Chakraborty Sandeep, Nascimento Rafael, Zaini Paulo A, Gouran Hossein, Rao Basuthkar J, Goulart Luiz R, Dandekar Abhaya M
Department of Plant Sciences, University of California, Davis (UC Davis) , CA , United States of America.
Department of Plant Sciences, University of California, Davis (UC Davis), CA, United States of America; Institute of Genetics and Biochemistry, Federal University of Uberlândia, Campus Umuarama, Uberlândia Minas Gerais, Brazil.
PeerJ. 2016 May 24;4:e2007. doi: 10.7717/peerj.2007. eCollection 2016.
Background. Xylella fastidiosa, the causative agent of various plant diseases including Pierce's disease in the US, and Citrus Variegated Chlorosis in Brazil, remains a continual source of concern and economic losses, especially since almost all commercial varieties are sensitive to this Gammaproteobacteria. Differential expression of proteins in infected tissue is an established methodology to identify key elements involved in plant defense pathways. Methods. In the current work, we developed a methodology named CHURNER that emphasizes relevant protein functions from proteomic data, based on identification of proteins with similar structures that do not necessarily have sequence homology. Such clustering emphasizes protein functions which have multiple copies that are up/down-regulated, and highlights similar proteins which are differentially regulated. As a working example we present proteomic data enumerating differentially expressed proteins in xylem sap from grapevines that were infected with X. fastidiosa. Results. Analysis of this data by CHURNER highlighted pathogenesis related PR-1 proteins, reinforcing this as the foremost protein function in xylem sap involved in the grapevine defense response to X. fastidiosa. β-1, 3-glucanase, which has both anti-microbial and anti-fungal activities, is also up-regulated. Simultaneously, chitinases are found to be both up and down-regulated by CHURNER, and thus the net gain of this protein function loses its significance in the defense response. Discussion. We demonstrate how structural data can be incorporated in the pipeline of proteomic data analysis prior to making inferences on the importance of individual proteins to plant defense mechanisms. We expect CHURNER to be applicable to any proteomic data set.
背景。木质部难养菌（Xylella fastidiosa）是包括美国皮尔斯病和巴西柑橘杂色黄化病在内的多种植物病害的病原体，仍然是持续令人担忧和造成经济损失的根源，特别是因为几乎所有商业品种都对这种γ-变形菌敏感。感染组织中蛋白质的差异表达是确定植物防御途径中关键要素的既定方法。方法。在当前工作中，我们开发了一种名为CHURNER的方法，该方法基于对具有相似结构但不一定具有序列同源性的蛋白质的鉴定，从蛋白质组学数据中强调相关蛋白质功能。这种聚类强调具有多个上调/下调拷贝的蛋白质功能，并突出显示差异调节的相似蛋白质。作为一个工作示例，我们展示了列举感染木质部难养菌的葡萄木质部汁液中差异表达蛋白质的蛋白质组学数据。结果。通过CHURNER对这些数据的分析突出了与发病机制相关的PR-1蛋白，强化了其作为参与葡萄对木质部难养菌防御反应的木质部汁液中最重要的蛋白质功能。具有抗微生物和抗真菌活性的β-1,3-葡聚糖酶也被上调。同时，CHURNER发现几丁质酶既有上调也有下调，因此这种蛋白质功能的净增益在防御反应中失去了意义。讨论。我们展示了在推断单个蛋白质对植物防御机制的重要性之前，如何将结构数据纳入蛋白质组学数据分析流程。我们预计CHURNER可应用于任何蛋白质组学数据集。
