Systems analysis of grass secondary cell wall development and regulation for biofuel production
EMSL Project ID
49510
Abstract
The objective of this proposal is to identify the proteins, phosphopeptides, transcripts, and metabolic signatures that mediate secondary cell wall (SCW) development in grasses. Grass cell walls are one of the most abundant potential sources of biomass for biofuel production. However, the biological conversion of grass biomass to fuel is limited by deconstruction of cell walls into component sugars. Grass cell walls have divergent content and tissue patterning and their cell wall synthesis and control is likely different from those of dicots. Therefore, understanding grass cell wall synthesis and control can be used to improve the quality of grasses as a biofuel feedstock. The first objective would gather and combine proteome, phosphoproteome, transcriptome, and cell wall chemical analysis of the elongating internode of rice, a model grass with a well-annotated genome. Microscopy demonstrates that the second internode at elongation stage exhibits a gradient of lignin, indicative of active cell wall synthesis in the basal and central segments of the internode and less deposition in the upper parts. Enrichment of protein phosphorylation events in a rice secondary cell wall network and a number of literature reports of protein kinases and phosphorylation events related to cell wall processes, justifies attainment of phosphoproteome data for this developmental gradient. This objective will test the hypothesis that the abundance of proteins with known roles in grass cell wall synthesis and regulation correlate with the deposition of appropriate cell wall components. If this is the case, modeling the relationship between the abundance of proteins and accumulation (or depletion) of cell wall components, will identify other proteins with similar relationships with cell wall components that may function in cell wall biology. Transcriptome data within the same samples will provide complementary information and extend the coverage of proteome. Combining these -omics studies will extend understanding of grass cell wall synthesis and its regulation and provide testable hypotheses about candidate regulatory genes and post-translational modifications of cell wall synthesis. The second objective of this proposal is to develop a transient assay that will accelerate functional studies of candidate cell wall regulators, currently a time-consuming process requiring generation of grass mutants via tissue culture and characterization of multiple generations. As an alternative, this objective would explore the use of metabolite profiling of transiently transformed protoplasts. The project will measure metabolic responses to transiently overexpressing characterized transcription factors in protoplasts. If metabolic response profiles for known regulatory proteins can be determined, the project will attempt to categorize and infer the function of additional candidate regulator genes based on their metabolics response profiles. As a control for the metabolic data and a useful experiment in itself for placing the transcription factors examined into the grass gene regulatory network, the project will also conduct transcriptomics of protoplasts with induced tranascription factor expression. By collaborating with EMSL on the proteome, phosphoproteome and metabolome analyses and with JGI on the transcriptomics, this project will extend our understanding of grass cell wall synthesis and its regulation by providing testable hypotheses and establish a platform to quickly test the functions of candidate regulators toward design of superior bioenergy grass crops. Project Details
Project type
FICUS Research
Start Date
2016-10-01
End Date
2018-09-30
Status
Closed
Released Data Link
Team
Principal Investigator
Team Members
Related Publications
Lin F, BJ Williams, PA Thangella, A Ladak, AA Schepmoes, HJ Olivos, K Zhao, SJ Callister, and LE Bartley. 2017. "Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode." Frontiers in Plant Science 8:1134. doi:10.3389/fpls.2017.01134