Proteomics: a powerful tool to study plant responses to biotic stress

Liu, Yahui; Song, Lei; Liu, Kefu; Wang, Sheng; Huang, Lusheng; Guo, Lanping

doi:10.1186/s13007-019-0515-8

Cited by 123 publications

(54 citation statements)

References 232 publications

(219 reference statements)

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“…Proteomics has emerged as a powerful tool to explore physiological changes at the cellular level 35,36 and has been used to study plant defense responses to herbivory 19,22,23,37 . The present study is a comprehensive analysis of changes occurring to the switchgrass proteome and phosphoproteome in response to GB herbivory.…”

Section: Discussionmentioning

confidence: 99%

Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)

Zogli

Alvarez

Naldrett

et al. 2020

Sci Rep

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Switchgrass (Panicum virgatum L.) is an important crop for biofuel production but it also serves as host for greenbugs (Schizaphis graminum Rondani; GB). Although transcriptomic studies have been done to infer the molecular mechanisms of plant defense against GB, little is known about the effect of GB infestation on the switchgrass protein expression and phosphorylation regulation. The global response of the switchgrass cultivar Summer proteome and phosphoproteome was monitored by label-free proteomics shotgun in GB-infested and uninfested control plants at 10 days post infestation. Peptides matching a total of 3,594 proteins were identified and 429 were differentially expressed proteins in GB-infested plants relative to uninfested control plants. Among these, 291 and 138 were up and downregulated by GB infestation, respectively. Phosphoproteome analysis identified 310 differentially phosphorylated proteins (DP) from 350 phosphopeptides with a total of 399 phosphorylated sites. These phosphopeptides had more serine phosphorylated residues (79%), compared to threonine phosphorylated sites (21%). Overall, KEGG pathway analysis revealed that GB feeding led to the enriched accumulation of proteins important for biosynthesis of plant defense secondary metabolites and repressed the accumulation of proteins involved in photosynthesis. Interestingly, defense modulators such as terpene synthase, papain-like cysteine protease, serine carboxypeptidase, and lipoxygenase2 were upregulated at the proteome level, corroborating previously published transcriptomic data.

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Section: Discussionmentioning

confidence: 99%

Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)

Zogli

Alvarez

Naldrett

et al. 2020

Sci Rep

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show abstract

“…Proteomics approach is used to detect and analyze proteins. This tool can identify wide array of proteins including observation of any change in protein level during specific developmental stage of plants or plants under stresses (Tan et al 2017;Liu et al 2019). Moreover, proteomics can reflect the metabolic processes and their possibilities to interact with important regulatory pathways.…”

Section: Introductionmentioning

confidence: 99%

Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

Rahman

et al. 2021

Rice

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Biotic stresses represent a serious threat to rice production to meet global food demand and thus pose a major challenge for scientists, who need to understand the intricate defense mechanisms. Proteomics and metabolomics studies have found global changes in proteins and metabolites during defense responses of rice exposed to biotic stressors, and also reported the production of specific secondary metabolites (SMs) in some cultivars that may vary depending on the type of biotic stress and the time at which the stress is imposed. The most common changes were seen in photosynthesis which is modified differently by rice plants to conserve energy, disrupt food supply for biotic stress agent, and initiate defense mechanisms or by biotic stressors to facilitate invasion and acquire nutrients, depending on their feeding style. Studies also provide evidence for the correlation between reactive oxygen species (ROS) and photorespiration and photosynthesis which can broaden our understanding on the balance of ROS production and scavenging in rice-pathogen interaction. Variation in the generation of phytohormones is also a key response exploited by rice and pathogens for their own benefit. Proteomics and metabolomics studies in resistant and susceptible rice cultivars upon pathogen attack have helped to identify the proteins and metabolites related to specific defense mechanisms, where choosing of an appropriate method to identify characterized or novel proteins and metabolites is essential, considering the outcomes of host-pathogen interactions. Despites the limitation in identifying the whole repertoire of responsive metabolites, some studies have shed light on functions of resistant-specific SMs. Lastly, we illustrate the potent metabolites responsible for resistance to different biotic stressors to provide valuable targets for further investigation and application.

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“…As an enormous amount of input protein material may be required for downstream processing prior LC-MS/MS (e.g., for the immunoprecipitation enrichment; acetylome analysis; Mo et al, 2015 ; Lv et al, 2016 ; Hartl et al, 2017 ; Basisty et al, 2018 ; Liu et al, 2019 ) 10 mg of A. thaliana total protein sample was used for testing of SP3 Carboxy protocol. Again, the SP3 method was directly employed without any previous protein precipitation step using SDS-containing protein extract.…”

Section: Resultsmentioning

confidence: 99%

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS

et al. 2021

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Quantitative protein extraction from biological samples, as well as contaminants removal before LC-MS/MS, is fundamental for the successful bottom-up proteomic analysis. Four sample preparation methods, including the filter-aided sample preparation (FASP), two single-pot solid-phase-enhanced sample preparations (SP3) on carboxylated or HILIC paramagnetic beads, and protein suspension trapping method (S-Trap) were evaluated for SDS removal and protein digestion from Arabidopsis thaliana (AT) lysate. Finally, the optimized carboxylated SP3 workflow was benchmarked closely against the routine FASP. Ultimately, LC-MS/MS analyses revealed that regarding the number of identifications, number of missed cleavages, proteome coverage, repeatability, reduction of handling time, and cost per assay, the SP3 on carboxylated magnetic particles proved to be the best alternative for SDS and other contaminants removal from plant sample lysate. A robust and efficient 2-h SP3 protocol for a wide range of protein input is presented, benefiting from no need to adjust the amount of beads, binding and rinsing conditions, or digestion parameters.

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Proteomics: a powerful tool to study plant responses to biotic stress

Cited by 123 publications

References 232 publications

Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)

Greenbug (Schizaphis graminum) herbivory significantly impacts protein and phosphorylation abundance in switchgrass (Panicum virgatum)

Proteomics and Metabolomics Studies on the Biotic Stress Responses of Rice: an Update

SP3 Protocol for Proteomic Plant Sample Preparation Prior LC-MS/MS

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