BIOLOGY. Regulation of Gene Expression CAMPBELL. Reece Urry Cain Wasserman Minorsky Jackson

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1 CAMPBELL BIOLOGY TENTH EDITION Reece Urry Cain Wasserman Minorsky Jackson 18 Regulation of Gene Expression Lecture Presentation by Nicole Tunbridge and Kathleen Fitzpatrick

2 Differential Expression of Genes Prokaryotes and eukaryotes precisely regulate gene expression in response to environmental conditions In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types RNA molecules play many roles in regulating gene expression in eukaryotes

3 Figure 18.1

4 Figure 18.1a

5 Concept 18.1: Bacteria often respond to environmental change by regulating transcription Natural selection has favored bacteria that produce only the products needed by that cell A cell can regulate the production of enzymes by feedback inhibition or by gene regulation One mechanism for control of gene expression in bacteria is the operon model

6 Figure 18.2 Precursor Feedback inhibition Enzyme 1 trpe Enzyme 2 trpd trpc Regulation of gene expression Enzyme 3 trpb trpa Tryptophan (a) Regulation of enzyme activity (b) Regulation of enzyme production

7 Operons: The Basic Concept A cluster of functionally related genes can be coordinately controlled by a single on-off switch The switch is a segment of DNA called an operator usually positioned within the promoter An operon is the entire stretch of DNA that includes the operator, the promoter, and the genes that they control

8 The operon can be switched off by a protein repressor The repressor prevents gene transcription by binding to the operator and blocking RNA polymerase The repressor is the product of a separate regulatory gene

9 The repressor can be in an active or inactive form, depending on the presence of other molecules A corepressor is a molecule that cooperates with a repressor protein to switch an operon off For example, E. coli can synthesize the amino acid tryptophan when it has insufficient tryptophan

10 By default the trp operon is on and the genes for tryptophan synthesis are transcribed When tryptophan is present, it binds to the trp repressor protein, which turns the operon off The repressor is active only in the presence of its corepressor tryptophan; thus the trp operon is turned off (repressed) if tryptophan levels are high

11 Figure 18.3 DNA Promoter mrna 5 trpr Regulatory gene 3 RNA polymerase trp operon Promoter Genes of operon trpe trpd trpc trpb trpa Operator Start codon Stop codon mrna 5 Protein Inactive repressor (a) Tryptophan absent, repressor inactive, operon on E D C B A Polypeptide subunits that make up enzymes for tryptophan synthesis DNA mrna 5 trpr 3 trpe No RNA made Protein Tryptophan (corepressor) Active repressor (b) Tryptophan present, repressor active, operon off

12 Figure 18.3a DNA trp operon Promoter Regulatory gene Promoter Genes of operon trpr trpe trpd trpc trpb trpa mrna 5 3 RNA polymerase Operator Start codon mrna 5 Stop codon Protein Inactive repressor (a) Tryptophan absent, repressor inactive, operon on E D C B A Polypeptide subunits that make up enzymes for tryptophan synthesis

13 Figure 18.3b DNA mrna 5 trpr 3 trpe No RNA made Protein Tryptophan (corepressor) Active repressor (b) Tryptophan present, repressor active, operon off

14 Repressible and Inducible Operons: Two Types of Negative Gene Regulation A repressible operon is one that is usually on; binding of a repressor to the operator shuts off transcription The trp operon is a repressible operon An inducible operon is one that is usually off; a molecule called an inducer inactivates the repressor and turns on transcription

15 The lac operon is an inducible operon and contains genes that code for enzymes used in the hydrolysis and metabolism of lactose By itself, the lac repressor is active and switches the lac operon off A molecule called an inducer inactivates the repressor to turn the lac operon on

16 Figure 18.4 DNA Regulatory gene Promoter Operator l a Ic IacZ mrna 5 3 RNA polymerase No RNA made Protein Active repressor (a) Lactose absent, repressor active, operon off DNA l a Ic lac operon lacz lacy laca mrna RNA polymerase Start codon Stop codon mrna 5 Protein β-galactosidase Permease Transacetylase Allolactose (inducer) Inactive repressor (b) Lactose present, repressor inactive, operon on

17 Figure 18.4a DNA Regulatory gene Promoter Operator lac I IacZ mrna 5 3 RNA polymerase No RNA made Protein Active repressor (a) Lactose absent, repressor active, operon off

18 Figure 18.4b DNA lac operon lac I lacz lacy laca mrna 3 RNA polymerase Start codon Stop codon 5 mrna 5 Protein β-galactosidase Permease Transacetylase Inactive repressor Allolactose (inducer) (b) Lactose present, repressor inactive, operon on

