Identification of Translational Hormone-Response Gene Networks and cis-Regulatory Elements

翻译激素反应基因网络和顺式调控元件的鉴定

基本信息

批准号：
1444561
负责人：
Jose Alonso
金额：
$ 319.94万
依托单位：
North Carolina State University
依托单位国家：
美国
项目类别：
Continuing Grant
财政年份：
2015
资助国家：
美国
起止时间：
2015-08-01 至 2024-07-31
项目状态：
已结题

来源：
https://www.nsf.gov/awardsearch/showAward?AWD_ID=1444561&HistoricalAwards=false
关键词：
Identification Translational Hormone Response Gene

项目摘要

Co-PIs: Anna Stepanova (Plant and Microbial Biology, North Carolina State University), Steffen Heber (Computer Science, North Carolina State University), Cranos Williams (Electrical and Computer Engineering, North Carolina State University)Unlike animals that can seek shelter to escape from bad weather, plants cannot move and must spend their entire lives in one place, rain or shine. Plants are able to adapt to challenging conditions by adjusting how they grow and how much nutrients they take in from the environment. Understanding these adjustments of plants in response to environmental challenge is important for a basic understanding of how plants may respond in rapidly changing environments, and will yield insights about ways to increase agricultural production to support a fast growing human population. Basic research suggests that plants, like animals, use a small set of signaling chemicals, hormones, to sense the environment, and to control their metabolism and growth. Since hormones play such a key role in regulating plant development and responses to the environment, it is important to identify the main 'genetic hubs', where environmental signals and hormonal changes are integrated in order to control a plant's life. This basic scientific knowledge will improve our understanding of how plants grow and react to stress and will help in the development of new crop varieties that perform well under extreme conditions. Traditionally scientists have studied how hormones influence gene activity by examining gene expression by measuring the copying of DNA into RNA, the first step in the transfer of genetic information into proteins, which play an enormous variety of functional roles in cells. However, an increase in expression does not always mean that more protein will be made because protein production from encoded RNA molecules is a highly regulated process. Fortunately, the recently developed Ribo-seq technology provides the capability of measuring protein production by every active gene in the genome at once. By using this technology, 'genetic hubs' that connect environmental sensing with the control of plant growth can be uncovered. Understanding how these hubs work at the molecular level will add new tools to the "biotechnological toolbox" that scientists can then use to develop better and more resilient crops.Genome-wide changes in translation activity in response to ethylene have been quantified at codon resolution by taking advantage of the recently developed ribosome footprinting technology, making it possible to identify new translational regulatory elements in Arabidopsis. Importantly, detailed characterization of one of the novel regulatory elements indicates that regulation of translation is not miRNA dependent, and that the element identified is also responsive to the plant hormone auxin, implicating this element in the interaction between ethylene and auxin. These findings not only confirm the basic biological importance of translational regulation and its potential as a signal integration mechanism, but also open new avenues for identifying, characterizing and utilizing additional regulatory modules of gene expression in plant species of economic importance. Towards that goal, a plant-optimized ribosome footprinting methodology will be deployed to examine the translation landscape of two plant species, tomato and Arabidopsis, in response to two plant hormones, ethylene and auxin. A time-course experiment will be performed to maximize the detection sensitivity and diversity (early vs. late activation) of translational regulatory elements. The resulting data, reflecting temporal changes, will be used to generate hierarchical transcriptional and translational interaction network models for the two hormones, and to identify key regulatory nodes. Finally, the comparison between two plant species will provide critical information about conservation of the regulatory elements, thereby informing research on future practical applications. All the sequence data will be made publicly available through the NCBI-SRA. All biological materials and genomic data will be available through a dedicated project website at brcwebportal.cos.ncsu.edu/plantriboprints). In addition, software and contents of the genome browser will be deposited at iPlant to ensure long-term public access. Arabidopsis seeds and DNA constructs will be deposited at the Arabidopsis Biological Resource Center. A new outreach program to promote interest among middle- and high-school kids in combining biology, computers, and engineering will be developed. A web-based bilingual dissemination tool, Plants4Teens, as well as live monthly demos at the North Carolina Museum of Natural Sciences and local schools, will be implemented in this new outreach program. Examples of demonstration modules will include comparisons between simple electronic and genetic circuits.

