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

主要研究者：Andreas Madlung（普吉特湾大学）高级合作者：Lars Tomanek（加州理工大学-圣路易斯奥比斯波）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得水和营养物质，并在三维空间中优化其身体的光合作用方向。许多发育决定是在幼苗从地面出现的第一个小时内做出的。这些决定直接响应于幼苗的环境，特别是关于可用的光。光的数量和质量都是使用精细的光受体机制来感知的，光受体机制将所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敏分子和一种叫做脱辅基蛋白的附着蛋白组成。一个小家族的基因编码多种类型的光敏色素脱辅基蛋白，可以结合到额外的相同或非常相似的分子。这些蛋白质复合物可以与DNA结合并指导基因的转录，从而最终允许植物中的多种生理反应。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变化。本研究有望揭示目前研究较少的光敏色素基因的新功能，并在转录水平和蛋白质水平上鉴定光响应基因在幼苗早期光响应过程中的相互作用。番茄既是重要的农作物，又是研究肉质果实的模式生物。了解在幼苗建立过程中光介导的反应的分子基础，可以在未来改善育种或工程植物增强结构完整性，优化架构，更早（或更晚）开花，并增加产量。这个项目的工作将主要由本科生进行，并通过与传统大学（华盛顿中部的一个少数民族服务机构）的合作，明确包括目前在科学领域代表性不足的学生。 该项目将为这些学生提供研究经验和培训机会。还将在华盛顿州农村地区举办分子生物学培训讲习班，以增加这一偏远地区的教育机会。该项目产生的生物材料将根据要求从牵头机构处获得。原始数据将通过适当的、可免费访问的储存库向公众提供，这些储存库包括NCBI Short Read Archive（SRA; http：//www.ncbi.nlm.nih.gov/sra/）和Gene Expression Omnibus（GEO; http：//www.ncbi.nlm.nih.gov/geo/）以及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/).