Control of Gene Expression

Control of Gene Expression

Gene Expression Points of Control

  • Transcriptional Control

  • Pre-mRNA Processing (Eukaryotes only)

  • Translational Control

  • Direct Regulation of Protein Activity

  • Protein Degradation

Transcriptional Control

  • Overview:

    • Most common point of control of gene expression.

    • Involves multiple factors:

      • Molecules that bind to DNA and/or the polymerase.

      • Most of these are protein complexes; some are RNA molecules (trans factors).

    • DNA Sequences:

      • Refers to cis factors, also known as "regulatory sequences.",

      • Includes:

      • Promoters

      • Operators

      • Enhancer Regions

      • Any other sequences that bind trans factors.

Regulatory Protein Complexes

  • Binding Domains:

    • Regulatory protein complexes typically have dimerized DNA binding domains.

    • Dimers can interact with DNA, enhancing the specificity and regulation of gene expression.

Gene Regulatory Proteins

  • Control Mechanism:

    • Often regulated by ligand binding which alters their conformation.

    • Types of Ligands Include:

      • Small proteins

      • Non-protein organic molecules

      • Inorganic molecules

Genetic “Switch” Systems

  • Composition:

    • Groups of integrated regulatory protein complexes.

    • Can be simple or complex, involving combinations of:

      • Repressors: Exert negative control on gene expression.

      • Activators: Exert positive control on gene expression.

Function of Regulatory Proteins

  • Activators:

    • Interact with DNA near promoter sites resulting in conformational changes that increase the affinity for RNA polymerase.

    • Can bind to the promoter directly to provide a surface for polymerase attachment.

    • May bind to polymerase directly to modify its conformation allowing binding.

  • Repressors:

    • Bind to DNA or polymerase and cause conformations that prevent or block transcription.

Positive and Negative Regulation

  • Negative Regulation:

    • Bound repressor protein prevents transcription by blocking access to the DNA.

  • Positive Regulation:

    • Bound activator protein promotes transcription by enhancing polymerase binding.

    • Ligand binding can remove the repressor or activate the activator, switching the gene on or off accordingly.

Examples of Transcriptional Control

  • Tryptophan Repressor in E. coli:

    • Controls transcription of genes coding for enzymes in tryptophan synthesis.

    • Mechanism:

      • When tryptophan is abundant (bound to repressor), it blocks the operator site.

      • This prevents transcription, leading to downregulation of tryptophan synthesis genes.

    • Diagram Explanation:

      • Free active repressor inhibits gene transcription, while inactive leads to genes being expressed.

  • Lac Operon in E. coli:

    • Functions as a two-part switch evaluating:

      • Is glucose present?

      • If no, check for lactose.

    • Part 1:

      • Presence of glucose influences cAMP levels. If glucose is present, low cAMP prevents CAP binding, leading to lac gene non-transcription.

    • Part 2:

      • If lactose is present, it is converted to allolactose which binds to the lac repressor, altering its conformation and leading to dissociation from DNA, thus allowing transcription to occur.

Eukaryotic Control of Transcription

  • Complexity:

    • Involves numerous transcription factors (TFII’s), both general and gene-specific, allowing for precise control.

    • Chromatin Structure:

      • Facilitates or restricts access to DNA, which is a unique aspect of eukaryotes compared to prokaryotes.

    • Operating Factors:

      • Often act over considerable distances from the gene.

Activation Mechanisms

  • Activation Involves:

    • DNA-binding sites for activators, modified by histone acetylase and remodeling complexes, facilitating transcription by the assembly of transcription factors and RNA polymerase.

Repression Mechanisms

  • Repression Techniques Include:

    • Competitive binding, masking activation surfaces on proteins, and recruitment of repressive chromatin remodeling complexes, ultimately hindering transcription.

Regulatory Protein Complexes in Detail

  • Complexes vs. Single Proteins:

    • Regulatory proteins seldom exist as isolated units; they typically form complexes with multiple subunits.

    • Certain subunits are responsible for DNA binding, while others function as coactivators or corepressors that modulate transcriptional activity.

Eukaryotic Genetic Switches

  • Integration of Components:

    • Eukaryotic gene control results from many interacting subunits, enabling fine-scale regulation.

    • The final expression state of a gene is a summation of these influences and can indicate whether a gene is completely on, off, or in a state of partial activation.

Integration of Regulatory Influences

  • Assemblies of Regulatory Proteins:

    • Different proteins interact to determine the probability of transcription initiation (

      • Strong activation vs. inhibition is balanced according to the assembly of regulatory proteins.

    • The spatial arrangement influences the likelihood of transcription activation from the promoter.