TABLE OF CONTENTS
DECLARATION ................................................................................................................. I
ACKNOWLEDGEMENTS.................................................................................................... II
SUMMARY ..................................................................................................................... IV
ABBREVIATIONS ............................................................................................................. V
TABLE OF CONTENTS .................................................................................................... VI
LIST OF FIGURES ........................................................................................................... X
LIST OF TABLES........................................................................................................... XII
INTRODUCTION .................................................................................................... 0-1
CHAPTER 1: METHODS TO STUDY EVOLUTION OF TRANSCRIPTION
FACTORS AND REGULATORY NETWORKS
1.1 INTRODUCTION ................................................................................................. 1-1
1.2 MOLECULAR MECHANISM FOR THE CONTROL OF GENE EXPRESSION 1-2
1.3 APPROACHES TO STUDY EVOLUTION OF TRANSCRIPTION FACTORS .. 1-3
1.3.1 COMPARISON OF PROTEIN SEQUENCES TO INFER HOMOLOGY ............................ 1-3
1.3.2 DOMAINS OF A PROTEINS CAN BE USED TO INFER EVOLUTIONARY HISTORY ......... 1-4
1.3.3 PROCEDURES TO ASSIGN DOMAINS TO PROTEIN SEQUENCES ............................. 1-7
1.3.4 PROTEIN EVOLUTION ....................................................................................... 1-8
1.4 APPROACHES TO STUDY GENE EXPRESSION PROGRAMS ................... 1-10
1.4.1 METHODS TO STUDY PROTEIN-DNA INTERACTIONS ........................................ 1-11
1.4.2 GENE EXPRESSION ANALYSIS ......................................................................... 1-12
1.5 STRUCTURE OF TRANSCRIPTIONAL REGULATORY NETWORKS .......... 1-17
1.5.1 MOTIFS......................................................................................................... 1-18
1.5.2 MODULES ..................................................................................................... 1-19
1.5.3 GLOBAL NETWORK ORGANISATION ................................................................. 1-20
1.6 REFERENCES .................................................................................................. 1-21
CHAPTER 2: EVOLUTION OF TRANSCRIPTION FACTORS IN E. COLI
2.1 INTRODUCTION ................................................................................................. 2-1
2.2 METHODS .......................................................................................................... 2-2
2.2.1 IDENTIFICATION OF TRANSCRIPTION FACTORS .................................................. 2-2
2.2.2 ACTIVATORS, REPRESSORS AND DUAL REGULATORS ......................................... 2-4
2.3 RESULTS AND DISCUSSION ........................................................................... 2-4
2.3.1 ELEVEN DNA-BINDING DOMAIN FAMILIES ......................................................... 2-4
2.3.2 TRANSCRIPTION FACTORS AND PARTNER DOMAINS ........................................... 2-6
2.3.3 TRANSCRIPTION FACTORS AND GENE DUPLICATION ........................................... 2-8
VI
2.3.4 PROTEIN FAMILIES AND REGULATORY FUNCTION ............................................... 2-9
2.3.5 BINDING SITE POSITION AND REGULATORY FUNCTION ...................................... 2-11
2.3.6 REPRESSOR BINDING SITES ........................................................................... 2-14
2.3.7 GLOBAL REGULATORS ................................................................................... 2-14
2.4 CONCLUSIONS ................................................................................................ 2-21
2.5 REFERENCES .................................................................................................. 2-22
CHAPTER 3: TRANSCRIPTIONAL REGULATORY NETWORK GROWTH
BY GENE DUPLICATION
3.1 INTRODUCTION ................................................................................................. 3-1
3.2 MATERIALS AND METHODS ........................................................................... 3-2
