In-silico definition of the Drosophila melanogaster matrisome.
In-silico definition of the Drosophila melanogaster matrisome.
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DOI：
10.1016/j.mbplus.2019.100015
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发表时间：
2019-11
影响因子：
--
通讯作者：
Naba A
中科院分区：
文献类型：
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作者：
Davis MN;Horne-Badovinac S;Naba A
细胞外基质 (ECM) 是数百种蛋白质的组合，在结构上支持其周围的细胞并在生化上调节其功能。黑腹果蝇已成为研究 ECM 蛋白分泌、ECM 组装和 ECM 在病理生理过程中作用的基本机制的强大模型生物。然而，截至今天，我们还没有形成该生物体 ECM 的成分的明确列表。我们之前报道了用于定义人类、小鼠、斑马鱼和线虫基质体（编码 ECM 和 ECM 相关蛋白的基因集合）的计算管道的开发。使用类似的方法，我们在此报告，我们的管道已识别出构成果蝇基质体的 641 个基因。我们进一步将这些基因分为不同的结构和功能类别，包括对编码形成顶端 ECM 的蛋白质的基因进行分类的扩展方法。我们说明了如何使用果蝇基质体蛋白的全面列表来注释大型蛋白质组数据集并确定 ECM 在病理生理过程中意想不到的作用。最后，为了帮助科学界传播和使用果蝇基质体的拟议定义和分类，我们的列表已通过三个公共门户网站提供：Matrisome Project (http://matrisome.org)、The FlyBase (https://flybase.org/) 和 GLAD (https://www.flyrnai.org/tools/glad/web/)。我们开发了一个结合基因和蛋白质序列分析的生物信息学管道来预测果蝇基质体。计算机模拟果蝇基质体包含 641 个基因。我们提出了对编码形成顶端 ECM 的蛋白质的基因进行全面的分类。果蝇基质体列表现已通过三个公共门户网站提供：The Matrisome Project、FlyBase 和 GLAD。
The extracellular matrix (ECM) is an assembly of hundreds of proteins that structurally supports the cells it surrounds and biochemically regulates their functions. Drosophila melanogaster has emerged as a powerful model organism to study fundamental mechanisms underlying ECM protein secretion, ECM assembly, and ECM roles in pathophysiological processes. However, as of today, we do not possess a well-defined list of the components forming the ECM of this organism. We previously reported the development of computational pipelines to define the matrisome - the ensemble of genes encoding ECM and ECM-associated proteins - of humans, mice, zebrafish and C. elegans. Using a similar approach, we report here that our pipeline has identified 641 genes constituting the Drosophila matrisome. We further classify these genes into different structural and functional categories, including an expanded way to classify genes encoding proteins forming apical ECMs. We illustrate how having a comprehensive list of Drosophila matrisome proteins can be used to annotate large proteomic datasets and identify unsuspected roles for the ECM in pathophysiological processes. Last, to aid the dissemination and usage of the proposed definition and categorization of the Drosophila matrisome by the scientific community, our list has been made available through three public portals: The Matrisome Project (http://matrisome.org), The FlyBase (https://flybase.org/), and GLAD (https://www.flyrnai.org/tools/glad/web/). We developed a bioinformatics pipeline combining gene- and protein-sequence analysis to predict the Drosophila matrisome. The in-silico Drosophila matrisome comprises 641 genes. We propose a comprehensive classification of genes encoding proteins forming apical ECMs. The Drosophila matrisome list is now available through three public portals: The Matrisome Project, FlyBase, and GLAD.