18 Regulation of Gene Expression


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  • Figure 18.2 Regulation of a metabolic pathway.
  • Figure 18.3 The trp operon in E. coli : regulated synthesis of repressible enzymes.
  • Figure 18.4 The lac operon in E. coli : regulated synthesis of inducible enzymes.
  • Figure 18.5 Positive control of the lac operon by catabolite activator protein (CAP).
  • Figure 18.6 Stages in gene expression that can be regulated in eukaryotic cells.
  • Figure 18.7 A simple model of histone tails and the effect of histone acetylation.
  • Figure 18.8 A eukaryotic gene and its transcript.
  • Figure 18.9 The structure of MyoD, a specific transcription factor that acts as an activator.
  • Figure 18.10 A model for the action of enhancers and transcription activators.
  • Figure 18.11 Cell type–specific transcription.
  • Figure 18.13 Alternative RNA splicing of the troponin T gene.
  • Figure 18.14 Degradation of a protein by a proteasome.
  • Figure 18.15 Regulation of gene expression by miRNAs.
  • Figure 18.16 From fertilized egg to animal: What a difference four days makes.
  • Figure 18.17 Sources of developmental information for the early embryo.
  • Figure 18.17 Sources of developmental information for the early embryo.
  • Figure 18.18 Determination and differentiation of muscle cells.
  • Figure 18.23 Genetic changes that can turn proto-oncogenes into oncogenes.
  • Figure 18.24 Signaling pathways that regulate cell division.
  • Figure 18.25 A multistep model for the development of colorectal cancer.
  • 18 Regulation of Gene Expression

    1. 1. LECTURE PRESENTATIONSFor CAMPBELL BIOLOGY, NINTH EDITIONJane B. Reece, Lisa A. Urry, Michael L. Cain, Steven A. Wasserman, Peter V. Minorsky, Robert B. Jackson© 2011 Pearson Education, Inc.Lectures byErin BarleyKathleen FitzpatrickRegulation of Gene ExpressionChapter 18
    2. 2. Bacteria often respond to environmentalchange by regulating transcription• Natural selection has favored bacteria thatproduce only the products needed by that cell• A cell can regulate the production of enzymes byfeedback inhibition or by gene regulation• Gene expression in bacteria is controlled by theoperon model© 2011 Pearson Education, Inc.
    3. 3. PrecursorFeedbackinhibitionEnzyme 1Enzyme 2Enzyme 3Tryptophan(a) (b)Regulation of enzymeactivityRegulation of enzymeproductionRegulationof geneexpression−−trpE genetrpD genetrpC genetrpB genetrpA geneFigure 18.2
    4. 4. Operons: The Basic Concept• A cluster of functionally related genes can beunder coordinated control by a single “on-offswitch”• The regulatory “switch” is a segment of DNAcalled an operator usually positioned within thepromoter• An operon is the entire stretch of DNA thatincludes the operator, the promoter, and the genesthat they control© 2011 Pearson Education, Inc.
    5. 5. • The operon can be switched off by a proteinrepressor• The repressor prevents gene transcription bybinding to the operator and blocking RNApolymerase• The repressor is the product of a separateregulatory gene© 2011 Pearson Education, Inc.
    6. 6. • The repressor can be in an active or inactive form,depending on the presence of other molecules• A corepressor is a molecule that cooperates witha repressor protein to switch an operon off• For example, E. coli can synthesize the aminoacid tryptophan© 2011 Pearson Education, Inc.
    7. 7. • By default the trp operon is on and the genes fortryptophan synthesis are transcribed• When tryptophan is present, it binds to the trprepressor protein, which turns the operon off• The repressor is active only in the presence of itscorepressor tryptophan; thus the trp operon isturned off (repressed) if tryptophan levels are high© 2011 Pearson Education, Inc.
