Control Of Gene Expression PDF

Chapter 18 Control of Gene Expression Lecture Presentations by Nicole Tunbridge and © 2018 Pearson Education Ltd....

Chapter 18 Control of Gene Expression Lecture Presentations by Nicole Tunbridge and © 2018 Pearson Education Ltd. Kathleen Fitzpatrick Beauty in the Eye of the Beholder ▪ 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 © 2018 Pearson Education Ltd. Figure 18.1 © 2018 Pearson Education Ltd. Figure 18.1a © 2018 Pearson Education Ltd. Concept 18.1: Bacteria often respond to environmental change by regulating transcription ▪ Natural selection has favored bacteria that produce only the gene 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 © 2018 Pearson Education Ltd. Figure 18.2 Precursor Genes that encode enzymes 1, 2, and 3 Feedback trpE inhibition Enzyme 1 trpD Regulation of gene expression Enzyme 2 trpC – trpB – Enzyme 3 trpA Tryptophan (a) Regulation of enzyme (b) Regulation of enzyme activity production © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. ▪ 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, located some distance from the operon itself © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. Figure 18.3 trp operon DNA trp promoter Promoter Regulatory gene Genes of operon trpR trpE trpD trpC trpB trpA RNA trp operator Stop codon polymerase Start codon 3′ Polypeptide mRNA mRNA 5′ 5′ subunits that make up enzymes Inactive trp E D C B A for tryptophan Protein repressor synthesis (a) Tryptophan absent, repressor inactive, operon on. DNA trpR trpE No RNA 3′ mRNA made 5′ Protein Active trp repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. © 2018 Pearson Education Ltd. Figure 18.3a trp operon DNA trp promoter Promoter Regulatory gene Genes of operon trpR trpE trpD trpC trpB trpA RNA trp operator Stop codon polymerase Start codon 3′ Polypeptide mRNA mRNA 5′ 5′ subunits that make up enzymes Inactive trp E D C B A for tryptophan Protein synthesis repressor (a) Tryptophan absent, repressor inactive, operon on. © 2018 Pearson Education Ltd. Figure 18.3b DNA trpR trpE No RNA 3′ made mRNA 5′ Protein Active trp repressor Tryptophan (corepressor) (b) Tryptophan present, repressor active, operon off. © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. Figure 18.4 Regulatory Promoter DNA gene Operator lacI lacZ No RNA 3′ made mRNA 5′ RNA polymerase Protein Active repressor (a) Lactose absent, repressor active, operon off. lac operon DNA lacI lacZ lacY lacA RNA polymerase Start codon Stop codon 3′ mRNA 5′ mRNA 5′ Protein β-Galactosidase Permease Transacetylase Inactive lac Allolactose repressor Enzymes for using lactose (inducer) (b) Lactose present, repressor inactive, operon on. © 2018 Pearson Education Ltd. Figure 18.4a Regulatory Promoter gene Operator DNA lacI lacZ No RNA 3′ made mRNA 5′ RNA polymerase Protein Active repressor (a) Lactose absent, repressor active, operon off. © 2018 Pearson Education Ltd. Figure 18.4b lac operon DNA lacI lacZ lacY lacA Start codon Stop codon RNA polymerase 3′ mRNA 5′ mRNA 5′ Protein β-Galactosidase Permease Transacetylase Inactive lac Allolactose Enzymes for using lactose repressor (inducer) (b) Lactose present, repressor inactive, operon on. © 2018 Pearson Education Ltd. Video: Cartoon Rendering of the lac Repressor from E. coli © 2018 Pearson Education Ltd. ▪ 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 both the trp and lac operons involves negative control of genes because operons are switched off by the active form of the repressor © 2018 Pearson Education Ltd. Positive Gene Regulation ▪ Some operons are also subject to positive control through a stimulatory protein, such as cyclic AMP receptor protein (CRP), an activator of transcription ▪ When glucose (a preferred food source of E. coli) is scarce, CRP is activated by binding with cyclic AMP (cAMP) ▪ Activated CRP attaches to the promoter of the lac operon and increases the affinity of RNA polymerase, thus accelerating transcription © 2018 Pearson Education Ltd. ▪ When glucose levels increase, CRP detaches from the lac operon, and transcription returns to a normal rate ▪ CRP helps regulate other operons that encode enzymes used in catabolic pathways ▪ The ability to catalyze compounds like lactose enables cells deprived of glucose to survive ▪ The compounds present in any given cell determine which genes are switched on © 2018 Pearson Education Ltd. Figure 18.5 Promoter Operator DNA lacI lacZ CRP-binding site RNA polymerase Active binds and cAMP CRP transcribes Inactive lac Inactive repressor CRP Allolactose (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. Promoter Operator DNA lacI lacZ CRP-binding site RNA polymerase less likely to bind Inactive Inactive lac CRP repressor (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. © 2018 Pearson Education Ltd. Figure 18.5a Promoter Operator DNA lacI lacZ CRP-binding site RNA polymerase Active binds and CRP transcribes cAMP Inactive lac Inactive repressor CRP Allolactose (a) Lactose present, glucose scarce (cAMP level high): abundant lac mRNA synthesized. © 2018 Pearson Education Ltd. Figure 18.5b Promoter Operator DNA lacI lacZ CRP-binding site RNA polymerase less likely to bind Inactive Inactive lac CRP repressor (b) Lactose present, glucose present (cAMP level low): little lac mRNA synthesized. © 2018 Pearson Education Ltd. Concept 18.2: Eukaryotic gene expression is regulated at many stages ▪ All organisms must regulate which genes are expressed at any given time ▪ Genes are turned on and off in response to signals from their external and internal environments ▪ In multicellular organisms, regulation of gene expression is essential for cell specialization © 2018 Pearson Education Ltd. Differential Gene Expression ▪ Almost all the cells in an organism contain an identical genome ▪ 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, but is often equated with transcription © 2018 Pearson Education Ltd. Figure 18.6 Signal Chromatin Chromatin modification: DNA unpacking DNA Gene available for transcription Transcription RNA Exon Primary Intron transcript RNA processing Tail mRNA in Cap nucleus Transport NUCLEUS to cytoplasm CYTOPLASM mRNA in cytoplasm Degradation Translation of mRNA Polypeptide Protein processing Active protein Degradation of protein Transport to cellular destination Cellular function (such as enzymatic activity or structural support) © 2018 Pearson Education Ltd. Figure 18.6a Signal Chromatin Chromatin modification: DNA unpacking DNA Gene available for transcription Transcription RNA Exon Primary transcript Intron RNA processing Tail mRNA in Cap nucleus Transport NUCLEUS to cytoplasm CYTOPLASM © 2018 Pearson Education Ltd. Figure 18.6b CYTOPLASM mRNA in cytoplasm Degradation Translation of mRNA Polypeptide Protein processing Active protein Degradation of protein Transport to cellular destination Cellular function (such as enzymatic activity or structural support) © 2018 Pearson Education Ltd. Animation: Protein Degradation © 2018 Pearson Education Ltd. Animation: Protein Processing © 2018 Pearson Education Ltd. Animation: Blocking Translation © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. Histone Modifications and DNA Methylation ▪ In histone acetylation, acetyl groups are attached to an amino acid in a histone tail ▪ This appears to open up the chromatin structure, thereby promoting the initiation of transcription ▪ The addition of methyl groups (methylation) can condense chromatin and reduce transcription © 2018 Pearson Education Ltd. Figure 18.7 Unacetylated histone tails Acetylated Histone DNA double Nucleosome histone tails tails helix DNA Acetylation Amino acids available for chemical modification DNA Nucleosome Compact: DNA not Looser: DNA accessible (end view) accessible for transcription for transcription (a) Histone tails protrude outward (b) Acetylation of histone tails promotes loose chromatin from a nucleosome. structure that permits transcription. © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. Organization of a Typical Eukaryotic Gene and Its Transcript ▪ 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 © 2018 Pearson Education Ltd. Figure 18.8 Enhancer (group of Proximal Transcription Poly-A signal Transcription distal control elements) control elements start site sequence termination region Exon Intron Exon Intron Exon DNA Upstream Downstream Promoter Transcription Poly-A signal Primary RNA Exon Intron Exon Intron Exon Cleaved 3′ end transcript 5′ of primary (pre-mRNA) transcript RNA processing Intron RNA Coding segment mRNA G P P P AAA···AAA 3′ Start Stop 5′ Cap 5′ UTR codon codon 3′ UTR Poly-A tail © 2018 Pearson Education Ltd. Figure 18.8a Enhancer (group of Proximal Transcription Poly-A signal Transcription distal control elements) control elements start site sequence termination region Exon Intron Exon Intron Exon DNA Upstream Downstream Promoter © 2018 Pearson Education Ltd. Figure 18.8b_1 Proximal Transcription Poly-A signal control elements start site sequence Exon Intron Exon Intron Exon DNA Promoter © 2018 Pearson Education Ltd. Figure 18.8b_2 Proximal Transcription Poly-A