19 Video: Cartoon Rendering of the lac Repressor from E. coli

20 Inducible enzymes usually function in catabolic pathways; their synthesis is induced by a chemical signal Repressible enzymes usually function in anabolic pathways; their synthesis is repressed by high levels of the end product Regulation of the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor

21 Positive Gene Regulation Some operons are also subject to positive control through a stimulatory protein, such as catabolite activator protein (CAP), an activator of transcription When glucose (a preferred food source of E. coli) is scarce, CAP is activated by binding with cyclic AMP (camp) Activated CAP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription

22 When glucose levels increase, CAP detaches from the lac operon, and transcription returns to a normal rate CAP helps regulate other operons that encode enzymes used in catabolic pathways

23 Figure 18.5 DNA Promoter Operator lac I lacz CAP-binding site camp Active CAP RNA polymerase binds and transcribes Inactive CAP Allolactose Inactive lac repressor (a) Lactose present, glucose scarce (camp level high): abundant lac mrna synthesized DNA Promoter lac I lacz CAP-binding site Inactive CAP Operator RNA polymerase less likely to bind Inactive lac repressor (b) Lactose present, glucose present (camp level low): little lac mrna synthesized

24 Figure 18.5a DNA lac I Promoter Operator lacz CAP-binding site camp Active CAP Inactive CAP Allolactose RNA polymerase binds and transcribes Inactive lac repressor (a) Lactose present, glucose scarce (camp level high): abundant lac mrna synthesized

25 Figure 18.5b DNA lac I Promoter lacz CAP-binding site Inactive CAP Operator RNA polymerase less likely to bind Inactive lac repressor (b) Lactose present, glucose present (camp level low): little lac mrna synthesized

26 Concept 18.2: Eukaryotic gene expression is regulated at many stages All organisms must regulate which genes are expressed at any given time In multicellular organisms regulation of gene expression is essential for cell specialization

27 Differential Gene Expression Almost all the cells in an organism are genetically identical Differences between cell types result from differential gene expression, the expression of different genes by cells with the same genome Abnormalities in gene expression can lead to diseases including cancer Gene expression is regulated at many stages

28 Figure 18.6 Signal Chromatin DNA Chromatin modification: DNA unpacking Gene available for transcription Transcription Cap RNA NUCLEUS CYTOPLASM Degradation of mrna Exon Intron Primary transcript RNA processing Tail mrna in nucleus Transport to cytoplasm mrna in cytoplasm Translation Polypeptide Protein processing Degradation of protein Active protein Transport to cellular destination Cellular function (such as enzymatic activity or structural support)

29 Figure 18.6a Signal Chromatin DNA Chromatin modification: DNA unpacking Gene available for transcription Transcription Cap RNA Exon Intron Primary transcript RNA processing Tail mrna in nucleus NUCLEUS Transport to cytoplasm CYTOPLASM

30 Figure 18.6b CYTOPLASM mrna in cytoplasm Degradation of mrna Translation Polypeptide Protein processing Degradation of protein Active protein Transport to cellular destination Cellular function (such as enzymatic activity or structural support)

31 Animation: Protein Degradation

32 Animation: Protein Processing

33 Animation: Blocking Translation

34 Regulation of Chromatin Structure The structural organization of chromatin helps regulate gene expression in several ways Genes within highly packed heterochromatin are usually not expressed Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

35 Histone Modifications and DNA Methylation In histone acetylation, acetyl groups are attached to positively charged lysines in histone tails This loosens chromatin structure, thereby promoting the initiation of transcription The addition of methyl groups (methylation) can condense chromatin; the addition of phosphate groups (phosphorylation) next to a methylated amino acid can loosen chromatin

36 Figure 18.7 Histone tails DNA double helix Amino acids available for chemical modification Nucleosome (end view) (a) Histone tails protrude outward from a nucleosome Acetyl groups DNA Unacetylated histones (side view) Acetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription

37 DNA methylation, the addition of methyl groups to certain bases in DNA, is associated with reduced transcription in some species DNA methylation can cause long-term inactivation of genes in cellular differentiation In genomic imprinting, methylation regulates expression of either the maternal or paternal alleles of certain genes at the start of development

38 Epigenetic Inheritance Although the chromatin modifications just discussed do not alter DNA sequence, they may be passed to future generations of cells The inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance

39 Regulation of Transcription Initiation Chromatin-modifying enzymes provide initial control of gene expression by making a region of DNA either more or less able to bind the transcription machinery

