New Cell Type-Specific Data Sets and Computational Approaches for Plant Stress Biology

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Drought is one of the primary causes of reduced crop yields. Understanding how plants respond to water limitation is therefore important. Much progress has been made on understanding guard cells, the cell types that define the stomata. These are pores on the leaf surface that open and close in response to a variety of signals, including the water status of the plant. Under drought, stomata must act to balance a plant's “hunger” (CO2 from the atmosphere still needs to enter the leaf through the stomata for photosynthesis to occur) with its “thirst” (stomata close to conserve water under drought). The discovery of the ABA co-receptors PYR1 and PYR1-like family in 2009 by Sean Cutler, Erwin Grill, and colleagues, along with extensive genetic work by, among others, Julian Schroeder's and Sally Assmann's groups, has helped towards elucidation of the signaling networks in guard cells.******New methods for the isolation of genetic material from specific cell types, such as INTACT (isolation of nuclei tagged in specific cell types) and targeted TRAP (translating ribosome affinity purification), as established in plants by the Henikoff and Bailey-Serres Laboratories, respectively, are allowing unprecedented understanding of biological responses at the resolution of specific cell types. The Provart Lab's proposed research program aims to use such tools to understand how plants react to drought at the level of guard cell transcriptional and epigenomic responses. Further, we will investigate predicted protein-protein interactions that could be mediated by the drought hormone abscisic acid, and, finally, we will investigate polymorphisms in the vicinity of active sites of guard cell-expressed signaling proteins for their effect on the function of these proteins. In all cases, we will continue to create innovative “cyberinfrastructural” community resources / “apps” for use by my own lab and by plant researchers worldwide. While we have developed an initial framework for exploring data sets from the kilometer to nanometer scales, we will create linkages between these scales and enable easy searching of the data so that questions such as “could this particular small molecule dock with any solved or predicted protein tertiary structure, and might a polymorphism affect its binding?” may be asked.******Significance: The in planta/in vitro part of these three projects will result in several novel candidate stress-tolerance genes that can be readily deployed agriculturally. The cyberinfrastructure developed by my laboratory will enable new insights based on large data sets, will leverage the value of these publicly-funded data sets, and will permit a better understanding of plant biology. This is critical to feeding 9 billion people by 2050 under a changing climate.**