signal control elements start site sequence Exon Intron Exon Intron Exon DNA Promoter Transcription Poly-A signal Cleaved 3′ Primary RNA Exon Intron Exon Intron Exon 5′ end of transcript primary (pre-mRNA) transcript © 2018 Pearson Education Ltd. Figure 18.8b_3 Proximal Transcription Poly-A signal control elements start site sequence Exon Intron Exon Intron Exon DNA Promoter Transcription Poly-A signal Cleaved 3′ Primary RNA Exon Intron Exon Intron Exon 5′ end of transcript primary (pre-mRNA) RNA processing transcript Intron RNA Coding segment mRNA G P P P AAA···AAA 3′ 5′ Cap 5′ UTR Start Stop 3′ UTR Poly-A codon codon tail © 2018 Pearson Education Ltd. Animation: mRNA Degradation © 2018 Pearson Education Ltd. The Roles of General and Specific 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 © 2018 Pearson Education Ltd. General Transcription Factors at the Promoter ▪ RNA polymerase requires the assistance of transcription factors to initiate transcription ▪ General transcription factors are essential for the transcription of all protein-coding genes ▪ A few bind to the TATA box within the promoter ▪ Many bind to proteins, including other transcription factors and RNA polymerase II © 2018 Pearson Education Ltd. ▪ Only when the complete initiation complex has assembled can the RNA polymerase begin to move along the template strand of the DNA ▪ It produces a complementary strand of RNA ▪ For genes that are not expressed all the time, high levels of transcription depend on the presence of another set of factors, specific transcription factors © 2018 Pearson Education Ltd. 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 ▪ Each enhancer is generally associated with only one gene and no other © 2018 Pearson Education Ltd. Figure 18.9 Activation domain DNA-binding domain DNA © 2018 Pearson Education Ltd. ▪ 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 protein- protein interactions that result in transcription of a given gene © 2018 Pearson Education Ltd. ▪ The currently accepted model suggests that protein- mediated bending of the DNA brings the bound activators into contact with a group of mediator proteins ▪ The mediator proteins interact with general transcription factors at the promoter ▪ This helps assemble and position the preinitiation complex © 2018 Pearson Education Ltd. Figure 18.10_1 Activators Promoter DNA Gene Enhancer Distal control TATA element box © 2018 Pearson Education Ltd. Figure 18.10_2 Activators Promoter DNA Gene Enhancer Distal control TATA element box General transcription factors DNA-bending protein Group of mediator proteins © 2018 Pearson Education Ltd. Figure 18.10_3 Activators Promoter DNA Gene Enhancer Distal control TATA element box General transcription factors DNA-bending protein Group of mediator proteins RNA polymerase II RNA polymerase II Transcription RNA synthesis initiation complex © 2018 Pearson Education Ltd. Animation: Initiation of Transcription © 2018 Pearson Education Ltd. ▪ Some transcription factors function as repressors, inhibiting expression of a particular gene in several different ways ▪ Some activators and repressors act indirectly by influencing chromatin structure to promote or silence transcription © 2018 Pearson Education Ltd. Combinatorial Control of Gene Activation ▪ A particular combination of control elements can activate transcription only when the appropriate activator proteins are present ▪ With only a dozen or so control elements, a large number of potential combinations is possible © 2018 Pearson Education Ltd. Figure 18.11 Enhancer for DNA in both albumin gene Promoter Albumin gene cells (activators not shown) Control Enhancer for elements crystallin gene Promoter Crystallin gene Liver cell DNA in liver cell DNA in lens cell Lens cell Liver cell nucleus Available Lens cell activators nucleus Available activators Albumin gene not expressed Albumin gene expressed Crystallin gene not expressed Crystallin gene expressed © 2018 Pearson Education Ltd. Figure 18.11a DNA in both Enhancer for cells albumin gene Promoter Albumin gene (activators not shown) Control Enhancer for elements crystallin gene Promoter Crystallin gene © 2018 Pearson Education Ltd. Figure 18.11b DNA in liver cell Liver cell Liver cell nucleus Available activators Albumin gene expressed Crystallin gene not expressed © 2018 Pearson Education Ltd. Figure 18.11c DNA in lens cell Lens cell Lens cell nucleus Available activators Albumin gene not expressed Crystallin gene expressed © 2018 Pearson Education Ltd. Coordinately Controlled Genes in Eukaryotes ▪ Co-expressed eukaryotic genes are not organized in operons (with a few exceptions) ▪ These genes can be scattered over different chromosomes, but each has the same combination of control elements ▪ Activator proteins in the nucleus recognize specific control elements and promote simultaneous transcription of the genes © 2018 Pearson Education Ltd. Nuclear Architecture and Gene Expression ▪ Chromosome conformation capture techniques allow identification of regions of chromosomes that interact with each other ▪ Loops of chromatin from different chromosomes may congregate at particular sites, some of which are rich in transcription factors and RNA polymerases ▪ These transcription factories are thought to be areas specialized for a common function © 2018 Pearson Education Ltd. Figure 18.12 Chromosomes in the interphase nucleus (fluorescence micrograph) Chromosome territory 5 µm Chromatin loop Transcription factory © 2018 Pearson Education Ltd. Figure 18.12a Chromosomes in the interphase nucleus (fluorescence micrograph) 5 µm © 2018 Pearson Education Ltd. Mechanisms of Post-Transcriptional Regulation ▪ Transcription alone does not constitute 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 © 2018 Pearson Education Ltd. 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 ▪ Alternative RNA splicing can significantly expand the repertoire of a eukaryotic genome ▪ It is a proposed explanation for the surprisingly low number of genes in the human genome ▪ More than 90% of the human protein-coding genes undergo alternative splicing © 2018 Pearson Education Ltd. Figure 18.13 Exons DNA 1 2 3 4 5 Troponin T gene Primary RNA 1 2 3 4 5 transcript RNA splicing mRNA 1 2 3 5 OR 1 2 4 5 © 2018 Pearson Education Ltd. Animation: RNA Processing © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. ▪ The life span of mRNA molecules in the cytoplasm is important in determining the pattern of protein synthesis in a cell ▪ Eukaryotic mRNA is more long-lived than prokaryotic mRNA ▪ Nucleotide sequences that influence the life span of mRNA in eukaryotes reside in the untranslated region (UTR) at the 3′ end of the molecule © 2018 Pearson Education Ltd. Protein Processing and Degradation ▪ After translation, polypeptides undergo processing, including cleavage, and chemical modifications ▪ The length of time each protein functions 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 © 2018 Pearson Education Ltd. Concept 18.3: Noncoding RNAs play multiple roles in controlling gene expression ▪ 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 ▪ In the past, genes that did not encode a protein product or known functional RNA were considered “junk DNA” ▪ A flood of recent data has contradicted this idea © 2018 Pearson Education Ltd. ▪ A significant fraction of the genome may be transcribed into noncoding RNAs (ncRNAs) ▪ Researchers are uncovering more evidence of biological roles for these ncRNAs every day ▪ This represents a major shift in the the thinking of biologists © 2018 Pearson Education Ltd. Effects on mRNAs by MicroRNAs and Small Interfering RNAs ▪ MicroRNAs (miRNAs) are small, single-stranded RNA molecules that can bind complementary sequences in mRNA ▪ The miRNAs and associated proteins cause degradation of the target mRNA or sometimes block its translation ▪ Biologists estimate that expression of at least one- half of human genes may be regulated by miRNAs © 2018 Pearson Education Ltd. Figure 18.14 miRNA miRNA- protein complex 1 The miRNA binds to a target mRNA mRNA OR mRNA degraded Translation blocked 2 If bases are complementary, mRNA is degraded (left); if the match is less complete, translation is blocked (right). © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. Chromatin Remodeling and Effects on Transcription by ncRNAs ▪ Some ncRNAs act to bring about remodeling of chromatin structure ▪ In some yeasts, siRNAs re-form heterochromatin at centromeres after chromosome replication © 2018 Pearson Education Ltd. Figure 18.15 Centromeric DNA 1 RNA transcripts RNA Sister (red) produced. polymerase chromatids (two DNA RNA molecules) transcript 2 Yeast enzyme synthesizes strands complementary to RNA transcripts. 3 Double-stranded RNA processed into siRNAs siRNA-protein that associate with proteins. 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 Chromatin- modifying enzymes 6 Formation of heterochromatin at the centromere. Heterochromatin at the centromere region © 2018 Pearson Education Ltd. Figure 18.15a Centromeric DNA 1 RNA transcripts RNA Sister (red) produced. polymerase chromatids RNA (two DNA transcript molecules) 2 Yeast enzyme synthesizes strands complementary to RNA transcripts. 