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Gene Regulation inGene Regulation in

ProkaryotesProkaryotes

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Outline of Chapter 16Outline of Chapter 16 There are many steps in gene expression and regulationThere are many steps in gene expression and regulation

can occur at any one of themcan occur at any one of them

Genetic and molecular studies show that most regulationGenetic and molecular studies show that most regulation

affects the initiation of RN transcriptsaffects the initiation of RN transcripts

!tudies of genes for lactose utili"ation!tudies of genes for lactose utili"ation Negati#e regulation $ %locks transcriptionNegati#e regulation $ %locks transcription

Positi#e regulation $ increases transcriptionPositi#e regulation $ increases transcription

&N %inding proteins acting on RN polymerase at promoter are main&N %inding proteins acting on RN polymerase at promoter are main

agents of regulationagents of regulation

ttenuation of expression $ tryptophan pathwayttenuation of expression $ tryptophan pathway Gene expression is fine tuned %y premature termination ofGene expression is fine tuned %y premature termination of

transcriptiontranscription

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Outline of Chapter 16Outline of Chapter 16 Glo%al regulatory mechanisms'Glo%al regulatory mechanisms' E.E.coliscolis

response to heat shock is an example of theresponse to heat shock is an example of the

%acterial a%ility to coordinate the expression of%acterial a%ility to coordinate the expression of

different sets of genes dispersed around thedifferent sets of genes dispersed around the

chromosome(chromosome( )icroarray analysis is an important new tool for)icroarray analysis is an important new tool for

detecting changes in gene expression in response todetecting changes in gene expression in response to

en#ironmental changesen#ironmental changes Comprehensi#e example' *owComprehensi#e example' *ow Vibrio choleraeVibrio cholerae

regulate their #irulence genesregulate their #irulence genes

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RN polymerase is the key en"ymeRN polymerase is the key en"yme

for transcriptionfor transcription

RN polymerase in#ol#ed in three phases ofRN polymerase in#ol#ed in three phases of

transcriptiontranscription +nitiation $ sigma su%unit , core en"yme -two alpha. one %eta.+nitiation $ sigma su%unit , core en"yme -two alpha. one %eta.

and one %eta/ su%unit0and one %eta/ su%unit0 inds to promoter. unwinds &N. %egins polymeri"ation of %asesinds to promoter. unwinds &N. %egins polymeri"ation of %ases

complementary to &N templatecomplementary to &N template

2longation $ mo#ement away from promoter sigma su%unit2longation $ mo#ement away from promoter sigma su%unit

released. polymeri"ationreleased. polymeri"ation

Termination $signal reached %y RN polymeraseTermination $signal reached %y RN polymerase Rho dependent termination $ Rho factor recogni"es se3uence in mRN.Rho dependent termination $ Rho factor recogni"es se3uence in mRN.

%inds to it. and pulls it away from RN polymerase%inds to it. and pulls it away from RN polymerase

Rho independent termination $ stem loop structure formed %y se3uenceRho independent termination $ stem loop structure formed %y se3uence

of 45 %ases with a run of 6 or more /s signals release of RNof 45 %ases with a run of 6 or more /s signals release of RN

polymerasepolymerase

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Fig. 16.2

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Translation in prokaryotes starts %efore transcriptionTranslation in prokaryotes starts %efore transcription

endsends

+nitiation sites for translation signal ri%osomes to %ind near 7/+nitiation sites for translation signal ri%osomes to %ind near 7/end of mRN while downstream transcription is still occurringend of mRN while downstream transcription is still occurring

Polycistronic mRNs often lead to the translation of se#eralPolycistronic mRNs often lead to the translation of se#eral

genes at the same time from one mRN transcriptgenes at the same time from one mRN transcript

The regulation of gene expression can occur at manyThe regulation of gene expression can occur at many

stepssteps inding of RN polymerase to promoterinding of RN polymerase to promoter

!hift from initiation to elongation!hift from initiation to elongation

Release of mRN at terminationRelease of mRN at termination

Posttranscriptional sta%ility of mRNPosttranscriptional sta%ility of mRN

2fficiency of ri%osomes to recogni"e translation initiation sites2fficiency of ri%osomes to recogni"e translation initiation sites

