The overarching goal of my research is to understand the molecular mechanisms governing plant responses to environmental stimuli and stress; in particular the involvement of the phosphoinositide signaling pathway. The membrane associated inositol phospholipids and soluble inositol phosphates provide a means of both intercepting a signal at the membrane and propagating it within the cell. Our current focus is on inositol pyrophosphates, a novel class of signaling molecules. Our hypothesis is that these molecules are involved in energy and nutrient sensing in plants and we are taking a multifaceted approach of molecular genetics, biochemistry, physiology, and systems biology to address this hypothesis as well as understand the global regulation of the pathway.
Another avenue of research in the lab is to characterize seedling responses to microgravity and the spaceflight environment. Our first flight experiment “Plant Signaling in Microgravity” was a comparative study of transcriptional profiles of wild type and transgenic Arabidopsis seedlings (altered in phosphoinositide-mediated signaling), grown on the International Space Station (ISS). In a second flight experiment “Plant RNA Regulation” we will extend this work to other aspects of gene regulation including changes in small RNAs. Plants will be an integral part of long distance space travel or habitation. An understanding of how plants respond to the spaceflight environment is an important step towards enabling them to withstand stresses and optimize their growth.
Ph.D. Plant Biology University of Illinois 1991
M.S. Plant Biology University of Illinois 1988
M.S. Biochemistry University of Colombo 1984
B.S. Biological Science University of Colombo 1982
Area(s) of Expertise
Inositol phosphate metabolism, plant nutrient and energy sensing, plant stress responses
- Evaluating the Effects of the Circadian and Time of Day on Plant Gravitropic Responses , (2022)
- A Role for Inositol Pyrophosphates in the Metabolic Adaptations to Low Phosphate in Arabidopsis , METABOLITES (2021)
- NASA GeneLab RNA-seq consensus pipeline: standardized processing of short-read RNA-seq data , ISCIENCE (2021)
- The Circadian-clock Regulates the Arabidopsis Gravitropic Response , Gravitational and Space Research (2021)
- Uncovering Transcriptional Responses to Fractional Gravity in Arabidopsis Roots , LIFE-BASEL (2021)
- Biosynthesis and possible functions of inositol pyrophosphates in plants , Frontiers in Plant Science (2015)
- Certain Malvaceae Plants Have a Unique Accumulation of myo-Inositol 1,2,4,5,6-Pentakisphosphate , Plants (2015)
- Methods for RNA Profiling of Gravi-Responding Plant Tissues , Methods in Molecular Biology (2015)
- Do phosphoinositides regulate membrane water permeability of tobacco protoplasts by enhancing the aquaporin pathway? , Planta (2014)
- Phosphoinositide-signaling is one component of a robust plant defense response , Frontiers in Plant Science (2014)
Plants are essential for life on earth and for long duration spaceflight and colonization. However, the spaceflight environment is not ideal for plant growth and understanding how plants sense and respond to this environment is critical for enabling plant growth in space. The objective of this study is to identify mechanisms regulating plant responses to spaceflight and microgravity. GeneLab contains several datasets of molecular responses of Arabidopsis grown in spaceflight or onboard the International Space Station. However, there is little overlap among these datasets suggesting that microgravity-specific responses may be masked by the differences in experimental conditions. We evaluated distinct gene sets and identified common cis-regulatory elements. We propose to investigate these top candidates and reveal overarching regulatory pathways. We will carry out Yeast 1Hybrid library screening to identify their target transcription factors. We will also generate Arabidopsis plants with either reduced (knockdown) or increased (over expression) expression of these factors and study their response to simulated microgravity and other stresses. This approach is more inclusive than the overlap of specific gene responses across experiments and is particularly beneficial for identifying patterns in limited data sets. The results from this study will provide valuable information on the potential primary effectors governing plant responses to spaceflight and microgravity.