3 Double-stranded RNA processed into siRNAs siRNA-protein that associate with proteins. complex 4 The siRNA-protein complexes bind RNA transcripts and become tethered to centromere region. © 2018 Pearson Education Ltd. Figure 18.15b 5 The siRNA-protein complexes recruit histone-modifying enzymes. Centromeric DNA Chromatin- modifying enzymes 6 Formation of heterochromatin at the centromere. Heterochromatin at the centromere region © 2018 Pearson Education Ltd. ▪ Small ncRNAs called piwi-interacting RNAs (piRNAs) induce formation of heterochromatin, blocking the expression of parasitic DNA elements in the genome known as transposons ▪ piRNAs help to reestablish appropriate methylation patterns during gamete formation in many animal species © 2018 Pearson Education Ltd. ▪ Long noncoding RNAs (lncRNAs) range from 200 to hundreds of thousands of nucleotides in length ▪ One type of lncRNA is responsible for X chromosome inactivation ▪ RNA-based regulation of chromatin structure plays an important role in gene regulation © 2018 Pearson Education Ltd. The Evolutionary Significance of Small ncRNAs ▪ Small ncRNAs can regulate gene expression at multiple steps and in many ways ▪ 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 © 2018 Pearson Education Ltd. 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 ▪ Cells are organized successively into tissues, organs, organ systems, and the whole organism ▪ Gene expression orchestrates the developmental programs of animals © 2018 Pearson Education Ltd. A Genetic Program for Embryonic Development ▪ The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis © 2018 Pearson Education Ltd. Figure 18.16 1 mm 2 mm (a) Fertilized eggs of a frog (b) Newly hatched tadpole © 2018 Pearson Education Ltd. Figure 18.16a 1 mm (a) Fertilized eggs of a frog © 2018 Pearson Education Ltd. Figure 18.16b 2 mm (b) Newly hatched tadpole © 2018 Pearson Education Ltd. ▪ 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 a program of gene regulation that is carried out as cells divide © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. ▪ The other major 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 changes in nearby target cells ▪ Thus, interactions between cells induce differentiation of specialized cell types © 2018 Pearson Education Ltd. Figure 18.17 (a) Cytoplasmic determinants in the egg Molecules of two different cytoplasmic determinants Nucleus Fertilization Unfertilized Mitotic egg cell division Sperm Zygote (fertilized egg) Two-celled embryo (b) Induction by nearby cells Early embryo (32 cells) NUCLEUS Signal transduction pathway Signal receptor Signaling molecule © 2018 Pearson Education Ltd. Figure 18.17a (a) Cytoplasmic determinants in the egg Molecules of two different cytoplasmic determinants Nucleus Fertilization Unfertilized egg Mitotic cell division Sperm Zygote (fertilized egg) Two-celled embryo © 2018 Pearson Education Ltd. Figure 18.17b (b) Induction by nearby cells Early embryo (32 cells) NUCLEUS Signal transduction pathway Signal receptor Signaling molecule © 2018 Pearson Education Ltd. Animation: Cell Signaling © 2018 Pearson Education Ltd. Sequential Regulation of Gene Expression During Cellular Differentiation ▪ Determination irreversibly commits a cell to becoming a particular cell type ▪ Determination precedes differentiation ▪ Cell differentiation is marked by the production of tissue-specific proteins © 2018 Pearson Education Ltd. ▪ Myoblasts are cells determined to form muscle cells and produce large amounts of muscle-specific proteins ▪ MyoD is a “master regulatory gene” that encodes a transcription factor that commits the cell to becoming skeletal muscle ▪ Some target genes for MyoD (protein) encode additional muscle-specific transcription factors © 2018 Pearson Education Ltd. Figure 18.18_1 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic OFF OFF precursor cell © 2018 Pearson Education Ltd. Figure 18.18_2 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic OFF OFF precursor cell mRNA OFF MyoD protein Myoblast (transcription factor) (determined) © 2018 Pearson Education Ltd. Figure 18.18_3 Nucleus Master regulatory gene myoD Other muscle-specific genes DNA Embryonic OFF OFF precursor cell mRNA OFF MyoD protein Myoblast (transcription factor) (determined) mRNA mRNA mRNA mRNA Myosin, other muscle proteins, MyoD A different and cell cycle- Part of a muscle fiber transcription factor blocking proteins (fully differentiated cell) © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. 