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UNIVERSITY of CALIFORNIA, SAN DIEGO Early Signaling in Plant UNIVERSITY OF CALIFORNIA, SAN DIEGO Early Signaling in plant immunity A dissertation submitted in partial satisfaction of the requirements for the degree Doctor of Philosophy in Biology by Tenai E. Eguen Committee in charge: Professor Steven Briggs, Chair Professor Marty Yanofsky, Co-Chair Professor Tracy Johnson Professor Bernhard Palsson Professor Yunde Zhao 2013 Copyright Tenai E. Eguen, 2013 All rights reserved The Dissertation of Tenai E. Eguen is approved, and it is acceptable in quality and form for publication on microfilm and electronically: _______________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ ________________________________________________________________________ Chair University of California, San Diego 2013 iii DEDICATION This dissertation is dedicated to all my friends and family who were supportive during my graduate studies. It is also dedicated to all the students, colleagues and my committee members who contributed to the success of this research. iv TABLE OF CONTENTS Signature Page ................................................................................................................................ iii Dedication ....................................................................................................................................... iv Table of Contents ............................................................................................................................. v List of Abbreviations ..................................................................................................................... vii List of Figures ................................................................................................................................. xi List of Tables ............................................................................................................................. xiviii Acknowledgments........................................................................................................................ xvv Vita................................................................................................................................................. xv Abstract of the Dissertation .......................................................................................................... xvi Chapter 1 .......................................................................................................................................... 1 Introduction ...................................................................................................................................... 1 Results .............................................................................................................................................. 7 Discussion ...................................................................................................................................... 19 Conclusion ..................................................................................................................................... 41 v Chapter 2 ........................................................................................................................................ 42 Introduction .................................................................................................................................... 42 Results ............................................................................................................................................ 44 Discussion ...................................................................................................................................... 52 Materials and methods ................................................................................................................... 54 Appendix ........................................................................................................................................ 59 References ...................................................................................................................................... 