Plants will be a crucial component for astronaut health and well-being during any long-distance spaceflight or colonization mission: as a source of food, for replenishing water and purifying air as well as physiological and psychological comfort. The challenge is to understand how plants respond to the spaceflight environment to enable plants to thrive in potentially hostile environments. As technologies have advanced for global gene expression, transcriptome level research has become an integral part of experiments and provides knowledge of gene expression resulting from the conditions of spaceflight. Steady state transcript abundance quantified by RNASeq is frequently used as measure of gene expression with the implicit assumption that transcriptional changes upon a treatment (such as a stress) are indicative of the downstream response. However, changes in mRNA abundance do not necessarily lead to corresponding changes in protein, and transcript and protein abundance are not highly correlated. The data from spaceflight experiments BRIC20 (PI Wyatt) and Plant Signaling (PI Perera) suggest that post-transcriptional regulation plays an integral role in gene expression differences between spaceflight and ground controls. The differential expression, abundance and phosphorylation of translational machinery in spaceflight leads to the obvious questions: What genes are being post transcriptionally regulated and by what mechanism(s)? To answer these questions, PIs Wyatt and Perera plan to combine expertise and resources to generate compatible multi-omics datasets and provide a comprehensive picture of transcriptional and post transcriptional regulation. This integrated approach will help answer fundamental questions regarding plant adaptation to spaceflight and this proposal is aligned with sub-topic PL-A of Appendix B. The novel datasets and analyses will address questions outlined in Research Emphasis 2 of the Space Biology Science Plan 2016-2025, specifically â€œ(a) Answer basic questions about how plants respond to changes in gravity and other environmental factors associated with spaceflight. And (b) Build on past plant research to provide a better understanding of physiological responses of plants to spaceflight, providing new knowledge that can facilitate the development of a bioregenerative life support systemâ€. Analyses will also addresses Research Emphasis 4: molecular and cellular biology, specifically â€œ(a) Studies designed to determine how spaceflight alters gene expression at the transcriptomic, metabolomics and proteomics levels in the different tissues or cell types within the same organism, and how these changes impact the organismâ€™s overall health during space travelâ€.
The circadian clock, an internal timekeeping mechanism, enables organisms to temporally organize their molecular and biochemical activities so that they are optimally timed with environmental conditions. Many environmental responses are gated by the circadian clock. Responses to environmental stimuli vary depending on the time of day or season that it is perceived by the organism. We examined microarray and RNA-Seq data sets available in GeneLab and found that components of the circadian clock are often identified as differentially expressed in response to gravity in multiple studies in Arabidopsis. This finding led us to investigate the potential for gating of gravitropic responses such as root bending. We observed that the time of day the stimulus is provided affects the magnitude of the gravitropic response. Further, this response is altered in a circadian clock mutant. Based on these findings we hypothesize that, like other environmental stimuli, the response to gravity is gated by the circadian clock. We propose to investigate if there is an integrated relationship between the circadian clock and gravity. First, we propose to determine if the time of day and year can impact the observed effects of microgravity indicating that these factors should be considered in all microgravity research. Secondly we will examine if microgravity affects circadian-regulated activities and the timing of all aspects of physiology and development.
Plants are a vital part of human life support systems for long-duration space flight and habitation. However, the space environment is not optimal for plant growth. Plants grown in space are subject to many unfamiliar stresses (in addition to the lack of gravity) and recent transcriptional profiling studies indicate that there are global changes in gene expression between space and ground controls. Post transcriptional regulation of RNA is emerging as an important mechanism of modulating gene expression under different environmental conditions. To date however, there have been no studies to examine the role of small regulatory RNAs in plant responses to the space environment. We propose to examine the transcriptional and post transcriptional mechanisms that regulate early seedling development in space and microgravity. Our hypothesis is that plant adaptation and response to the space environment will involve novel regulatory small RNAs. Our previous flight experiment â€œPlant Signalingâ€ has revealed novel regulatory mechanisms and provides the foundation for further investigation and the proposed research. The long term goals are to understand the molecular mechanisms by which plants sense and adapt to changes in their environment and to characterize the regulatory networks that mediate these responses. This knowledge will be valuable for designing plants which are better able to withstand space flight, microgravity, and adverse environmental conditions.
Myo-inositol phosphates (InsPs) are signaling molecules that are critically important in a number of developmental, metabolic and signaling processes in eukaryotes. The fully phosphorylated form, inositol hexakisphosphate or InsP6, plays important roles in many eukaryotes. A new frontier for InsP signaling is the study of unique signaling roles for a novel group of InsPs containing diphospho- or triphospho- moieties (PPx) at one or more positions on the Ins ring. In some ways, these PPx-InsPs are analogous to ATP in that they contain high-energy pyrophosphate bonds, and in addition, have been linked to communicating the energy status of the cell in other organisms. In this collaborative project, we previously developed analytical methods to detect and quantify PPx-InsPs in plant tissues, identified and cloned genes encoding the VIP kinases that are responsible for inositol pyrophosphate production in plants, and developed genetic resources to examine function of the Vip genes. Our preliminary data using mutants lacking both Vip genes reveal these genes are key in signaling the energy status of the plant cell. Further, we have identified a possible mechanistic link between inositol pyrophosphate signaling and a major regulator of eukaryotic metabolism, the Sucrose non-fermenting related kinase 1 (SnRK1). Given the immediate need to understand and manipulate plant bioenergy, the long-term goal of this project is to understand how InsP6, InsP7 and InsP8 convey signaling information within the cell. We focus on these molecules in plants, but point out that our model and findings are applicable to understanding the InsP6 signaling hub in other eukaryotes. During the proposed project, we plan to address several unresolved questions pertaining to PPx-InsPs and energy by first adding to a preliminary kinetic model of this signaling pathway.