    8. 8. PromoterDNARegulatorygenemRNAtrpR5′3′Protein InactiverepressorRNApolymerasePromotertrp operonGenes of operonOperatormRNA 5′Start codon Stop codontrpE trpD trpC trpB trpAE D C B APolypeptide subunits that make upenzymes for tryptophan synthesis(a) Tryptophan absent, repressor inactive, operon on(b) Tryptophan present, repressor active, operon offDNAmRNAProteinTryptophan(corepressor)ActiverepressorNo RNAmadeFigure 18.3
    9. 9. Repressible and Inducible Operons: TwoTypes of Negative Gene Regulation• A repressible operon is one that is usually on;binding of a repressor to the operator shuts offtranscription• The trp operon is a repressible operon• An inducible operon is one that is usually off; amolecule called an inducer inactivates therepressor and turns on transcription© 2011 Pearson Education, Inc.
    10. 10. • The lac operon is an inducible operon andcontains genes that code for enzymes used in thehydrolysis and metabolism of lactose• By itself, the lac repressor is active and switchesthe lac operon off• A molecule called an inducer inactivates therepressor to turn the lac operon on© 2011 Pearson Education, Inc.
    11. 11. (a) Lactose absent, repressor active, operon off(b) Lactose present, repressor inactive, operon onRegulatorygenePromoterOperatorDNA lacZlacIlacIDNAmRNA5′3′NoRNAmadeRNApolymeraseActiverepressorProteinlac operonlacZ lacY lacADNAmRNA5′3′ProteinmRNA 5′InactiverepressorRNA polymeraseAllolactose(inducer)β-Galactosidase Permease TransacetylaseFigure 18.4
    12. 12. • Inducible enzymes usually function in catabolicpathways; their synthesis is induced by a chemicalsignal• Repressible enzymes usually function in anabolicpathways; their synthesis is repressed by highlevels of the end product• Regulation of the trp and lac operons involvesnegative control of genes because operons areswitched off by the active form of the repressor© 2011 Pearson Education, Inc.
    13. 13. Positive Gene Regulation• Some operons are also subject to positive controlthrough a stimulatory protein, such as cataboliteactivator protein (CAP), an activator oftranscription• When glucose (a preferred food source of E. coli)is scarce, CAP is activated by binding with cyclicAMP (cAMP)• Activated CAP attaches to the promoter of the lacoperon and increases the affinity of RNApolymerase, thus accelerating transcription© 2011 Pearson Education, Inc.
    14. 14. • When glucose levels increase, CAP detaches fromthe lac operon, and transcription returns to anormal rate• CAP helps regulate other operons that encodeenzymes used in catabolic pathways© 2011 Pearson Education, Inc.
    15. 15. Figure 18.5PromoterDNACAP-binding sitelacZlacIRNApolymerasebinds andtranscribesOperatorcAMPActiveCAPInactiveCAPAllolactoseInactive lacrepressor(a) Lactose present, glucose scarce (cAMP level high):abundant lac mRNA synthesizedPromoterDNACAP-binding sitelacZlacIOperatorRNApolymerase lesslikely to bindInactive lacrepressorInactiveCAP(b) Lactose present, glucose present (cAMP level low):little lac mRNA synthesized
    16. 16. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display Detailed genetic and crystallographic studies haveshown that the binding of the lac repressor is morecomplex than originally thought In all, three operator sites have been discovered O1  Next to the promoter O2  Downstream in the lacZ coding region O3  Slightly upstream of the CAP siteThe lac Operon Has Three Operator Sitesfor the lac Repressor14-36
    17. 17. 14-37The identification of three lac operator sitesFigure 14.9Repression is 1,300 foldTherefore, transcription is 1/1,300the level when lactose is presentNo repressionie: Constitutive expression
    18. 18. Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or display The results of Figure 14.9 supported the hypothesisthat the lac repressor must bind to two of the threeoperators to cause repression It can bind to O1 and O2 , or to O1 and O3 But not O2 and O3 If either O2 or O3 is missing maximal repression is notachieved Binding of the lac repressor to two operator sitesrequires that the DNA form a loop A loop in the DNA brings the operator sites closer togetherThis facilitates the binding of the repressor protein14-38
    19. 19. 14-39Figure 14.10Copyright ©The McGraw-Hill Companies, Inc. Permission required for reproduction or displayEach repressordimer binds toone operator siteEach repressordimer binds toone operator site
    20. 20. Differential Gene Expression• Almost all the cells in an organism are geneticallyidentical• Differences between cell types result fromdifferential gene expression, the expression ofdifferent genes by cells with the same genome• Abnormalities in gene expression can lead todiseases including cancer• Gene expression is regulated at many stages© 2011 Pearson Education, Inc.
