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Biochemical Regulation of Brassica Napus Diacylglycerol Acyltransferase 1

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Biochemical Regulation of Brassica Napus Diacylglycerol Acyltransferase 1 ! Biochemical Regulation of Brassica napus Diacylglycerol Acyltransferase 1 by Kristian Mark P. Caldo A thesis submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy in Plant Science Department of Agricultural, Food and Nutritional Science University of Alberta ©Kristian Mark P. Caldo, 2017 ! ! ABSTRACT Diacylglycerol acyltransferase 1 (DGAT1) is an integral membrane enzyme catalyzing the final and committed step in acyl-CoA-dependent triacylglycerol (TAG) biosynthesis. Previous metabolic control analysis showed that DGAT1 plays a substantial role in modulating the flow of carbon into seed oil in Brassica napus. In B. napus and many other organisms, DGAT1 has been used as a biotechnological tool to boost oil accumulation. Despite its key role in primary metabolism and biotechnological importance, no detailed structure-function information is available on the enzyme. This doctoral thesis aimed to shed light on the mechanism of action and regulation of DGAT1 by employing various techniques in molecular biology, and protein and lipid biochemistry. The first part of this dissertation involved the development of a purification protocol for recombinant B. napus DGAT1 (BnaDGAT1) produced in Saccharomyces cerevisiae. The optimized protocol included solubilization of membrane-bound BnaDGAT1 in n-dodecyl-!-D-maltopyranoside micelles (DDM), cobalt affinity chromatography, and size-exclusion chromatography. BnaDGAT1 was eluted mainly as a dimer from the last chromatographic step. The purified enzyme was well-folded, intact, and active and utilized acyl-CoAs which represent the major fatty acids in canola- type B. napus seed oil. In the second part of this dissertation, the hydrophilic N-terminal domain of BnaDGAT1 was identified as the enzyme’s regulatory domain that is not essential for catalysis. This regulatory domain has an intrinsically disordered region (IDR) and a folded segment. The IDR exhibited an autoinhibitory function and appeared to facilitate ! ""! ! positive cooperativity through dimerization. The folded segment has an allosteric site for acyl-CoA/CoA. Acyl-CoA, a substrate of the enzyme, was found to serve as a homotropic allosteric activator. On the other hand, CoA was identified as a non- competitive feedback inhibitor through interaction with the same allosteric site. The three-dimensional solution structure of the allosteric site and the amino acid residues interacting with CoA were elucidated, revealing details on this important regulatory element for allosteric regulation. In the third part of this dissertation, the purified enzyme in DDM micelles was lipidated and subjected to detailed kinetic analysis. Purified and lipidated BnaDGAT1 exhibited hyperbolic and sigmoidal responses to increasing concentrations of 1, 2- diacyl-sn-glycerol and acyl-CoA, respectively. Phosphatidate (PA) was identified as a feedforward activator of BnaDGAT1. The presence of PA may have facilitated the transition of the enzyme into the more active state that is also desensitized to substrate inhibition. PA may also relieve possible autoinhibition of BnaDGAT1 brought about by the N-terminal region. Furthermore, BnaDGAT1 was found to be a substrate of the sucrose non-fermenting kinase 1, which can phosphorylate the enzyme and convert it to a less active form. Based on these findings, an enzyme model is proposed illustrating the biochemical regulation of BnaDGAT1 through the aforementioned mechanisms. ! """! ! PREFACE The work presented in chapters 3-5 of this dissertation is based on the findings reported in the following papers. My contributions are summarized below each paper. Chapter 3: Caldo KMP, Greer MS, Chen G, LemieuxMJ, Weselake RJ (2015). Purification and properties of Brassica napus diacylglycerol acyltransferase 1. FEBS Lett. 589: 773–778. Copyright (2017), with permission from John Wiley and Sons. License #4159460347317 Contributions: I designed and performed all the experiments under the guidance of my supervisors. I wrote the first draft of the manuscript and further revised the manuscript with the co-authors. Chapter 4: Caldo KMP, Acedo JZ, Panigrahi R, Vederas JC, Weselake RJ, Lemieux MJ (2017). Diacylglycerol acyltransferase 1 is regulated by its N-terminal domain in response to allosteric effectors. Plant Physiology 175: 667–680 www.plantphysiol.org Copyright (2017) American Society of Plant Biologists Contributions: I designed and performed most of the experiments under the guidance of my supervisors. I performed the NMR experiments together with JZA. I wrote the first draft of the manuscript and further revised the manuscript with the co-authors. Chapter 5: Caldo KMP, Shen W, Xu Y, Hanley-Bowdoin