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Proteome-wide mapping of early events connected to oxidative stress in Arabidopsis

ABSTRACT: Changes in environmental conditions are associated with the fast accumulation of reactive oxygen species, which may rapidly generate an oxidative environment. For efficient survival, plants respond by rapid changes in protein turnover, gene expression and posttranslational protein modifications. For this reason, the regulation of ROS levels requires rapid protective mechanisms including of antioxidant defense. Here, we aimed to delineate the early events associated with the response of Arabidopsis to methyl viologen on proteome level.

INSTRUMENT(S): LTQ Orbitrap Velos

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

TISSUE(S): Plant Cell, Whole Body

SUBMITTER: Tibor Pechan

LAB HEAD: Tibor Pechan

PROVIDER: PXD038495 | Pride | 2024-01-26

REPOSITORIES: Pride

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			Action	DRS
	F1_M_1.pdResult	Other
	F1_M_1.raw	Raw
	F1_M_2.pdResult	Other
	F1_M_2.raw	Raw
	F1_M_3.pdResult	Other

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Publications

Methyl viologen-induced changes in the Arabidopsis proteome implicate PATELLIN 4 in oxidative stress responses.

Melicher Pavol P Dvořák Petr P Řehák Jan J Šamajová Olga O Pechan Tibor T Šamaj Jozef J Takáč Tomáš T

Journal of experimental botany 20240101 1

The photosynthesis-induced accumulation of reactive oxygen species in chloroplasts can lead to oxidative stress, triggering changes in protein synthesis, degradation, and the assembly/disassembly of protein complexes. Using shot-gun proteomics, we identified methyl viologen-induced changes in protein abundance in wild-type Arabidopsis and oxidative stress-hypersensitive fsd1-1 and fsd1-2 knockout mutants, which are deficient in IRON SUPEROXIDE DISMUTASE 1 (FSD1). The levels of proteins that are ...[more]

PMID: 37728561

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Proteomic analysis of Arabidopsis fsd1 mutants in response to methyl viologen

Project description:Within this project, two Arabidopsis tDNA mutants deficient in iron superoxide dismutase FSD1 were exposed to 8h long treatment with methyl viologen. Differential, LC MSMS base proteomics was performed in order to elucidate the mechanisms of the role of FSD1 in oxidative stress tolerance

2022-03-18 | PXD028328 | Pride

Arabidopsis MED8 functions in oxidative stress

Project description:In this work, we describe a TDNA insertion mutant for Mediator complex subunit 8 (MED8) that regulates the oxidative stress responses. Wild-type Col-0 and med8 seedlings were growth under control condition or oxidative stress (induced by methyl viologen treatment) and were subjected to RNA-seq profiling. Total mRNA fractions were isolated and subjected to signle-end deep sequencing (approx.30M reads/sample) to reveal differential expression between genotypes and conditions.

2021-03-14 | GSE141547 | GEO

Mutation of Arabidopsis SME1 improves oxidative stress resilience

Project description:Alternative splicing is an important posttranscriptional gene regulatory process, acting in diverse adaptive and basal plant processes. Splicing of precursor-messenger RNA (pre-mRNA) is catalyzed by a dynamic ribonucleoprotein complex, termed the spliceosome. In a suppressor screen, we identified a nonsense mutation in the Sm protein SME1 to alleviate photorespiratory H2O2-dependent cell death in catalase-deficient plants. Furthermore, sme1-2 mutants showed increased tolerance to the superoxide-generating herbicide methyl viologen. mRNA-seq and proteomic analyses indicated a constitutive stress response and pre-mRNA splicing alterations in sme1-2 mutants under control conditions. With a pulldown experiment, using SME1 as a bait, we provide experimental evidence for proteins associated with Arabidopsis thaliana spliceosome complexes, by identifying almost 50 proteins homologous to mammalian spliceosome-associated proteins and propose four novel proteins previously not-reported or hypothesized to be part of plant spliceosome complexes. Mutation of one of these interactors, the Sm core assembly protein ICLN also resulted in a decreased sensitivity to methyl viologen. Taken together, we show that SME1 mutation and impaired snRNP assembly result in enhanced resilience to oxidative stress.

2023-03-03 | PXD024816 | Pride

Global transcriptional changes of Clostridium acetobutylicum cultures with increased butanol-acetone ratios

Project description:Artificial electron carriers have been widely used to shift the solvent ratio towards butanol in acetone-butanol-ethanol (ABE) fermentation of solventogenic clostridia according to decreased hydrogen production. In this study, first insights on the molecular level were gained to explore the effect of methyl viologen addition to cultures of Clostridium acetobutylicum. Employing batch fermentation in mineral salts medium, the butanol:acetone ratio was successively increased from 2.3 to 12.4 on a 100 ml scale in serum bottles and from 1.4 to 16.5 on a 1,300 ml scale in bioreactors, respectively. The latter cultures were used for DNA microarray analyses to provide new information on the transcriptional changes referring to methyl viologen exposure and thus, exhibing gene expression patterns according to the manipulation of the cellular redox balance.