40 Organization of a Typical Eukaryotic Gene Associated with most eukaryotic genes are multiple control elements, segments of noncoding DNA that serve as binding sites for transcription factors that help regulate transcription Control elements and the transcription factors they bind are critical to the precise regulation of gene expression in different cell types

41 Figure 18.8 Enhancer (group of distal control elements) DNA Proximal control elements Transcription start site Exon Intron Exon Intron Poly-A signal sequence Exon Transcription termination region Upstream Primary RNA transcript (pre-mrna) Promoter 5 Exon Intron Exon Transcription Intron Downstream Poly-A signal Exon Cleaved 3 end of primary transcript Intron RNA RNA processing Coding segment mrna G P P P 5 Cap 5 UTR Start codon Stop codon AAA AAA 3 UTR Poly-A tail 3

42 Figure 18.8a DNA Enhancer (group of distal control elements) Upstream Proximal control elements Transcription start site Poly-A signal sequence Exon Intron Exon Intron Exon Promoter Transcription termination region Downstream

43 Figure 18.8b-1 Proximal control elements Transcription start site Poly-A signal sequence Exon Intron Exon Intron Exon DNA Promoter

44 Figure 18.8b-2 Proximal control elements Transcription start site Poly-A signal sequence Exon Intron Exon Intron Exon DNA Primary RNA transcript (pre-mrna) Promoter 5 Exon Transcription Poly-A signal Intron Exon Intron Exon Cleaved 3 end of primary transcript

45 Figure 18.8b-3 Proximal control elements Transcription start site Poly-A signal sequence Exon Intron Exon Intron Exon DNA Primary RNA transcript (pre-mrna) Promoter 5 Intron RNA Exon Transcription Poly-A signal Intron Exon Intron Exon RNA processing Cleaved 3 end of primary transcript Coding segment mrna G P P P 5 Cap 5 UTR Start codon Stop codon AAA AAA 3 3 UTR Poly-A tail

46 Animation: mrna Degradation

47 The Roles of Transcription Factors To initiate transcription, eukaryotic RNA polymerase requires the assistance of transcription factors General transcription factors are essential for the transcription of all protein-coding genes In eukaryotes, high levels of transcription of particular genes depend on control elements interacting with specific transcription factors

48 Enhancers and Specific Transcription Factors Proximal control elements are located close to the promoter Distal control elements, groupings of which are called enhancers, may be far away from a gene or even located in an intron

49 Figure 18.9 Activation domain DNA-binding domain DNA

50 An activator is a protein that binds to an enhancer and stimulates transcription of a gene Activators have two domains, one that binds DNA and a second that activates transcription Bound activators facilitate a sequence of proteinprotein interactions that result in transcription of a given gene

51 Figure DNA Activators Promoter Enhancer Distal control element TATA box Gene

52 Figure DNA Activators Promoter Enhancer Distal control element TATA box Gene DNAbending protein General transcription factors Group of mediator proteins

53 Figure DNA Activators Promoter Enhancer Distal control element TATA box Gene DNAbending protein General transcription factors Group of mediator proteins RNA polymerase II RNA polymerase II Transcription initiation complex RNA synthesis

54 Animation: Initiation of Transcription

55 Some transcription factors function as repressors, inhibiting expression of a particular gene by a variety of methods Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription

56 Combinatorial Control of Gene Activation A particular combination of control elements can activate transcription only when the appropriate activator proteins are present

57 Figure DNA in both cells contains the albumin gene and the crystallin gene: Control elements Enhancer for albumin gene Promoter Enhancer for crystallin gene Promoter Albumin gene Crystallin gene LIVER CELL NUCLEUS Available activators LENS CELL NUCLEUS Available activators Albumin gene expressed Albumin gene not expressed Crystallin gene not expressed Crystallin gene expressed (a) Liver cell (b) Lens cell

58 Figure 18.11a DNA in both cells contains the albumin gene and the crystallin gene: Enhancer for albumin gene Promoter Albumin gene Control elements Enhancer for crystallin gene Promoter Crystallin gene

59 Figure 18.11b LIVER CELL NUCLEUS Available activators Albumin gene expressed Crystallin gene not expressed (a) Liver cell

60 Figure 18.11c LENS CELL NUCLEUS Available activators Albumin gene not expressed (b) Lens cell Crystallin gene expressed

61 Coordinately Controlled Genes in Eukaryotes Co-expressed eukaryotic genes are not organized in operons (with a few minor exceptions) These genes can be scattered over different chromosomes, but each has the same combination of control elements Copies of the activators recognize specific control elements and promote simultaneous transcription of the genes

62 Nuclear Architecture and Gene Expression Loops of chromatin extend from individual chromosome territories into specific sites in the nucleus Loops from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases These may be areas specialized for a common function

