Arabidopsis 2010: Whole proteome tools to benchmark gene functions and reveal networks

所有有生命的有机体都是由蛋白质和其他由蛋白质组成的物质组成的，这些蛋白质包括脂肪、糖和DNA。蛋白质完成生命的工作；它们提供形状，传递分子“消息”，制造细胞的所有部分，捕获和利用能量，提供武器和防御，并复制传递给下一代所需的基因。尽管蛋白质很重要，但科学家很少首先测量蛋白质，因为现有技术只揭示了总蛋白质的一小部分。这项提议有两个主要目标。一是提高了蛋白质质谱学鉴定的灵敏度和精密度。目标是识别样本中90%的蛋白质，即大约10,000种蛋白质。目前最先进的技术只识别了大约10%的蛋白质。与现有的定性方法(蛋白质被指定为存在或不存在)相比，将开发该方法的定量方面，以检测每种蛋白质水平的两倍或更大的变化。这样的改进可以被所有的科学家使用，应该有广泛的应用。第二个目标是用这项新技术来回答一个具有农业意义的重要科学问题：根结线虫是如何感染植物的？线虫引起了许多最严重的农作物疾病。它们钻入根部，激活不正常的生长模式，最终扰乱根的功能，导致水分和营养胁迫。将确定其水平受感染影响的植物蛋白质。这些变化将在感染同一线虫的不同植物物种之间进行比较，以了解哪些变化是共同的。这些常见的或保守的变化可能是最重要的，因为它们已经持续了数百万年。将在植物中进行基因改变，以模仿或防止感染引起的变化，作为测试线虫引起的变化是否对感染发生所必需的一种方式。这将有助于对如何培育抗病作物的基本理解。该项目将为博士后研究人员和研究生提供最新的蛋白质组学培训机会。

All living organisms are composed of proteins plus other substances made by proteins including fat, sugar, and DNA. Proteins do the work of life; they provide shape, transmit molecular "news", make all of the parts of a cell, capture and utilize energy, provide weapons and defenses, and copy genes required for transmittal to the next generation. Despite their importance, proteins are rarely the first things measured by scientists because existing technologies reveal only a small fraction of the total. This proposal has two principal aims. The first is to increase the sensitivity and precision of protein identification by mass spectrometry. The goal is to identify 90% of the proteins in a sample, or about 10,000 proteins. Current state-of-the-art technology identifies only about 10% of the proteins. Quantitative aspects of the method will be developed to detect changes of two-fold or greater in the level of each protein, compared with existing methods that are qualitative (proteins are designated as either present or absent). Such improvements could be used by all scientists and should have broad application. The second aim is to use this new technology to answer an important scientific question with agricultural significance: how does the root knot nematode infect plants? Nematodes cause many of the most serious diseases of crops. They burrow into the roots and activate abnormal growth patterns which eventually disrupt root functions, leading to water and nutrient stress. Plant proteins will be identified whose levels are affected by infection. These changes will be compared between different plant species infected by the same nematode to learn which changes are in common. These common or conserved changes may be the most important because they have persisted over millions of years. Genetic alterations will be made in the plant that either mimic or prevent the changes caused by infection, as a way to test whether the changes caused by nematodes are necessary for the infection to take place. This will aid in the basic understanding of how to make crops that resist disease. This project will provide training opportunities in state-of-the-art proteomics for postdoctoral researchers and graduate students.