3.2.1 GENE REGULATORY NETWORKS AND MOTIFS .................................................... 3-2
3.2.2 IDENTIFICATION OF DUPLICATED GENES ............................................................ 3-2
3.2.3 IDENTIFICATION OF DUPLICATED EDGES AND SIMULATION PROCEDURE ............... 3-3
3.2.4 METHOD TO INTRODUCING ERRONEOUS INTERACTIONS INTO THE NETWORK ....... 3-3
3.3 RESULTS AND DISCUSSION ........................................................................... 3-4
3.3.1 CHARACTERISTICS OF THE REGULATORY NETWORKS ........................................ 3-4
3.3.2 DUPLICATION AND DOMAINS ............................................................................. 3-7
3.3.3 FORMATION OF THE REGULATORY NETWORK BY GENE DUPLICATIONS................. 3-9
3.3.4 DUPLICATION AND NETWORK TOPOLOGY ........................................................ 3-17
3.3.5 DUPLICATION AND NETWORK MOTIFS .............................................................. 3-19
3.4 CONCLUSIONS ................................................................................................ 3-23
3.5 REFERENCES .................................................................................................. 3-23
CHAPTER 4: EVOLUTIONARY CHANGES IN THE BLUEPRINT FOR
TRANSCRIPTIONAL REGULATION IN PROKARYOTES
4.1 INTRODUCTION ................................................................................................. 4-1
4.2 MATERIALS AND METHODS ........................................................................... 4-2
4.2.1 ALGORITHM TO RECONSTRUCT TRANSCRIPTIONAL NETWORKS. .......................... 4-2
4.2.2 PROCEDURE TO IDENTIFY ORTHOLOGOUS PROTEINS ......................................... 4-3
4.2.3 PROCEDURE TO EVALUATE SIGNIFICANCE OF THE BIAS IN GENE CONSERVATION. 4-4
4.2.4 ALGORITHM TO RECONSTRUCT ANCESTRAL NETWORKS. .................................... 4-5
4.2.5 PROCEDURE TO GROUP GENOMES BY INTERACTIONS AND GENES CONSERVED. .. 4-6
4.2.6 PROCEDURE TO ANALYSE SCALE FREE BEHAVIOUR OF CONSERVED NETWORKS. . 4-7
4.2.7 ALGORITHM TO ANALYSE CONSERVATION OF ‘NETWORK MOTIFS’........................ 4-8
4.2.8 PROCEDURE TO EVALUATE SIGNIFICANCE OF MOTIF INTERACTION CONSERVATION4-9
4.3 RESULTS AND DISCUSSION ......................................................................... 4-10
4.3.1 RECONSTRUCTION OF TRANSCRIPTIONAL REGULATORY NETWORKS ................. 4-10
4.3.2 CONSERVATION OF TRANSCRIPTION FACTORS AND TARGET GENES .................. 4-13
4.3.3 CONSERVATION OF TRANSCRIPTIONAL REGULATORY NETWORKS ..................... 4-17
4.3.4 EVOLUTION OF GLOBAL NETWORK STRUCTURE ............................................... 4-20
4.3.5 EVOLUTION OF LOCAL NETWORK STRUCTURE ................................................. 4-23
4.4 CONCLUSIONS ................................................................................................ 4-29
4.5 REFERENCES .................................................................................................. 4-30
VII
CHAPTER 5: GENOME SCALE ANALYSIS OF REGULATORY
NETWORK DYNAMICS
5.1 INTRODUCTION ................................................................................................. 5-1
5.2 MATERIALS AND METHODS ........................................................................... 5-2
5.2.1 DATASETS ...................................................................................................... 5-2
5.2.2 BACK-TRACKING ALGORITHM ........................................................................... 5-3
5.2.3 INTERCHANGE INDEX ....................................................................................... 5-4
5.2.4 TOPOLOGICAL MEASURES ................................................................................ 5-4
5.2.5 NORMALIZATION FOR REGULATORY HUBS ......................................................... 5-5
5.2.6 REGULATORY MOTIFS ...................................................................................... 5-5
5.2.7 RANDOM NETWORKS ....................................................................................... 5-6
5.2.8 SENSITIVITY ANALYSIS ..................................................................................... 5-6
5.3 RESULTS AND DISCUSSION ........................................................................... 5-6