63 Figure Chromosomes in the interphase nucleus (fluorescence micrograph) Chromosome territory 5 µm Chromatin loop Transcription factory

64 Figure 18.12a Chromosomes in the interphase nucleus (fluorescence micrograph) 5 µm

65 Mechanisms of Post-Transcriptional Regulation Transcription alone does not account for gene expression Regulatory mechanisms can operate at various stages after transcription Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes

66 RNA Processing In alternative RNA splicing, different mrna molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns

67 Figure Exons DNA Troponin T gene Primary RNA transcript RNA splicing mrna OR

68 Animation: RNA Processing

69 Initiation of Translation and mrna Degradation The initiation of translation of selected mrnas can be blocked by regulatory proteins that bind to sequences or structures of the mrna Alternatively, translation of all mrnas in a cell may be regulated simultaneously For example, translation initiation factors are simultaneously activated in an egg following fertilization

70 The life span of mrna molecules in the cytoplasm is a key to determining protein synthesis Eukaryotic mrna is more long lived than prokaryotic mrna Nucleotide sequences that influence the lifespan of mrna in eukaryotes reside in the untranslated region (UTR) at the 3 end of the molecule

71 Protein Processing and Degradation After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control The length of time each protein function is regulated by selective degradation Cells mark proteins for degradation by attaching ubiquitin to them This mark is recognized by proteasomes, which recognize and degrade the proteins

72 Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression Only a small fraction of DNA codes for proteins, and a very small fraction of the non-protein-coding DNA consists of genes for RNA such as rrna and trna A significant amount of the genome may be transcribed into noncoding RNAs (ncrnas) Noncoding RNAs regulate gene expression at two points: mrna translation and chromatin configuration

73 Effects on mrnas by MicroRNAs and Small Interfering RNAs MicroRNAs (mirnas) are small single-stranded RNA molecules that can bind to mrna These can degrade mrna or block its translation It is estimated that expression of at least half of all human genes may be regulated by mirnas

74 Figure mirna mirnaprotein complex 1 The mirna binds to a target mrna. OR mrna degraded Translation blocked 2 If bases are completely complementary, mrna is degraded. If match is less than complete, translation is blocked.

75 Small interfering RNAs (sirnas) are similar to mirnas in size and function The blocking of gene expression by sirnas is called RNA interference (RNAi) RNAi is used in the laboratory as a means of disabling genes to investigate their function

76 Chromatin Remodeling by ncrnas Some ncrnas act to bring about remodeling of chromatin structure In some yeasts sirnas re-form heterochromatin at centromeres after chromosome replication

77 Figure Centromeric DNA 1 RNA transcripts (red) produced. RNA polymerase RNA transcript Sister chromatids (two DNA molecules) 2 Yeast enzyme synthesizes strands complementary to RNA transcripts. 3 Double-stranded RNA processed into sirnas that associate with proteins. sirna-protein complex 4 The sirna-protein complexes bind RNA transcripts and become tethered to centromere region. 5 The sirna-protein complexes recruit histone-modifying enzymes. Centromeric DNA 6 Chromatin condensation is initiated and heterochromatin is formed. Heterochromatin at the centromere region Chromatinmodifying enzymes

78 Figure 18.15a Centromeric DNA 1 2 RNA transcripts (red) produced. Yeast enzyme synthesizes strands complementary to RNA transcripts. RNA polymerase RNA transcript Sister chromatids (two DNA molecules) 3 Double-stranded RNA processed into sirnas that associate with proteins. sirna-protein complex 4 The sirna-protein complexes bind RNA transcripts and become tethered to centromere region.

79 Figure 18.15b 5 The sirna-protein complexes recruit histone-modifying enzymes. Centromeric DNA 6 Chromatin condensation is initiated and heterochromatin is formed. Heterochromatin at the centromere region Chromatinmodifying enzymes

80 Small ncrnas called piwi-associated RNAs (pirnas) induce heterochromatin, blocking the expression of parasitic DNA elements in the genome, known as transposons RNA-based regulation of chromatin structure is likely to play an important role in gene regulation

81 The Evolutionary Significance of Small ncrnas Small ncrnas can regulate gene expression at multiple steps An increase in the number of mirnas in a species may have allowed morphological complexity to increase over evolutionary time sirnas may have evolved first, followed by mirnas and later pirnas

82 Concept 18.4: A program of differential gene expression leads to the different cell types in a multicellular organism During embryonic development, a fertilized egg gives rise to many different cell types Cell types are organized successively into tissues, organs, organ systems, and the whole organism Gene expression orchestrates the developmental programs of animals

