Proteomics analysis reveals differentially activated pathways that operate in peanut gynophores at different developmental stages
BackgroundCultivated peanut (Arachis hypogaea. L) is one of the most important oil crops in the world. After flowering, the peanut plant forms aboveground pegs (gynophores) that penetrate the soil, giving rise to underground pods. This means of reproduction, referred to as geocarpy, distinguishes peanuts from most other plants. The molecular mechanism underlying geocarpic pod development in peanut is poorly understood.ResultsTo gain insight into the mechanism of geocarpy, we extracted proteins from aerial gynophores, subterranean unswollen gynophores, and gynophores that had just started to swell into pods. We analyzed the protein profiles in each of these samples by combining 1 DE with nanoLC-MS/MS approaches. In total, 2766, 2518, and 2280 proteins were identified from the three samples, respectively. An integrated analysis of proteome and transcriptome data revealed specifically or differentially expressed genes in the different developmental stages at both the mRNA and protein levels. A total of 69 proteins involved in the gravity response, light and mechanical stimulus, hormone biosynthesis, and transport were identified as being involved in geocarpy. Furthermore, we identified 91 genes that were specifically or abundantly expressed in aerial gynophores, including pectin methylesterase and expansin, which were presumed to promote the elongation of aerial gynophores. In addition, we identified 35 proteins involved in metabolism, defense, hormone biosynthesis and signal transduction, nitrogen fixation, and transport that accumulated in subterranean unswellen gynophores. Furthermore, 26 specific or highly abundant proteins related to fatty acid metabolism, starch synthesis, and lignin synthesis were identified in the early swelling pods.ConclusionsWe identified thousands of proteins in the aerial gynophores, subterranean gynophores, and early swelling pods of peanut. This study provides the basis for examining the molecular mechanisms underlying peanut geocarpy pod development.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-015-0582-6) contains supplementary material, which is available to authorized users.
[…] Raw data files obtained from the Orbitrap were converted into MGF files using Proteome Discoverer 1.2 (Thermo, USA). Protein annotation was performed using the Mascot search engine (Matrix Science, UK; version 2.3.02) against the peanut transcriptome database, which contained 72, 527 unigenes . The parameters for protein identification are listed in Additional file : Table S9, and the false discovery rate (FDR) was set to 0.05 for both peptides and proteins.Functional annotation of the proteins was performed using the Blast2 GO program against the non-redundant protein database at NCBI . KEGG pathway analysis was performed by comparing the identified proteins with the KEGG database (http://www.genome.jp/kegg/). COG classification was carried out by comparing the identified proteins with the Cluster of Orthologous Groups database (http://www.ncbi.nlm.nih.gov/COG/). […]
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