Leveraging mass spectrometry-based proteomics and post-translational modifications for system-wide understanding of bioenergy plants and their environment

Bioenergy research focuses on utilizing renewable biomass feedstocks to produce biofuels and bioproducts to address growing concerns about energy security and climate change. To better understand the details of bioenergy crop production and conversion to bioproducts, it is essential to characterize bioenergy plants and their environments at a molecular systems level. Mass spectrometry has emerged as a promising technique for detailed proteomic information, including post-translational modifications (PTMs), of molecular processes and cellular functions of biological systems. In this dissertation, proteomic approaches have been optimized and implemented to deepen our understanding of the interaction of plants and their environment in a bioenergy research context. Growing studies support the concept of the plant holobiont, where plant growth and fitness are a result of the collective genome expression of both the plant and its associated microbes. This dissertation illustrates the optimization of proteomic workflows to understand how the poplar plant and its associated microbes respond to complex ecological interactions occurring in the rhizosphere, such as a key protein kinase that controls plant-fungal symbiosis. Similarly, abiotic factors such as the diurnal cycle play a key role in synchronizing plant behavior with external cues and are important for a plant\u27s phenotypic plasticity. We have utilized an advanced bioinformatic workflow with de novo-assisted database searching to provide the first molecular evidence of how both proteins and their PTMs are regulated by the diurnal cycle in poplar plants. For the goal of efficient conversion of biomass to biofuels, the plant’s lignin content has been a key bottleneck because it limits the accessibility of cellulosic sugar. Genetic modification of the lignin biosynthesis pathway can help reduce lignin, but this often results in stunted growth phenotype. Multi-omics analysis of lignin-modified model grass, Brachypodium distachyon provided a deeper understanding of the undesired phenotypic effects caused by lignin modification and revealed key molecular signals that could be targeted for genetic manipulations. Overall, this dissertation research is one of the first concerted proteomics investigations of the biotic and abiotic details of poplar and revealed key aspects of symbiotic microbial associations as well as the pleiotropic effects caused by lignin modification in Brachypodium