83 A Genetic Program for Embryonic Development The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis

84 Figure mm 2 mm (a) Fertilized eggs of a frog (b) Newly hatched tadpole

85 Figure 18.16a 1 mm (a) Fertilized eggs of a frog

86 Figure 18.16b 2 mm (b) Newly hatched tadpole

87 Cell differentiation is the process by which cells become specialized in structure and function The physical processes that give an organism its shape constitute morphogenesis Differential gene expression results from genes being regulated differently in each cell type Materials in the egg set up gene regulation that is carried out as cells divide

88 Cytoplasmic Determinants and Inductive Signals An egg s cytoplasm contains RNA, proteins, and other substances that are distributed unevenly in the unfertilized egg Cytoplasmic determinants are maternal substances in the egg that influence early development As the zygote divides by mitosis, cells contain different cytoplasmic determinants, which lead to different gene expression

89 The other important source of developmental information is the environment around the cell, especially signals from nearby embryonic cells In the process called induction, signal molecules from embryonic cells cause transcriptional changes in nearby target cells Thus, interactions between cells induce differentiation of specialized cell types

90 Figure (a) Cytoplasmic determinants in the egg (b) Induction by nearby cells Unfertilized egg Sperm Molecules of two different cytoplasmic determinants Nucleus Fertilization Zygote (fertilized egg) Mitotic cell division Two-celled embryo Signal transduction pathway Signal receptor Signaling molecule Early embryo (32 cells) NUCLEUS

91 Figure 18.17a (a) Cytoplasmic determinants in the egg Molecules of two different cytoplasmic determinants Unfertilized egg Nucleus Fertilization Mitotic cell division Sperm Zygote (fertilized egg) Two-celled embryo

92 Figure 18.17b (b) Induction by nearby cells Early embryo (32 cells) NUCLEUS Signal transduction pathway Signal receptor Signaling molecule

93 Animation: Cell Signaling

94 Sequential Regulation of Gene Expression During Cellular Differentiation Determination irreversibly commits a cell to its final fate Determination precedes differentiation Cell differentiation is marked by the production of tissue-specific proteins

95 Myoblasts are cells determined to produce muscle cells and begin producing muscle-specific proteins MyoD is a master regulatory gene encodes a transcription factor that commits the cell to becoming skeletal muscle The MyoD protein can turn some kinds of differentiated cells fat cells and liver cells into muscle cells

96 Figure Nucleus Master regulatory gene myod Other muscle-specific genes Embryonic precursor cell DNA OFF OFF

97 Figure Nucleus Master regulatory gene myod Other muscle-specific genes Embryonic precursor cell DNA OFF OFF mrna OFF Myoblast (determined) MyoD protein (transcription factor)

98 Figure Nucleus Master regulatory gene myod Other muscle-specific genes Embryonic precursor cell DNA OFF OFF mrna OFF Myoblast (determined) MyoD protein (transcription factor) mrna mrna mrna mrna Part of a muscle fiber (fully differentiated cell) MyoD Another transcription factor Myosin, other muscle proteins, and cell cycle blocking proteins

99 Pattern Formation: Setting Up the Body Plan Pattern formation is the development of a spatial organization of tissues and organs In animals, pattern formation begins with the establishment of the major axes Positional information, the molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells

100 Pattern formation has been extensively studied in the fruit fly Drosophila melanogaster Combining anatomical, genetic, and biochemical approaches, researchers have discovered developmental principles common to many other species, including humans

101 The Life Cycle of Drosophila In Drosophila, cytoplasmic determinants in the unfertilized egg determine the axes before fertilization After fertilization, the embryo develops into a segmented larva with three larval stages

102 Figure Developing egg within ovarian follicle Follicle cell Nucleus Egg Nurse cell 2 Mature, unfertilized egg Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg Head Thorax Abdomen Embryonic development 0.5 mm 4 Segmented embryo 0.1 mm BODY AXES Anterior Left Dorsal Ventral Right Posterior 5 Larva Body segments Hatching (a) Adult (b) Development from egg to larva

103 Figure 18.19a Head Thorax Abdomen 0.5 mm Dorsal Right BODY AXES Anterior Left Ventral Posterior (a) Adult

104 Figure 18.19b-1 1 Developing egg within ovarian follicle Follicle cell Nurse cell Nucleus Egg (b) Development from egg to larva

105 Figure 18.19b-2 1 Developing egg within ovarian follicle Follicle cell Nurse cell Nucleus Egg 2 Mature, unfertilized egg Depleted nurse cells Egg shell (b) Development from egg to larva

