8.1 Major Modes of Regulation Gene expression: transcription of gene into mRNA followed by translation of mRNA into protein (Figure 8.1) Most proteins are enzymes that carry out biochemical reactions Constitutive proteins are needed at the same level all the time Microbial genomes encode many proteins that are not needed all the time Regulation helps conserve energy and resources © 2012 Pearson Education, Inc.

DNA mRNA Protein Upstream region Downstream region Figure 8.1 Upstream region Downstream region DNA Transcription terminator Start of transcription Shine-Dalgarno sequence (ribosome- binding site) Transcription mRNA Start codon: Translation starts here Stop codon: Translation ends here Figure 8.1 Components of a bacterial gene. Translation Protein © 2012 Pearson Education, Inc.

8.2 DNA-Binding Proteins mRNA transcripts generally have a short half-life Prevents the production of unneeded proteins Regulation of transcription typically requires proteins that can bind to DNA Small molecules influence the binding of regulatory proteins to DNA Proteins actually regulate transcription © 2012 Pearson Education, Inc.

8.2 DNA-Binding Proteins Most DNA-binding proteins interact with DNA in a sequence-specific manner Specificity provided by interactions between amino acid side chains and chemical groups on the bases and sugar–phosphate backbone of DNA Major groove of DNA is the main site of protein binding Inverted repeats frequently are binding site for regulatory proteins © 2012 Pearson Education, Inc.

8.2 DNA-Binding Proteins Homodimeric proteins: proteins composed of two identical polypeptides Protein dimers interact with inverted repeats on DNA Each of the polypeptides binds to one inverted repeat (Figure 8.2) © 2012 Pearson Education, Inc.

Figure 8.2 Domain containing protein–protein contacts, holding protein dimer together DNA-binding domain fits in major grooves and along sugar–phosphate backbone Inverted repeats Figure 8.2 DNA-binding proteins. Inverted repeats © 2012 Pearson Education, Inc.

8.2 DNA-Binding Proteins Several classes of protein domains are critical for proper binding of proteins to DNA Helix-turn-helix (Figure 8.3) First helix is the recognition helix Second helix is the stabilizing helix Many different DNA-binding proteins from Bacteria contain helix-turn-helix lac and trp repressors of E. coli © 2012 Pearson Education, Inc.

Subunits of binding protein Figure 8.3 Stabilizing helix Turn Recognition helix DNA Subunits of binding protein Figure 8.3 The helix-turn-helix structure of some DNA-binding proteins. © 2012 Pearson Education, Inc.

8.2 DNA-Binding Proteins Multiple outcomes after DNA binding are possible DNA-binding protein may catalyze a specific reaction on the DNA molecule (i.e., transcription by RNA polymerase) The binding event can block transcription (negative regulation) The binding event can activate transcription (positive regulation) © 2012 Pearson Education, Inc.

8.3 Negative Control of Transcription: Repression and Induction Several mechanisms for controlling gene expression in bacteria These systems are greatly influenced by environment in which the organism is growing Presence or absence of specific small molecules Interactions between small molecules and DNA-binding proteins result in control of transcription or translation © 2012 Pearson Education, Inc.

8.3 Negative Control of Transcription: Repression and Induction Negative control: a regulatory mechanism that stops transcription Repression: preventing the synthesis of an enzyme in response to a signal (Figure 8.5) Enzymes affected by repression make up a small fraction of total proteins Typically affects anabolic enzymes (e.g., arginine biosynthesis) © 2012 Pearson Education, Inc.

8.3 Negative Control of Transcription: Repression and Induction Negative Control (cont’d) Induction: production of an enzyme in response to a signal (Figure 8.6) Typically affects catabolic enzymes (e.g., lac operon) Enzymes are synthesized only when they are needed no wasted energy © 2012 Pearson Education, Inc.

Repression Cell number Relative increase Total protein Arginine added Figure 8.5 Repression Cell number Total protein Relative increase Arginine added Figure 8.5 Enzyme repression. Arginine biosynthesis enzymes Time © 2012 Pearson Education, Inc.

