Dataset Information

Wheat leaf phosphoproteome - Integrative Network Analysis of the Signaling Cascades in Seedling Leaves of Bread Wheat by Large-Scale Phosphoproteomic Profiling

ABSTRACT: In this study, we performed a large-scale leaf phosphoproteomic analysis of two wheat genotypes HX10 and NC47 to explore the complex protein phosphorylation network of signaling and regulatory events affecting rapid vegetative growth in wheat. We used TiO2 affinity chromatography combined with LC-MS/MS and Maxquant software to identify phosphopeptides and phosphorylated sites. Finally, 2,336 phosphopeptides containing 2,734 phosphorylation sites were identified from the two wheat genotypes HX10 and NC47 in our study.

INSTRUMENT(S): LTQ Orbitrap

ORGANISM(S): Triticum Aestivum (wheat)

TISSUE(S): Leaf

SUBMITTER: Dong-Wen Lv

LAB HEAD: Yue-Ming Yan

PROVIDER: PXD000540 | Pride | 2014-04-01

REPOSITORIES: Pride

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Integrative network analysis of the signaling cascades in seedling leaves of bread wheat by large-scale phosphoproteomic profiling.

Lv Dong-Wen DW Lv Dong-Wen DW Ge Pei P Zhang Ming M Cheng Zhi-Wei ZW Li Xiao-Hui XH Yan Yue-Ming YM

Journal of proteome research 20140328 5

Here, we conducted the first large-scale leaf phosphoproteome analysis of two bread wheat cultivars by liquid chromatography-tandem mass spectrometry. Altogether, 1802 unambiguous phosphorylation sites representing 1175 phosphoproteins implicated in various molecular functions and cellular processes were identified by gene ontology enrichment analysis. Among the 1175 phosphoproteins, 141 contained 3-10 phosphorylation sites. The phosphorylation sites were located more frequently in the N- and C- ...[more]

PMID: 24679076

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Project description:Our understanding of the mechanisms that govern the cellular process of meiosis is limited in higher plants with polyploid genomes. Bread wheat is an allohexaploid that behaves as a diploid during meiosis. Chromosome pairing is restricted to homologous chromosomes despite the presence of homoeologues in the nucleus. The importance of wheat as a crop and the extensive use of wild wheat relatives in breeding programs has prompted many years of cytogenetic and genetic research to develop an understanding of the control of chromosome pairing and recombination. The rapid advance of biochemical and molecular information on meiosis in model organisms such as yeast provides new opportunities to investigate the molecular basis of chromosome pairing control in wheat. However, building the link between the model and wheat requires points of data contact. We report here a large-scale transcriptomics study using the Affymetrix wheat GeneChipÂ® aimed at providing this link between wheat and model systems and at identifying early meiotic genes. Analysis of the microarray data identified 1,350 transcripts temporally-regulated during the early stages of meiosis. Expression profiles with annotated transcript functions including chromatin condensation, synaptonemal complex formation,recombination and fertility were identified. From the 1,350 transcripts, 30 displayed at least an eight-fold expression change between and including pre-meiosis and telophase II, with more than 50% of these having no similarities to known sequences in NCBI and TIGR databases. This resource is now available to support research into the molecular basis of pairing and recombination control in the complex polyploid, wheat. Experiment Overall Design: The seven stages collected were pre-meiosis (PM), leptotene to pachytene (LP), diplotene to anaphase I (DA), telophase I to telophase II (TT), tetrads (T), immature pollen (IP) and mature anthers (MAN). Immediately after determining the stage, the remaining two anthers from the floret were placed into liquid nitrogen. After collecting at least 25 staged anthers for each time point from several biological samples, anthers from the respective stages were pooled. Leaf material used in this study was collected from glasshouse-grown plants (six weeks) and total RNA isolated using TrizolÂ® (Gibco BRL, Australia) according to the manufacturerâs protocol. Experiment Overall Design: Twenty micrograms of aRNA of from each of the seven samples were fragmented for hybridization to each microarray. In total three technical replicates were conducted for each of the seven stages examined. Affymetrix GeneChipÂ® Wheat Genome Arrays were used for all samples. The arrays were hybridized and processed according to the manufacturerâs specifications. Experiment Overall Design: Normalization of the microarray data was conducted using RMA. The software package Acuity 4 (Molecular Devices, CA, USA) was then used to analyze the microarray data.

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