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 ▪ The larva then forms a pupa, which undergoes metamorphosis into the adult fly © 2018 Pearson Education Ltd. Figure 18.19 Dorsal Head Thorax Abdomen Right Anterior Posterior Left 0.5 mm Ventral BODY AXES (a) Adult. Follicle cell 1 Developing egg Nucleus Egg Nurse cell 2 Mature, unfertilized egg. Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg. Embryonic development 4 Segmented embryo. Body 0.1 mm 5 Larva. segments Hatching (b) Development from egg to larva. © 2018 Pearson Education Ltd. Figure 18.19a Dorsal Head Thorax Abdomen Right Anterior Posterior Left 0.5 mm Ventral BODY AXES (a) Adult. © 2018 Pearson Education Ltd. Figure 18.19b_1 Follicle cell 1 Developing egg. Nucleus Egg Nurse cell © 2018 Pearson Education Ltd. Figure 18.19b_2 Follicle cell 1 Developing egg. Nucleus Egg Nurse cell 2 Mature, unfertilized egg. Egg shell Depleted nurse cells © 2018 Pearson Education Ltd. Figure 18.19b_3 Follicle cell 1 Developing egg. Nucleus Egg Nurse cell 2 Mature, unfertilized egg. Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg. © 2018 Pearson Education Ltd. Figure 18.19b_4 Follicle cell 1 Developing egg. Nucleus Egg Nurse cell 2 Mature, unfertilized egg. Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg. Embryonic development 4 Segmented embryo. Body 0.1 mm segments © 2018 Pearson Education Ltd. Figure 18.19b_5 Follicle cell 1 Developing egg. Nucleus Egg Nurse cell 2 Mature, unfertilized egg. Egg shell Depleted nurse cells Fertilization Laying of egg 3 Fertilized egg. Embryonic development 4 Segmented embryo. Body 0.1 mm 5 Larva. segments Hatching (b) Development from egg to larva. © 2018 Pearson Education Ltd. 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 homeotic genes, which control pattern formation in the late embryo, larva, and adult stages © 2018 Pearson Education Ltd. Figure 18.20 Eye Leg Normal Wild instead of antenna type antenna Mutant © 2018 Pearson Education Ltd. Figure 18.20a Eye Normal Wild antenna type © 2018 Pearson Education Ltd. Figure 18.20b Leg instead of antenna Mutant © 2018 Pearson Education Ltd. ▪ 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 about 120 genes essential for normal segmentation © 2018 Pearson Education Ltd. 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 egg- polarity genes because they control orientation of the egg and consequently the fly © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. Figure 18.21 Head Tail A8 T1 T2 T3 A7 A5 A6 A1 A2 A3 A4 Wild-type larva 250 µm Tail Tail A8 A8 A7 A6 A7 Mutant larva (bicoid ) © 2018 Pearson Education Ltd. Figure 18.21a Head Tail A8 T1 T2 T3 A7 A1 A2 A4 A5 A6 A3 Wild-type larva 250 µm © 2018 Pearson Education Ltd. Figure 18.21b Tail Tail A8 A8 A7 A6 A7 Mutant larva (bicoid ) © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. Figure 18.22 100 µm Anterior end Fertilization, translation of bicoid mRNA Bicoid mRNA in mature Bicoid protein in unfertilized egg early embryo © 2018 Pearson Education Ltd. Figure 18.22a Bicoid mRNA in mature unfertilized egg © 2018 Pearson Education Ltd. Figure 18.22b 100 µm Anterior end Bicoid protein in early embryo © 2018 Pearson Education Ltd. Animation: Development of Head-Tail Axis in Fruit Flies © 2018 Pearson Education Ltd. ▪ The bicoid research was groundbreaking 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 that a gradient of molecules can determine polarity and position in the embryo © 2018 Pearson Education Ltd. Evolutionary Developmental Biology (“Evo-Devo”) ▪ The fly with legs emerging from its head in Figure 18.20 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” © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. Types of Genes Associated with Cancer ▪ Cancer can be caused by mutations to genes that normally 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 © 2018 Pearson Education Ltd. ▪ 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 © 2018 Pearson Education Ltd. ▪ Proto-oncogenes can be converted to oncogenes by ▪ movement of DNA within the genome ▪ amplification of a proto-oncogene ▪ point mutations in the proto-oncogene or its control elements © 2018 Pearson Education Ltd. Figure 18.23 Proto-oncogene Proto-oncogene Proto-oncogene Translocation or Gene amplification: Point mutation Point mutation transposition: gene multiple copies of the gene within a control element within the gene moved to new locus, under new controls New Oncogene Oncogene Oncogene promoter Normal