Regulation of Gene Expression

Differential Gene Expression

• Prokaryotes and eukaryotes regulate gene expression based on environmental conditions.
• In multicellular eukaryotes, gene expression regulates development and cell type differences.

Bacterial Response to Environmental Change

• Bacteria adapt to environmental changes by regulating transcription to preserve resources.
• This occurs at two levels:
  • Adjusting enzyme activity via negative feedback.
  • Gene regulation.

Feedback Inhibition and Gene Regulation

• Enzymes can be regulated via:
  • Feedback inhibition.
  • Regulation of enzyme production through gene expression.
• Example: Tryptophan synthesis regulation.

Operons

• Operons are a mechanism for controlling gene expression in bacteria.
• A cluster of functionally related genes is controlled by a single on/off switch.
• The operator is a DNA segment, the switch, usually located within the promoter.
• An operon includes the operator, promoter, and the genes they control.

Components of the trp Operon

• The trp operon contains:
  • Promoter: where RNA polymerase binds.
  • Operator: the on/off switch.
  • Genes: trpE, trpD, trpC, trpB, trpA which code for enzymes that synthesize tryptophan.

Repressors

• The operon can be switched off by a repressor protein.
• The repressor binds to the operator, blocking RNA polymerase and preventing transcription.
• The repressor is produced by a separate regulatory gene.

Regulation of the trp Operon

• The repressor molecule isn't always active; it requires a corepressor to become active.
• E. coli synthesizes tryptophan only when levels are low.

trp Operon Mechanism

• The trp operon is on by default, allowing transcription of genes for tryptophan synthesis.
• The tryptophan repressor is inactive on its own.
• When tryptophan is present, it binds to the repressor, activating it. The activated repressor binds to the operator, turning the operon off.
• The operon is repressed when tryptophan levels are high.

Repressible vs. Inducible Operons

• A repressible operon is usually on; repressor binding turns it off (e.g., trp operon).
• An inducible operon is usually off; an inducer inactivates the repressor, turning it on.

lac Operon

• The lac operon is an inducible operon containing genes for lactose hydrolysis and metabolism.
• The lac repressor is active by itself, switching the lac operon off.
• An inducer molecule inactivates the repressor to turn the lac operon on.

lac Operon Mechanism

• When lactose is absent, the repressor is active, and the operon is off.
• When lactose is present, allolactose (an inducer) binds to the repressor, inactivating it and turning the operon on.

Enzyme Function

• Inducible enzymes usually function in catabolic pathways and are induced by a chemical signal.
• Repressible enzymes usually function in anabolic pathways and are repressed the end product.
• Regulation of trp and lac operons involves negative control because operons are switched off by the active repressor.

Positive Gene Regulation

• Some operons are subject to positive control via stimulatory proteins like catabolite activator protein (CAP), activated by cAMP.
• Bacteria prefer glucose as an energy source but can switch to lactose if glucose is scarce.
• Low glucose levels increase cAMP, activating CAP.
• Activated CAP binds to the lac operon promoter, increasing RNA polymerase affinity and transcription.

CAP Regulation

• When glucose is scarce, cAMP levels rise, activating CAP, which then increases lac operon transcription.
• When glucose is abundant, CAP detaches, and transcription returns to normal.
• CAP regulates other operons involved in catabolic pathways.
• Repressors act as on/off switches; CAP acts as a volume control.

Eukaryotic Gene Expression

• Regulation of gene expression is essential for cell specialization in multicellular organisms.
• Almost all cells in an organism are genetically identical.
• Differences between cell types result from differential gene expression.
• Abnormal gene expression can lead to diseases, including cancer.
• Gene expression is regulated at multiple stages.

Steps of Gene Expression Regulation

• Chromatin modification (DNA unpacking).
• Transcription.
• RNA processing.
• mRNA transport to the cytoplasm.
• mRNA degradation.
• Translation.
• Protein processing.
• Protein degradation.
• Transport to cellular destination.

Regulation of Transcription Initiation

• Eukaryotic genes have multiple control elements, which are noncoding DNA segments that serve as binding sites for transcription factors.
• Control elements and transcription factors are crucial for precise gene expression regulation in different cell types.

Transcription Factors

• Eukaryotic RNA polymerase requires transcription factors to initiate transcription.
• General transcription factors are essential for transcribing all protein-coding genes.
• High transcription levels depend on control elements interacting with specific transcription factors.

Enhancers and Control Elements

• Proximal control elements are located near the promoter.
• Distal control elements (enhancers) can be far from the gene.

Activators

• An activator is a protein that binds to an enhancer, stimulating gene transcription.
• Activators have a DNA-binding domain and a protein-binding domain.
• Bound activators facilitate protein-protein interactions, resulting in gene transcription.
• General transcription factors initiate low-level transcription; enhancer interactions cause large increases.

Repressors as Transcription Factors

• Some transcription factors act as repressors, inhibiting gene expression by blocking activator binding or interacting directly with activators.

Combinatorial Control of Gene Activation

• A combination of control elements regulates expression for each gene.
• A specific control element combination activates transcription only when appropriate activator proteins are present.