Induction Total protein Cell number Relative increase Figure 8.6 Induction Total protein Cell number Relative increase -Galacto- sidase Figure 8.6 Enzyme induction. Lactose added Time © 2012 Pearson Education, Inc.

8.3 Negative Control of Transcription: Repression and Induction Inducer: substance that induces enzyme synthesis Corepressor: substance that represses enzyme synthesis Effectors: collective term for inducers and repressors Effectors affect transcription indirectly by binding to specific DNA-binding proteins Repressor molecules bind to an allosteric repressor protein Allosteric repressor becomes active and binds to region of DNA near promoter called the operator © 2012 Pearson Education, Inc.

Transcription proceeds Figure 8.7 arg Promoter arg Operator argC argB argH RNA polymerase Transcription proceeds Repressor arg Promoter arg Operator argC argB argH RNA polymerase Corepressor (arginine) Figure 8.7 Enzyme repression in the arginine operon. Transcription blocked Repressor © 2012 Pearson Education, Inc.

Transcription blocked Figure 8.8 lac Promoter lac Operator lacZ lacY lacA RNA polymerase Transcription blocked Repressor lac Promoter lac Operator lacZ lacY lacA RNA polymerase Transcription proceeds Figure 8.8 Enzyme induction in the lactose operon. Repressor Inducer © 2012 Pearson Education, Inc.

8.4 Positive Control of Transcription Positive control: regulator protein activates the binding of RNA polymerase to DNA (Figure 8.9) Maltose catabolism in E. coli Maltose activator protein cannot bind to DNA unless it first binds maltose Activator proteins bind specifically to certain DNA sequence Called activator-binding site, not operator © 2012 Pearson Education, Inc.

Activator- binding site Figure 8.9 Activator- binding site mal Promoter malE malF malG No transcription RNA polymerase Maltose activator protein Activator- binding site mal Promoter malE malF malG Figure 8.9 Positive control of enzyme induction in the maltose operon. RNA polymerase Transcription proceeds Maltose activator protein Inducer © 2012 Pearson Education, Inc.

8.4 Positive Control of Transcription Promoters of positively controlled operons only weakly bind RNA polymerase Activator protein helps RNA polymerase recognize promoter May cause a change in DNA structure May interact directly with RNA polymerase Activator-binding site may be close to the promoter or several hundred base pairs away (Figure 8.11) © 2012 Pearson Education, Inc.

Activator- binding site Figure 8.11 Activator- binding site Promoter RNA polymerase Transcription proceeds Activator protein Promoter RNA polymerase Transcription proceeds Figure 8.11 Activator protein interactions with RNA polymerase. Activator protein Activator- binding site © 2012 Pearson Education, Inc.

8.5 Global Control and the lac Operon Cyclic AMP and CRP In catabolite repression, transcription is controlled by an activator protein and is a form of positive control (Figure 8.14) Cyclic AMP receptor protein (CRP) is the activator protein Cyclic AMP is a key molecule in many metabolic control systems It is derived from a nucleic acid precursor It is a regulatory nucleotide © 2012 Pearson Education, Inc.

DNA mRNA mRNA Figure 8.14 CRP protein cAMP RNA polymerase lac Structural genes DNA Active repressor binds to operator and blocks tran- scription Transcription Transcription lacI mRNA mRNA lacZ lacY lacA Figure 8.14 Overall regulation of the lac system. Translation Translation Inducer Active repressor Lactose catabolism Inactive repressor © 2012 Pearson Education, Inc.

8.5 Global Control and the lac Operon Dozens of catabolic operons affected by catabolite repression Enzymes for degrading lactose, maltose, and other common carbon sources Flagellar genes are also controlled by catabolite repression No need to swim in search of nutrients © 2012 Pearson Education, Inc.

8.7 Two-Component Regulatory Systems Prokaryotes regulate cellular metabolism in response to environmental fluctuations External signal is transmitted directly to the target External signal detected by sensor and transmitted to regulatory machinery (Signal transduction) Most signal transduction systems are two-component regulatory systems © 2012 Pearson Education, Inc.