    21. 21. Figure 18.6 SignalNUCLEUSChromatinChromatin modification:DNA unpacking involvinghistone acetylation andDNA demethylationDNAGeneGene availablefor transcriptionRNA ExonPrimary transcriptTranscriptionIntronRNA processingCapTailmRNA in nucleusTransport to cytoplasmCYTOPLASMmRNA in cytoplasmTranslationDegradationof mRNAPolypeptideProtein processing, suchas cleavage andchemical modificationActive proteinDegradationof proteinTransport to cellulardestinationCellular function (suchas enzymatic activity,structural support)Stages in gene expressionthat can be regulated ineukaryotic cells
    22. 22. Regulation of Chromatin Structure• Genes within highly packed heterochromatin areusually not expressed• Chemical modifications to histones and DNA ofchromatin influence both chromatin structure andgene expression© 2011 Pearson Education, Inc.
    23. 23. Histone Modifications• In histone acetylation, acetyl groups areattached to positively charged lysines in histonetails• This loosens chromatin structure, therebypromoting the initiation of transcription• The addition of methyl groups (methylation) cancondense chromatin; the addition of phosphategroups (phosphorylation) next to a methylatedamino acid can loosen chromatin© 2011 Pearson Education, Inc.
    24. 24. Figure 18.7Amino acidsavailablefor chemicalmodificationHistonetailsDNAdoublehelixNucleosome(end view)(a) Histone tails protrude outward from a nucleosomeUnacetylated histones Acetylated histones(b) Acetylation of histone tails promotes loose chromatinstructure that permits transcription
    25. 25. • The histone code hypothesis proposes thatspecific combinations of modifications, as well asthe order in which they occur, help determinechromatin configuration and influence transcription© 2011 Pearson Education, Inc.
    26. 26. DNA Methylation• DNA methylation, the addition of methyl groupsto certain bases in DNA, is associated withreduced transcription in some species• DNA methylation can cause long-term inactivationof genes in cellular differentiation• In genomic imprinting, methylation regulatesexpression of either the maternal or paternalalleles of certain genes at the start of development© 2011 Pearson Education, Inc.
    27. 27. Epigenetic Inheritance• Although the chromatin modifications justdiscussed do not alter DNA sequence, they maybe passed to future generations of cells• The inheritance of traits transmitted bymechanisms not directly involving the nucleotidesequence is called epigenetic inheritance© 2011 Pearson Education, Inc.
    28. 28. The Roles of Transcription Factors• To initiate transcription, eukaryotic RNApolymerase requires the assistance of proteinscalled transcription factors• General transcription factors are essential for thetranscription of all protein-coding genes• In eukaryotes, high levels of transcription ofparticular genes depend on control elementsinteracting with specific transcription factors© 2011 Pearson Education, Inc.
    29. 29. • Proximal control elements are located close to thepromoter• Distal control elements, groupings of which arecalled enhancers, may be far away from a geneor even located in an intronEnhancers and Specific Transcription Factors© 2011 Pearson Education, Inc.