!ta%ility of polypeptide product!ta%ility of polypeptide product

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The utili"ation of lactose %yThe utili"ation of lactose %yE. coliE. coli''

model system for gene regulation model system for gene regulation

The presence of lactose induces expression of the genesThe presence of lactose induces expression of the genes

re3uired for lactose utili"ationre3uired for lactose utili"ation +nduction+nduction$ stimulation of protein synthesis$ stimulation of protein synthesis

+nducer+nducer$ molecule that stimulates synthesis$ molecule that stimulates synthesis 8actose8actose$ inducer of genes for lactose utili"ation$ inducer of genes for lactose utili"ation

1975s and 1965s $ Golden era of %acterial genetics1975s and 1965s $ Golden era of %acterial genetics d#antages ofd#antages ofE. coliE. coliand lactose utili"ation systemand lactose utili"ation system

Culture large num%ers of %acteria allow isolation of rare mutantsCulture large num%ers of %acteria allow isolation of rare mutants 8actose genes not essential for sur#i#al -can use glucose as car%on8actose genes not essential for sur#i#al -can use glucose as car%on

source0source0

+nduction increases expression 1555 fold making mutant identification+nduction increases expression 1555 fold making mutant identification

easyeasy

Color changes usingColor changes using :galactosidase en"yme -e(g(. OPNG. ;:gal0 make:galactosidase en"yme -e(g(. OPNG. ;:gal0 makemeasurement of expression le#els efficientmeasurement of expression le#els efficient

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Coordinate repression and induction of three genesCoordinate repression and induction of three genes

re#ealed %y studies of lactose:utili"ation mutantsre#ealed %y studies of lactose:utili"ation mutants

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Complementation nalysis of mutants identifiesComplementation nalysis of mutants identifies

lactose utili"ation geneslactose utili"ation genes

)onod et al( isolated many 8ac)onod et al( isolated many 8ac::mutants una%le tomutants una%le to

utili"e lactoseutili"e lactose Complementation analysis identified three genesComplementation analysis identified three genes

-lac>. lac?. and lac0 in a tightly linked cluster-lac>. lac?. and lac0 in a tightly linked cluster

Fig. 16.5

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2xperimental e#idence for repressor protein2xperimental e#idence for repressor protein

+solated mutant in+solated mutant in lacIlacIgenegene

Constituti#eConstituti#emutant $ synthesi"edmutant $ synthesi"ed ::

galactosidase and lac permease e#en in a%sencegalactosidase and lac permease e#en in a%sence

of lactose -inducer0of lactose -inducer0

lacIlacImust %e amust %e a repressorrepressor$ cells must need$ cells must need lacIlacI

protein product to pre#ent expression ofprotein product to pre#ent expression of lacYlacY

andand lacZlacZin a%sence of inducerin a%sence of inducer

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Pa

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+nducer releases repressor to trigger+nducer releases repressor to trigger

en"yme synthesisen"yme synthesis

ddition of lactose inducer causedddition of lactose inducer caused $$

galactosidase synthesis to continuegalactosidase synthesis to continue

Conclusion' +nducer %inds to repressor soConclusion' +nducer %inds to repressor so

repressor can not %ind to &Nrepressor can not %ind to &N

llostericllostericeffect : inducer %ound toeffect : inducer %ound to

promotor changes conformation of proteinpromotor changes conformation of protein

so it can not %ind to &Nso it can not %ind to &N

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Repressor has %inding domains forRepressor has %inding domains for

operator and for the induceroperator and for the inducer

Fig. 16.7

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Changes in the operator can alsoChanges in the operator can also

affect repressor acti#ityaffect repressor acti#ity

Fig. 16.8

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Proteins act inProteins act in transtrans

