Control of Gene Expression in Bacteria and Eukaryotes

Control of Gene Expression in Bacteria

Introduction to Gene Expression Regulation

Cells do not express all of their genes at all times. Regulation of gene expression is essential for cellular function and adaptation to environmental changes.

• Gene expression: Occurs when a gene product is synthesized and becomes active in a cell.

• Cells are selective about:

  • Which genes they express

  • In what amounts genes are expressed

  • When genes are expressed

• Regulation of gene expression is critical for cell survival and efficiency.

Mechanisms of Regulation

Information flow in cells follows the central dogma: DNA → mRNA → protein → activated protein. Regulation can occur at multiple steps:

• Transcriptional control: Determines whether mRNA is synthesized from DNA. Most efficient but slowest.

• Translational control: Determines whether an mRNA is translated into protein. Allows rapid changes.

• Post-translational control: Determines whether a protein is activated by chemical modification. Fastest response.

Equation:

$\text{DNA} \rightarrow \text{mRNA} \rightarrow \text{protein} \rightarrow \text{activated protein}$

Transcriptional Control

Transcriptional control is the most resource-efficient but slowest form of regulation. It prevents unnecessary synthesis of mRNA and proteins.

• Regulatory proteins can block RNA polymerase from binding the promoter, preventing transcription.

• Example: An enzyme is not produced if regulatory proteins block RNA polymerase.

Translational Control

Translational control allows rapid changes because mRNA is already present.

• Regulatory molecules can speed up mRNA degradation.

• The ability of mRNA to be translated can be affected by regulatory proteins or small RNAs.

Post-Translational Control

Post-translational control provides the most rapid response, as only one step is needed to activate an existing protein.

• Proteins may require chemical modification (e.g., phosphorylation) to become active.

• Some genes are transcribed constitutively (all the time).

Comparison: Transcriptional control is slow but efficient; post-translational control is fast but energetically expensive.

Metabolizing Lactose—A Model System

Escherichia coli (E. coli) uses lactose as an energy source only when glucose is depleted. The metabolism of lactose involves two key proteins:

• Galactoside permease: Transports lactose into the cell.

• β-galactosidase: Cleaves lactose into glucose and galactose.

E. coli produces high levels of β-galactosidase only when lactose is present. Lactose acts as an inducer—a molecule that triggers transcription of a specific gene.

• If glucose is present, β-galactosidase is not produced in high levels. Glucose negatively regulates β-galactosidase expression.

Identifying Regulated Genes

Monod and Jacob isolated and analyzed E. coli mutants that could not metabolize lactose to identify genes and their regulators.

• Mutants were generated using mutagens (X-rays, UV light, chemicals).

• Screening involved identifying individuals with defects in lactose metabolism.

• Replica plating was used to identify mutant cells by transferring colonies to plates with different media.

Three Classes of Lactose Metabolism Mutants

Observed Phenotype	Interpretation	Genotype
Cells cannot cleave lactose, even in the presence of inducer (lactose)	No β-galactosidase; gene for β-galactosidase is defective	lacZ-
Cells cannot accumulate lactose	No membrane protein (galactoside permease) to import lactose; gene for galactoside permease is defective	lacY-
Cells can cleave lactose even if lactose is absent as an inducer	Constitutive expression of lacZ and lacY; gene for regulatory protein that shuts down lacZ and lacY is defective	lacI-

Negative Control of Transcription

Transcription can be regulated by:

• Negative control: A regulatory protein called a repressor binds to DNA and shuts down transcription.

• Positive control: A regulatory protein called an activator binds to DNA and triggers transcription.

The lacI gene encodes a repressor protein that binds on or near the lacZ and lacY promoter. Lactose acts as an inducer by binding the repressor and removing it, allowing transcription.

• lacI- mutants lack a functional repressor; lacZ and lacY are expressed with or without lactose.

The Operon Model

Jacob and Monod coined the term operon for a set of coordinately regulated bacterial genes transcribed together into one mRNA. The lac operon includes lacZ, lacY, and lacA genes.

• lacI is a repressor of the lac operon, expressed constitutively.

• Lactose is the inducer that changes the shape of lacI, causing it to release from the operator (allosteric regulation).

• lacA encodes transacetylase, which exports excess sugar from the cell.

Regulation by Glucose

Transcription of the lac operon is greatly reduced when glucose is present. Two mechanisms:

• Inducer exclusion: Transport of lactose into the cell is inhibited when glucose is high.

• Inhibition of CAP: Catabolite Activator Protein (CAP) is inhibited when glucose is high. When glucose is low, CAP-cAMP complex stimulates RNA polymerase binding and transcription.