2012-03-31 | E-MEXP-3417 | biostudies-arrayexpress

The Arabidopsis Mediator complex subunit 8 regulates oxidative stress responses

Project description:Hydrogen peroxide (H2O2) signals regulate plant growth and defense by orchestrating genome-wide transcriptional re-programming, however, the specific mechanisms that regulate H2O2-dependent gene expression are poorly understood. Here we report the identification of the Mediator complex subunit MED8 as regulator of H2O2 responses, through a genetic screen of EAL4 promoter. Interestingly, the introduction of med8 mutation in the catalase-deficient background was associated with enhanced activation of salicylic acid biosynthesis and signaling pathways. Surprisingly, however, med8 seedlings were more tolerant to oxidative stress generated by methyl viologen. This tolerance phenotype is associated with the hyperactivation of defense and hormone signaling pathways in particular salicylic acid and jasmonic acid-related pathways. In addition, analysis of MED8 interactomes revealed interaction with novel pathways expanding Mediator complex function to processes beyond transcription, including miRNA biogenesis and and mRNA processing. We establish MED8 as a new component within the regulation of oxidative stress responses and demonstrate that MED8 act as negative regulator of H2O2 -driven activation of defense gene expression.

2021-09-17 | PXD016615 | Pride

Transcription profiling of Arabidopsis seedlings treated with the herbicide methyl viologen

Project description:We exposed plants to methyl viologen (MV), a redox cycling herbicide in the light, and perform biochemical and Affymetrix ATH1 GeneChip experiments under conditions in which photosynthesis was active and the antioxidant response well conserved. Samples of total RNA were obtained from a pool of 25 Arabidopsis specimens from two independent biological replicates from the aerial parts of 2h MV-treated and non-treated control seedlings.

2008-01-08 | E-ATMX-28 | biostudies-arrayexpress

Clostridium thermocellum DSM 1313 Transcriptional Responses to Redox Perturbation

Project description:Clostridium thermocellum is a promising CBP candidate organism capable of directly converting lignocellulosic biomass to ethanol. Low yields, productivities and growth inhibition prevent industrial deployment of this organism for commodity fuel production. Symptoms of potential redox imbalance such as incomplete substrate utilization, and fermentation products characteristic of overflow metabolism, have been observed during growth. This perceived redox imbalance may be in part responsible for the mentioned bioproductivity limitations. Toward better understanding the redox metabolism of C. thermocellum, we analyzed gene expression, using microarrays, during addition of two stress chemicals (methyl viologen and hydrogen peroxide) which we observed to change fermentation redox potential. High quality RNA was extracted from C. thermocellum grown on cellobiose in chemostat culture and exposed, separately, to methyl viologen and hydrogen peroxide. Transcriptome profiles were obtained at seven time points during actively growing fermentations, 3 minutes, 15 minutes, 35 minutes, 7 hours, 14 hours, 50 hours, and 60 hours after beginning exposure to each stressor. Exposure treatments were carried out in duplicate and reference/untreated samples were taken before and between treatments, after flushing of stressor chemicals and re-equilibration of growth conditions.

2015-07-29 | E-GEOD-71465 | biostudies-arrayexpress

Transcription profiling of S. cerevisiae mRNAs following oxidative stress and DNA damage

Project description:We subjected yeast to two stresses, oxidative stress, which under current settings induces a fast and transient response in mRNA abundance, and DNA damage, which triggers a slow enduring response. Using microarrays, we performed a transcriptional arrest experiment to measure genome-wide mRNA decay profiles under each condition. Genome-wide decay kinetics in each condition were compared to decay experiments that were performed in a reference condition (only transcription inhibition without an additional stress) to quantify changes in mRNA stability in each condition. We found condition-specific changes in mRNA decay rates and coordination between mRNA production and degradation. In the transient response, most induced genes were surprisingly destabilized, while repressed genes were somewhat stabilized, exhibiting counteraction between production and degradation. This strategy can reconcile high steady-state level with short response time among induced genes. In contrast, the stress that induces the slow response displays the more expected behavior, whereby most induced genes are stabilized, and repressed genes destabilized. Our results show genome-wide interplay between mRNA production and degradation, and that alternative modes of such interplay determine the kinetics of the transcriptome in response to stress. Experiment Overall Design: We used Affymetrix microarrays to measure the decay profiles of all genes following transcription inhibition in four separate experiments. In two reference experiments, only transcription inhibtion was applied. In two other experiments, an additional stress was applied prior to transcription inhibition: oxidative stress (0.3mM hydrogen peroxide) or DNA damage (0.1% methyl methanesulfonate).

2008-10-26 | E-GEOD-12221 | biostudies-arrayexpress

Arabidopsis thaliana

Project description:Expression data from Arabidopsis thaliana (Ler) rosette leaves treated with paraquat (methyl viologen)

| PRJNA108021 | ENA

Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids

Project description:The notion that plants use specialized metabolism to protect against environmental stresses needs to be experimentally proven by addressing the question of whether stress tolerance by specialized metabolism is directly due to metabolites such as flavonoids. We report that flavonoids with radical scavenging activity mitigate against oxidative and drought stress in Arabidopsis thaliana. Metabolome and transcriptome profiling and experiments with oxidative and drought stress in wild-type, single overexpressors of MYB12/PFG1 (PRODUCTION OF FLAVONOL GLYCOSIDES1) or MYB75/PAP1 (PRODUCTION OF ANTHOCYANIN PIGMENT1), double overexpressors of MYB12 and PAP1, transparent testa4 (tt4) as a flavonoid-deficient mutant, and flavonoid-deficient MYB12 or PAP1 overexpressing lines (obtained by crossing tt4 and the individual MYB overexpressor) demonstrated that flavonoid overaccumulation was key to enhanced tolerance to such stresses. Antioxidative activity assays using 2,2-diphenyl-1-picrylhydrazyl, methyl viologen, and 3,3'-diaminobenzidine clearly showed that anthocyanin overaccumulation with strong in vitro antioxidative activity mitigated the accumulation of reactive oxygen species in vivo under oxidative and drought stress. These data confirm the usefulness of flavonoids for enhancing both biotic and abiotic stress tolerance in crops.

2013-12-06 | MTBLS57 | MetaboLights

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