106 Figure 18.19b-3 1 Developing egg within ovarian follicle Follicle cell Nurse cell Nucleus Egg 2 Mature, unfertilized egg Depleted nurse cells Egg shell Fertilization Laying of egg 3 Fertilized egg (b) Development from egg to larva

107 Figure 18.19b-4 1 Developing egg within ovarian follicle Follicle cell Nurse cell Nucleus Egg 2 Mature, unfertilized egg Depleted nurse cells Egg shell Fertilization Laying of egg 3 Fertilized egg Embryonic development 4 Segmented embryo 0.1 mm Body segments (b) Development from egg to larva

108 Figure 18.19b-5 1 Developing egg within ovarian follicle Follicle cell Nurse cell Nucleus Egg 2 Mature, unfertilized egg Depleted nurse cells Egg shell Fertilization Laying of egg 3 Fertilized egg Embryonic development 4 Segmented embryo 0.1 mm Body segments Hatching 5 Larva (b) Development from egg to larva

109 Genetic Analysis of Early Development: Scientific Inquiry Edward B. Lewis, Christiane Nüsslein-Volhard, and Eric Wieschaus won a Nobel Prize in 1995 for decoding pattern formation in Drosophila Lewis discovered the homeotic genes, which control pattern formation in late embryo, larva, and adult stages

110 Figure Wild type Mutant Eye Antenna Leg

111 Figure 18.20a Wild type Eye Antenna

112 Figure 18.20b Mutant Leg

113 Nüsslein-Volhard and Wieschaus studied segment formation They created mutants, conducted breeding experiments, and looked for corresponding genes Many of the identified mutations were embryonic lethals, causing death during embryogenesis They found 120 genes essential for normal segmentation

114 Axis Establishment Maternal effect genes encode cytoplasmic determinants that initially establish the axes of the body of Drosophila These maternal effect genes are also called eggpolarity genes because they control orientation of the egg and consequently the fly

115 Bicoid: A Morphogen That Determines Head Structures One maternal effect gene, the bicoid gene, affects the front half of the body An embryo whose mother has no functional bicoid gene lacks the front half of its body and has duplicate posterior structures at both ends

116 Figure Head Tail T1 T2 T3 A1 A2 A3 A4 A5 A6 A7 A8 Wild-type larva 250 µm Tail Tail A8 A7 A6 A7 Mutant larva (bicoid) A8

117 Figure 18.21a Head Tail T1 T2 T3 A1 A2 A3 A4 A5 A6 A7 A8 Wild-type larva 250 µm

118 Figure 18.21b Tail Tail A8 A7 A6 A7 Mutant larva (bicoid) A8

119 This phenotype suggests that the product of the mother s bicoid gene is essential for setting up the anterior end of the embryo This hypothesis is an example of the morphogen gradient hypothesis, in which gradients of substances called morphogens establish an embryo s axes and other features of its form Experiments showed that bicoid protein is distributed in an anterior to posterior gradient in the early embryo

120 Figure Results Anterior end 100 µm Bicoid mrna in mature unfertilized egg Fertilization, translation of bicoid mrna Bicoid protein in early embryo

121 Figure 18.22a 100 µm Bicoid mrna in mature unfertilized egg

122 Figure 18.22b Anterior end 100 µm Bicoid protein in early embryo

123 Animation: Development of Head-Tail Axis in Fruit Flies

124 The bicoid research was ground breaking for three reasons It identified a specific protein required for some early steps in pattern formation It increased understanding of the mother s role in embryo development It demonstrated a key developmental concept that a gradient of molecules can determine polarity and position in the embryo

125 Evolutionary Developmental Biology ( Evo-Devo ) The fly with legs emerging from its head in Figure is the result of a single mutation in one gene Some scientists considered whether these types of mutations could contribute to evolution by generating novel body shapes This line of inquiry gave rise to the field of evolutionary developmental biology, evo-devo

126 Concept 18.5: Cancer results from genetic changes that affect cell cycle control The gene regulation systems that go wrong during cancer are the very same systems involved in embryonic development

127 Types of Genes Associated with Cancer Cancer can be caused by mutations to genes that regulate cell growth and division Mutations in these genes can be caused by spontaneous mutation or environmental influences such as chemicals, radiation, and some viruses

128 Oncogenes are cancer-causing genes in some types of viruses Proto-oncogenes are the corresponding normal cellular genes that are responsible for normal cell growth and division Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle

129 Proto-oncogenes can be converted to oncogenes by Movement of DNA within the genome: if it ends up near an active promoter, transcription may increase Amplification of a proto-oncogene: increases the number of copies of the gene Point mutations in the proto-oncogene or its control elements: cause an increase in gene expression