L, Chen G, Lemieux MJ, Weselake RJ. Brassica napus diacylglycerol acyltransferase 1 is feedforward activated by phosphatidate and inhibited by SnRK1-catalyzed phosphorylation. To be submitted. Contributions: I designed and performed all the experiments under the guidance of my supervisors, except the phosphorylation assay, which was performed by WS. I ! "#! ! wrote the first draft of the manuscript and further revised the manuscript with the co- authors. ! #! ! ACKNOWLEDGEMENTS I acknowledge the following people who had been instrumental in the completion of this thesis. Firstly, I would like to extend my deepest gratitude and appreciation to my supervisor, Dr. Randall Weselake, for providing me with continuous guidance, wisdom and support throughout the course of my doctoral studies. Thank you for sharing your knowledge of and passion for plant biochemistry and biotechnology, for providing a very stimulating and well-equipped research environment, and for giving me many opportunities for professional development. I am also very grateful to my co-supervisor, Dr. Joanne Lemieux, for sharing her knowledge and expertise on membrane proteins, and for her guidance and encouragement during my graduate work. I am also thankful to my committee members, Dr. Nat Kav and Dr. Jianping Wu, for their valuable advice and suggestions on various parts of my research. I am also thankful to Dr. Rene Jacobs for his helpful counsel and, together with Dr. Lingyun Chen, for serving as my arm’s length examiners. I would also like to thank Dr. Timothy Durrett and Dr. Michael Gänzle for serving as external examiner and chair of my final PhD examination, respectively. I am very grateful to my collaborators namely Dr. Wei Shen from North Carolina State University for performing the phosphorylation assays involving 32P, Jeella Acedo and Dr. John Vederas from the Department of Chemistry for their help with NMR analysis, and Dr. Rashmi Panigrahi from the Department of Biochemistry for her help in protein work. I would also like to thank Dr. Sten Stymne for providing yeast strain H1246, which had been very useful to my research. I am also thankful to Dr. Elena Arutyunova for sharing her knowledge on membrane protein work and enzyme kinetics, and Yang Xu for her help and valuable suggestions in some of my experiments. I also ! #"! ! thank Dr. Guanqun Chen and Dr. Elzbieta Mietkewska for helping me get started in the lab with the proper techniques in lipid biochemistry and molecular biology. I am also thankful to the rest of the members of the Weselake group and Lemieux group who supported me in my graduate studies. I also acknowledge the financial support for my PhD work provided by the Natural Sciences and Engineering Research Council of Canada, Alberta Innovates Bio Solutions, Alberta Innovates Technology Futures, and Alberta Canola Producers Commission. I am also thankful to my grandparents, parents and siblings for their steadfast love and encouragement. I am extremely grateful to my wonderful wife for her unwavering love and support, and for always pushing me to continuously persevere and move forward throughout my graduate studies. And lastly, I am thankful to the One above for giving me the opportunity to explore His wonderful molecular creations. ! #""! ! TABLE OF CONTENTS CHAPTER 1. Introduction ............................................................................................. 1 CHAPTER 2. Literature Review .................................................................................... 6 2.1. Glycerolipids, including triacylglycerol .................................................................. 6 2.2. Plant fatty acid and triacyglycerol biosynthesis ...................................................... 8 2.2.1. Overview .......................................................................................................... 9 2.2.2. Fatty acid biosynthesis ..................................................................................... 9 2.2.2.1. Acetyl-CoA carboxylase ......................................................................... 10 2.2.2.2. Fatty acid synthase .................................................................................. 12 2.2.2.3. Fatty acid export from the plastid and re-esterification .......................... 13 2.2.3. The first three reactions of the Kennedy pathway ......................................... 14 2.2.3.1. sn-Glycerol-3-phosphate acyltransferase ................................................ 14 2.2.3.2. Lysophosphatidate acyltransferase .......................................................... 14 2.2.3.3. Phosphatidic acid phosphatase ............................................................... 15 2.2.4. Diacylglycerol acyltransferase ....................................................................... 18 2.2.5. Acyl-CoA-independent
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