CHLOROPLAST SOLUBLE PROTEASES AND THEIR PHYSIOLOGICAL SUBSTRATES: An integrated genetic and targeted systems analysis of chloroplast proteolysis

蛋白质水解，即蛋白质或多肽分解为氨基酸，对于去除不需要或受损的蛋白质和调节细胞过程（如新陈代谢）至关重要。叶绿体是植物生产力和农业中必不可少的细胞器，但叶绿体蛋白寿命和降解的决定因素尚不清楚。细胞和细胞器包含数百个蛋白质水解系统；它们必须通过顺序、平行和/或共享蛋白质底物的方式相互补充。这项研究将提供对叶绿体蛋白酶网络的深入了解，并作为在其他亚细胞区室中发现蛋白酶网络的一个例子。研究结果也可以应用于分子农业和合成生物学，因为叶绿体等细胞区室倾向于过度表达具有营养或药物价值的产品。该研究结果将为叶绿体蛋白的稳定积累提供更合理的蛋白质设计，从而直接影响这些应用。该项目将为本科生、研究生和博士后提供蛋白质组学、质谱学、分子遗传学、生物化学和生物信息学方面的培训。暑期实习将通过美国国家科学基金会资助的REU项目和康奈尔大学4H扩展项目向高中生提供。为了帮助培养下一代科学家，将在第二年组织一个植物蛋白水解研讨会，邀请蛋白酶和降解组学技术方面的专家。本研究建立在对拟南芥蛋白酶单阶和高阶突变体、先前确定的蛋白酶底物、特定生化工具和基于质谱的蛋白质降解事件检测工作流程（例如TAILS）的投资基础上。在AIM 1中，研究者将研究主要叶绿体代谢途径的关键酶（如四吡咯和shikimate）是如何被Clp蛋白酶系统识别和降解的。这个必不可少的Clp系统是最复杂和丰富的可溶性叶绿体寡聚蛋白酶，由16种不同的基因产物组成，包括底物选择器和伴侣。在AIM 2中，将使用亲和和捕获方法鉴定额外的Clp候选底物和适配器，随后进行体内生理和体外相互作用研究。目标3。在体外分析的基础上，提出了另外两种叶绿体肽酶，PREP和OOP，用于降解更小的蛋白质和蛋白质片段，包括剪切的叶绿体转运肽。初步的分子遗传学数据表明，Clp、PREP和OOP之间存在功能相互作用。这些肽酶的体内生理作用将通过非靶向和靶向方法确定，并研究它们是否以及如何形成功能性蛋白酶网络。

Proteolysis, the breakdown of proteins or peptides to amino acids, is critical for removal of unwanted or damaged proteins and regulation of cellular processes such as metabolism. Chloroplasts are essential organelles in plant productivity and agriculture, but determinants of chloroplast protein life-time and degradation are poorly understood. Cells and organelles contain hundreds of proteolytic systems; these must complement each other, by acting in sequence, in parallel and/or by sharing protein substrates. This research will provide insight into the network of chloroplast protease and serve as an example for protease network discovery in other subcellular compartments. The research findings can also be implemented in molecular farming and synthetic biology, since cellular compartments such as chloroplasts are favored for overexpression of products with nutritional or pharmaceutical value. The outcome of this research will allow more rational protein design for stable accumulation of chloroplast proteins, thus directly impacting these applications. This project will provide training in proteomics, mass spectrometry, molecular genetics, biochemistry and bioinformatics at the undergraduate, graduate and post-doctoral levels. Summer internships will be offered through our NSF-sponsored REU program and to high school students through the Cornell 4H extension program. To help to train the next generation scientists, a plant proteolysis workshop with invited experts on proteases and degradomics technology will be organized in year 2.This research is built upon investments in Arabidopsis protease single and higher order mutants, previously identified protease substrates, specific biochemical tools and mass spectrometry-based workflows for detection of protein degradation events (e.g. TAILS). In AIM 1, investigators will study how key enzymes of major chloroplast metabolic pathways (e.g. tetrapyrroles and shikimate) are recognized and degraded by the Clp protease system in vivo. This essential Clp system is the most complex and abundant soluble chloroplast oligomeric protease consisting of 16 different gene products, including substrate selectors and chaperones. In AIM 2, additional Clp candidate substrates and perhaps adaptors will be identified, using affinity and trapping approaches, followed by in vivo physiological and in vitro interaction studies. AIM 3. Based on in vitro analysis, two additional chloroplast peptidases, PREP and OOP were proposed to degrade smaller proteins and protein fragments, including cleaved chloroplast transit peptides. Preliminary molecular genetics data indicate functional interactions between Clp, PREP and OOP. The in vivo physiological role of these peptidases will be determined by untargeted and targeted approaches and investigate if and how they form a functional protease network.