Plant RiboPrints Research

Brief project overview:

   Plants, as sessile organisms, need to constantly adjust their intrinsic programs of growth and development to the environmental conditions. This adaptation often involves changes in the developmentally predefined patterns of activity of one or more phytohormones. In turn, these hormonal fluctuations lead to alterations at the gene expression level and to the concurrent changes of the cellular activities. In general, the hormone-mediated regulation of plant development is achieved, at least in part, by modulating the transcriptional activity of hundreds of genes. The study of these transcriptional regulatory networks not only provides a conceptual framework to understand the fundamental biology behind these hormone-mediated processes, but also the molecular tools needed to accelerate the progress of modern agriculture. Although often overlooked, understanding of the translational regulatory networks behind complex biological processes has the potential to empower similar advances in both basic and applied plant biology arenas. By taking advantage of the recently developed ribosome footprinting technology, genome-wide changes in translation activity in response to ethylene were quantified at codon resolution, and new translational regulatory elements have been identified in Arabidopsis. Importantly, the detailed characterization of one of the novel regulatory elements indicates that this 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 general 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 large amount and dynamic nature of the generated data will be also utilized to generate hierarchical transcriptional and translational interaction network models for the two hormones and to explore the possible use of these diverse types of information to identify key regulatory nodes.  Finally, the comparison between two plant species will provide critical information on the conservation of the regulatory elements identified and, thus, inform research on future practical applications.

Objectives of the Project:

In order to achieve the general goals described above the following specific aims are being pursued:
AIM 1) Identify genes affected at the translational level in response to ethylene and/or auxin in both Arabidopsis and tomato seedlings.
AIM 2) Determine the hierarchical relationships between ethylene and auxin transcriptional and translational responses.
AIM 3) Identify cis-regulatory elements involved in translational regulation.
Aim 4) Determine the physiological significance of the translation regulation mediated by the identified cis-elements and their potential as signal integration nodes.