growth- Normal growth-stimulating Normal growth- Hyperactive or stimulating protein in excess stimulating protein degradation- protein in excess in excess resistant protein © 2018 Pearson Education Ltd. Figure 18.23a Proto-oncogene Translocation or transposition: gene moved to new locus, under new controls New Oncogene promoter Normal growth- stimulating protein in excess © 2018 Pearson Education Ltd. Figure 18.23b Proto-oncogene Gene amplification: multiple copies of the gene Normal growth-stimulating protein in excess © 2018 Pearson Education Ltd. Figure 18.23c Proto-oncogene Point mutation Point mutation within a control element within the gene Oncogene Oncogene Normal growth- Hyperactive or stimulating protein degradation- in excess resistant protein © 2018 Pearson Education Ltd. ▪ Tumor-suppressor genes normally inhibit cell division ▪ Mutations that decrease protein products of tumor- suppressor 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 © 2018 Pearson Education Ltd. 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 ▪ The Ras protein is a G protein that relays a signal from a growth factor receptor on the cell surface ▪ The response to the resulting cascade stimulates cell division © 2018 Pearson Education Ltd. Figure 18.24 1 Growth factor 3 G protein P P NUCLEUS 6 Protein that P P Ras P P stimulates GTP 5 Transcription the cell cycle factor (activator) 2 Receptor 4 Protein kinases Normal cell division (a) Normal cell cycle–stimulating pathway. MUTATION Ras Overexpression of protein GTP NUCLEUS Transcription factor (activator) Ras protein active with or without growth factor. Increased cell division (b) Mutant cell cycle–stimulating pathway. © 2018 Pearson Education Ltd. Figure 18.24a 1 Growth factor 3 G protein P P Protein that NUCLEUS 6 stimulates P P Ras P P 5 Transcription the cell cycle GTP factor (activator) 2 Receptor 4 Protein kinases Normal cell division (a) Normal cell cycle–stimulating pathway. © 2018 Pearson Education Ltd. Figure 18.24b MUTATION Overexpression Ras of protein GTP NUCLEUS Transcription factor (activator) Ras protein active with or without growth factor. Increased cell division (b) Mutant cell cycle–stimulating pathway. © 2018 Pearson Education Ltd. ▪ Mutations in the p53 gene prevent suppression of the cell cycle ▪ Suppression of the cell cycle can be important in the case of damage to a cell’s DNA; normal p53 prevents a cell from passing on mutations ▪ It also activates expression of miRNAs that inhibit the cell cycle, and can turn on genes directly involved in DNA repair ▪ If DNA is irreparable, p53 activates cell “suicide” genes © 2018 Pearson Education Ltd. Figure 18.25 2 Protein kinases 5 Protein that Damaged DNA inhibits the is not replicated. NUCLEUS cell cycle UV light 1 DNA damage 3 Active form 4 Transcription in genome of p53 No cell division (a) Normal cell cycle–inhibiting pathway Cell cycle is Inhibitory protein not inhibited. Defective or absent UV missing light MUTATION transcription DNA damage factor in genome Increased cell division (b) Mutant cell cycle–inhibiting pathway © 2018 Pearson Education Ltd. Figure 18.25a 2 Protein kinases 5 Protein that Damaged DNA inhibits the is not replicated. NUCLEUS cell cycle UV light 1 DNA damage 3 Active form 4 Transcription in genome of p53 No cell division (a) Normal cell cycle–inhibiting pathway © 2018 Pearson Education Ltd. Figure 18.25b Cell cycle is Inhibitory not inhibited. Defective or protein missing absent UV light MUTATION transcription factor DNA damage in genome Increased cell division (b) Mutant cell cycle–inhibiting pathway © 2018 Pearson Education Ltd. The Multistep Model of Cancer Development ▪ Multiple mutations are generally needed for full- fledged 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 © 2018 Pearson Education Ltd. Figure 18.26 Colon 1 Loss of tumor- 2 Activation of 4 Loss of Colon wall suppressor gene ras oncogene tumor-suppressor APC (or other) gene p53 3 Loss of 5 Additional tumor-suppressor mutations gene SMAD4 Normal colon Small benign Larger benign Malignant tumor epithelial cells growth (polyp) growth (adenoma) (carcinoma) © 2018 Pearson Education Ltd. Figure 18.26a 1 Loss of tumor- suppressor gene Colon wall APC (or other) Normal colon Small benign epithelial cells growth (polyp) 2 Activation of 4 Loss of ras oncogene tumor-suppressor gene p53 3 Loss of 5 Additional tumor-suppressor mutations gene SMAD4 Larger benign Malignant tumor growth (adenoma) (carcinoma) © 2018 Pearson Education Ltd. ▪ Routine screening for some cancers, such as colorectal