Dataset Information

Large-scale qualitative and quantitative research of dityrosine crosslinking omics in Escherichia coli

ABSTRACT: Excessive reactive oxygen species cause oxidative stress in cells. Two molecules of tyrosine can generate dityrosine, which is not only a product of natural posttranslational processes, but also a putative biomarker for protein oxidation. Few studies have investigated dityrosine crosslinking under endogenous or exogenous oxidative conditions in Escherichia coli at the proteome level so far. In this study, in order to investigate qualitative and quantitative dityrosine crosslinking, two mutant strains were constructed as endogenous oxidative stress model, as well as one mutant strain added with 1mM H2O2 as exogenous oxidative stress model. We integrated label-free LC-MS/MS and bioinformatics to research dityrosine crosslinking in Escherichia coli. A large-scale dataset of dityrosine crosslinking was provided. 352 proteins were identified to participate in dityrosine crosslinking by pLink. The subcellular localization included cytoplasmic (61.93%), periplasmic (21.31%), outer membrane (7.95%), inner membrane (5.97%) and extracellular (2.84%). Quantitative analysis of dityrosine crosslinking indicated that the three oxidative stress models could be separated at dityrosine linked peptides level. We expect that our research will guide efforts to comprehend the detailed features of dityrosine crosslinking in future.

INSTRUMENT(S): Q Exactive HF

ORGANISM(S): Escherichia Coli

TISSUE(S): Cell Culture

SUBMITTER: Zhou Xiangzhe

LAB HEAD: Yongqian Zhang

PROVIDER: PXD039132 | Pride | 2023-05-10

REPOSITORIES: Pride

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Publications

Large-Scale Qualitative and Quantitative Assessment of Dityrosine Crosslinking Omics in Response to Endogenous and Exogenous Hydrogen Peroxide in <i>Escherichia coli</i>.

Zhou Xiangzhe X Liu Feng F Li Nuomin N Zhang Yongqian Y

Antioxidants (Basel, Switzerland) 20230323 4

Excessive hydrogen peroxide causes oxidative stress in cells. The oxidation of two tyrosine residues in proteins can generate <i>o,o'</i>-dityrosine, a putative biomarker for protein oxidation, which plays critical roles in a variety of organisms. Thus far, few studies have investigated dityrosine crosslinking under endogenous or exogenous oxidative conditions at the proteome level, and its physiological function remains largely unknown. In this study, to investigate qualitative and quantitative ...[more]

PMID: 37107161

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Project description:Guanosine 3 ,5 -bispyrophosphate (ppGpp), also known as ‘‘magic spot,’’ has been shown to bind prokaryotic RNA polymerase to down-regulate ribosome production and increase transcription of amino acid biosynthesis genes during the stringent response to amino acid starvation. Because many environmental growth perturbations cause ppGpp to accumulate, we hypothesize ppGpp to have an overarching role in regulating the genetic program that coordinates transitions between logarithmic growth (feast) and growth arrest (famine). We used the classic glucose-lactose diauxie as an experimental system to investigate the temporal changes in transcription that accompany growth arrest and recovery in wildtype Escherichia coli and in mutants that lack RelA (ppGpp synthetase) and other global regulators, i.e., RpoS and Crp. When cultured on a mixture of glucose and lactose, E. coli grows preferentially on glucose until it is exhausted, resulting in growth arrest while the cells adjust to growth on lactose, i.e., diauxie. Diauxie was delayed in the relA mutant and was accompanied by a 15% decrease in the number of carbon sources used and a 3-fold overall decrease in the induction of RpoS and Crp regulon genes. Thus the data significantly expand the previously known role of ppGpp and support a model wherein the ppGpp-dependent redistribution of RNA polymerase across the genome is the driving force behind control of the stringent response, general stress response, and starvation-induced carbon scavenging. Our conceptual model of diauxie describes these global control circuits as dynamic, interconnected, and dependent upon ppGpp for the efficient temporal coordination of gene expression that programs the cell for transitions between feast and famine. E. coli MG1655 and isogenic mutants were cultured in a 2 l Biostat B fermentor (B. Braun Biotech International) containing 1 liter of Morpholinepropanesulfonic acid (MOPS) minimal medium with 0.5 g/l of glucose and 1.5 g/l of lactose. The temperature was maintained at 37 ºC and pH was kept constant at 7.2 by the addition of 2 M NaOH. The dissolved oxygen level was maintained above 20% of saturation by adjusting the agitation speeds in the range of 270-500 rpm with fixed 1 l/min air flow.

Dataset Information

Large-scale qualitative and quantitative research of dityrosine crosslinking omics in Escherichia coli

Publications

Large-Scale Qualitative and Quantitative Assessment of Dityrosine Crosslinking Omics in Response to Endogenous and Exogenous Hydrogen Peroxide in <i>Escherichia coli</i>.

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