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Assessing the Contribution of Han Family Gata Factors To ASSESSING THE CONTRIBUTION OF HAN FAMILY GATA FACTORS TO ARABIDOPSIS EMBRYOGENESIS by MATTHEW FRANCIS VOLNY (Under the Direction of Wolfgang Lukowitz) ABSTRACT The diverse architecture of many plant species belies their similar developmental origin; each was derived from a single fertilized egg cell. Subsequent divisions of this cell and its daughters, produces a simplified version of the adult plant, comprised of an apical and basal meristem interconnected by a central vascular cylinder. But how is the spatial arrangement of the meristems decided upon, and what comprises the molecular network regulating this process? In this dissertation I detail my efforts towards elucidating the molecular mechanisms regulating embryonic polarity in Arabidopsis thaliana. Previously, it was shown that the GATA transcription factor HANABA TARANU is required for positioning the inductive boundary at which the root initiates; han mutants display an apical shift in gene expression domains normally delimited by the proembryo boundary, yet often recover to form complete seedlings. I show that their recovery is due to the action of two closely related genes, HAN-LIKE 1 (HANL1) and HANL2. Loss of all three HAN genes produces embryos that are initially similar to han single mutants, but over time deteriorate and arrest as blimp-shaped structures lacking a discernible shoot or root apical meristem, and vascular precursors. Molecular markers of embryonic polarity, such as WUS and PLT1, remain unchanged in these embryos, yet many regulators of organogenesis or meristem maintenance, such as FIL, TMO5, and CLV3 are never expressed. Strikingly, genes normally confined to the basal side of the proembryo boundary, such as WOX5 and WOX8, which are normally transcribed in the precursors of the root quiescent center and distal root, expand into sub-surface and surface cell layers. I interpret this effect as partial radialization of the apical/basal pattern. HAN family genes are characterized by a short, deeply conserved amphiphilic stretch at their N-terminus, called the HAN domain. Through a number of approaches, I show that this domain is required for normal activity, and functions to mediate interactions between HAN and transcriptional co-repressors of the TPL family. These results suggest that HAN genes, which are transcribed in the proembryo, may function to directly antagonize the expression of basal or suspensor transcripts in this domain. INDEX WORDS: Embryogenesis, Patterning, Development, Arabidopsis thaliana, ASSESSING THE CONTRIBUTION OF HAN FAMILY GATA FACTORS TO ARABIDOPSIS EMBRYOGENESIS by MATTHEW FRANCIS VOLNY B.S., State University of New York at Oswego, 2008 A Dissertation Submitted to the Graduate Faculty of The University of Georgia in Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY ATHENS, GEORGIA 2015 © 2015 Matthew Francis Volny All Rights Reserved ASSESSING THE CONTRIBUTION OF HAN FAMILY GATA FACTORS TO ARABIDOPSIS EMBRYOGENESIS by MATTHEW FRANCIS VOLNY Major Professor: Wolfgang Lukowitz Committee: Kelly Dawe Xiaoyu Zhang Richard Meagher Douglas Menke Electronic Version Approved: Suzanne Barbour Dean of the Graduate School The University of Georgia August 2015 DEDICATION For Kristin and Roo. iv ACKNOWLEDGEMENTS I would like to acknowledge my committee - Dr. Kelly Dawe, Dr. Xiaoyu Zhang, Dr. Rich Meagher, and Dr. Doug Menke, and I would especially like to thank my advisor Dr. Wolfgang Lukowitz for his invaluable help. v TABLE OF CONTENTS Page ACKNOWLEDGEMENTS ............................................................................................................ v LIST OF TABLES ....................................................................................................................... viii LIST OF FIGURES ........................................................................................................................ ix CHAPTER 1 INTRODUCTION AND LITERATURE REVIEW ..................................................... 1 Auxin transport, perception, and signal transduction .............................................. 3 Initiation and organization of the root apical meristem – auxin gradients and a radial pattern of tissues ............................................................................................ 7 Antagonistic interactions enforce root and shoot fates ......................................... 16 Embryonic polarity – how are root and shoot fates first established? .................. 18 Establishing developmental domains in the pre-globular embryo ........................ 22 Conclusions ........................................................................................................... 26 References ............................................................................................................. 27 2 ANALYSIS OF HAN-FAMILY MUTANTS REVEALS EMBRYOS WITH A PARTIALLY RADIALIZED PRIMARY AXIS ........................................................ 55 Abstract ................................................................................................................. 56 Introduction ........................................................................................................... 58 Results ................................................................................................................... 64 Discussion ............................................................................................................. 74 vi Conclusions ........................................................................................................... 78 Materials and Methods .......................................................................................... 79 References ............................................................................................................. 84 3 STRUCTURAL BASIS OF HAN FUNCTION IN ARABIDOPSIS THALIANA EMBRYOGENESIS ................................................................................................. 102 Abstract ............................................................................................................... 103 Introduction ......................................................................................................... 105 Results ................................................................................................................. 108 Discussion ........................................................................................................... 114 Perspective and open questions ........................................................................... 118 Materials and Methods ........................................................................................ 119 References ........................................................................................................... 126 4 CONCLUSIONS AND FUTURE DIRECTIONS .................................................... 139 References ........................................................................................................... 145 APPENDICES A CHAPTER 2 SUPPLEMENTARY .......................................................................... 147 B CHAPTER 3 SUPPLEMENTARY .......................................................................... 153 vii LIST OF TABLES Page Table S2.1: HANL1/2 rescue constructs ..................................................................................... 150 Table S2.2: Primers for complementation assays, reporter gene construction, and in situ hybridizations .................................................................................................................. 151 Table S3.1: Complementation assays testing the functional equivalency of HAN and B-class GATA factors, and mutant and chimeric variants of HAN, GATA29, and GATA16 .... 157 Table S3.2: Primers for complementation assays ....................................................................... 158 Table S3.3: Sequences for mutating/deleting/changing GATA29/HAN/IAA17 domains for swaps… ........................................................................................................................... 159 viii LIST OF FIGURES Page Figure 1.1: Dynamics of WOX gene expression in embryogenesis ............................................. 50 Figure 1.2: Auxin transport and accumulation during embryogenesis ......................................... 51 Figure 1.3: Positioning and maintenance of the root stem cell niche ........................................... 52 Figure 1.4: Regulation of phyllotaxis and maintenance of the shoot apical meristem ................. 53 Figure 1.5: Transcriptional control of lateral organ polarity in leaves and embryos .................... 54 Figure 2.1: Divergence and expression of HAN-family genes in Arabidopsis ............................. 94 Figure 2.2: han hanl1 hanl2 mutants arrest as blimp-like structures with abnormally enlarged surface cells ....................................................................................................................... 96 Figure 2.3: Expression of genes regulating embryo polarity, tissue formation, and organogenesis in triple mutant embryos ................................................................................................... 98 Figure 2.4: Genes expressed in the provascular domain ............................................................... 99 Figure 2.5: Auxin responses and radialization of apical/basal axis ............................................ 100 Figure
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