No description available.

<p>Plants naturally deposit a significant amount of carbon towards lignin, a polymer that imparts mechanical strength to cell walls but impedes our utilization of the polysaccharides in lignocellulosic biomass. Genetic engineering of lignin has demonstrated profound success in improving the processing of the biomass. Lignin is derived from the phenylpropanoid pathway, the architecture of which is well understood based upon the biochemical and genetic studies conducted to date. In contrast, we lack a systematic and quantitative view of the factors that determine carbon flux into and within this branched metabolic pathway in plants. To explore the control of carbon allocation for phenylalanine and lignin biosynthesis, we have developed a kinetic model of the pathway in Arabidopsis to test the regulatory role of several key enzymatic steps. We first established a ¹³C isotope feeding system for the measurement of flux using excised wild-type Arabidopsis stems. The excised stems continued to grow and lignify in our feeding system. When ring ¹³C₆-labeled phenylalanine ([¹³C₆]-Phe) was supplied to excised stems, isotope label was rapidly incorporated into soluble intermediates and lignin. Using this approach, we then analyzed metabolite pool sizes and isotope abundances of the pathway intermediates in a time course from stems fed with [¹³C₆]-Phe of different concentrations, and used these data to parameterize a kinetic model constructed with Michaelis-Menten kinetics. Our model of the general phenylpropanoid pathway captured the dynamic trends of metabolite pools <i>in vivo</i>and predicted the metabolic profiles of an independent feeding experiment. Based on the model simulation, we found that subcellular sequestration of pathway intermediates is necessary to maintain lignification homeostasis when metabolites are over-accumulated. Both the measurements and simulation suggested that theavailability of substrate Phe is one limiting factor for lignin flux in developing stems. This finding indicates new gene targets for lignin manipulation in plants. To extend our kinetic model to simulate flux distribution in response to genetic perturbations, we conducted an RNA-sequencing experiment in wild type and 13 plants with modified lignification, and integrated the transcriptional data with the metabolic profiles. We found that the biosynthesis of Phe and lignification are tightly coordinated at transcriptional level. The coregulation of the shikimate and phenylpropanoid pathways involves transcriptional and post-translational regulatory mechanisms to maintain pathway homeostasis. Our results also indicate that induction of Phe supply and enhancement of PAL activity are both effective strategies to increase carbon flux into the phenylpropanoid network.</p><p>In this interdisciplinary project, we have taken various system biology approaches to understand metabolic flux towards lignin, the second most abundant carbon sink in nature. We have combined isotope labeling aided flux measurements and mathematical simulation, and have integrated metabolome data with transcriptome profiles. The experiments and analysis have been conducted in both wild-type Arabidopsis and those with perturbed lignification. The novel work not only provides insight into our knowledge of phenylpropanoid metabolism, but also creates a framework to systematically assemble gene expression, enzyme activity, and metabolite accumulation to study metabolic fluxes, the ultimate functional phenotypes of biochemical networks.</p>

<p>The phenylpropanoid pathway gives rise to a wide variety of specialized metabolites, but the majority of carbon flux going through this pathway is directed towards the synthesis of the lignin monomers: <i>p</i>-coumaryl alcohol, coniferyl alcohol and sinapyl alcohol. Lignin is a major impediment in biomass saccharification, which negatively affects animal feed and biofuel production. In an effort to improve biomass for the latter purposes, researchers have altered the polymer through genetic manipulations and generated biomass with lower recalcitrance to saccharification; however, in many cases these efforts have resulted in plant dwarfism. To date, we do not have a full understanding of the extent of lignin modifications a plant is able to tolerate without affecting its growth. More importantly, the mechanism that links dwarfism and modifications in lignin content and composition remains unknown. To contribute to answering these questions, we designed a strategy to incorporate a novel monomer into the lignin of <i>Arabidopsis thaliana</i>. We used mutants in genes that code for enzymes and regulators of the phenylpropanoid pathway to redirect the pathway’s flux towards the synthesis of <i>p</i>-coumaraldehyde and prevent the incorporation of <i>p-</i>coumaryl alcohol. Despite being mutated for the genes typically considered to be required for monolignol biosynthesis, the plants we generated continue to incorporate <i>p-</i>coumaryl alcohol into their lignin. This result suggests that the pathway’s architecture has not been completely elucidated and that there are more enzymes involved in lignification than previously thought. Additionally, we explored the connection between perturbations in phenylpropanoid metabolism and plant growth, by using an inducible system to track the changes in gene expression and metabolism that occur when phenylpropanoid metabolism is restored in a lignin biosynthetic mutant. The use of an inducible system allowed us to not only determine the metabolic processes affected in this mutant, but the proximal sequence of events that lead to restored growth when a functional copy of the mutant gene is induced. Finally, we redirected the flux through the pathway to assess the effects of simultaneously modulating lignin content and composition. Through this project we discovered that redirecting phenylpropanoid flux towards the synthesis of sinapyl alcohol in lignin-deficient mutant backgrounds, results in plant dwarfism. The growth impairment of these mutants can be overcome by providing exogenous coniferyl alcohol, suggesting that dwarfism in these mutants is caused by deficiency in coniferyl alcohol and/or derivatives thereof and not lignin alone. Altogether these projects allowed us to define the cellular processes affected by perturbations in phenylpropanoid homeostasis and the role of other phenylpropanoids besides lignin in this process.</p>