    30. 30. Figure 18.8-3Enhancer(distal controlelements)DNAUpstreamPromoterProximalcontrolelementsTranscriptionstart siteExon Intron Exon ExonIntronPoly-AsignalsequenceTranscriptionterminationregionDownstreamPoly-AsignalExon Intron Exon ExonIntronTranscriptionCleaved3′ end ofprimarytranscript5′Primary RNAtranscript(pre-mRNA)Intron RNARNA processingmRNACoding segment5′ Cap 5′ UTRStartcodonStopcodon 3′ UTR3′Poly-AtailPPPG AAA ⋅⋅⋅ AAA
    31. 31. • An activator is a protein that binds to an enhancerand stimulates transcription of a gene• Activators have two domains, one that binds DNAand a second that activates transcription• Bound activators facilitate a sequence of protein-protein interactions that result in transcription of agiven gene© 2011 Pearson Education, Inc.
    32. 32. Figure 18.9DNAActivationdomainDNA-bindingdomain
    33. 33. • Some transcription factors function as repressors,inhibiting expression of a particular gene by avariety of methods• Some activators and repressors act indirectly byinfluencing chromatin structure to promote orsilence transcription© 2011 Pearson Education, Inc.
    34. 34. ActivatorsDNAEnhancerDistal controlelementPromoterGeneTATA boxGeneraltranscriptionfactorsDNA-bendingproteinGroup of mediator proteinsRNApolymerase IIRNApolymerase IIRNA synthesisTranscriptioninitiation complexFigure 18.10-3Activator proteins bind to distal controlelements grouped as an enhancer in theDNA. This enhancer has three binding sites,each called a distal control element.A DNA-bending protein brings thebound activators closer to thepromoter.General transcription factors, mediatorproteins, and RNA polymerase II arenearby.The activators bind to certain mediatorproteins and general transcriptionfactors, helping them form an activetranscription initiation complex onthe promoter.
    35. 35. Figure 18.11ControlelementsEnhancer PromoterAlbumin geneCrystallingeneLIVER CELLNUCLEUSAvailableactivatorsAlbumin geneexpressedCrystallin genenot expressed(a) Liver cellLENS CELLNUCLEUSAvailableactivatorsAlbumin genenot expressedCrystallin geneexpressed(b) Lens cell
    36. 36. Mechanisms of Post-TranscriptionalRegulation• Transcription alone does not account for geneexpression• Regulatory mechanisms can operate at variousstages after transcription• Such mechanisms allow a cell to fine-tune geneexpression rapidly in response to environmentalchanges© 2011 Pearson Education, Inc.
    37. 37. RNA Processing• In alternative RNA splicing, different mRNAmolecules are produced from the same primarytranscript, depending on which RNA segments aretreated as exons and which as introns© 2011 Pearson Education, Inc.
    38. 38. ExonsDNATroponin T genePrimaryRNAtranscriptRNA splicingormRNA111 1222 2333444555 5Figure 18.13
    39. 39. Protein Processing and Degradation• After translation, various types of proteinprocessing, including cleavage and the addition ofchemical groups, are subject to control• Proteasomes are giant protein complexes thatbind protein molecules and degrade them© 2011 Pearson Education, Inc.
    40. 40. Figure 18.14Protein tobe degradedUbiquitinUbiquitinatedproteinProteasomeProtein enteringa proteasomeProteasomeand ubiquitinto be recycledProteinfragments(peptides)
    41. 41. Noncoding RNAs play multiple roles incontrolling gene expression• Only a small fraction of DNA codes for proteins,and a very small fraction of the non-protein-codingDNA consists of genes for RNA such as rRNA andtRNA• A significant amount of the genome may betranscribed into noncoding RNAs (ncRNAs)• Noncoding RNAs regulate gene expression at twopoints: mRNA translation and chromatinconfiguration© 2011 Pearson Education, Inc.
    42. 42. Effects on mRNAs by MicroRNAs andSmall Interfering RNAs• MicroRNAs (miRNAs) are small single-strandedRNA molecules that can bind to mRNA• These can degrade mRNA or block its translation© 2011 Pearson Education, Inc.
