Inheritance and Mutation: Gene Regulation and Expression

LU3: Inheritance and Mutation

Gene Regulation and Expression

Learning Objectives

1. To describe the basic transcriptional and translational process in eukaryotic and prokaryotic organisms.

2. To describe the basic functions of different parts of genomes for gene regulation and expression.

3. To explain the basic mechanism of gene regulation and expression, and relate the mechanisms to regulation during organism’s development.

4. To understand the basic between environmental, genetic, and epigenetic effects on DNA regulation and expression.

How and Why Genes Are Regulated and Expressed?

• E.g., In human cells.

• Share the same genome, but what makes them different?

• In gene expression:

  • certain genes are turned on and off.

  • a gene is turned on and transcribed into RNA.

  • information flows from genes to proteins, genotype to phenotype.

• In cellular level, the occurrence of differentiation, dedifferentiation, redifferentiation, and trans-differentiation.

• Cells become specialized in structure and function.

• Gene expression must be regulated in several different dimensions; in time, space, and abundance (strong or weak).

Gene Expression Regulation

• Prokaryotes and eukaryotes alter gene expression in response to changing environment.

• In multicellular eukaryotes, gene expression regulates development and responsible for differences in cell types.

• RNA molecules (mRNA) play many roles in regulating gene expression in eukaryotes.

Categories of Genes

• Housekeeping:

  • Always turned on in all cells.

  • E.g., transcription and translation machinery, energy conversion, etc.

• Cell type specific:

  • Turned on in each cell that give a cell its special properties and function.

• Developmental regulatory:

  • Specific to certain stages during growth and development.

• Inducible:

  • Not normally expressed but can be in response to external stimuli.

  • E.g., hormone.

• Gene regulation has been well studied in E. coli

Operons: The Basic Concept

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

• Operon

  • The entire stretch of DNA that includes the operator, promoter, and genes that they control.

• Operator

  • The regulatory switch, and a segment of DNA.

  • Positioned between the enzyme genes and the promoter.

• Promoter

  • A control sequences.

  • Site where the transcription enzyme initiates transcription when RNA polymerases and transcription factors, TFs bind.

• Repressor

  • Can switch on-off operon.

  • Prevents gene transcription by binding to the operator and blocking RNA polymerase.

  • Product of a separate regulatory gene.

  • Can be in an active or inactive form, depending on the presence of other molecules.

• Inducer

  • Activate or inactivate the repressor to turn the operon on or off.

• Activator

  • Accelerate transcription.

• Enhancer

  • Distal control elements in operon.

Bacteria Respond to Environmental Change by Regulating Transcription

• Natural selection has favoured bacteria to produce only the products needed by the cell.

• A cell can regulate the production of enzymes by feedback inhibition or by gene regulation on a stretch of DNA that coordinate gene expression.

• Gene expression in bacteria is controlled by the operon model.

The trp Operon

• E.g., The tryptophan, trp operon is on and the genes for tryptophan synthesis are transcribed.

• When tryptophan is present, it binds to the trp repressor, which turns the operon off.

• The repressor is active only in the presence of its corepressor; thus the trp operon is turned off (repressed) if tryptophan levels are high.

The lac Operon

• E.g., The lactose, lac operon, contains genes that code for enzymes used in hydrolysis and metabolism of lactose.

• By itself, lac repressor is active and switches the lac operon off.

• An inducer inactivates the repressor to turn the lac operon on.

Repressible vs. Inducible Operons

• Repressible operon

  • Usually on.

  • Binding of a repressor to the operator shuts off transcription.

  • E.g., trp operon

• Inducible operon

  • Usually off

  • An inducer inactivates the repressor and turns on transcription.

  • E.g., lac operon

• Repressible enzymes (trp)

  • Usually function in anabolic pathways.

  • Their synthesis is repressed by high levels of the product.

• Inducible enzymes (lac)

  • Usually function in catabolic pathways.

  • Their synthesis is induced by a chemical signal.

• Regulation of 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 Adenosine Monophosphate (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.

Eukaryotic Gene Expression Regulated At Many Stages

• All organisms must regulate which genes are expressed at any given time and at many stages.

• In multicellular organisms, regulation of gene expression is essential for cell specialization.

• Differential Gene Expression

  • Almost all 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.

Regulation of Chromatin Structure

1. Heterochromatin

   • Genes, highly packed.

   • Usually not expressed.

2. Euchromatin

   • Genes, loosens.

   • Usually expressed.

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

• Histone acetylation (acetyl groups attached to positively charged lysines in histone tails)

  • Loosens chromatin structure, thereby promoting the initiation of transcription.

• Methylation (addition of methyl groups)

  • Condense chromatin.

• Phosphorylation (addition of phosphate groups next to a methylated amino acid)

  • 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.

Histone Acetylation

Switching a gene on and off through histone modification.

• Some other post-translational modifications: Biotinylation, Glycosylation, Alkylation, Glutamylation, Glycylation, Isoprenylation, Lipoylation, Phosphopantetheinylation, Sulfation, Selenation and C-terminal amidation.

DNA Methylation

Switching a gene on and off through DNA methylation.

• The addition of methyl groups to certain bases in DNA, associated with reduced transcription in some species.

• 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 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.

Organization of a Typical Eukaryotic Gene

• Multiple control elements (segments of non-coding DNA) serve as binding sites for Transcription Factors (TFs) that help regulate transcription.

• Control elements and the TF they bind are critical to the precise regulation of gene expression in different cell types.

• TFBS transcription factor binding site (TFBS)

• cis-regulatory module (CRM)

The Roles of Transcription Factors

1. To initiate transcription, RNA polymerase requires the assistance of proteins called transcription factors, TF.

2. General TF are essential for the transcription of all protein-coding genes.

3. High/low levels of transcription of genes depend on control elements interacting with specific TF.

4. Control the development/cell cycle.

5. Response to intercellular signals and/or environment.

Regulation of Transcription Initiation

• Transcriptional regulation in eukaryotes is complex.

• It involves many proteins collectively called Transcription Factors (TFs).

• TFs bind to DNA sequences called Enhancers (cis-regulatory module).

• The sequences to which TFs bind are called TFBSs (cis-regulatory elements).

• Repressor inhibit transcription by binding to DNA sequences called Silencers.

• 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.

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.

• An activator 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.

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.

Mechanisms of Post-Transcriptional Regulation

• The processes include:

  • addition of a cap and tail to the RNA

  • removal of any introns

  • splicing together of the remaining exons

• 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.

• RNA Processing

  • Such mechanisms allow a cell to fine-tune gene expression rapidly in response to environmental changes.

  • Regulatory mechanisms can operate at various stages after transcription.

  • Transcription alone does not account for gene expression.

mRNA Degradation

• The life span of mRNA molecules in the cytoplasm is a key to determining protein synthesis.

• Can have different lifetimes and are all eventually broken down and their parts recycled.

• 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.

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.

Post-Translational Control Mechanisms

• Occur after translation.

• Involve cutting polypeptides into smaller, active final products.

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.