<div>L-phenylalanine (Phe) is an important amino acid which is the precursor of various plant secondary metabolisms. Its biosynthesis and consumption are governed by different levels of regulatory mechanisms, yet our understanding to them are still far from complete. The plant has evolved a complex regulation over Phe, likely due to the fact that a significant portion of carbon assimilated by photosynthesis is diverted to its downstream products. In particular, lignin as one of them, is among the most abundant polymers in plant secondary cell wall. Studies have unraveled the interconnected metabolism involved in lignin biosynthesis, and a hierarchical gene regulatory network on top of it is also being uncovered by different research groups. These biological processes function together for sufficient lignification to ensure cell wall hydrophobicity and rigidity for plant normal growth. Yet on the other hand, the presence of lignin hinders the efficient saccharification process for biofuel production. Therefore, it is fundamental to understand lignin biosynthesis and its upstream Phe biosynthesis in a systematic way, to guide rational metabolic engineering to either reduce lignin content or manipulate its composition <i>in planta</i>.</div><div> </div><div> Phe biosynthesis was predominantly existed in plastids according to previous studies, and there exists a cytosolic synthetic route as well. Yet how two pathways are metabolically coordinated are largely under-explored. Here I describe a flux analysis using time course datasets from ¹⁵N L-tyrosine (Tyr) isotopic labeling studies to show the contributions from two alternative Phe biosynthetic routes in Petunia flower. The flux split between cytosolic and plastidial routes were sensitive to genetic perturbations to either upstream chorismate mutase within shikimate pathway, or downstream plastidial cationic amino-acid transporter. These results indicate the biological significance of having an alternative biosynthetic route to this important amino acid, so that defects of the plastidial route can be partially compensated to maintain Phe homeostasis.</div><div> </div><div> To understand the metabolic dynamics of the upstream part of lignin biosynthesis, we developed a multicompartmental kinetic model of the general phenylpropanoid metabolism in Arabidopsis basal lignifying stems. The model was parameterized by Markov Chain Monte Carlo sampling, with data from feeding plants with ring labeled [¹³C₆]-Phe. The existence of vacuole storage for both Phe and <i>p</i>-coumarate was supported by an information theoretic approach. Metabolic control analysis with the model suggested the plastidial cationic amino-acid transporter to be the step with the highest flux controlling coefficient for lignin deposition rate. This model provides a deeper understanding of the metabolic connections between Phe biosynthesis and phenylpropanoid metabolism, suggesting the transporter step to be the promising target if one aims to manipulate lignin pathway flux.</div><div> </div><div> Hundreds of gene regulatory interactions between transcription factors and structural genes involved in lignin biosynthesis has been reported with different experimental evidence in model plant Arabidopsis, however, a public database is missing to summarize and present all these findings. In this work, we documented all reported gene regulatory interactions in Arabidopsis lignin biosynthesis, and ended up with a gene regulatory network consisting of 438 interactions between 72 genes. A network is then constructed with linear differential equations, and its parameters were estimated and evaluated with RNA-seq datasets from 13 genetic backgrounds in Arabidopsis basal stems. We combined this network with a kinetic model of lignin biosynthesis starting from Phe and ending with all monolignols participated in lignin polymerization. This hierarchical kinetic model is the first model integrating dynamic information between transcriptional machinery and metabolic network for lignin biosynthesis. We showed that it is able to provide mechanistic explanations for most of experimental findings from different genotypes. It also provides the opportunity to systematically test all possible genetic manipulation strategies targeting to lignification relevant genes to predict the lignin phenotypes <i>in silico</i>.</div>

Mémoire (M.Ress.Renouv.)-- Université du Québec à Chicoutimi, 1994. / Résumé disponible sur Internet. CaQCU Document électronique également accessible en format PDF. CaQCU