130 Figure Proto-oncogene Proto-oncogene Proto-oncogene Translocation or transposition: gene moved to new locus, under new controls New promoter Gene amplification: multiple copies of the gene within a control element Point mutation: within the gene Oncogene Oncogene Oncogene Normal growthstimulating protein in excess Normal growth-stimulating protein in excess Normal growthstimulating protein in excess Hyperactive or degradationresistant protein

131 Figure 18.23a Proto-oncogene Translocation or transposition: gene moved to new locus, under new controls New promoter Oncogene Normal growthstimulating protein in excess

132 Figure 18.23b Proto-oncogene Gene amplification: multiple copies of the gene Normal growth-stimulating protein in excess

133 Figure 18.23c Proto-oncogene Point mutation: within a control element within the gene Oncogene Oncogene Normal growthstimulating protein in excess Hyperactive or degradationresistant protein

134 Tumor-Suppressor Genes Tumor-suppressor genes normally help prevent uncontrolled cell growth Mutations that decrease protein products of tumorsuppressor genes may contribute to cancer onset Tumor-suppressor proteins Repair damaged DNA Control cell adhesion Act in cell-signaling pathways that inhibit the cell cycle

135 Interference with Normal Cell-Signaling Pathways Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers Mutations in the ras gene can lead to production of a hyperactive Ras protein and increased cell division

136 Figure Growth factor 3 G protein P P P P P P Ras GTP NUCLEUS 5 Transcription factor (activator) 6 Protein that stimulates the cell cycle 2 Receptor 4 Protein kinases MUTATION Ras GTP Ras protein active with or without growth factor. NUCLEUS Transcription factor (activator) Overexpression of protein

137 Suppression of the cell cycle can be important in the case of damage to a cell s DNA; p53 prevents a cell from passing on mutations due to DNA damage Mutations in the p53 gene prevent suppression of the cell cycle

138 Figure Protein kinases UV light NUCLEUS 5 Protein that inhibits the cell cycle 1 DNA damage 3 Active form 4 in genome of p53 Transcription UV light DNA damage in genome MUTATION Defective or missing transcription factor. Inhibitory protein absent

139 The Multistep Model of Cancer Development Multiple mutations are generally needed for fullfledged cancer; thus the incidence increases with age At the DNA level, a cancerous cell is usually characterized by at least one active oncogene and the mutation of several tumor-suppressor genes

140 Figure Colon 1 Loss of tumorsuppressor gene ras oncogene 2 Activation of APC (or other) 4 Loss of tumor-suppressor gene p53 Normal colon epithelial cells Colon wall Small benign growth (polyp) 3 Loss of tumorsuppressor gene SMAD4 Larger benign growth (adenoma) 5 Additional mutations Malignant tumor (carcinoma)

141 Figure 18.26a 1 Loss of tumorsuppressor gene APC (or other) Colon wall Normal colon epithelial cells Small benign growth (polyp) 2 Activation of ras oncogene 4 Loss of tumor-suppressor gene p53 3 Loss of tumorsuppressor gene SMAD4 Larger benign growth (adenoma) 5 Additional mutations Malignant tumor (carcinoma)

142 Routine screening for some cancers, such as colorectal cancer, is recommended In such cases, any suspicious polyps may be removed before cancer progresses Breast cancer is a heterogeneous disease that is the commonest form of cancer in women in the United States A genomics approach to profiling breast tumors has identified four major types of breast cancer

143 Figure MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Normal Breast Cells in a Milk Duct ERα + PR + HER2 + Duct Estrogen interior receptor alpha (ERα) Progesterone receptor (PR) Breast Cancer Subtypes Luminal A Luminal B HER2 (a receptor tyrosine kinase) ERα +++ PR ++ HER2 40% of breast cancers Best prognosis ERα ++ PR ++ HER2 (shown); some HER % of breast cancers Poorer prognosis than luminal A subtype Support cell Extracellular matrix HER2 Basal-like ERα PR HER % of breast cancers Poorer prognosis than luminal A subtype ERα PR HER % of breast cancers More aggressive; poorer prognosis than other subtypes

144 Figure 18.27a MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Normal Breast Cells in a Milk Duct ERα + PR + HER2 + Estrogen receptor alpha (ERα) Duct interior Progesterone receptor (PR) HER2 (a receptor tyrosine kinase) Support cell Extracellular matrix

145 Figure 18.27b MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Breast Cancer Subtypes Luminal A Luminal B ERα +++ PR ++ HER2 40% of breast cancers Best prognosis ERα ++ PR ++ HER2 (shown); some HER % of breast cancers Poorer prognosis than luminal A subtype

