Chapter 6 Regulation of Prokaryotic Gene Expression

6.1 Overview 1. What are Gene Expression and Regulation? (1) Gene expression  Constitutive Expression  Regulated/Adaptive Expression (2) Gene regulation/control

2. Influencing factors Nutritional status Environmental factors Hormone level Developmental stage

3. Operon (1) What is an operon? (2) Operon types  Inducible operon  Repressible operon (3) Gene regulation of operon  Negative regulation  Positive regulation

负控诱导系统 正控诱导系统

正控阻遏系统 负控阻遏系统

1. Organization of lac operon lacI Regulatory gene lacZ lacY lacA DNA mRNA β -Galactosidase Permease Transacetylase Protein Structural Genes P lacI P lac O lac repressor 6.2 The Regulation of lac Operon

3. Positive control of lac operon cAMP CAP (catabolite activator protein) or cAMP receptor protein (CRP)

4. Negative contral of lac operon p t p t lacI lacZ lacY lacA Repressor  -galactosidase transcripts Permease Transacetylase 1. + Inducer (lactose/ allolactose) o Induced Repressor cannot bind

2. No Inducer p t lacI lacZ lacY lacA o Repressed Repressor binds to lac o transcript Animation

1. Organization of trp operon 6.3 The Regulation of trp Operon

2. The Repression of trp Operon trpR → Repressor Corepressor

 Attenuator 3. The Attenuation Mechanism of trp Operon  Mechanism of Attenuation When Ribosome reaches Trp codon  Trp is scarce  Trp is aboudant

Attenuation model in Trp starved cells.

Attenuation model in Trp non-starved cells Animation

5. Generality of Attenuation

1. The Regulation of ara Operon (1) organization 6.4 The Regulation of Other Operons P t P t araC araB araA araD Activator/ Repressor I 1 I 2 AraC dimer CRP O2O2 O1O1

Arabinose absent →Negative control araB A D O 1 CRP araI araC O2O2 PCPC P BAD Blocked

Arabinose present → Positive control araB A D O 1 CRP araI araC PCPC P BAD O2O2 Transcription

2. The Regulation of rRNA Operon (1) organization

6.5 Riboswitches 1. What is a riboswitch? Riboswitches have two important domains:  an aptamer  an expression platform

2. Mechanism of Riboswitches (1) Inhibition of Translation Initiation (2) Transcription termination (3) Auto-cleavage

3. Tempting Targets

4. Riboswitches and the RNA World hypothesis 5. Riboswitches as Antibiotic Targets Blount KF, Breaker RR. Riboswitches as antibacterial drug targets". Nat Biotechnol, 2006, 24 (12): Brantl, S. Bacterial gene regulation: from transcription attenuation to riboswitches and ribozymes. Trends Microbiol, 2004, 12: Mandal, M. and R. R. Breaker. Gene Regulation by Riboswitches. Nat Rev Mol Cell Biol, 2004, 5:

6.6 Time Regulation Different sigma factors recognize different promoters and thus, the availability of sigma factors can regulate the transcription of genes associated with these promoters. 1. Time Regulation of Sigma Factors

Early Middle Late

 Uncommitted. 2. Time Regulation of λ phage

 Committed.  Lysogeny  Lysis

 Execution  Lysogeny

 Lysis

1. Translation Initiation of Regulation (1) Ribosome binding site (rbs) (2) SD sequencing (3) mRNA secondary structure (4) Initiational codon 2. Regulation of Rare Codon 3. Transcriptional Regulation of Overlapping Gene 4. Translational Repression 6.7 Post-Transcriptional Regulation

Summary 1. Concepts Gene ExpressionOperonAttenuator Constitutive ExpressionInducible OperonAttenuation Regulated ExpressionRepressible OperonRiboswitch Gene Regulation 2. Differences between inducible operon and repressible operon 3. The regulation mechanism of lac operon 4. The regulation mechanism of trp operon (attenuation) 5. The regulation mechanism of ara operon 6. The regulation mechanism of riboswitches