Gene Regulation. Bacteria. Chapter 18: Regulation of Gene Expression

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1 Chapter 18: Regulation of Gene Expression A Biology Gene Regulation rokaryotes and eukaryotes alter their gene expression in response to their changing environment In multicellular eukaryotes, gene expression regulates development and is responsible for differences in cell types molecules play a role in regulating this 2 Bacteria Feedback inhibition recursor trpe gene Natural selection favors bacteria that produce only those products needed by the cell Enzyme 1 Enzyme 2 trpd gene trpc gene Regulation of gene expression A cell can regulate the production of enzymes by feedback inhibition or by gene regulation - Enzyme 3 Tryptophan trpb gene trpa gene - In bacteria this is controlled by operons (a) Regulation of enzyme activity (b) Regulation of enzyme production Fig

2 Operons Cluster of functionally related genes under coordinated control by a single on-off switch that includes the operator, promoter, and genes they control Regulatory switch is a segment of called an operator which is usually positioned within the promoter Operon can be switched off by a protein (works by binding to the operator and blocking polymerase) Repressor is the product of a separate regulatory gene Repressor can be in an active or inactive form depending on the presence of other molecules Co is a molecule that cooperates with a protein to shut off an operon 4 trp operon Regulatory gene m rotein 5! trpr 3! Operator Start codon polymerase m 5! Inactive (a) Tryptophan absent, inactive, operon on Genes of operon trpe trpd trpc trpb trpa Stop codon E D C B A olypeptide subunits that make up enzymes for tryptophan synthesis Fig No made E. coli synthesizes the amino acid tryptophan m Trp operon is on by default rotein Tryptophan (co) (b) Tryptophan present, active, operon off Active Ex. Trp Operon When tryptophan is present, it binds to the trp protein which turns the operon off (acts as a co) 5 Repressible and Inducible Operons m 5! rotein laci polymerase 3! m 5! lac operon lacz lacy laca β-galactosidase ermease Transacetylase Fig m rotein Regulatory gene 5! laci 3! polymerase Active Allolactose (inducer) (a) Lactose absent, active, operon off (b) Lactose present, inactive, operon on Operator lacz Inactive No made Repressible operon is usually on (binding of a shuts it off) Ex. trp operon Inducible operon is usually off (binding of an inducer inactivates the and turns on transcription) Ex. lac operon - contains genes that code for enzymes used in hydrolysis and metabolism of lactose 6

3 ositive Gene Regulation ositive control caused by a stimulatory protein called an activator of transcription (ex. catabolite activator protein - CA) When glucose is scarce, CA is activated by binding with cyclic AM (cam) Activated CA attaches to the promoter of the lac operon and increases the affinity of polymerase (accelerating transcription) When glucose levels increase, CA detaches from the lac operon and transcription returns to a normal rate CA helps regulate other operons that encode enzymes used in catabolic pathways laci CA-binding site cam Active CA Inactive CA Allolactose polymerase binds and transcribes lacz Operator Inactive lac (a) Lactose present, glucose scarce (cam level high): abundant lac m synthesized laci CA-binding site Inactive CA Fig lacz Operator polymerase less likely to bind Inactive lac (b) Lactose present, glucose present (cam level low): little lac m synthesized 7 Eukaryote Gene Expression Fig All organisms must regulate which genes are expressed at any given time In multicellular organisms, regulation of gene expression is essential for cell specialization Since almost all cells in an organism are genetically identical, differences between cell types result from differential gene expression (expression of different genes by cells with the same genome) Signal Cap Degradation of m Gene NUCLEUS Chromatin Chromatin modification: unpacking involving histone acetylation and demethylation Exon Intron Gene available for transcription rimary transcript processing Tail m in nucleus Transport to cytoplasm CYTOLASM m in cytoplasm Translation olypeptide rotein processing, such as cleavage and chemical modification Abnormalities in gene expression can lead to diseases including cancer Gene expression is regulated at many stages Degradation of protein Active protein Transport to cellular destination Cellular function (such as enzymatic activity, structural support) 8 Regulation of Chromatin Structure Genes with highly packed heterochromatin are usually not expressed Fig Amino acids available for chemical modification Histone tails double helix Nucleosome (end view) (a) Histone tails protrude outward from a nucleosome Chemical modifications to histones and of chromatin influence both chromatin structure and gene expression Histone acetylation - acetyl groups are attached to positively charged lysines in histone tails which loosens chromatin structure (promoting transcription) Unacetylated histones Acetylated histones (b) Acetylation of histone tails promotes loose chromatin structure that permits transcription Adding methyl groups (methylation) condenses chromatin If phosphate groups are added to the methylated amino acid, the chromatin is loosened. 9

