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PROTEIN-PROTEIN INTERACTION MAP of Arabidopsis Thaliana GENERAL TRANSCRIPTION FACTORS A, B, D, E, and F

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PROTEIN-PROTEIN INTERACTION MAP of Arabidopsis Thaliana GENERAL TRANSCRIPTION FACTORS A, B, D, E, and F PROTEIN-PROTEIN INTERACTION MAP OF Arabidopsis thaliana GENERAL TRANSCRIPTION FACTORS A, B, D, E, AND F By SHAI JOSHUA LAWIT A DISSERTATION PRESENTED TO THE GRADUATE SCHOOL OF THE UNIVERSITY OF FLORIDA IN PARTIAL FULFILLMENT OF THE REQUIREMENTS FOR THE DEGREE OF DOCTOR OF PHILOSOPHY UNIVERSITY OF FLORIDA 2003 Copyright 2003 by Shai Joshua Lawit This document is dedicated to my family, both genetic and scientific. ACKNOWLEDGMENTS I thank my dearest wife, Kristel Lynn, for her undying support for me. I also thank my son, Benjamin Owen, for constant interest in this document as I wrote and unending smiles and hugs at all times. I thank my parents and all of my family for instilling me with a desire for education and excellence. Of course, I have a great appreciation for the members of the Gurley lab (past, present, and future) who continually contribute to this field of research. John Davis and the members of his lab (especially Chris Dervinis for helping me to get access to the Poplar genomic sequences and Ram Kishore Alavalapati for running all the PAUP analyses) deserve special thanks for technical assistance, collaboration, and helpful discussions. I would finally like to thank William B. Gurley, Eva Czarnecka-Verner, Robert Ferl, Alice Harmon, Karen Koch, Donald McCarty, Thomas Yang, Robert R. Schmidt, Waltraud I. Dunn, and the entire teaching faculty who have molded me into the scientist that I am. iv TABLE OF CONTENTS Page ACKNOWLEDGMENTS ................................................................................................. iv LIST OF TABLES........................................................................................................... viii LIST OF FIGURES ........................................................................................................... ix ABSTRACT...................................................................................................................... xii CHAPTER 1 INTRODUCTION TO THE LITERATURE ...............................................................1 General Transcription Factors ......................................................................................1 TATA Binding Protein and TFIID........................................................................3 TATA Binding Protein-Associated Factors ..........................................................6 Histone-like TAFs ..........................................................................................6 TAF1 family...................................................................................................8 Other TAFs and interactions of TFIID.........................................................13 Alternative TBP- or TAF-Containing Complexes ..............................................17 TAFs: Required Factors or Optional Accessories...............................................23 Interplay of GTFs ................................................................................................26 Transcriptional Activators That Bind DNA ...............................................................36 2 PHYLOGENETIC ANALYSIS OF POPLAR, Arabidopsis AND OTHER PLANT GENERAL TRANSCRIPTION FACTORS ..............................................................51 Introduction.................................................................................................................51 Methods ......................................................................................................................53 Results.........................................................................................................................56 TFIIA Large and Small Subunits ........................................................................56 TFIIB Family.......................................................................................................57 Representative TFIID Components.....................................................................58 TFIIEα and TFIIEβ Subunits ..............................................................................59 TFIIFα and TFIIFβ Subunits ..............................................................................60 Discussion...................................................................................................................60 TFIIA Large and Small Subunits ........................................................................60 TFIIB Family.......................................................................................................62 Representative TFIID Components.....................................................................65 v TFIIEα and TFIIEβ Subunits ..............................................................................68 TFIIFα Family.....................................................................................................68 TFIIFβ Family.....................................................................................................69 3 BINARY PROTEIN-PROTEIN INTERACTIONS OF THE Arabidopsis thaliana GENERAL TRANSCRIPTION FACTOR IID..........................................................89 Introduction.................................................................................................................89 Materials and Methods ...............................................................................................90 Results.........................................................................................................................96 Discussion...................................................................................................................98 4 BINARY PROTEIN-PROTEIN INTERACTIONS OF Arabidopsis TFIIA, TFIIB, TFIID, TFIIE, AND TFIIF .......................................................................................118 Introduction...............................................................................................................118 Materials and Methods .............................................................................................119 Results.......................................................................................................................121 Discussion.................................................................................................................123 5 DISCUSSION...........................................................................................................147 TFIIA Large and Small Subunits..............................................................................147 TFIIB Family............................................................................................................149 TFIID Components...................................................................................................152 TFIIEα and TFIIEβ Subunits ...................................................................................154 TFIIFα and TFIIFβ Subunits....................................................................................155 Conclusion ................................................................................................................157 APPENDIX A NUCLEOTIDE AND AMINO ACID SEQUENCES OF GENERAL TRANSCRIPTION FACTORS................................................................................161 TFIIA Small Subunit Sequences ..............................................................................161 TFIIA Large Subunit Sequences ..............................................................................163 TFIIB Family Sequences ..........................................................................................165 TATA Binding Protein Sequences ...........................................................................172 TAF6 Sequences.......................................................................................................176 TAF9 Sequences.......................................................................................................179 TAF10 Sequences.....................................................................................................182 TAF11 Sequences.....................................................................................................185 TFIIEα Sequences ....................................................................................................186 TFIIEβ Sequences ....................................................................................................189 TFIIFα Sequences ....................................................................................................192 TFIIFβ Sequences.....................................................................................................194 vi B AMINO ACID MULTIPLE SEQUENCE ALIGNMENTS FOR CORE DOMAINS OF THE GENERAL TRANSCRIPTION FACTORS .............................................197 TFIIA Small Subunit Alignment ..............................................................................197 TFIIA Large Subunit Alignment ..............................................................................198 TFIIB Family Alignment..........................................................................................200 TBP Alignment.........................................................................................................205 TAF6 Alignment.......................................................................................................208 TAF9 Alignment.......................................................................................................211
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