Transcription Regulation in Prokaryotes

1 GENERAL INTRODUCTION FLOW OF GENETIC INFORMATION DISTINCTIVE FEATURES OF PROKARYOTIC GENE REGULATION BIOCHEMICAL NATURE OF THE TRANSCRIPTION REACTION WHAT MAKES RNA TRANSCRIPTION DIFFERENT FROM DNA REPLICATION? THE PRODUCTS OF TRANSCRIPTION 2 THE PLAYERS OR CELLULAR COMPONENTS NECESSARY FOR TRANSCRIPTION 2.1 TRANSCRIPTION START SITES: THE PROMOTER 2.2 RNA POLYMERASE 2.3 ALTERNATIVE ( FACTORS 2.4 THE 3-DIMENSIONAL STRUCTURE OF RNA POLYMERASE 2.5 IS RNA POLYMERASE MODIFIED DURING DIFFERENT STAGES OF TRANSCRIPTION? INITIATION OF TRANSCRIPTION 3.1 PROMOTOR LOCATION 3.2 THE CLOSED RNA POLYMERASE-PROMOTOR COMPLEX 3.3 FORMATION OF OPEN COMPLEXES 3.4 BINDING OF SUBSTRATE NTPS THE TERNARY COMPLEXES PROMOTOR CLEARANCE AND THE FORMATION OF ELONGATING COMPLEXES THE THERMODYNAMICS AND KINETICS OF TRANSCRIPTION INITIATION TRANSCRIPTION ELONGATION 4.1 THE ARCHITECTURE OF ELONGATING COMPLEXES WHAT IS KNOWN ABOUT THE DIFFERENT FUNCTIONAL SITE? 4.2 THE RATE OF ELONGATION 4.3 RNA POLYMERASES DURING TRANSCRIPTION 4.4 TRANSCRIPT CLEAVAGE FACTORS 'TRAFFIC PROBLEMS' AT THE BACTERIAL GENOME INEVITABLE COLLISIONS BETWEEN TRANSCRIPTION AND REPLICATION MACHINERIES TERMINATION OF TRANSCRIPTION 5.1 FACTOR-INDEPENDENT TERMINATION 5.2 FACTOR DEPENDENT TERMINATION 5.3 ATTENUATION OF TRANSCRIPTION 5.4 ANTITERMINATION THE ROLE OF DNA STRUCTURE IN TRANSCRIPTION REGULATION 6.1 IS DNA METHYLATION INVOLVED IN REGULATION? 6.2 EFFECTS OF DNA CURVATURE ON TRANSCRIPTION INHIBITION 6.3 DNA SUPERCOILING AND TRANSCRIPTION REGULATION BY TRANSCRIPTION FACTORS 7.1 REPRESSORS AND OPERATORS THE CLASSICAL MODEL 7.2 THE MODULAR STRUCTURE OF TRANSCRIPTION FACTORS 7.3 LYSR A REPRESENTATIVE OF A LARGE TRANSCRIPTION FACTOR FAMILY 7.4 DNA LOOPS REGULATION THROUGH DYNAMIC STRUCTURES REGULATION BY DNA STRUCTURING PROTEINS TWO COMPONENT REGULATORY SYSTEMS REGULATORY NETWORKS 8.1 THE SOS RESPONSE 8.2 THE HEAT-SHOCK RESPONSE 8.3 STATIONARY PHASE CONTROL 8.4 THE LRP REGULON THE STRINGENT CONTROL GROWTH RATE REGULATION LESSONS FROM A MANY-FOLD REGULATED SYSTEM THE SYNTHESIS OF RIBOSOMAL RNA