146 Figure 18.27c MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Breast Cancer Subtypes HER2 Basal-like ERα PR HER % of breast cancers Poorer prognosis than luminal A subtype ERα PR HER % of breast cancers More aggressive; poorer prognosis than other subtypes

147 Inherited Predisposition and Environmental Factors Contributing to Cancer Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes Inherited mutations in the tumor-suppressor gene adenomatous polyposis coli are common in individuals with colorectal cancer Mutations in the BRCA1 or BRCA2 gene are found in at least half of inherited breast cancers, and tests using DNA sequencing can detect these mutations

148 The Role of Viruses in Cancer A number of tumor viruses can also cause cancer in humans and animals Viruses can interfere with normal gene regulation in several ways if they integrate into the DNA of a cell Viruses are powerful biological agents

149 Figure 18.UN01 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mrna DEGRADATION TRANSLATION PROTEIN PROCESSING AND DEGRADATION

150 Figure 18.UN02 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mrna DEGRADATION TRANSLATION PROTEIN PROCESSING AND DEGRADATION

151 Figure 18.UN03a Enhancer with possible control elements Promoter Reporter gene Relative level of reporter mrna (% of control)

152 Figure 18.UN03b

153 Figure 18.UN04 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mrna DEGRADATION TRANSLATION PROTEIN PROCESSING AND DEGRADATION

154 Figure 18.UN05 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mrna DEGRADATION TRANSLATION PROTEIN PROCESSING AND DEGRADATION

155 Figure 18.UN06 Promoter Operon Genes A B C Operator RNA polymerase A B C Polypeptides

156 Figure 18.UN07 Repressible operon: Promoter Genes expressed Operator Genes Inactive repressor: no corepressor present Genes not expressed Corepressor Active repressor: corepressor bound

157 Figure 18.UN08 Inducible operon: Genes not expressed Promoter Genes expressed Operator Genes Active repressor: no inducer present Inducer Inactive repressor: inducer bound

158 Figure 18.UN09 Chromatin modification Genes in highly compacted chromatin are generally not transcribed. Histone acetylation seems to loosen chromatin structure, enhancing transcription. DNA methylation generally reduces transcripton. Transcription Regulation of transcription initiation: DNA control elements in enhancers bind specific transcription factors. Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription. Coordinate regulation: CHROMATIN MODIFICATION Enhancer for liver-specific genes Enhancer for lens-specific genes mrna DEGRADATION TRANSCRIPTION RNA PROCESSING TRANSLATION PROTEIN PROCESSING AND DEGRADATION mrna degradation Each mrna has a characteristic life span, determined in part by sequences in the 5 and 3 UTRs. RNA processing Alternative RNA splicing: Primary RNA transcript mrna OR Translation Initiation of translation can be controlled via regulation of initiation factors. Protein processing and degradation Protein processing and degradation are subject to regulation.

159 Figure 18.UN09a CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mrna DEGRADATION TRANSLATION PROTEIN PROCESSING AND DEGRADATION

160 Figure 18.UN09b Chromatin modification Genes in highly compacted chromatin are generally not transcribed. Histone acetylation seems to loosen chromatin structure, enhancing transcription. DNA methylation generally reduces transcription. mrna degradation Each mrna has a characteristic life span, determined in part by sequences in the 5 and 3 UTRs. RNA processing Alternative RNA splicing: Primary RNA transcript mrna OR Translation Initiation of translation can be controlled via regulation of initiation factors. Protein processing and degradation Protein processing and degradation are subject to regulation.

161 Figure 18.UN09c Transcription Regulation of transcription initiation: DNA control elements in enhancers bind specific transcription factors. Bending of the DNA enables activators to contact proteins at the promoter, initiating transcription. Coordinate regulation: Enhancer for liver-specific genes Enhancer for lens-specific genes

162 Figure 18.UN10 CHROMATIN MODIFICATION TRANSCRIPTION Chromatin modification Small and/or large noncoding RNAs can promote heterochromatin formation in certain regions, which can block transcription. mrna DEGRADATION RNA PROCESSING TRANSLATION Translation mirna or sirna can block the translation of specific mrnas. PROTEIN PROCESSING AND DEGRADATION mrna degradation mirna or sirna can target specific mrnas for destruction.

163 Figure 18.UN11 EFFECTS OF MUTATIONS Protein overexpressed Protein absent Cell cycle overstimulated Increased cell division Cell cycle not inhibited

164 Figure 18.UN12 Enhancer Promoter Gene 1 Gene 2 Gene 3 Gene 4 Gene 5

165 Figure 18.UN13