Characterization of the Tomato Secretome Using Integrated Functional and Computational Strategies

植物细胞壁在植物生物学的许多不同方面起着核心作用，包括器官生长和分化，对微生物病原体的防御，营养物质的代谢和运输以及对环境胁迫的反应。此外，植物细胞壁可以被认为是一个重要的隔室，作为与环境的界面，因此大量的分子信号在细胞壁环境中发生。根据其多功能性质，植物细胞壁容纳了大量复杂的蛋白质群或蛋白质组，包括具有广泛催化功能的酶以及结构蛋白。然而，越来越明显的是，对细胞壁蛋白质组（也称为“分泌组”）的范围、组成和动态特性的了解仍然非常有限。该项目将采用综合方法对番茄分泌组进行编目，将一套新开发的功能筛选与高度纯化的壁蛋白提取物测序、生物信息学工具和计算预测相结合。该基础设施将用于评估细胞壁蛋白质组在与细胞壁生物学密切相关的两个生物过程中的定性和定量动态：果实成熟和植物防御反应。为此，我们将在一个标准的实验番茄基因型中研究蛋白质和mRNA的表达，并与几个非软化番茄突变体进行对比。这项研究将生成一系列番茄组织中植物分泌组的全面目录，重要的是，提供对细胞外蛋白的见解，这些蛋白在果实成熟过程和对病原体攻击的反应中似乎有助于信号传导并发挥作用。由此产生的信息应该能够对如何提高水果质量和农业生产力提供重要的见解。将开发一个可公开访问的番茄分泌组数据库（SecreTom），以容纳项目数据，提供对所有相关计算工具的访问，并作为植物壁蛋白质组研究的中心。SecreTom将通过茄科植物基因组数据库（SGN: http://www.sgn.cornell.edu/）访问，该数据库也将作为项目数据的长期存储库。此外，每年的夏季蛋白质组学研讨会将举行，包括一系列研讨会，海报展示和实验室实践培训。通过康奈尔大学现有项目网络的支持，本科生和研究生阶段代表性不足的群体的参与将得到保证。

The plant cell wall plays a central role in many diverse aspects of plant biology, including organ growth and differentiation, defence against microbial pathogens, metabolism and transport of nutrients and responses to environmental stresses. In addition, the plant cell wall can be thought of as a vital compartment that acts as the interface with the environment and so substantial molecular signaling occurs in and across the wall environment. In accordance with its multifunctional nature, the plant cell wall houses a large and complex protein population, or proteome, including enzymes with a broad range of catalytic functions as well as structural proteins. However, it is increasingly evident that there is still a very limited understanding of the extent, composition and dynamic properties of the cell wall proteome, also termed the 'secretome'. This project will use an integrated approach to catalog the tomato secretome, coupling a suite of newly developed functional screens with sequencing of highly purified wall protein extracts, bioinfomatic tools and computational prediction. This infrastructure will be used to evaluate the qualitative and quantitative dynamics of the cell wall proteome during two biological processes that are intimately associated with wall biology: fruit ripening and plant defence responses. To this end, protein and mRNA expression will be studied in a standard experimental tomato genotype and contrasted with those in several non-softening tomato mutants.This research will generate a comprehensive catalog of the plant secretome in a range of tomato tissues and importantly, provide insights into the extracellular proteins that appear to contribute to, and play a role in, signaling during fruit ripening and in response to pathogen attack. The resulting information should allow important insights into how to improve fruit quality and agricultural productivity. A publicly accessible tomato secretome database (SecreTom) will be developed to house the project data, to provide access to all associated computational tools, and to act as a hub for plant wall proteome research. SecreTom will be accessible through the Solanaceous Genomes Database (SGN: http://www.sgn.cornell.edu/), which will also serve as the long-term repository for the project data. In addition, an annual summer Proteomics Workshop will be held, comprising a seminar series, poster presentations, and lab-based practical training. The participation of under-represented groups at the undergraduate and graduate levels will be ensured through the support of a network of existing Cornell programs.