Gene Expression at the Molecular Level III: Gene Regulation

Chapter 14: Gene Expression at the Molecular Level III: Gene Regulation

Overview of Gene Regulation

  • Gene expression

    • Definition: The process by which a gene is made into a functional product.

    • Majority of genes are regulated to ensure

    • Correct timing of protein production

    • Correct amounts of protein synthesis

    • Energy savings: Producing proteins only as needed.

    • Constitutive genes: Genes expressed at constant levels in all conditions over time.

Prokaryotic Gene Regulation

  • Regulation in prokaryotes is often responsive to environmental changes.

  • Example: E. coli and Lactose Metabolism

    • E. coli can use various sugars for energy, including lactose (a sugar found in milk).

    • Genes code for proteins that enable the uptake and metabolism of lactose.

    • Regulatory Response:

    • Presence of lactose  Two proteins produced:

      • Lactose permease: Transports lactose into the cell.

      • β-galactosidase: Breaks down lactose.

    • Absence of lactose  Proteins are no longer synthesized.

Gene Regulation in Eukaryotes

  • Essential for producing different cell types in an organism through cell differentiation.

  • All cells have the same genome but express different proteomes due to gene regulation.

    • Result: Different proteins and varying amounts of the same protein.

Developmental Gene Regulation in Mammals

  • Fetal stage characterized by:

    • Refinement of body parts

    • Increase in size

    • Different oxygen demands between the embryo and mother.

  • Hemoglobin: Delivers oxygen throughout the body.

    • Gene regulation determines which globin polypeptides are made to create functional hemoglobin.

    • Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin, aiding in oxygen transfer from maternal blood.

Levels of Gene Regulation - Bacteria

  • Most regulation occurs at the transcription level.

  • Regulation may also occur at:

    • Rate of translation

    • Protein or post-translation levels.

Levels of Gene Regulation - Eukaryotes

  • Common levels of regulation include:

    • Transcriptional regulation

    • RNA modification

    • Translation control

    • Post-translation control

Bacterial Transcriptional Regulation

Transcription Factors

  • Involves regulatory transcription factors that:

    • Bind to regulatory sequences near a promoter and affect transcription of adjacent genes.

    • Repressors: Inhibit transcription (Negative control).

    • Activators: Increase transcription rates (Positive control).

Small Effector Molecules

  • Small effector molecules influence transcription by

    • Binding to regulatory transcription factors, causing conformational changes.

    • Factors have two domains:

    • DNA binding site

    • Effector molecule binding site

The Operon Concept

Operon Definition

  • An operon: A set of genes under the transcriptional control of one promoter and transcribed as polycistronic mRNA, encoding multiple proteins.

    • Allows coordinated regulation of a gene group with a common function.

lac Operon

  • E. coli contains genes for lactose metabolism.

    • lacP: Lac promoter

    • Genes:

    • lacZ: Codes for β-galactosidase.

    • lacY: Codes for lactose permease.

    • lacA: Codes for galactoside transacetylase.

Regulatory Sites in the lac Operon

  • lacO: Operator site for repressor binding.

  • CAP site: Binding site for activator protein

  • lacI gene: Codes for lac repressor with its own promoter.

Regulation of the lac Operon

  • Under negative control when lactose is absent, the lac repressor binds to the operator, inhibiting transcription.

  • When lactose is present:

    • Allolactose: Acts as a small effector molecule and inducer, binding to the repressor and preventing its DNA binding, thus enabling transcription.

Positive Control via CAP

  • CAP (catabolite activator protein) activates the lac operon in synergy with cAMP.

  • Catabolite repression: When glucose is present, it inhibits cAMP production, repressing the lac operon.

  • Activation occurs when lactose levels are high and glucose levels are low, facilitating transcription.

trp Operon

  • trp operon encodes enzymes for the synthesis of the amino acid tryptophan.

    • Regulated by trpR gene which encodes the trp repressor.

  • When tryptophan is low: trp repressor remains inactive, allowing transcription.

  • When tryptophan is high: Repressor is activated and binds to the operator, shutting down transcription.

Distinctions Between lac and trp Repressors

  • Lac repressor: Binds in the absence of its effector (inducible system).

  • Trp repressor: Binds only in the presence of its corepressor (repressible system).

Regulation of Transcription in Eukaryotes

Roles of Transcription Factors and Mediator

  • Similar principles to prokaryotes: Activators and repressors influence RNA polymerase initiation.

  • Eukaryotic regulation is more complex with individual gene organization.

Combinatorial Control

  • Expression determined by a combination of:

    • Activators

    • Repressors

    • Modulation by small effector molecules and protein interactions

    • Chromatin structure alterations through activator proteins and DNA methylation effects on transcription.

Promoter Features

  • Core promoter includes:

    • TATA box: 5′ – TATAAAA – 3′, located 25 bp upstream from the transcription start site.

    • Transcriptional start site: Where transcription begins.

    • Regulatory elements: Recognized by proteins controlling transcription initiation (enhancers and silencers).

Proteins for Eukaryotic Transcription

  • Needed:

    • RNA polymerase II

    • 5 General transcription factors (GTFs)

    • Mediator: A protein complex mediating activator/repressor interactions with RNA polymerase II.

Transcriptional Regulation

  • Activators enhance transcription by binding to enhancers while repressors inhibit transcription via silencers.

Chromatin Structure and Methylation

  • Transcription is difficult in the closed chromatin conformation, allowing access in the open conformation.

  • Chromatin remodeling through ATP-dependent complexes makes DNA more transcriptionally accessible.

  • DNA methylation affects gene expression, often silencing genes.

Alternative Splicing of pre-mRNAs

  • Pre-mRNA processing in eukaryotes can produce multiple mRNA variants from a single gene.

  • Mechanisms allow for different proteins from the same gene, regulated by splicing factors.

  • Example: α-tropomyosin pre-RNA can splice differently, leading to protein variants with specialized functions.

  • Alternative splicing increases the complexity of proteomes relative to genome size.

Regulation of Translation

  • Iron regulatory protein (IRP) regulates translation in response to iron levels, controlling ferritin synthesis:

    • Low iron: IRP binds to iron regulatory element (IRE), inhibiting translation.

    • High iron: Binds to IRP, preventing it from inhibiting translation, allowing ferritin production for iron storage.