&N sites act only in&N sites act only in ciscis

TransTransacting elementsacting elementscan diffuse throughcan diffuse through

cytoplasm and act at target &N sites oncytoplasm and act at target &N sites on

any &N molecule in cellany &N molecule in cell

CisCisacting elementsacting elementscan only influencecan only influence

expression of ad@acent genes on same &Nexpression of ad@acent genes on same &N

moleculemolecule

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Three experiments elucidateThree experiments elucidate ciscisandand transtrans

acting elements using =/ plasmidacting elements using =/ plasmid

+nduci%le synthesis+nduci%le synthesis

lacIlacI,,gene encodes agene encodes a

diffusi%le element thatdiffusi%le element that

acts inacts in transtrans%y%y

%inding to any%inding to any

operator it encountersoperator it encounters

regardless ofregardless ofchromosomal locationchromosomal location

Insert Figure 16.9ahere

Fi . 16.9 a

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Noninduci%leNoninduci%le

ll operator sites -O,0ll operator sites -O,0e#entually occupied %ye#entually occupied %ysuperrepressorsuperrepressor

lacIlacIsupperrepressor cansupperrepressor cannot %ind inducernot %ind inducer lacIlacIss mutant encodes amutant encodes a

diffusi%le element thatdiffusi%le element that%inds to operator%inds to operatorregardless of chromosomalregardless of chromosomallocation -trans actinglocation -trans actingelement0element0

Insert Figure 16.9bhere

Fig. 16.9 b

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Constituti#eConstituti#e

Presence of OPresence of O,,plasmidplasmid

does not compensatedoes not compensate

for Ofor Occ

mutation onmutation on%acterial chromosome%acterial chromosome

Operator isOperator is ciscisactingacting

elementelement

Insert Figure 16.9chere

Fig. 16.9 c

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The Operon TheoryThe Operon Theory

The playersThe players

laczlacz.. lacYlacY.. lacZlacZgenes that split lactose into glucose and galactosegenes that split lactose into glucose and galactose

Promotor site to which RN polymerase %indsPromotor site to which RN polymerase %inds

cis acting operator sitecis acting operator site

trans:acting repressor that can %ind to operator -encoded %ytrans:acting repressor that can %ind to operator -encoded %y lacIlacIgene0gene0

+nducer that pre#ents repressor from %inding to operator+nducer that pre#ents repressor from %inding to operator

Fi . 16.10 a

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RepressionRepression +n a%sence of lactose. repressor %inds to operator which+n a%sence of lactose. repressor %inds to operator which

pre#ents transcriptionpre#ents transcription

Negati#e regulatory elementNegati#e regulatory element

Fig. 16.10 b

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+nduction+nduction 8actose present8actose present

llolactose %inds tollolactose %inds to

repressor(repressor(

Repressor changes shapeRepressor changes shape

and can not %ind toand can not %ind tooperatoroperator

RN polymerase %indsRN polymerase %inds

to promotor andto promotor and

initiates transcription ofinitiates transcription of

polycistronic mRNpolycistronic mRN

Fig. 16.10 c

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Positi#e control increasesPositi#e control increases

transcription oftranscription of lacZlacZ.. lacYlacY. and. and lacAlacA c)P %inds toc)P %inds to

CRP -c)PCRP -c)P

receptor protein0receptor protein0

when glucose is lowwhen glucose is low

CRP %inds toCRP %inds to

regulatory regionregulatory region

2nhances acti#ity2nhances acti#ity

of RN polymeraseof RN polymeraseat lac promotorat lac promotor

Fi . 16.11

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!ome positi#e regulators increase!ome positi#e regulators increase

transcription of genes in only one pathwaytranscription of genes in only one pathway

AraCAraCis a positi#eis a positi#e

regulator for allregulator for all

ara%inose genesara%inose genes

which %reak downwhich %reak downsugar ara%inosesugar ara%inose

8oss of function8oss of function

mutation results inmutation results in

little or nolittle or noexpression of genesexpression of genes

Fig. 16.12

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)olecular studies help fill in details)olecular studies help fill in details

of control mechanismsof control mechanisms Radioacti#e tag attachedRadioacti#e tag attached

to lac repressorto lac repressor Repressor fromRepressor from lacIlacI,,cellscells

purified and mixed withpurified and mixed with

operator &N. cosedimentoperator &N. cosedimentoccurredoccurred

Repressor fromRepressor from lacIlacI,,mixedmixed

with mutant operator &N.with mutant operator &N.

