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.