4 Methylation Adding methyl groups to certain bases in is associated with reduced transcription in some species 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 10 Epigenetic Inheritance Although chromatin modifications do not alter sequences, they can be passed on to future generations of cells Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence is called epigenetic inheritance 11 Organization of a Typical Eukaryotic Gene Most eukaryotic genes are associated with multiple control elements (segments of noncoding that serve as binding sites for transcription factors that regulate transcription) Enhancer (distal control elements) roximal control elements oly-a start site Exon Intron Exon signal sequence Intron Exon termination region Upstream rimary transcript (pre-m) 5! Intron Downstream oly-a signal Exon Intron Exon Intron Exon Cleaved 3! end of processing primary transcript Coding segment Fig m G 5! Cap 5! UTR Start codon Stop codon 3! UTR AAA AAA 3! oly-a tail 12

5 Factors Activation domain -binding domain To initiate transcription, eukaryotic polymerase requires the assistance of proteins called transcription factors (essential for transcription of all protein-coding genes) Fig roximal control elements are located close to the promoter. Distal control elements (called enhancers) may be far away from a gene or even located in an intron. An activator binds to an enhancer and stimulates transcription of a gene. (Activator has two domains - one binds to and second activates transcription) 13 Factors Some act as s (inhibiting expression of a gene) Some activators and s act indirectly by influencing chromatin structure to promote or silence transcription Enhancer Activators Distal control element bending protein initiation complex Gene TATA box General transcription factors Group of mediator proteins polymerase II polymerase II synthesis Fig ost-al Regulation alone does not account for gene expression Regulatory mechanisms can operate at various stages after transcription (allow cell to fine-tune gene expression rapidly in response to environmental changes) 1 2 Exons Alternative Splicing - different m molecules are produced from the same primary transcript (depending on what is treated as exons and introns) m Degradation - life-span of m molecule in cytoplasm (eukaryotic m lasts longer than prokaryotic m) rimary transcript 1 2 Troponin T gene splicing m or Fig

6 ost-al Regulation rotein processing roteasomes are complexes that bind protein molecules and degrade them Ubiquitin roteasome roteasome and ubiquitin to be recycled rotein to be degraded Ubiquitinated protein rotein entering a proteasome rotein fragments (peptides) Fig Noncoding Small fraction of codes for proteins and a very small fraction of non-protein-coding consists of genes for r or t Significant amounts of the genome may be transcribed into noncoding s (ncs) which can regulate gene expression at m translation and chromatin configuration 5! 3! Hairpin (a) rimary mi transcript mi mi Hydrogen bond Dicer miprotein complex m degraded Translation blocked (b) Generation and function of mis Fig Micros (mis) are small single-stranded that can bind to m to degrade or block translation 17 Noncoding Inhibition of gene expression by molecules is called interference (i) i is caused by small interfering s (sis) - sis and mis are similar but form from different precursors An increase in the number of mis in a species may have allowed morphological complexity to increase over evolutionary time 18

7 Differential Gene Expression During embryonic development, a fertilized egg gives rise to many different cell types which are organized into tissues, organs, organ systems, and the whole organism Transformation from a zygote to adult results from cell division, cell differentiation, and morphogenesis 1 mm 2 mm (a) Fertilized eggs of a frog (b) Newly hatched tadpole Figs & Cell differentiation - process by which cells become specialized in structure and function Morphogenesis - physical processes that give an organism its shape Cytoplasmic determinants - maternal substances in the egg that influence early development (a) Cytoplasmic determinants in the egg Sperm Fertilization Zygote (fertilized egg) Two-celled embryo Mitotic cell division Unfertilized egg Nucleus Molecules of two different cytoplasmic determinants (b) Induction by nearby cells Early embryo (32 cells) NUCLEUS Signal transduction pathway Signal receptor Signaling molecule (inducer) 19 Sequential Regulation Determination commits a cell to its final fate (happens before differentiation) Differentiation is marked by the production of tissue-specific proteins Nucleus Embryonic precursor cell Master regulatory gene myod OFF Other muscle-specific genes OFF Ex. Myoblasts produce musclespecific proteins and form skeletal muscle cells Myoblast (determined) m MyoD protein (transcription factor) OFF MyoD is one of several master regulatory genes the produce proteins that commit the cell to becoming skeletal muscle MyoD protein is a transcription factor that binds to enhancers of various target genes art of a muscle fiber (fully differentiated cell) m m m m MyoD Another transcription factor Myosin, other muscle proteins, and cell cycle blocking proteins Fig Setting Up the Body lan BODY AXES Head Thorax Abdomen 0.5 mm Dorsal Right Anterior osterior Left Ventral Fig attern formation - development of spatial organization of tissues and organs (in animals begins with establishment of major axes) ositional information - molecular cues that control pattern formation, tells a cell its location relative to the body axes and to neighboring cells Ex. Drosophila melanogaster (fruit fly) - cytoplasmic determinants in the egg determine the axes before fertilization (a) Adult 1 2 Egg developing within ovarian follicle Nurse cell Unfertilized egg Depleted nurse cells 3 Fertilized egg 4 Segmented embryo 5 Larval stage Body segments Follicle cell (b) Development from egg to larva Nucleus Egg Egg shell Fertilization Laying of egg Embryonic development Hatching 0.1 mm 21