    43. 43. (a) Primary miRNA transcriptHairpinmiRNAmiRNAHydrogenbondDicermiRNA-proteincomplexmRNA degraded Translation blocked(b) Generation and function of miRNAs5′ 3′Figure 18.15
    44. 44. • The phenomenon of inhibition of gene expressionby RNA molecules is called RNA interference(RNAi)• RNAi is caused by small interfering RNAs(siRNAs)• siRNAs and miRNAs are similar but form fromdifferent RNA precursors© 2011 Pearson Education, Inc.
    45. 45. A program of differential gene expressionleads to the different cell types in amulticellular organism• During embryonic development, a fertilized egggives rise to many different cell types• Cell types are organized successively into tissues,organs, organ systems, and the whole organism• Gene expression orchestrates the developmentalprograms of animals© 2011 Pearson Education, Inc.
    46. 46. A Genetic Program for EmbryonicDevelopment• The transformation from zygote to adult resultsfrom cell division, cell differentiation, andmorphogenesis© 2011 Pearson Education, Inc.
    47. 47. Figure 18.16(a) Fertilized eggs of a frog (b) Newly hatched tadpole1 mm 2 mm
    48. 48. • Cell differentiation is the process by which cellsbecome specialized in structure and function• The physical processes that give an organism itsshape constitute morphogenesis• Differential gene expression results from genesbeing regulated differently in each cell type• Materials in the egg can set up gene regulationthat is carried out as cells divide© 2011 Pearson Education, Inc.
    49. 49. Cytoplasmic Determinants and InductiveSignals• An egg’s cytoplasm contains RNA, proteins, andother substances that are distributed unevenly inthe unfertilized egg• Cytoplasmic determinants are maternalsubstances in the egg that influence earlydevelopment• As the zygote divides by mitosis, cells containdifferent cytoplasmic determinants, which lead todifferent gene expression© 2011 Pearson Education, Inc.
    50. 50. Figure 18.17a(a) Cytoplasmic determinants in the eggUnfertilized eggSpermFertilizationZygote(fertilized egg)Mitoticcell divisionTwo-celledembryoNucleusMolecules of twodifferent cytoplasmicdeterminants
    51. 51. • The other important source of developmentalinformation is the environment around the cell,especially signals from nearby embryonic cells• In the process called induction, signal moleculesfrom embryonic cells cause transcriptionalchanges in nearby target cells• Thus, interactions between cells inducedifferentiation of specialized cell types© 2011 Pearson Education, Inc.
    52. 52. Figure 18.17b(b) Induction by nearby cellsEarly embryo(32 cells)NUCLEUSSignaltransductionpathwaySignalreceptorSignalingmolecule(inducer)
    53. 53. Sequential Regulation of Gene ExpressionDuring Cellular Differentiation• Determination commits a cell to its final fate• Determination precedes differentiation• Cell differentiation is marked by the production oftissue-specific proteins© 2011 Pearson Education, Inc.
    54. 54. • Myoblasts produce muscle-specific proteins andform skeletal muscle cells• MyoD is one of several “master regulatory genes”that produce proteins that commit the cell tobecoming skeletal muscle• The MyoD protein is a transcription factor thatbinds to enhancers of various target genes© 2011 Pearson Education, Inc.
    55. 55. NucleusEmbryonicprecursor cellMyoblast(determined)Part of a muscle fiber(fully differentiated cell)DNAMaster regulatorygene myoDOFF OFFOFFmRNAOther muscle-specific genesMyoD protein(transcriptionfactor)mRNA mRNA mRNA mRNAMyoD AnothertranscriptionfactorMyosin, othermuscle proteins,and cell cycle–blocking proteinsFigure 18.18-3
    56. 56. Cancer results from genetic changes thataffect cell cycle control• The gene regulation systems that go wrong duringcancer are the very same systems involved inembryonic development© 2011 Pearson Education, Inc.
    57. 57. Types of Genes Associated with Cancer• Cancer can be caused by mutations to genes thatregulate cell growth and division• Tumor viruses can cause cancer in animalsincluding humans© 2011 Pearson Education, Inc.
