Low Temperature Transcriptional Networks

PI: M. Thomashow（密歇根州立大学）合著者：C. Chan（密歇根州立大学）和T. Chen（俄勒冈州立大学）合作者：S.-H。Shiu（密歇根州立大学）：该项目的长期目标是在系统层面上了解植物对非生物胁迫的反应，并利用所获得的第一原理开发新的策略来提高农业重要作物的抗逆性。这些目标很重要，因为非生物胁迫限制了作物可以种植的地理位置，并造成了每年产量的大部分损失。总体目标是确定低温转录网络，植物已经进化到生存的寒冷。由于冷冻和脱水损伤之间存在直接联系，该结果还应进一步深入了解赋予耐旱性和其他脱水压力的基因模块的性质。该项目的具体目标有两个方面。首先是详细了解拟南芥的低温转录网络，并确定哪些成分有助于抗冻性。这将通过鉴定转录因子和其他在低温转录组配置中起关键作用的调节蛋白来完成；识别顺式作用的DNA调控元件，这些调控蛋白通过这些元件发挥作用；并确定有助于抗冻性的调控程序和基因模块（以及对干旱和其他非生物胁迫的潜在耐受性）。该项目的第二个目的是确定赋予拟南芥耐冻性的低温转录网络和基因模块是否在冷环境下的植物中保存（即，对低非冷冻温度的抗冻能力增加），以及这些网络和模块中的“缺陷”是否有助于那些不冷环境的植物的冷冻敏感性。这一目标将通过比较基因组分析三个密切相关的茄属物种，不同的耐寒性：商业茄、马铃薯和番茄。总之，拟议的研究包括基因组水平的基因表达测定，模型和作物物种的比较基因组分析，以及计算分析和实证测试的整合，以重建和模拟对植物生命至关重要的转录调控网络，并在农业中具有重要意义。更广泛的影响提高作物的非生物抗逆性对于满足未来对食物和纤维的需求至关重要。此外，在美国，每年生产足够的生物质，用可再生资源生产的生物燃料取代相当大比例的石油基运输燃料，这是一个新兴的国家愿景的关键组成部分。本文提出的研究直接关系到这些重要领域，因为它们将提供对植物进化以应对非生物胁迫的基因组机制的更深入理解，并有可能提供遗传工具来提高植物的非生物胁迫耐受性。在这些研究过程中产生的微阵列数据将通过项目网站（http://aztec.stanford.edu/cold/index.html）以及GEO和ArrayExpress提供。该项目还将有助于培训下一代科学家，这些科学家在将基因组学、生物信息学和计算方法应用于生物学的基本问题方面经验丰富。最后，该项目包括一个夏季本科教育和研究培训计划，目标是纳入我们社会中代表性不足的群体。目标是为学生提供机会，了解更多关于基因组研究的不同领域，并广泛和非正式地讨论与追求科学事业有关的问题。

PI: M. Thomashow (Michigan State University)CoPIs: C. Chan (Michigan State University) and T. Chen (Oregon State University; subawardee)Collaborator: S.-H. Shiu (Michigan State University)The long range goals of the project are to gain a systems level understanding of plant responses to abiotic stress and to use the first principles gained to develop novel strategies to improve the stress tolerance of agriculturally important crops. These goals are important as abiotic stresses limit the geographical locations where crops can be grown and account for the majority of losses in yield on an annual basis. The overall objective is to identify the low temperature transcriptional networks that plants have evolved to survive freezing. As there is a direct link between freezing and dehydration injury, the results should also provide further insights into the nature of gene modules that impart tolerance to drought and other dehydration stresses. The specific aims of the project are two-fold. The first is to develop a detailed understanding of the low temperature transcriptional network of Arabidopsis and determine which components contribute to freezing tolerance. This will be accomplished by identifying transcription factors and other regulatory proteins that have key roles in configuring the low temperature transcriptome; identifying the cis-acting DNA regulatory elements through which these regulatory proteins function; and identifying the regulatory programs and gene modules that contribute to freezing tolerance (and potentially tolerance to drought and other abiotic stresses). The second aim of this project is to determine whether the low temperature transcriptional networks and gene modules that impart freezing tolerance in Arabidopsis are conserved in plants that cold acclimate (i.e., increase in freezing tolerance in response to low non-freezing temperatures) and whether "deficiencies" in these networks and modules contribute to the freezing sensitivity of those plants that do not cold acclimate. This aim will be accomplished through comparative genomic analysis of three closely related Solanum species which differ in cold tolerance: S. commersonii, potato and tomato. Together, the proposed studies incorporate the determination of gene expression at a genome level, a comparative genomic analysis of model and crop species, and the integration of computational analysis and empirical testing to reconstruct and model transcriptional regulatory networks that are fundamental to plant life and have importance in agriculture. Broader ImpactsImproving the abiotic stress tolerance of crops is crucial to meeting future demands for food and fiber. In addition, it is a key component of an emerging national vision to produce sufficient biomass per year in the U.S. to replace significant percentages of petroleum-based transportation fuels with biofuels produced from renewable resources. The studies proposed here directly relate to these important areas as they will provide a deeper understanding of the genomic mechanisms that plants have evolved to cope with abiotic stress and have the potential to provide genetic tools to improve the abiotic stress tolerance of plants. Microarray data generated in the course of these studies will be available through a project website (http://aztec.stanford.edu/cold/index.html) and through GEO and ArrayExpress. The project will also contribute to the training of a next generation of scientists who are experienced in bringing genomic, bioinformatic and computational approaches to bear on fundamental questions in biology. Finally, the project includes a summer undergraduate education and research training program which will target inclusion of underrepresented groups of our society. The goal is to provide the students with opportunities to learn more about different areas of genomic research and to discuss broadly and informally issues that relate to pursuing careers in science.