THE REGULATORY MECHANISM OF SECONDARY CELL WALL BIOSYNTHESIS IN GRASSES

Grass cell walls are environmentally and economically important, including being an abundant and sustainable carbon source to produce lignocellulosic biofuels. However, the crosslinked structure of cell walls limits polysaccharide extraction efficiency, which is a bottleneck for biofuel production. Based on knowledge in Arabidopsis, multiple transcription factors from various protein families can regulate cell wall biosynthesis by forming a series of feed-forward loops. Diverged from dicotyledonous plants approximately 150 million years ago, grasses have evolved different cell wall components and vascular bundle patterning in vegetative organs. In this dissertation, I aimed to characterize transcription factors and corresponding DNA binding sites that control cell wall biosynthesis in grasses. I hypothesized that unstudied grass cell wall transcription factors might fall into the following three categories: (1) orthologs of known dicot cell wall regulators that have conserved functions in regulating the cell wall network; (2) uncharacterized cell wall-associated transcription factors that also likely maintain similar functions with those in dicots; (3) uncharacterized grass cell wall-associated transcription factors that do not exist or have different functions in dicots. In Chapter 2, to analyze conservation and divergence between known dicot cell wall-associated transcription factors and their orthologs in grasses, we examined the phylogeny of R2R3 MYB protein family across selected dicots and grasses. Though we observed dicot-specific, grass-specific, and two panicoid grass-expanded clades, in general, most R2R3 MYBs that regulate SCW in Arabidopsis show evidence of conservation in the grasses. In Chapter 3, we developed a Rice Combined mutual Ranked (RCR) network to identify regulators of grass-specific genes and other uncharacterized cell wall-associated transcription factors in grasses. The RCR network covers approximately 90% of the rice genome and shows high quality in GO-term-based evaluations. Network prediction and further molecular genetic validation suggest that OsMYB61a can directly or indirectly regulate grass cell wall-specific genes, among others. The RCR network includes a cell wall sub-network with 96 novel transcription factors. Eight out of eleven of them altered expression of cell wall-related genes in a transient gene expression assays in rice protoplast. In Chapter 4, I further examined the conservation of cell wall-associated cis-elements in grasses using comparative de novo motif discovery and explored various scenarios for incorporation of grass-specific genes into cell wall biosynthesis pathways. Firstly, we observed that known dicots cell wall-associated cis-elements, such as MYB and NAC DNA binding sites, are significantly enriched within the promoters of CESA, lignin biosynthesis genes, as well as grass cell wall-specific genes. This provides support for the generally held hypothesis that known dicot cell wall-associated cis-elements are conserved in grasses. In addition, cis-elements that are potentially associated with AP2/ERF, C2H2, C2C2, and homeodomain proteins are also significantly enriched within promoters of grass cell wall biosynthesis genes. These results support the prediction and characterization of novel cell wall-associated transcription factors and binding sites. In all, this dissertation provides guidance toward functional characterization of cell wall-associated regulatory elements in grasses, knowledge of which will promote terrestrial biofuel production

Interdependent iron and phosphorus availability controls photosynthesis through retrograde signaling

International audienceAbstract Iron deficiency hampers photosynthesis and is associated with chlorosis. We recently showed that iron deficiency-induced chlorosis depends on phosphorus availability. How plants integrate these cues to control chlorophyll accumulation is unknown. Here, we show that iron limitation downregulates photosynthesis genes in a phosphorus-dependent manner. Using transcriptomics and genome-wide association analysis, we identify two genes, PHT4;4 encoding a chloroplastic ascorbate transporter and bZIP58 , encoding a nuclear transcription factor, which prevent the downregulation of photosynthesis genes leading to the stay-green phenotype under iron-phosphorus deficiency. Joint limitation of these nutrients induces ascorbate accumulation by activating expression of an ascorbate biosynthesis gene, VTC4 , which requires bZIP58. Furthermore, we demonstrate that chloroplastic ascorbate transport prevents the downregulation of photosynthesis genes under iron-phosphorus combined deficiency through modulation of ROS homeostasis. Our study uncovers a ROS-mediated chloroplastic retrograde signaling pathway to adapt photosynthesis to nutrient availability

Plant Metabolic Network 15: A resource of genome-wide metabolism databases for 126 plants and algae.

To understand and engineer plant metabolism, we need a comprehensive and accurate annotation of all metabolic information across plant species. As a step towards this goal, we generated genome-scale metabolic pathway databases of 126 algal and plant genomes, ranging from model organisms to crops to medicinal plants (https://plantcyc.org). Of these, 104 have not been reported before. We systematically evaluated the quality of the databases, which revealed that our semi-automated validation pipeline dramatically improves the quality. We then compared the metabolic content across the 126 organisms using multiple correspondence analysis and found that Brassicaceae, Poaceae, and Chlorophyta appeared as metabolically distinct groups. To demonstrate the utility of this resource, we used recently published sorghum transcriptomics data to discover previously unreported trends of metabolism underlying drought tolerance. We also used single-cell transcriptomics data from the Arabidopsis root to infer cell type-specific metabolic pathways. This work shows the quality and quantity of our resource and demonstrates its wide-ranging utility in integrating metabolism with other areas of plant biology