8 Fig Developmental Genes in Drosophila Head T1 T2 T3 A8 A6 A7 A1 A2 A3 A4 A5 Wild-type larva 250 µm Tail Homeotic genes - control pattern formation in late embryo, larva, and adult stages Tail A8 A7 A6 A7 A8 Tail Embryonic lethals - mutations that cause death during embryogenesis Maternal effect genes - encode for cytoplasmic determinants that establish the axes (also called egg-polarity genes) RESULTS Bicoid m in mature unfertilized egg Mutant larva (bicoid) Fertilization, translation of bicoid m Anterior end Bicoid protein in early embryo 100 µm Ex. Bicoid gene - if it is not functional, the fly will lack a front half and have duplicate posterior structures at both ends Bicoid m in mature unfertilized egg Bicoid protein in early embryo Fig Cancer Gene regulation systems that go wrong in cancer are the same systems involved in embryonic development Cancer is caused by mutations in genes that regulate cell growth and division Tumor viruses can also cause cancer in animals including humans Oncogenes - cancer-causing genes roto-oncogenes - normal cellular genes responsible for normal cell growth and division Conversion of a proto-oncogene to an oncogene can lead to abnormal stimulation of the cell cycle Conversion can be caused by movement of near a promoter, amplification of a proto-oncogene, point mutations in the proto-oncogene or its control elements 23 Conversion of a roto-oncogene roto-oncogene Fig Translocation or transposition: gene moved to new locus, under new controls Gene amplification: multiple copies of the gene within a control element oint mutation: within the gene New promoter Oncogene Oncogene Normal growthstimulating protein in excess Normal growth-stimulating protein in excess Normal growthstimulating protein in excess Hyperactive or degradationresistant protein 24

9 Tumor Suppressor Genes Help prevent uncontrolled cell growth Mutations that decrease production of tumor suppressor genes contribute to cancer onset Tumor suppressor proteins repair damaged, control cell adhesion, and inhibit the cell cycle Mutations in the ras proto-oncogene and p53 tumor suppressor gene are common in human cancers Mutations in the ras gene leads to hyperactive Ras protein and increased cell division p53 prevents a cell from passing on mutations due to damage 25 roto-oncogenes and Tumor Suppressor Genes 1 Growth factor 3 G protein GT Ras 2 Receptor 4 rotein kinases (phosphorylation cascade) (a) Cell cycle stimulating pathway 5 GT Ras factor (activator) MUTATION Hyperactive Ras protein (product of oncogene) issues signals on its own. Gene expression rotein that stimulates the cell cycle NUCLEUS UV light 2 rotein kinases 1 damage in genome (b) Cell cycle inhibiting pathway rotein overexpressed 3 Active form of p53 rotein that inhibits the cell cycle EFFECTS OF MUTATIONS MUTATION Defective or missing transcription factor, such as p53, cannot activate transcription. rotein absent Cell cycle overstimulated (c) Effects of mutations Increased cell division Cell cycle not inhibited 26 Multistep Model of Cancer Development Multiple mutations are generally needed for full-fledged cancer (this is why incidence increases with age) Usually requires at least one active oncogene and mutations in several tumorsuppressor genes Individuals can inherit oncogenes or mutant alleles of tumor suppressor genes Colon Fig Loss of tumorsuppressor gene AC (or other) 2 Activation of ras oncogene 4 Loss of tumorsuppressor gene p53 Normal colon epithelial cells Colon wall Small benign growth (polyp) 3 Loss of tumorsuppressor gene DCC Larger benign growth (adenoma) 5 Additional mutations Malignant tumor (carcinoma) 27