RUI: Comparative Transcriptomic and Proteomic Analysis of Phytochrome Responses in Tomato

高级合作者：Lars Tomanek（加州理工大学-圣路易斯奥比斯波分校）和Lukas Mueller（博伊斯汤普森植物研究所）植物对外部环境和内部信号做出反应，以优化生理过程，使它们能够从地面获取水分和营养物质，并优化它们的身体在三维空间中的光合作用方向。许多发育的决定都是在幼苗从地里长出来的最初几个小时内做出的。这些决定是对幼苗环境的直接反应，特别是对可用光的反应。光的数量和质量都是通过复杂的光受体机制来感知的，这些机制将获得的信息转化为各种生长反应。其中一种光受体叫做光敏色素，它由一种叫做发色团的光感应分子和一种叫做载脂蛋白的附着蛋白组成。一个小的基因家族编码多种类型的光敏色素载脂蛋白，这些载脂蛋白可以与其他相同或非常相似的分子结合。这些蛋白质复合物可以与DNA结合并指导基因的转录，从而最终允许植物产生多种生理反应。该项目将使用全基因组方法直接比较番茄幼苗和几种光敏色素突变体在早期发育过程中的转录和蛋白质组学变化。该项目有望揭示光敏色素基因的新功能，并在幼苗早期光响应过程中发现光响应基因在转录和蛋白水平上的新相互作用。番茄既是一种重要的农用作物，又是研究肉质果实的模式生物。了解幼苗建立过程中光介导反应的分子基础，可以在未来改善植物的育种或工程，增强结构完整性，优化结构，提前（或推迟）开花，提高产量。该项目的工作将主要由本科生进行，并通过与传统大学（Heritage University）的合作，明确包括目前在科学领域代表性不足的学生。传统大学是华盛顿市中心的一所少数族裔服务机构。该项目将为这些学生提供研究经验和培训机会。分子生物学培训讲习班也将在华盛顿州农村地区举行，以增加这个偏远地区的教育机会。本项目生成的生物材料将根据要求从牵头机构公开提供。原始数据将通过适当的、免费访问的存储库向公众提供，这些存储库包括NCBI Short Read Archive （SRA; http://www.ncbi.nlm.nih.gov/sra/）、Gene Expression Omnibus （GEO; http://www.ncbi.nlm.nih.gov/geo/）和Sol Genomics Network （SGN; http://solgenomics.net/）。

PI: Andreas Madlung (University of Puget Sound)Senior Collaborators: Lars Tomanek (California Polytechnical University - San Luis Obispo) and Lukas Mueller (Boyce Thompson Institute for Plant Research)Plants respond both to external environmental and internal signals to optimize physiological processes that allow them to access water and nutrients from the ground and optimally orient their bodies for photosynthesis in three-dimensional space. Many developmental decisions are made within the first hours of emergence of the seedling from the ground. These decisions are in direct response to the seedling's environment, particularly with respect to the available light. Both light quantity and quality are sensed using elaborate light receptor mechanisms, which translate the obtained information into various growth responses. One of these light receptors is called phytochrome, which consists of a light-sensing molecule called the chromophore and an attached protein called the apoprotein. A small family of genes encodes multiple types of phytochrome apoproteins that can bind to additional identical or very similar molecules. These protein complexes can bind to DNA and direct the transcription of genes, thus ultimately allowing for a multitude of physiological responses in the plant. This project will use a genome wide approach to directly compare transcriptional and proteomic changes in tomato seedlings and several phytochrome mutants during early development. It is expected that this project will reveal novel functions of the lesser-studied phytochrome genes, and identify new interactions of light-response genes, both on the transcript and the protein level during early seedling responses to light.Tomato is both a major agronomic crop and a model organism for the study of fleshy fruits. Understanding the molecular underpinnings of light-mediated responses during seedling establishment may in the future improve breeding or engineering of plants with enhanced structural integrity, optimized architecture, earlier (or later) flowering, and increased yield. Work on this project will be conducted primarily by undergraduates, and explicitly include students currently underrepresented in the sciences through a collaboration with Heritage University, a minority serving institution in central Washington. This project will provide these students with research experiences and training opportunities. Training workshops in molecular biology will also be held in rural Washington State to enhance educational opportunities in this remote area. Biological materials generated by this project will be publically available from the lead institution on request. Raw data will be made available to the public via appropriate, freely accessible repositories that include the NCBI Short Read Archive (SRA; http://www.ncbi.nlm.nih.gov/sra/) and Gene Expression Omnibus (GEO; http://www.ncbi.nlm.nih.gov/geo/) and the Sol Genomics Network (SGN; http://solgenomics.net/).