Proteome Profiling of Wheat Shoots from Different Cultivars

Vu, Lam Dai; Verstraeten, Inge; Stes, Elisabeth; Bel, Michiel Van; Coppens, Frederik; Gevaert, Kris; Smet, Ive De

doi:10.3389/fpls.2017.00332

Cited by 18 publications

(17 citation statements)

References 51 publications

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“…Recent years, two‐dimensional LC‐MS/MS separations demonstrated great resolving power and enables the throughput of deep proteome beyond 3,000 proteins (Batth et al, ; Yang, Shen, Camp, & Smith, ). Such two‐dimensional LC‐MS/MS analysis strategies have been applied to the study of other cereals (Li, Liu, Chen, & Cheng, ; Vu et al, ). Here, a high‐throughput proteomic workflow based on two‐dimensional LC‐MS/MS, which was connected by high‐pH RPLC fractionation and LC‐MS/MS, was used to deeply identify the proteome of TBS, and 3,363 proteins were identified, providing a comprehensive information at the protein molecular level for the future research of tartary buckwheat.…”

Section: Resultsmentioning

confidence: 99%

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Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

et al. 2019

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The whole seed of tartary buckwheat (Fagopyrum tataricum) is considered as a healthy and functional food, which is rich in kinds of flavonoids and with potential antioxidant effect. An in‐depth analysis of tartary buckwheat seed (TBS) proteome was performed using a shotgun proteomics strategy. Total protein of TBS was extracted and digested, then the peptides were separated by offline two‐dimensional liquid chromatography and identified by tandem mass spectrometry. Total of 3,363 high‐confidence proteins were identified from 13,730 matched peptides, in which, 2,499 proteins were annotated by the Gene Ontology (GO) analysis with 1,720 involved in “biological process,” 2,241 in “molecular function,” and 693 in “cellular components.” Based on the GO functional enrichment and Kyoto Encyclopedia of Genes and Genomes pathway enrichment results, buckwheat seed proteins were mostly enriched in metabolism of nucleic acid, respiration and energy metabolism, as well as synthesis and metabolism of protein. Practical applications This study characterized the tartary buckwheat seed proteome on a scale of 3,000+ proteins and provide important information and clues for future research, especially in the mechanism of seed germination, nutrient composition changes, and metabolite production seed germination and material metabolism.

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Section: Resultsmentioning

confidence: 99%

“…Recent years, two-dimensional LC-MS/MS separations demonstrated great resolving power and enables the throughput of deep proteome beyond 3,000 proteins(Batth et al, 2014;Yang, Shen, Camp, & Smith, 2012). Such two-dimensional LC-MS/MS analysis strategies have been applied to the study of other cereals(Li, Liu, Chen, & Cheng, 2018;Vu et al, 2017).…”

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confidence: 99%

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

et al. 2019

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“…Total protein extraction was conducted on three biological replicates of approximately 50 pooled 14-DAS-old whole CYCA3;4 OE 11.2 x Col-0 and Col-0 x Col-0 F1 seedlings, as previously described (Vu et al, 2017). Phosphopeptides were enriched as previously described with minor modifications (Vu et al, 2017). A total of 100 μL of the re-suspended peptides were incubated with 3 mg MagReSyn Ti-IMAC microspheres for 20 min at room temperature.…”

Section: Methodsmentioning

confidence: 99%

CYCA3;4 Is a Post-Prophase Target of the APC/C^CCS52A2E3-Ligase Controlling Formative Cell Divisions in Arabidopsis