cancer, is recommended ▪ Suspicious polyps may be removed before cancer progresses ▪ Breast cancer is a heterogeneous disease that is the second most common form of cancer in women in the United States; it also occurs in some men ▪ A genomics approach to profiling breast tumors has identified four major types of breast cancer © 2018 Pearson Education Ltd. Figure 18.27 MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Luminal A Luminal B Basal-like ERα PR ERα− PR− HER2− ERα++ 15–20% of breast cancers ERα+++ PR++ More aggressive; poorer PR++ prognosis than other subtypes HER2− (shown here); HER2– some HER2++ 40% of breast cancers 15–20% of breast cancers Best prognosis Poorer prognosis than luminal A subtype A research scientist examines DNA sequencing data from breast cancer samples. HER2 HER2 ERα− Normal Breast Cells in a Milk Duct PR− In a normal breast cell, the three signal receptors HER2++ HER2 10–15% of breast are at normal levels (indicated by +): receptor cancers ERα+ Duct Dimer Poorer prognosis PR+ interior than luminal HER2+ A subtype Estrogen Milk receptor duct alpha (ERα) Signaling molecule Progesterone receptor (PR) P P P P Response P P ATP ADP (cell division) HER2 Mammary Epithelial receptor Treatment with Herceptin for the HER2 subtype gland milk-secreting lobule Herceptin molecule cell Support Extracellular cell matrix HER2 receptors © 2018 Pearson Education Ltd. Figure 18.27a A research scientist examines DNA sequencing data from breast cancer samples. © 2018 Pearson Education Ltd. Figure 18.27b MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Normal Breast Cells in a Milk Duct In a normal breast cell, the three signal receptors are at normal levels (indicated by +): ERα+ Duct PR+ interior HER2+ Estrogen receptor Milk alpha (ERα) duct Progesterone receptor (PR) HER2 Mammary Epithelial receptor gland milk-secreting lobule cell Support Extracellular cell matrix © 2018 Pearson Education Ltd. Figure 18.27ba Milk duct Mammary Epithelial gland milk-secreting cell lobule Support cell © 2018 Pearson Education Ltd. Figure 18.27bb Normal Breast Cells in a Milk Duct In a normal breast cell, the three signal receptors are at normal levels (indicated by +): ERα+ Duct PR+ interior HER2+ Estrogen receptor alpha (ERα) Support cell Progesterone receptor (PR) HER2 receptor Extracellular matrix © 2018 Pearson Education Ltd. Figure 18.27c MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer Luminal A Luminal B Basal-like ERα PR ERα− ERα+++ ERα++ PR− PR++ PR++ HER2− HER2− HER2− (shown here); 15–20% of breast cancers 40% of breast cancers some HER2++ More aggressive; poorer Best prognosis 15–20% of breast cancers prognosis than other subtypes Poorer prognosis than luminal A subtype HER2 HER2 ERα− PR− HER2++ 10−15% of breast cancers Poorer prognosis than luminal A subtype © 2018 Pearson Education Ltd. Figure 18.27ca Luminal A Luminal B ERα PR ERα+++ ERα++ PR++ PR++ HER2− HER2− (shown here); some HER2++ 40% of breast cancers 15–20% of breast cancers Best prognosis Poorer prognosis than luminal A subtype © 2018 Pearson Education Ltd. Figure 18.27cb Basal-like HER2 HER2 ERα− ERα− PR− PR− HER2− HER2++ 15–20% of breast cancers 10−15% of breast cancers More aggressive; poorer Poorer prognosis than prognosis than other subtypes luminal A subtype © 2018 Pearson Education Ltd. Figure 18.27d MAKE CONNECTIONS: Genomics, Cell Signaling, and Cancer HER2 HER2 ERα− PR− HER2++ 10–15% of breast cancers Poorer prognosis than luminal A subtype Signaling HER2 molecule receptor Dimer P P P P Response P P ATP ADP (cell division) Treatment with Herceptin for the HER2 subtype Herceptin molecule HER2 receptors © 2018 Pearson Education Ltd. Figure 18.27da HER2 Signaling HER2 molecule receptor Dimer P P P P Response P P ATP ADP (cell division) © 2018 Pearson Education Ltd. Figure 18.27db Treatment with Herceptin for the HER2 subtype Herceptin molecule HER2 receptors © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. 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 © 2018 Pearson Education Ltd. Figure 18.UN01 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mRNA TRANSLATION DEGRADATION PROTEIN PROCESSING AND DEGRADATION © 2018 Pearson Education Ltd. Figure 18.UN02 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mRNA TRANSLATION DEGRADATION PROTEIN PROCESSING AND DEGRADATION © 2018 Pearson Education Ltd. Figure 18.UN03 CHROMATIN MODIFICATION TRANSCRIPTION RNA PROCESSING mRNA TRANSLATION DEGRADATION PROTEIN PROCESSING AND DEGRADATION © 2018 Pearson Education Ltd. Figure 18.UN04a © 2018 Pearson