Regulation of Gene ExpressionIn Prokaryotes

Regulation of Gene Expression

• Constituitive Gene Expression (promoters)

• Regulating Metabolism (promoters and operators)

• Regulating Development (sigma switches)

Constituitive Gene Expression (promoters)

promoter coding sequence

Regulating Metabolism (promoters and operators)

promoter coding sequenceoperator

Major and minor grooves - protein binding

Major and minor grooves - protein binding

Recognition involves the major groove

Regulatory Proteins Bind DNA

Many regulatory proteins are dimers and bind to palindromes

negative control positive control

repressor activatedgenes OFF

repressor deactivatedgenes ON

repressor activatedgenes OFF

repressor deactivatedgenes ON

precursor molecules macromolecule

energy

energy

substrate

product

Synthetic Pathway

Degredative Pathway

Repressors & metabolic pathways

Metabolic signals and repressor activity

metabolic signal

molecule

DNAbinding

site

repressorprotein

gene off

gene ongene off

gene on

the lac operon

Lactose Metabolism

the metabolic signal for repression

Negative ControlWhen activated by binding of the metabolic signal molecule,

the lac repressor binds to the operator, blocking RNA polymerase

Negative control in the lac operon

the lac operon

Conventional interpretation of dominance - focusing on enzyme function

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Conventional interpretation of codominance - focusing on enzyme function

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But alternatively, control regions can be involved - a recessive operator mutation

But alternatively, control regions can be involved - a dominant operator mutation

But alternatively, control regions can be involved - one inducer mutation

But alternatively, control regions can be involved - another inducer mutation

the Lac control region

Cyclic AMP

Positive ControlcAMP is present when glucose is unavailable

cAMP binds to CAP protein, which then binds to the promoterbinding of the CAP-cAMP complex to the promoter, activates it

CAP-cAMP positioning of CTD

CAP-cAMP acts in formation of closed promoter

The Lactose Operon:Control of a degredative pathway

Practice

Answers

Trp operon, control of aa biosynthetic pathway

The Tryptophan Operon:Control of a synthetic pathway

TryptophanSynthesis

allosteric

protein

Attenuation of trp

The leader sequence:two trp codons and a stop codon

The mechanism of attenuation - termination

Region 2 can bind with 1 or 3, but affinity for 1 is higher

Over riding attentuation if shortage of trp causes ribosome to stall, 2 binds with 3

…no terminator hairpin forms

Control of development:Sigma switching

Different sigmas and their regions of homology

RNA polymerase in bacteria

core enzyme

sigma

Sigma factors recognize promoters and disassociate when the RNA polymerase binds to the promoter, leaving the core

enzyme to make the transcript

RNA polymerase

Phage SPOI (in B. subtilis)

• 3 phases of gene expression

– Early phase– Mid phase– Late phase

• Each phase uses a different sigma, each recognizing a different promoter

• The genes of each phase all have the same kind of promoter, recognized by one of the sigma factors

• Early phase. Early genes have promoters recognized by the host’s RNA polymerase. gp28 is an early protein that acts as a sigma factor for the middle phase genes. gp28 has a higher affinity for the CORE’s binding site than it’s own sigma, thus displacing the host’s sigma and turning off the early genes and turning on the mid genes.

• Middle phase . Middle phase genes have promoters recognized by gp28. Gp33 and gp34 are middle proteins that act as a sigma factor for the late genes.

• Late phase

early transcripts

early proteins,including gp28host

sigma

late transcripts

late proteinsgp33-34 sigma

middle transcripts

middle proteins,including gp33, gp34gp28

sigma

Sigma Switching

Lambda

Lysogenic Life Cycles - Temperate Viruses

Genetic map of Lambda

3 phases again

N antitermination

Q antitermination

cI and cro duke it out

Establishing Lysogeny

Maintaining Lysogeny

InductionSOS

Prokaryote versus Eukaryote Comparison

Step 1

promoter

Step 2

Prokaryotes

Step 1

promoter

Step 2

Eukaryotes

promotersigma

Transcription Factor(eukaryotic sigma)

Positive control in eukaryotes - gene enhancers

Gene activation in Eukaryotes: A different complicated initiation complex for each different context in which a gene is expressed