Dataset Information

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action Prajita Pandey 1,‡, Khadiza Zaman 2, ‡, Laszlo Prokai 2 , and Vladimir Shulaev 1,*

ABSTRACT: The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remains largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of yeast Saccharomyces cerevisiae on proteome level to oxidants with different mechanism of action as early as 3 min after treatment with four oxidants, namely H2O2, cumene hydroperoxide (CHP), menadione and diamide, when protein abundances were compared using label-free quantification relying on a high-resolution mass analyzer (Orbitrap). We identified significant regulation of 196 proteins in response to H2O2, 569 proteins in response to CHP, 369 proteins in response to menadione and 207 proteins in response to diamide. Only 17 proteins were common across all treatments, but several more proteins were shared between two or three oxidants. Pathway analyses revealed that each oxidant triggered unique signaling mechanism associated with cell survival and repair. Signaling pathways mostly regulated by oxidants were Ran, mTOR, Rho, and eIEF2. Furthermore, each oxidant regulated these pathways in a unique way indicating specificity of response to oxidants having different mode of action. We hypothesize that interplay of these signaling pathway may be important in recognizing different oxidants to trigger different downstream MAPK signaling cascades and induce specific responses.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Saccharomyces Cerevisiae (baker's Yeast)

SUBMITTER: Laszlo Prokai

LAB HEAD: Dr. Vladimir Shulaev

PROVIDER: PXD022685 | Pride | 2021-01-04

REPOSITORIES: Pride

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Publications

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action.

Pandey Prajita P Zaman Khadiza K Prokai Laszlo L Shulaev Vladimir V

International journal of molecular sciences 20201226 1

The early signaling events involved in oxidant recognition and triggering of oxidant-specific defense mechanisms to counteract oxidative stress still remain largely elusive. Our discovery driven comparative proteomics analysis revealed unique early signaling response of the yeast Saccharomyces cerevisiae on the proteome level to oxidants with a different mechanism of action as early as 3 min after treatment with four oxidants, namely H2O2, cumene hydroperoxide (CHP), ...[more]

PMID: 33375274

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Project description:Packaging of eukaryotic genomes into chromatin has wide-ranging effects on gene transcription. Curiously, it is commonly observed that deletion of a global chromatin regulator affects expression of only a limited subset of genes bound to or modified by the regulator in question. However, in many single-gene studies it has become clear that chromatin regulators often do not affect steady-state transcription, but instead are required for normal transcriptional reprogramming by environmental cues. We therefore have systematically investigated the effects of 83 histone mutants, and 119 deletion mutants, on induction/repression dynamics of 200 transcripts in response to diamide stress in yeast. Importantly, we find that chromatin regulators play far more pronounced roles during gene induction/repression than they do in steady-state expression. Furthermore, by jointly analyzing the substrates (histone mutants) and enzymes (chromatin modifier deletions) we identify specific interactions between histone modifications and their regulators. Combining these functional results with genome-wide mapping of several histone marks in the same time course, we systematically investigated the correspondence between histone modification occurrence and function. We follow up on one pathway, finding that Set1-dependent H3K4 methylation primarily acts as a gene repressor during diamide stress, specifically at genes involved in ribosome biosynthesis. Set1-dependent repression of ribosomal genes occurs via distinct pathways for ribosomal protein genes and ribosomal biogenesis genes, which can be separated based on genetic requirements for repression and based on chromatin changes during gene repression. Together, our dynamic studies provide a rich resource for investigating chromatin regulation, and show that the M-bM-^@M-^\activatingM-bM-^@M-^] mark H3K4me3 functions largely as a repressor in yeast. We set to track how histone modifications change during transcriptional reprogramming. We perfomed a time course experiment following treatment of mid-log growing yeast (BY4741) with diamide. Samples were collected at t=0,4,8,15,30,60 and fixed by crosslinking. We extracted mononucleosomes by MNase digestion and then applied ChIP for selected histone modifications. The IPed material was hybridized to genomic tiling arrays against the input material.

Dataset Information

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of Saccharomyces cerevisiae to Oxidants with Different Mechanism of Action Prajita Pandey 1,‡, Khadiza Zaman 2, ‡, Laszlo Prokai 2 , and Vladimir Shulaev 1,*

Publications

Comparative Proteomics Analysis Reveals Unique Early Signaling Response of <i>Saccharomyces cerevisiae</i> to Oxidants with Different Mechanism of Action.

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