no cosediment occurredno cosediment occurred

Fig. 16.13

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)any &N:inding proteins contain)any &N:inding proteins contain

a helix:turn:helix motifa helix:turn:helix motif

TwoTwo AA:helical regions:helical regions

separated %y a turn inseparated %y a turn in

the protein structurethe protein structure

*elix:turn:helix motif*elix:turn:helix motif

fits into ma@or groo#efits into ma@or groo#e

of &Nof &N

)ost repressor)ost repressorproteinsproteins

Fig. 16.14 a

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!pecific amino acids in the a:helix determine!pecific amino acids in the a:helix determine

the %inding specificity of repressor proteinsthe %inding specificity of repressor proteins

*y%rid BB:P44 repressor engineered to ha#e amino acid*y%rid BB:P44 repressor engineered to ha#e amino acid

se3uence that will %ind to %acterial #irus BB andse3uence that will %ind to %acterial #irus BB and

%acteriophage P44%acteriophage P44 Fig. 16.14 b

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)ost regulatory proteins are)ost regulatory proteins are

oligomericoligomeric

More than one

binding domain

DNase footrint

identifies bindingregion

DNase cannot

digest rotein

co!ered sites

Fig. 16.15 a

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The looping of &N is a commonThe looping of &N is a common

feature of regulatory proteinsfeature of regulatory proteins

AraCAraCacts as %oth aacts as %oth arepressor and acti#atorrepressor and acti#ator No ara%inoseNo ara%inose

inding toinding to araOaraOandand

araIaraI11causes looping andcauses looping andpre#ents RN frompre#ents RN fromtranscri%ingtranscri%ing

ra%inose presentra%inose present AraCAraC %inds to%inds to araIaraI11andand

araIaraI44%ot not to%ot not to araOaraO( RN( RNpolymerase interacts withpolymerase interacts witharaCaraCat theat the araIaraIsites andsites andtranscri%es genestranscri%es genes

Fig. 16.16

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*ow regulatory proteins interact*ow regulatory proteins interact

with RN polymerasewith RN polymerase

Negati#e regulators -Negati#e regulators -laclacrepressor0repressor0

Physically %lock &N:%inding sites of RNPhysically %lock &N:%inding sites of RN

polymerasepolymerase

Positi#e regulatorsPositi#e regulators

2sta%lish physical contact with RN2sta%lish physical contact with RN

polymerase enhancing en"yme/s a%ility topolymerase enhancing en"yme/s a%ility to

initiate transcriptioninitiate transcription

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sing the lac> gene as a reporter ofsing the lac> gene as a reporter of

gene expressiongene expression

Reporter gene $ protein encoding geneReporter gene $ protein encoding gene

whose expression in the cell is 3uantifia%lewhose expression in the cell is 3uantifia%le

%y techni3ues of protein detection(%y techni3ues of protein detection(

=usion of reporter gene to cis acting=usion of reporter gene to cis acting

regulatory regions allows assessment generegulatory regions allows assessment gene

acti#ity %y monitoring amount of reporteracti#ity %y monitoring amount of reporter

gene productgene product

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=usion used to perform genetic studies of the=usion used to perform genetic studies of the

regulatory region of gene ;regulatory region of gene ;

Fig. 16.18 a

C iC ti

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Creating aCreating a

collection ofcollection of

lac>lac>insertions ininsertions in

thethe

chromosomechromosome

Fig. 16.18 b

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se of a fusion tose of a fusion to

o#erproduce a geneo#erproduce a gene

productproduct

Fig. 16.18 c

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The attenuation of gene expression' =ine tuning of theThe attenuation of gene expression' =ine tuning of the trptrp

operon through termination of transcriptionoperon through termination of transcription