Positive Control of Transcription: The ara Operon

The ara operon provides an example of positive control. It contains genes that allow E. coli to use arabinose. Transcription is turned on by an activator protein called AraC.

• AraC is allosterically regulated by arabinose.

• In the absence of arabinose, AraC acts as a repressor.

Global Gene Regulation

Global gene regulation is the coordinated regulation of many genes, necessary for responses requiring the expression of dozens or hundreds of genes.

Control of Gene Expression in Eukaryotes

Introduction to Gene Expression Regulation in Eukaryotes

Gene expression regulation is more complex in eukaryotes than in prokaryotes. Differential gene expression is responsible for creating different cell types, arranging them into tissues, and coordinating their activity.

Gene Regulation in Eukaryotes—An Overview

Eukaryotes can regulate gene expression at multiple levels:

• Transcription

• Translation

• Post-translation

• Chromatin remodeling

• RNA processing (to produce mature mRNA)

• Regulation of mRNA life span or stability

The Structure of Chromatin

In eukaryotes, DNA is wrapped around proteins to form chromatin. Chromatin consists of DNA wrapped around histones and other proteins, forming nucleosomes—repeating, beadlike structures.

• Chromatin structure allows DNA to fit in the nucleus and plays a key role in gene regulation.

Chromatin Remodeling

Chromatin must be unpacked at particular genes so they can be transcribed. RNA polymerase cannot access DNA when it is tightly coiled.

• Chromatin remodeling is the process of unpacking DNA to allow transcription.

DNA Methylation

Chromatin must be decondensed to expose the promoter for RNA polymerase to bind. DNA methylation causes chromatin to condense and represses gene expression.

• DNA methyltransferases add methyl groups (–CH3) to cytosines in DNA.

• Actively transcribed genes usually have low levels of methylation near their promoters.

Histone Modification

Acetylation of histones is usually associated with activation of genes.

• Histone acetyltransferases (HATs) add acetyl groups to histones, decondensing chromatin.

• Histone Accessibility Hypothesis: More condensed chromatin = less gene activity.

• Histone modifications are a method cells use to alter gene expression.

Chromatin Modifications Can Be Inherited

Patterns of methylation and acetylation can be passed on when a cell divides. This is known as epigenetic inheritance—any inheritance mechanism not due to differences in DNA sequence.

• Daughter cells can inherit patterns of gene expression.

Epigenetic Regulation of Ant Size (Research Example)

Research on Florida carpenter ants showed that differences in ant size are due to epigenetic regulation, specifically DNA methylation.

• Larvae with high DNA methylation have certain key genes inactivated and grow up to be small adults.

• Larvae with low DNA methylation have these genes decondensed and active, resulting in larger ants.

Summary Table: Mechanisms of Gene Regulation in Bacteria and Eukaryotes

Level of Regulation	Bacteria	Eukaryotes
Transcriptional	Regulatory proteins (repressors/activators) control RNA synthesis	Regulatory proteins, chromatin structure, transcription factors
Translational	Regulatory molecules affect mRNA stability and translation	Regulatory molecules, RNA processing, mRNA stability
Post-translational	Protein modification (e.g., phosphorylation)	Protein modification, localization, degradation
Chromatin Remodeling	Not present	Chromatin structure affects gene accessibility
RNA Processing	Not present	Splicing, capping, polyadenylation

Key Terms

• Operon: A set of coordinately regulated bacterial genes transcribed together into one mRNA.

• Inducer: A molecule that triggers transcription of a specific gene.

• Repressor: A protein that binds to DNA and shuts down transcription.

• Activator: A protein that binds to DNA and triggers transcription.

• Chromatin: DNA-protein complex that packages eukaryotic DNA.

• Epigenetic inheritance: Inheritance of gene expression patterns not due to DNA sequence changes.

Examples and Applications

• Lac operon: Classic model for gene regulation in bacteria, demonstrating negative and positive control.

• Ara operon: Example of positive control in bacteria.

• Chromatin remodeling: Key to gene regulation in eukaryotes, affecting cell differentiation and development.

• Epigenetic regulation: Explains phenotypic variation without changes in DNA sequence, as seen in ant size.

Learning Objectives

• Explain how regulons allow bacteria to coordinate the expression of large sets of genes in response to changing environments.

• Explain the role of repressors and inducers in negative control of gene expression.

• Explain the role of CAP protein and cAMP in positive control of gene expression.

• Describe the basic structure of chromatin and relate its structure to gene regulation.