Willems

Heyman

Eekhout

et al. 2020

Preprint

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32The Anaphase Promoting Complex/Cyclosome (APC/C) controls unidirectional progression 33 through the cell cycle by marking key cell cycle proteins for proteasomal turnover. Its 34 activity is temporally regulated by the docking of different activating subunits, known in 35 plants as CDC20 and CCS52. Despite the importance of the APC/C during cell 36 proliferation, the number of identified targets in the plant cell cycle is limited. Here, we 37 used the growth and meristem phenotypes of Arabidopsis CCS52A2-deficient plants in a 38 suppressor mutagenesis screen to identify APC/C CCS52A2 substrates or regulators, resulting 39 in the identification of a mutant cyclin CYCA3;4 allele. CYCA3;4 deficiency partially 40 rescues the early ccs52a2-1 phenotypes, whereas increased CYCA3;4 levels enhances them. 41 Furthermore, whereas CYCA3;4 proteins are promptly broken down after prophase in 42 wild-type plants, they remain present in later stages of mitosis in ccs52a2-1 mutant plants, 43 marking them as APC/C CCS52A2 substrates. Strikingly, CYCA3;4 overexpression results in 44 aberrant root meristem and stomatal divisions, mimicking phenotypes of plants with 45 reduced RBR1 activity. Correspondingly, RBR1 hyperphosphorylation was observed in 46 CYCA3;4-overproducing plants. Our data thus demonstrate that an inability to timely 47 destroy CYCA3;4 attributes to disorganized formative divisions, likely in part caused by 48 the inactivation of RBR1.49 4 109 ENHANCER (TE) / TILLERING AND DWARF (TAD1) was shown to mediate the 110 ubiquitination and subsequent degradation of MONOCULM 1 (MOC1), called LATERAL 111 6SUPPRESSOR (LAS) in Arabidopsis, a GRAS-family transcription factor that promotes shoot 112 branching and tillering (Lin et al., 2012; Xu et al., 2012). 113 Here, we have utilized an ethyl methanesulfonate (EMS) suppressor screen to identify 114 novel APC/C CCS52A2 targets, based on the growth inhibitory phenotype of ccs52a2-1 knockout 115 plants. We show that one of the identified revertants encodes a mutant allele of the CYCA3;4 116 gene and demonstrate this cyclin to be a specific target of APC/C CCS52A2 to ensure correct stem 117 cell organization. 118 119 RESULTS 120 Identification of pkn2 as a ccs52a2-1 Suppressor Mutant 121 Compared to wild type (WT, Col-0) plants, ccs52a2-1 mutant seedlings display a short root 122 phenotype (Figures 1A and 1B; Supplemental Figures 1A and 1B) (Vanstraelen et al., 2009; 123 Heyman et al., 2013). This phenotype was used to screen for putative targets or regulators of the 124 APC/C CCS52A2 ubiquitin ligase complex through a mutagenesis revertant screen. Therefore, ethyl 125 methanesulfonate (EMS)-mutagenized ccs52a2-1 plants were screened in the M 2 generation for a 126 recovered root growth. Out of a total of 260 initially identified revertants, 33 were confirmed in 127 the next generation. Among these, one revertant mutation, named pikmin 2 (pkn2), yielded a root 128 length in between that of WT and ccs52a2-1 mutant plants (Figures 1A to 1C; Supplemental 129 Figures 1A to 1C). 1...

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“…Total protein extraction was conducted on three biological replicate samples (leaf and spikelet material from independent plants) per wheat cultivar according to our previously described procedure with minor modifications (Vu et al , 2017). Details can be found in the Supplementary Information .…”

Section: Methodsmentioning

confidence: 99%

“…Details can be found in the Supplementary Information . Phosphopeptides were enriched as previously described (Vu et al , 2017).…”

Section: Methodsmentioning

confidence: 99%

Temperature-induced changes in wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

Zhu

Verstraeten

et al. 2018

Preprint

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Wheat (Triticum ssp.) is one of the most important human food sources. However, this crop is very sensitive to temperature changes. Specifically, processes during wheat leaf, flower and seed development and photosynthesis, which all contribute to the yield of this crop, are affected by high temperature. While this has to some extent been investigated on physiological, developmental and molecular levels, very little is known about early signalling events associated with an increase in temperature. Phosphorylation-mediated signalling mechanisms, which are quick and dynamic, are associated with plant growth and development, also under abiotic stress conditions. Therefore, we probed the impact of a short-term increase in temperature on the wheat leaf and spikelet phosphoproteome. The resulting data set provides the scientific community with a first large-scale plant phosphoproteome under the control of higher ambient temperature, which will be valuable for future studies. Our analyses also revealed a core set of common proteins between leaf and spikelet, suggesting some level of conserved regulatory mechanisms. Furthermore, we observed temperature-regulated interconversion of phosphoforms, which likely impacts protein activity.

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Proteome Profiling of Wheat Shoots from Different Cultivars

Cited by 18 publications

References 51 publications

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

CYCA3;4 Is a Post-Prophase Target of the APC/C^CCS52A2E3-Ligase Controlling Formative Cell Divisions in Arabidopsis

Temperature-induced changes in wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

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Proteome Profiling of Wheat Shoots from Different Cultivars

Cited by 18 publications

References 51 publications

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

Analysis of tartary buckwheat ( Fagopyrum tataricum ) seed proteome using offline two‐dimensional liquid chromatography and tandem mass spectrometry

CYCA3;4 Is a Post-Prophase Target of the APC/CCCS52A2E3-Ligase Controlling Formative Cell Divisions in Arabidopsis

Temperature-induced changes in wheat phosphoproteome reveal temperature-regulated interconversion of phosphoforms

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CYCA3;4 Is a Post-Prophase Target of the APC/C^CCS52A2E3-Ligase Controlling Formative Cell Divisions in Arabidopsis