The presence of tryptophan acti#ates aThe presence of tryptophan acti#ates a

repressor of the trp operonrepressor of the trp operon

trpR gene produces repressortrpR gene produces repressor CorepressorCorepressor$ tryptophan %inds to trp repressor$ tryptophan %inds to trp repressor

allowing it to %ind to operator &N and inhi%itallowing it to %ind to operator &N and inhi%it

transcriptiontranscription

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Termination of transcription fineTermination of transcription fine

tunes regulation oftunes regulation of trptrpoperonoperon

trpRtrpR::mutants are not constituti#emutants are not constituti#e Repressor independent change inRepressor independent change in trptrpexpressionexpression

Two alternati#e transcripts lead to differentTwo alternati#e transcripts lead to different

transcriptional outcomestranscriptional outcomes 8eader se3uence can fold in two different sta%le8eader se3uence can fold in two different sta%le

conformationsconformations Tryptophan present $ ri%osome mo#es 3uickly past codons inTryptophan present $ ri%osome mo#es 3uickly past codons in

leader allowing stem:loop to form terminating transcriptionleader allowing stem:loop to form terminating transcription

Tryptophan a%sent $ ri%osome stalls allowing normal stem loopTryptophan a%sent $ ri%osome stalls allowing normal stem loop

structure to form and transcription proceeds normallystructure to form and transcription proceeds normally

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Glo%al regulatory mechanisms coordinate theGlo%al regulatory mechanisms coordinate the

expression of many genesexpression of many genes

Normal sigma factor -Normal sigma factor -D5D50 %inds to RN polymerase and0 %inds to RN polymerase and

recogni"es se3uence in promoter to initiate transcriptionrecogni"es se3uence in promoter to initiate transcription

*eat shock disa%les*eat shock disa%les D5D5

Product ofProduct of rpoHrpoHgene.gene. 44%inds to se3uence in promoter of%inds to se3uence in promoter of

heat shock genes when heat stressed and starts transcriptionheat shock genes when heat stressed and starts transcription

Fig. 16.21 a

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=actors influencing increase in=actors influencing increase in 44acti#ity after heat shockacti#ity after heat shock

+ncrease in transcription of the rpo* gene+ncrease in transcription of the rpo* gene +ncrease in the translation of+ncrease in the translation of C4C4mRNmRN

stemming from greater sta%ility of rpo* mRNstemming from greater sta%ility of rpo* mRN

+ncrease in the sta%ility and acti#ity of the+ncrease in the sta%ility and acti#ity of the C4C4protein( Chaperones &na

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hat ena%les transcription ofhat ena%les transcription of 44during heat shockHduring heat shockH

Normal temperatures.Normal temperatures. rpoHrpoHgene -encodesgene -encodesC4C40 has promoter se3uence recogni"ed %y0 has promoter se3uence recogni"ed %y D5D5

which starts transcriptionwhich starts transcription

*igh temperatures -no*igh temperatures -no D5D5

0 a different promoter0 a different promoter

se3uence of these3uence of the rpoHrpoHgene is recogni"ed %y agene is recogni"ed %y a

different sigma factor.different sigma factor. 4B4B

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!ummary!ummary

E. colisE. colisheat shock response is controlled %yheat shock response is controlled %y

alternati#e sigma factors that recogni"e differentalternati#e sigma factors that recogni"e different

promoter se3uencespromoter se3uences

lternati#e sigma factors %ind to RN polymeraselternati#e sigma factors %ind to RN polymerase

as temperatures change to start transcription ofas temperatures change to start transcription of

heat shock proteinsheat shock proteins

The induction of alternati#e sigma factors thatThe induction of alternati#e sigma factors thatrecogni"e different promoter se3uences ser#e asrecogni"e different promoter se3uences ser#e as

glo%al control regulatory mechanisms inglo%al control regulatory mechanisms inE. coliE. coliand many other %acteriaand many other %acteria