    58. 58. • Oncogenes are cancer-causing genes• Proto-oncogenes are the corresponding normalcellular genes that are responsible for normal cellgrowth and division• Conversion of a proto-oncogene to an oncogenecan lead to abnormal stimulation of the cell cycle© 2011 Pearson Education, Inc.
    59. 59. • Proto-oncogenes can be converted to oncogenesby– Movement of DNA within the genome: if it ends upnear an active promoter, transcription mayincrease– Amplification of a proto-oncogene: increases thenumber of copies of the gene– Point mutations in the proto-oncogene or itscontrol elements: cause an increase in geneexpression© 2011 Pearson Education, Inc.
    60. 60. Figure 18.23Proto-oncogeneDNATranslocation ortransposition: genemoved to new locus,under new controlsGene amplification:multiple copies ofthe geneNewpromoterNormal growth-stimulatingprotein in excessNormal growth-stimulatingprotein in excessPoint mutation:within a controlelementwithinthe geneOncogene OncogeneNormal growth-stimulatingprotein inexcessHyperactive ordegradation-resistantprotein
    61. 61. Tumor-Suppressor Genes• Tumor-suppressor genes help preventuncontrolled cell growth• Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset• Tumor-suppressor proteins– Repair damaged DNA– Control cell adhesion– Inhibit the cell cycle in the cell-signaling pathway© 2011 Pearson Education, Inc.
    62. 62. Interference with Normal Cell-SignalingPathways• Mutations in the ras proto-oncogene and p53tumor-suppressor gene are common in humancancers• Mutations in the ras gene can lead to productionof a hyperactive Ras protein and increased celldivision© 2011 Pearson Education, Inc.
    63. 63. Figure 18.24Growthfactor1234512ReceptorG proteinProtein kinases(phosphorylationcascade)NUCLEUSTranscriptionfactor (activator)DNAGene expressionProtein thatstimulatesthe cell cycleHyperactive Ras protein(product of oncogene)issues signals on itsown.(a) Cell cycle–stimulating pathwayMUTATIONRasRasGTPGTPPPP PPP(b) Cell cycle–inhibiting pathwayProtein kinasesUVlightDNA damagein genomeActiveformof p53DNAProtein thatinhibitsthe cell cycleDefective or missingtranscription factor,such asp53, cannotactivatetranscription.MUTATIONEFFECTS OF MUTATIONS(c) Effects of mutationsProteinoverexpressedCell cycleoverstimulatedIncreased celldivisionProtein absentCell cycle notinhibited3
    64. 64. • Suppression of the cell cycle can be important inthe case of damage to a cell’s DNA; p53 preventsa cell from passing on mutations due to DNAdamage• Mutations in the p53 gene prevent suppression ofthe cell cycle© 2011 Pearson Education, Inc.
    65. 65. The Multistep Model of CancerDevelopment• Multiple mutations are generally needed for full-fledged cancer; thus the incidence increases withage• At the DNA level, a cancerous cell is usuallycharacterized by at least one active oncogene andthe mutation of several tumor-suppressor genes© 2011 Pearson Education, Inc.
    66. 66. Figure 18.25ColonNormal colonepithelial cellsLossof tumor-suppressorgene APC(or other)12345Colon wallSmall benigngrowth(polyp)Activationof rasoncogeneLossof tumor-suppressorgene DCCLossof tumor-suppressorgene p53AdditionalmutationsMalignanttumor(carcinoma)Largerbenign growth(adenoma)
    67. 67. Inherited Predisposition and OtherFactors Contributing to Cancer• Individuals can inherit oncogenes or mutant allelesof tumor-suppressor genes• Inherited mutations in the tumor-suppressor geneadenomatous polyposis coli are common inindividuals with colorectal cancer• Mutations in the BRCA1 or BRCA2 gene are foundin at least half of inherited breast cancers, andtests using DNA sequencing can detect thesemutations© 2011 Pearson Education, Inc.