistic information on how RNA expression patterns are orchestrated, are scarce. Results Here, we explored RIC in Arabidopsis to identify proteins interacting with a single mRNA, using the circadian clock-regulated Arabidopsis thaliana GLYCINE RICH RNA-BINDING PROTEIN 7 (AtGRP7) transcript, one of the most abundant transcripts in Arabidopsis, as a showcase. Seed-lings were treated with UV light to covalently crosslink RNA and proteins. The AtGRP7 transcript was captured from cell lysates with antisense oligonucleotides directed against the 5´untranslated region. The efficiency of RNA capture was greatly enhanced by the use of locked nucleic acid (LNA)/DNA oligonucleotides, as done in the enhanced RIC protocol. In total, we identified more than 300 proteins interacting with the AtGRP7 RNA. These were benchmarked against proteins pulled down by AtGRP7 in vitro transcripts from nuclear lysates. Among the proteins validated by in vitro interaction we found the family of Acetylation Lowers Binding Affinity (ALBA) proteins. Interaction of ALBA4 with the AtGRP7 RNA was independently validated via individual-nucleotide resolution crosslinking and immunoprecipitation. The circadian expression of the AtGRP7 transcript was slightly changed in an alba loss-of-function mutant compared to wild-type, demonstrating the functional relevance of the interaction. Conclusion We adapted specific RNP capture with LNA/DNA oligonucleotides for use in plants using AtGRP7 as a showcase. We anticipate that with further optimization and up-scaling of the protocol should be applicable for less abundant transcripts. Continuous improvements of mass spectrometry sensitivity will also help to increase the range of proteins that can be identified.

			Action	DRS
	638_20220830_E_ULG_SBK_HDMSE_MEMB.csv	Csv
	638_20220830_E_ULG_SBK_HDMSE_SN.csv	Csv
	C_A1_1.raw.zip	Raw
	C_A1_2.raw.zip	Raw
	C_A1_3.raw.zip	Raw