8.1 major modes of regulation gene expression: transcription of gene into mrna followed by...

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.

Figure 8.1 Upstreamregion

Downstreamregion

Start oftranscription Shine-Dalgarno

sequence (ribosome-binding site)

Start codon:Translationstarts here

Stop codon:Translation ends here

Transcriptionterminator

Transcription

Translation

Protein

DNA

mRNA


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



• 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



• 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)


Figure 8.2

Domain containing protein–proteincontacts, holding protein dimer together

DNA-binding domain fits inmajor grooves and alongsugar–phosphate backbone

Inverted repeats

Inverted repeats



• 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


Figure 8.3

Stabilizinghelix

Recognitionhelix

Subunitsof bindingprotein

Turn

DNA



• Multiple outcomes after DNA binding are possible1. DNA-binding protein may catalyze a specific

reaction on the DNA molecule (i.e., transcription by RNA polymerase)

2. The binding event can block transcription (negative regulation)

3. The binding event can activate transcription (positive regulation)


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


• 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)




• 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


Figure 8.5

Repression

Cell numberTotal protein

Arginine added

Argininebiosynthesisenzymes

Time

Re

lati

ve

inc

rea

se


Figure 8.6

Induction

Cell number

Total protein

Lactose added

-Galacto-sidase

Time

Re

lati

ve

inc

rea

se



• 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.

Figure 8.7

RNApolymerase

Repressor

Repressor

RNApolymerase

Corepressor(arginine)

Transcription proceeds

Transcription blocked

arg Promoter arg Operator argC argB argH

arg Promoter arg Operator argC argB argH


Figure 8.8

RNApolymerase

Repressor

Repressor

RNApolymerase

Inducer


Transcription blocked

lac Promoter lac Operator lacZ lacY lacA

lac Promoter lac Operator lacZ lacY lacA


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


Figure 8.9

Activator-binding site

RNApolymerase


mal Promoter malE malF malG

No transcription


Maltose activator protein

Maltose activator protein

Inducer

RNApolymerase

mal Promoter malE malF malG


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)


Figure 8.11


Activatorprotein


Activator protein

RNApolymerase

RNApolymerase

Promoter

Promoter

Transcriptionproceeds

Transcriptionproceeds


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


Figure 8.14 CRP protein

cAMP

RNApolymerase

lac Structural genes

Activerepressor

Inducer

Inactiverepressor

Lactose catabolism

DNA

mRNA mRNA

TranscriptionTranscription

TranslationTranslation

lacZ lacY lacAlacI

Activerepressorbinds tooperatorandblockstran-scription


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


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



• 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


Figure 8.16Environmental signal

Phosphataseactivity

Transcription blockedRNApolymerase

Sensorkinase

Cytoplasmicmembrane

Response regulator

DNA

Promoter Operator Structural genes© 2012 Pearson Education, Inc.


• 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


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)


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


Figure 8.18

Acyl homoserine lactone (AHL)

AHLActivator protein

Other cellsof the samespecies

Chromosome AHL synthase

AHL

Quorum-specificproteins


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


Figure 8.19


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


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


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


Figure 8.21

RpoHDnaK

Degradation ofRpoH by protease

RpoH

RpoH isreleased

Proteins unfold athigh temperature

DnaK bindsunfoldedproteins

RpoH is freeto transcribeheat shockgenes

Hig

h t

em

pe

ratu

reL

ow

te

mp

era

ture


IV. Regulation of Development in Model Bacteria

• 8.12 Sporulation in Bacillus• 8.13 Caulobacter Differentiation


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)


8.1 major modes of regulation gene expression: transcription of gene into mrna followed by...

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