Co-expressed Genes in Eukaryotes

• Co-expressed eukaryotic genes are not organized in operons (with minor exceptions).
• These genes are scattered on different chromosomes but share control elements.
• Activators recognize control elements, promoting simultaneous transcription.

Post-Transcriptional Regulation

• Transcription alone doesn't account for gene expression.
• Regulatory mechanisms operate after transcription to fine-tune gene expression in response to environmental changes.

RNA Processing

• Alternative RNA splicing produces different mRNA molecules from the same primary transcript, depending on which RNA segments are exons or introns.

Noncoding RNAs

• A small fraction of DNA codes for proteins; a very small fraction of 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 mRNA translation and chromatin configuration.

MicroRNAs and Small Interfering RNAs

• MicroRNAs (miRNAs) are small single-stranded RNA molecules that bind to mRNA.
• miRNAs degrade mRNA or block its translation.
• Estimated that miRNAs regulate at least half of all human genes.
• Small interfering RNAs (siRNAs) are similar to miRNAs in size and function.
• Blocking gene expression by siRNAs is called RNA interference (RNAi).
• RNAi is used in the lab to disable genes and study their function.

Gene Expression in Multicellular Organisms

• During embryonic development, a fertilized egg gives rise to different cell types.
• Cell types are organized into tissues, organs, organ systems, and the whole organism.
• Gene expression orchestrates developmental programs.

Cell Differentiation

• Cell differentiation is the process by which cells become specialized in structure and function.
• Morphogenesis involves the physical processes that give an organism its shape.
• Differential gene expression results from genes being regulated differently in each cell type.
• Materials in the egg (cytoplasmic determinants) set up gene regulation that is carried out as cells divide.

Cytoplasmic Determinants

• An egg’s cytoplasm contains RNA, proteins, and other substances distributed unevenly in the unfertilized egg.
• Cytoplasmic determinants are maternal substances that influence early development.
• As the zygote divides, cells contain different cytoplasmic determinants, leading to different gene expression.

Sequential Gene Expression Regulation

• Cell differentiation is marked by tissue-specific protein production.
• Cells are committed to specific cell types at the molecular level before differentiation is obvious.
• Determination is when a cell is irreversibly committed to its final fate.
• Determination precedes differentiation.

MyoD as a Master Regulatory Gene

• Determination is mediated by master genes.
• MyoD is a master regulatory gene that encodes a transcription factor committing cells to becoming skeletal muscle.
• Myoblasts are cells determined to produce muscle cells and begin producing muscle-specific proteins.
• MyoD can turn differentiated cells (fat and liver cells) into muscle cells.

Cancer Genes

• Cancer is caused by mutations in genes that regulate cell growth and division.
• Mutations can be spontaneous or caused by environmental factors (chemicals, radiation, viruses).

Oncogenes and Proto-oncogenes

• Oncogenes are cancer-causing genes in viruses.
• Proto-oncogenes are normal cellular genes responsible for cell growth and division.
• Conversion of a proto-oncogene to an oncogene leads to abnormal cell cycle stimulation.

Proto-oncogene Conversion to Oncogenes

• Proto-oncogenes can be converted via:
  • DNA movement within the genome (ends up near an active promoter, increasing transcription).
  • Amplification of the proto-oncogene (increases gene copies).
  • Point mutations in the proto-oncogene or its control elements (increase gene expression).

Tumor-Suppressor Genes

• Tumor-suppressor genes normally prevent uncontrolled cell growth.
• Mutations that decrease tumor-suppressor protein products may contribute to cancer onset.
• Tumor-suppressor proteins:
  • Repair damaged DNA.
  • Control cell adhesion.
  • Act in cell-signaling pathways that inhibit the cell cycle.

Cell-Signaling Pathways

• Mutations in the ras proto-oncogene and p53 tumor-suppressor gene are common in human cancers.
• Mutations in the ras gene lead to hyperactive Ras protein production and increased cell division.

p53 Tumor-Suppressor Gene

• Suppression of the cell cycle is vital when DNA is damaged; p53 prevents cells from passing on mutations.
• Mutations in the p53 gene prevent cell cycle suppression.

Multistep Cancer Development Model

• Multiple mutations are needed for cancer; incidence increases with age.
• At the DNA level, cancer cells usually have at least one active oncogene and several mutated tumor-suppressor genes.
• Tumor suppressor genes are normally recessive, requiring knockout of both alleles.
• Oncogenes are normally dominant.

Inherited Predisposition and Environmental Factors

• Individuals can inherit oncogenes or mutant alleles of tumor-suppressor genes (e.g., 15% of colorectal cancers involve inherited mutations).
• Mutations in BRCA1 or BRCA2 are found in at least half of inherited breast cancers, detectable via DNA sequencing.

Viruses in Cancer

• Tumor viruses can cause cancer by interfering with gene regulation if they integrate into a cell’s DNA.
• They can insert an oncogene, disrupt transcription of tumor-suppressing genes, or suppress P53 and other tumor-suppressing proteins.
• Viruses are responsible for approximately 15% of all cancers worldwide.