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Defense Response to Caterpillar Feeding Stress in Wild Pinus tabuliformis Unveiled by Quantitative Integrated Proteomic and Phosphoproteomic Analyses

ABSTRACT: To study the alteration pattern and defensive response mechanism triggered by herbivorous feeding stimuli under natural conditions, we built a biological model of the interrelationship between the Chinese pine (Pinus tabuliformis Carr.) and the Chinese pine caterpillar (Dendrolimus tabulaeformis Tsai et Liu) within their native habitat. We integrated proteomic and phosphoproteomic data, normalized the results, and combined them with bioinformatics to evaluate and analyze variations in phosphoproteomics in pine needles' response to the caterpillar's feeding stimulus. We systematically identified differentially significant phosphorylated proteins implicated in the pine's defense mechanism against caterpillar stress. Furthermore, we predicted upstream kinases of phosphorylation sites and their activities. Similarly, through an analysis of the Motif patterns of phosphorylated proteins, Mfuzz clustering of phosphorylation sites, kinase regulatory networks and functional modules of phosphorylated protein interaction networks in response to stress within pine, we can investigate the mechanisms behind resistance formation and regulation of caterpillar feeding incentives in pine. The identification results of partially phosphorylated proteins were additionally confirmed through PRM technology. Furthermore, genes upstream of differentially expressed proteins were validated through RT-qPCR detection.

INSTRUMENT(S): Q Exactive Plus

ORGANISM(S): Pinus Fenzeliana

TISSUE(S): Leaf

SUBMITTER: Tianhua Sun

LAB HEAD: Sun tianhua

PROVIDER: PXD022064 | Pride | 2024-01-16

REPOSITORIES: Pride

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Project description:Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.Hepatocellular carcinoma is one of the most frequently diagnosed cancers in the world. Post-translational modifications (PTMs) play an essential role during cancer development. Phosphorylation is an important PTMs. To identify the modifications of phosphorylation in HCC, a multiplexed tandem mass tag (TMT) approach combined with LC−MS/MS was used. A total of 4,780 phosphorylated sites distributed on 2,209 proteins were identified and quantified, including 74 and 459 phosphorylated up-regulated and down-regulated proteins, respectively. Bio-informatic analysis revealed the differences and commonalities between HCC and normal tissues. Gene ontology enrichment analysis provided the information on biological processes, molecular functions, cellular components, and sub-cellular localizations. Protein domains enrichment of differentially expressed proteins were analyzed by InterPro database. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis revealed the pathways that could potentially be involved in HCC. Integrative analysis of the functions, pathways, motifs of phosphorylated peptides, protein domains and protein interactions could establish a profile of phosphoproteome of HCC, which may contribute to identify new biomarkers for diagnosis and prognosis for HCC and novel therapeutic targets for HCC treatment.

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Defense Response to Caterpillar Feeding Stress in Wild Pinus tabuliformis Unveiled by Quantitative Integrated Proteomic and Phosphoproteomic Analyses

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