8.7 Two-Component Regulatory Systems Two-component regulatory systems (Figure 8.16) Made up of two different proteins: Sensor kinase: (in cytoplasmic membrane) detects environmental signal and autophosphorylates Response regulator: (in cytoplasm) DNA-binding protein that regulates transcription Also has feedback loop Terminates signal © 2012 Pearson Education, Inc.

Sensor kinase Cytoplasmic membrane Response regulator DNA Figure 8.16 Environmental signal Sensor kinase Cytoplasmic membrane Response regulator Figure 8.16 The control of gene expression by a two-component regulatory system. Phosphatase activity RNA polymerase DNA Transcription blocked Promoter Operator Structural genes © 2012 Pearson Education, Inc.

8.7 Two-Component Regulatory Systems Almost 50 different two-component systems in E. coli Examples include phosphate assimilation, nitrogen metabolism, and osmotic pressure response Some signal transduction systems have multiple regulatory elements Some Archaea also have two-component regulatory systems © 2012 Pearson Education, Inc.

8.9 Quorum Sensing Prokaryotes can respond to the presence of other cells of the same species Quorum sensing: mechanism by which bacteria assess their population density Ensures sufficient number of cells are present before initiating a response that requires a certain cell density to have an effect (e.g., toxin production in pathogenic bacterium) © 2012 Pearson Education, Inc.

8.9 Quorum Sensing Each species of bacterium produces a specific autoinducer molecule (Figure 8.18) Diffuses freely across the cell envelope Reaches high concentrations inside cell only if many cells are near Binds to specific activator protein and triggers transcription of specific genes © 2012 Pearson Education, Inc.

Quorum- specific proteins Figure 8.18 Acyl homoserine lactone (AHL) AHL Activator protein AHL Quorum- specific proteins Other cells of the same species Figure 8.18 Quorum sensing. Chromosome AHL synthase © 2012 Pearson Education, Inc.

8.9 Quorum Sensing Several different classes of autoinducers Acyl homoserine lactone was the first autoinducer to be identified Quorum sensing first discovered as mechanism regulating light production in bacteria including Aliivibrio fischeri (Figure 8.19) Lux operon encodes bioluminescence © 2012 Pearson Education, Inc.

Figure 8.19 Figure 8.19 Bioluminescent bacteria producing the enzyme luciferase. © 2012 Pearson Education, Inc.

8.9 Quorum Sensing Examples of quorum sensing P. aeruginosa switches from free living to growing as a biofilm Virulence factors of Staphylococcus aureus Quorum sensing is present in some microbial eukaryotes Quorum sensing likely exists in Archaea © 2012 Pearson Education, Inc.

8.11 Other Global Control Networks Several other global control systems Aerobic and anaerobic respiration Catabolite repression Nitrogen utilization Oxidative stress SOS response Heat shock response © 2012 Pearson Education, Inc.

8.11 Other Global Control Networks Heat shock response: Largely controlled by alternative sigma factors (Figure 8.21) Heat shock proteins: counteract damage of denatured proteins and help cell recover from temperature stress Very ancient proteins Heat shock response also occurs in Archaea © 2012 Pearson Education, Inc.

Low temperature High temperature DnaK RpoH Figure 8.21 DnaK RpoH Low temperature Proteins unfold at high temperature Degradation of RpoH by protease RpoH is released RpoH High temperature Figure 8.21 Control of heat shock in Escherichia coli. DnaK binds unfolded proteins RpoH is free to transcribe heat shock genes © 2012 Pearson Education, Inc.

IV. Regulation of Development in Model Bacteria 8.12 Sporulation in Bacillus 8.13 Caulobacter Differentiation © 2012 Pearson Education, Inc.

8.12 Sporulation in Bacillus Regulation of development in model bacteria Some prokaryotes display the basic principle of differentiation Endospore formation in Bacillus (Figure 8.22) Controlled by 4 sigma factors Forms inside mother cell Triggered by adverse external conditions (i.e., starvation or desiccation) © 2012 Pearson Education, Inc.