CO-PIS：Anna Stepanova（北卡罗来纳州立大学的植物和微生物生物学），Steffen Heber（北卡罗来纳州立大学计算机科学），Cranos Williams（北卡罗来纳州州立大学电气和计算机工程大学），不像那些可以寻求避难所的动物不同，植物无法逃脱，植物必须在一个地方移动并在一个地方度过一生。植物能够通过调整其生长方式以及从环境中获得多少营养来适应具有挑战性的条件。了解植物对环境挑战的这些调整对于对植物在迅速变化的环境中如何反应的基本了解非常重要，并将产生有关增加农业生产的方法以支持快速增长的人口的见解。基础研究表明，植物（例如动物）使用一小部分信号化学物质，激素来感知环境并控制其新陈代谢和生长。由于激素在调节植物的发育和对环境的反应中起着如此关键作用，因此必须确定主要的“遗传枢纽”，在这种情况下，环境信号和激素变化是为了控制植物生命的。这种基本科学知识将提高我们对植物如何成长和对压力的反应的理解，并有助于发展在极端条件下表现良好的新作物品种。传统上，科学家研究了激素如何通过测量将DNA复制到RNA中检查基因表达，这是将遗传信息转移到蛋白质中的第一步，遗传信息转移到蛋白质中，这些信息在细胞中扮演着各种各样的功能作用。但是，表达的增加并不总是意味着将产生更多的蛋白质，因为编码的RNA分子产生蛋白质是一个高度调节的过程。幸运的是，最近开发的Ribo-Seq技术提供了一次测量基因组中每个活性基因的蛋白质产生的能力。通过使用这项技术，可以发现将环境传感与植物生长控制的“遗传枢纽”被发现。了解这些枢纽如何在分子水平上起作用将为“生物技术工具箱”添加新工具，然后科学家可以使用该工具来开发更好，更弹性的农作物。通过利用最近开发的核糖体足迹技术的优势，可以在CODON分辨率上量化了对乙烯的转换活动的基因组变化，从而使其成为了新的翻译元素。重要的是，新型调节元件之一的详细表征表明，翻译的调节不是miRNA的依赖性，并且所鉴定的元素也对植物激素生长素的响应也有响应，这意味着该元素在乙烯与生长素之间的相互作用中。这些发现不仅证实了转化调节及其作为信号整合机制的潜力的基本生物学重要性，而且还开辟了新的途径，以识别，表征和利用基因表达的其他调节模块，这是经济重要性的植物种类。为了实现这一目标，将部署一种植物性优化的核糖体足迹方法，以检查两种植物物种番茄和拟南芥的翻译景观，以响应两种植物激素，即乙烯和生长素。将进行时间课程实验，以最大程度地提高转化调节元件的检测灵敏度和多样性（早期激活）。所得数据反映时间变化，将用于为两种激素生成层次转录和翻译交互网络模型，并识别关键的调节节点。最后，两种植物物种之间的比较将提供有关监管元素保护的关键信息，从而为未来的实际应用研究提供了信息。所有序列数据将通过NCBI-SRA公开提供。所有生物材料和基因组数据都将通过brcwebportal.cos.ncsu.edu/plantriboprints的专用项目网站获得。此外，基因组浏览器的软件和内容将存放在iPlant上，以确保长期的公众访问。拟南芥种子和DNA构建体将沉积在拟南芥生物资源中心。将开发一项新的外展计划，以促进中学和高中生在结合生物学，计算机和工程方面的兴趣。这项新的外展计划将实施基于网络的双语传播工具，即植物4teens，以及北卡罗来纳州自然科学博物馆和当地学校的现场演示。示范模块的示例将包括简单电子和遗传回路之间的比较。