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)icroarrays $ a tool for unco#ering)icroarrays $ a tool for unco#ering

changes in gene expressionchanges in gene expression

Cellular responses to glo%al en#ironmentalCellular responses to glo%al en#ironmental

changes can %e measured %y microarraychanges can %e measured %y microarray

analysis of mRN isolated from culturesanalysis of mRN isolated from cultures

grown in different en#ironmental conditionsgrown in different en#ironmental conditions Comparisons of wild:type cultures withComparisons of wild:type cultures with

strains containing mutations in keystrains containing mutations in key

regulatory regions help identify genes andregulatory regions help identify genes and

regulatory elements in#ol#ed in response toregulatory elements in#ol#ed in response to

specific en#ironmental changesspecific en#ironmental changes

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Fig. 1.13

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Regulation of Iirulence Genes inRegulation of Iirulence Genes in V.V.

choleraecholerae

acterial agents of cholera sense changes inacterial agents of cholera sense changes in

en#ironment and transmit signals toen#ironment and transmit signals to

regulators that initiate. enhance. diminish.regulators that initiate. enhance. diminish.

or repress expression of #arious genes(or repress expression of #arious genes(

Three regulatory proteins $ ToxR. Tox!.Three regulatory proteins $ ToxR. Tox!.

and ToxT $ turn on the genes for #irulenceand ToxT $ turn on the genes for #irulence

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2xperiments generate model for regulation of2xperiments generate model for regulation of

#irulence genes in#irulence genes in V. choleraeV. cholerae

Cloned two genes encoding su%units ofCloned two genes encoding su%units of

cholera toxin'cholera toxin' ctxActxAandand ctxBctxB

)ade)ade ctxAlacZctxAlacZreporter gene fusionreporter gene fusion

Created #ector li%rary ofCreated #ector li%rary of V. choleraeV. cholerae

genomic &Ngenomic &N

sedsed

E. coliE. coli

to perform geneticto perform genetic

manipulationsmanipulations

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+solated a gene that regulates expression of+solated a gene that regulates expression of ctxctxoperonoperon TransformedTransformedE. coliE. colicontainingcontaining ctxlacZctxlacZconstruct with clonesconstruct with clones

containingcontaining V. choleraeV. cholerae&N&N

Clones that contain a positi#e regulator should turn onClones that contain a positi#e regulator should turn on ctxlacZctxlacZconstructconstruct

+dentified+dentified ToxRToxR. a transmem%rane protein. a transmem%rane protein

+dentified+dentified Tox!Tox!. helps. helps ToxRToxRform dimers which helps it %ind to &Nform dimers which helps it %ind to &N

hat genes doeshat genes does ToxRToxRregulateHregulateH

Gene fusions created to constituti#e promoterGene fusions created to constituti#e promoter =usion introduced into strains of=usion introduced into strains of V. choleraeV. choleraewithwith lacZlacZrandomly insertedrandomly inserted

around the genomearound the genome

+dentified intermediate regulator gene+dentified intermediate regulator gene ToxTToxT. a transcriptional acti#ator. a transcriptional acti#ator

that %inds to promoters of many genes. includingthat %inds to promoters of many genes. including ctxctx

ToxRE! or ToxT can acti#ate the ctx genes that produce toxinToxRE! or ToxT can acti#ate the ctx genes that produce toxin

ToxT alone acti#ates additional #irulence genes which encode pili andToxT alone acti#ates additional #irulence genes which encode pili and

other proteinsother proteins

Transcription of ToxT is regulated %y ToxRE!Transcription of ToxT is regulated %y ToxRE!

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Fig. 16.22

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nanswered Juestions Remainnanswered Juestions Remain

hy is there a cascade -ToxR and ToxT0 ofhy is there a cascade -ToxR and ToxT0 of

regulatory factorsHregulatory factorsH

hat &N se3uence in the promoters doeshat &N se3uence in the promoters does

ToxR recogni"eHToxR recogni"eH hat is the signal that/s makes the cholerahat is the signal that/s makes the cholera

%acteria start to coloni"e the small%acteria start to coloni"e the small

intestineHintestineH *ow does ToxR regulatory protein find*ow does ToxR regulatory protein find

%inding sites on the chromosomeH%inding sites on the chromosomeH

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21807 Ch17