86 vi LIST OF ABBREVIATIONS 1 AGO4: ARGONAUTE 4 2 AgriGO: GO Analysis Toolkit and Database for Agricultural Community 3 APY1: APYRASE 1 4 APY2: APYRASE 2 5 Apyrase: ATP-diphosphohydrolases 6 ARF-GEF: adenosine diphosphate ribosylation factor guanine nucleotide exchange factor 7 ATGDI2: RAB GDP DISSOCIATION INHIBITOR 2 8 AtMIN7: HOPM INTERACTOR 7 9 ATP: Adenosine triphosphate 10 BAK1: BRI1-ASSOCIATED KINASE 1 11 BES1: BRI1-EMS-SUPPRESSOR 1 12 BIN2: BRASSINOSTEROID INSENSITIVE 2 13 Botrytis: Botrytis cinerea (also B.cinerea) 14 BRI1: BRASSINOSTEROID INSENSITIVE 1 15 BRZ1: BRASSINAZOLE-RESISTANT 1 16 BSU: BRI1 SUPPRESSOR 1 17 BTH: benzo-(1,2,3)-thiadiazole-7-carbothioic S-methyl ester vii 18 Col-0: Wildtype Columbia ecotype plants 19 COR: coronatine 20 CXIP1: CAX INTERACTING PROTEIN 1 21 CYP86A2: CYTOCHROME P450 86A2 22 DC3000: Pseudomonas syringae pv. (Pto) DC3000 23 DNA: Deoxyribonucleic acid 24 Dpi: days post inoculation 25 EDA10: EMBRYO SAC DEVELOPMENT ARREST 10 26 ELF6: EARLY FLOWERING 6 27 ENTPD1: ECTONUCLOSIDE TRIPHOSPHATE DIPHOSPHOYDROLASE 1 28 ETI: effector triggered immunity 29 FLC: FLOWERING LOCUS C 30 FLS2: FLAGELLIN-SENSITIVE 2 31 GDP: guanosine diphosphate 32 GO term: Gene ontology term 33 GPAT4: GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 4 34 GPAT8: PROBABLE GLYCEROL-3-PHOSPHATE ACYLTRANSFERASE 8 35 GTP: guanosine triphosphate viii 36 Hpa: Hyaloperonospora arabidopsidis (also H.arabidopsidis) 37 HR: hypersensitive response 38 IR: induced resistance 39 IRK: INFLORESENCE AND ROOT APICES RECEPTOR LIKE KINASE 40 JA: jasmonic acid 41 LAR: local acquired resistance 42 LHCB1: LIGHT HARVESTING CHLOROPHYLL B-BINDING PROTEIN 1 43 LHCB2: LIGHT HARVESTING CHLOROPHYLL B-BINDING PROTEIN 2 44 LHCB3: LIGHT HARVESTING CHLOROPHYLL B-BINDING protein 3 45 LHCII: light-harvesting complex II 46 LRR: leucine rich repeat 47 MAMPs: microbe-associated molecular patterns 48 mRNA: messenger RNA 49 NBS: nucleotide binding site 50 NPH3: NON-PHOTOTROPIC HYPOCOTYL 3 51 NPR1: NONEXPRESSER OF PR GENES1 52 NPR3: NPR1-LIKE PROTEIN 3 53 NPR4: NPR1-LIKE PROTEIN 4 ix 54 OPP: oxidative pentose phosphate pathway 55 P2: NADP-DEPENDENT ALKENAL DOUBLE BOND REDUCTASE P2 56 PAMPs: pathogen associated molecular patterns 57 PER63: PEROXIDASE 63 58 PHOT1: PHOTOTROPIN 1 59 PKP-ALPHA: PLASTIDIAL PYRUVATE KINASE 1 60 PR: PATHOGENESIS RELATED 61 PRR: Pattern recognition receptor 62 PRXCB: PEROXIDASE CB 63 PTI: PAMP triggered immunity 64 R proteins: RESISTANCE proteins 65 RAT5: RESISTANT TO AGROBACTERIUM TRANSFORMATION 5 66 REF6: RELATIVE OF EARLY FLOWERING 67 RIN4: RPM1-INTERACTING PROTEIN 4 68 RNA: Ribonucleic acid 69 ROS: reactive oxygen species 70 RPM1: RESISTANCE TO P. SYRINGAE PV MACULICOLA 1 71 SA: salicylic acid x 72 SAR: systemic acquired resistance 73 TAIR: The Arabidopsis information resource 74 TCA: tricarboxylic acid cycle 75 Ws: Wassilewskija ecotype 76 WT: wild-type 77 ZAP1: ZINC-DEPENDENT ACTIVATOR PROTEIN- xi LIST OF FIGURES Figure 1.1: Stomata closure is an important part of early response that limits pathogen invasion...1 Figure 1.2: PTI and ETI…………………………………………………………... ………………3 Figure 1.3: NPR1 monomerization is essential for SAR………………………….. ………………4 Figure 1.4: Phytohormone crosstalk……………………………………………………………….5 Figure 1.5: Go annotation of the biological processes of the total proteome……………………...9 Figure 1.6: Hpa infection reveals the role of 8 selected proteins in defense against Hpa Emwa1 isolate ………………………………………………………………………………….................12 Figure 1.7: Hpa infection reveals the role of 8 selected proteins in defense against Hpa Noco2 isolate..............................................................................................................................................13 Figure 1.8: Hpa infection reveals the role of 8 selected proteins in defense against Hpa Emco5 isolate..............................................................................................................................................13 Figure 1.9: Knockout mutant wrky1 displays enhanced disease susceptibility phenotype.............15 Figure 1.10: Response of selected proteins to B. Cinerea………………………………………..16 Figure 1.11: STRING output of interaction between proteins from the total proteome, phosphoproteome and npr1-1 proteome analysis………………………………………………...18 Figure 1.12: STRING network of cutin biosynthesis related proteins GPAT4, CYP86A2 and GPAT8……………………………………………………………………………………………21 Figure 1.13: STRING network of vesicle transport related proteins……………………………..23 xii Figure 1.14: STRING network of NPR1-dependent proteins that are associated with increasing the synthesis of energy and carbon skeleton in response to BTH treatment...……………………30 Figure 1.15: Primary metabolism pathway involved in defense………………………………….31 Figure 1.16: STRING network of WRKY1………………………………………………………34 Figure 1.17: STRING network of PER63, IRK and AGO4……………………………………..36 Figure 1.18: STRING network of NADP-DEPENDENT ALKENAL DOUBLE BOND REDUCTASE P2…………………………………………………………………………………37 Figure 1.19: STRING network of NPR1- dependent chloroplast proteins …………………........40 Figure 2.1: REF6 is required for disease resistance………………………………………………45 Figure 2.2: REF6 is required for defense against Hpa Emwa isolate...……………………...…...46
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