Overview: Conducting the Genetic Orchestra

Prokaryotes and eukaryotes alter gene expression in response to their changing environment

            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

 

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

            Gene expression in bacteria is controlled by the operon model

Operons: The Basic Concept

            A cluster of functionally related genes can be under coordinated control by a single “on-off switch”

            The regulatory “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

            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

            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

            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

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

            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

 

            nducible 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

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

            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

 

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

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

Regulation of Chromatin Structure

            Genes within highly packed heterochromatin are usually not expressed

            Chemical modifications to histones and DNA of chromatin influence both chromatin structure and gene expression

Histone Modifications

            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

            The histone code hypothesis proposes that specific combinations of modifications, as well as the order in which they occur, help determine chromatin configuration and influence transcription

DNA Methylation

            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

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

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

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

The Roles of Transcription Factors

            To initiate transcription, eukaryotic RNA polymerase requires the assistance of proteins called 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

            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

            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

            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

            A particular combination of control elements can activate transcription only when the appropriate activator proteins are present

Coordinately Controlled Genes in Eukaryotes

            Unlike the genes of a prokaryotic operon, each of the co-expressed eukaryotic genes has a promoter and control elements

            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

Nuclear Architecture and Gene Expression

            Loops of chromatin extend from individual chromosomes 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

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

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

mRNA Degradation

            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 3Ę end of the molecule

Initiation of Translation

            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

Protein Processing and Degradation

            After translation, various types of protein processing, including cleavage and the addition of chemical groups, are subject to control

            Proteasomes are giant protein complexes that bind protein molecules and degrade them

 

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

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

 

            The phenomenon of inhibition of gene expression by RNA molecules is called RNA interference (RNAi)

            RNAi is caused by small interfering RNAs (siRNAs)

            siRNAs and miRNAs are similar but form from different RNA precursors

Chromatin Remodeling and Effects on Transcription by ncRNAs

            In some yeasts siRNAs play a role in heterochromatin formation and can block large regions of the chromosome

            Small ncRNAs called piwi-associated RNAs (piRNAs) induce heterochromatin, blocking the expression of parasitic DNA elements in the genome, known as transposons

            RNA-based mechanisms may also block transcription of single genes

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

 

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

A Genetic Program for Embryonic Development

            The transformation from zygote to adult results from cell division, cell differentiation, and morphogenesis

            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 can set up gene regulation that is carried out as cells divide

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

            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

Sequential Regulation of Gene Expression During Cellular Differentiation

            Determination commits a cell to its final fate

            Determination precedes differentiation

            Cell differentiation is marked by the production of tissue-specific proteins

            Myoblasts produce muscle-specific proteins and form skeletal muscle cells

            MyoD is one of several “master regulatory genes” that produce proteins that commit the cell to becoming skeletal muscle

            The MyoD protein is a transcription factor that binds to enhancers of various target genes

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

            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

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

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

            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

Axis Establishment

            Maternal effect genes encode for 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

            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

            This phenotype suggests that the product of the mother’s bicoid gene is concentrated at the future anterior end

            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

            The bicoid research is important 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 principle that a gradient of molecules can determine polarity and position in the embryo

 

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

Types of Genes Associated with Cancer

            Cancer can be caused by mutations to genes that regulate cell growth and division

            Tumor viruses can cause cancer in animals including humans

 

            Oncogenes are cancer-causing genes

            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

            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

Tumor-Suppressor Genes

            Tumor-suppressor genes help prevent uncontrolled cell growth

            Mutations that decrease protein products of tumor-suppressor genes may contribute to cancer onset

            Tumor-suppressor proteins

         Repair damaged DNA

         Control cell adhesion

         Inhibit the cell cycle in the cell-signaling pathway

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

            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

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

Inherited Predisposition and Other 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