5.3.1 REGULATORY NETWORK IN YEAST .................................................................... 5-6
5.3.2 DIFFERENTIAL USE OF THE REGULATORY NETWORK .......................................... 5-9
5.3.3 DYNAMICS OF REGULATORY INTERACTIONS ...................................................... 5-9
5.3.4 REGULATORY SPECIFICITY THROUGH TF COMBINATIONS ................................. 5-14
5.3.5 LARGE-SCALE TOPOLOGICAL CHANGES .......................................................... 5-15
5.3.6 TF HUBS IN THE REGULATORY NETWORK ........................................................ 5-18
5.3.7 PREFERENTIAL USE OF NETWORK MOTIFS ....................................................... 5-21
5.3.8 INTER-REGULATION OF TFS IN THE CELL CYCLE AND SPORULATION .................. 5-23
5.4 CONCLUSIONS ................................................................................................ 5-28
5.5 REFERENCES .................................................................................................. 5-28
CHAPTER 6: DISCUSSION AND CONCLUSIONS .................................... 6-1
APPENDIX A: SUPPLEMENTARY MATERIAL
CHAPTER 2: EVOLUTION OF TRANSCRIPTION FACTORS IN E. COLI .............A-1
CHAPTER 3: TRANSCRIPTIONAL REGULATORY NETWORK GROWTH BY
GENE DUPLICATION ........................................................................A-1
3.1 PSEUDOCODES .................................................................................................. A-1
3.2 REPRESENTATION OF THE TRANSCRIPTIONAL REGULATORY NETWORK .................. A-1
3.3 CHARACTERIZATION OF THE VERTICES IN THE NETWORK ...................................... A-2
3.4 CHARACTERIZATION OF THE EDGES IN THE NETWORK ........................................... A-2
3.5 IDENTIFICATION OF NETWORK MOTIFS.................................................................. A-4
3.6 IDENTIFICATION OF DIRECTLY AND INDIRECTLY REGULATED GENES ....................... A-5
3.7 SIMULATION PROCEDURE.................................................................................... A-5
3.8 INTERNAL DUPLICATION IN THE YEAST SIMS ........................................................ A-6
3.9 INTERNAL DUPLICATIONS IN THE E. COLI SIMS ..................................................... A-7
3.10 INTERNAL DUPLICATIONS IN THE YEAST FFMS.................................................... A-7
CHAPTER 4: EVOLUTIONARY CHANGES IN THE BLUEPRINT FOR
TRANSCRIPTIONAL REGULATION IN PROKARYOTES ...............A-8
4.1 ALGORITHM TO SIMULATE NETWORK EVOLUTION .................................................. A-8
4.2 ALGORITHM TO EVALUATE OBSERVED NUMBER OF WHOLE MOTIFS IN GENOMES
BY CREATING RANDOM NETWORKS ...................................................................... A-9
4.3 ALGORITHM TO EVALUATE OBSERVED CONSERVATION OF INTERACTIONS IN
MOTIFS IN GENOMES ........................................................................................... A-9
4.4 CONSERVATION OF GENES, INTERACTIONS, GENOME SIZE AND NUMBER OF
PREDICTED TRANSCRIPTION FACTORS FOR EACH OF THE 176 GENOMES ............. A-11
VIII
CHAPTER 5: GENOME SCALE ANALYSIS OF REGULATORY NETWORK
DYNAMICS .......................................................................................A-15
APPENDIX B: OTHER PUBLISHED WORKS
1. NON-CANONICAL INTERACTIONS IN PROTEIN STRUCTURES
1.1 NCI: A SERVER TO IDENTIFY NON-CANONICAL INTERACTIONS IN PROTEINS ............ B-1
1.2 A C-H..O HYDROGEN BOND STABILISED POLYPEPTIDE CHAIN REVERSAL MOTIF ..... B-2
1.3 REGISTERING HELICES AND STRANDS USING C-H..O HYDROGEN BONDS ............... B-3
2. PROTEIN INTERACTION AND GENE EXPRESSION
2.1 CONSERVATION OF GENE COREGULATION............................................................ B-4
2.2 INTRODUCTION TO MICROARRAY DATA ANALYSIS .................................................. B-5
2.3 UNIVERSAL MICROARRAYS ................................................................................. B-6
2.4 STATISTICAL ANALYSIS OF DOMAINS IN INTERACTING PROTEIN PAIRS ..................... B-7
3. MICROBIAL GENOME EVOLUTION
3.1 DOLOP – DATABASE OF BACTERIAL LIPOPROTEINS ............................................. B-8
3.2 LOSS OF SIGMA FACTORS AND PSEUDOGENE ACCUMULATION IN M. LEPRAE .......... B-9
LIST OF PUBLICATIONS ..................................................................................C-1
IX