DNA-Binding Proteins and Genetic Regulation

DNA-Binding Proteins

• Regulatory proteins bind to DNA to control transcription, either turning it on or off
• Binding can be site-specific or nonspecific
• Proteins primarily bind to the major groove of DNA through amino acid-DNA interactions

Key Structures

• Inverted repeats serve as binding sites for regulatory proteins
• Homodimeric proteins consist of two identical polypeptides that bind to inverted repeats
• Helix-Turn-Helix motifs use a recognition helix to bind DNA and a stabilizing helix to maintain structure, found in lac and trp repressors of E. coli
• Leucine zipper motifs hold recognition helices in the correct orientation

DNA-Binding Outcomes

• Outcomes include catalyzing reactions on DNA such as transcription
• Negative regulation blocks transcription when a protein binds to DNA
• Positive regulation activates transcription when a protein binds to DNA

Negative Control

• Negative control stops transcription through repression or induction
• Repression inhibits enzyme synthesis when a product is sufficient, common for anabolic enzymes, i.e. trp operon
• Induction promotes enzyme synthesis in response to a substrate, common for catabolic enzymes, i.e. lac operon

Key Terms

• Inducer: Stimulates enzyme production
• Corepressor: Inhibits enzyme production
• Effectors: Includes inducers and repressors like IPTG and allolactose
• Mechanism: Corepressors bind allosteric repressor proteins, causing the activated repressor to bind DNA near the promoter (operator)

Positive Control

• A regulatory protein enhances RNA polymerase binding to DNA
• Example: Maltose catabolism in E. coli, where maltose activator protein binds maltose (inducer), activating transcription

Activator Binding

• Activator binding involves binding to an activator-binding site (not an operator) which helps RNA polymerase recognize the promoter by bending DNA or interacting directly with RNA polymerase
• A regulon is a group of operons controlled by one regulatory protein, such as the maltose regulon

Global Control

• Global control systems regulate many genes simultaneously

Examples

• The Lac operon
• Maltose regulon

Catabolite Repression (Glucose Effect)

• Ensures the best carbon source (glucose) is used first
• Glucose inhibits the synthesis of other catabolic enzymes like lactose and maltose

Diauxic Growth

• Two growth phases occur when two energy sources are available
• The better energy source is consumed first, followed by a lag, and then growth resumes with the second source

Cyclic AMP (cAMP) and CRP

• cAMP receptor protein (CRP) activates transcription
• CRP binds DNA only when bound to cAMP, which is high when glucose is low

Conditions for lac operon transcription

• High cAMP levels for CRP binding
• Presence of lactose (or another inducer) to prevent lacI repressor binding

Two-Component Regulatory Systems

• Regulate cellular metabolism in response to environmental changes
• Consists of a sensor kinase in the cytoplasmic membrane, which detects a signal and autophosphorylates
• Response regulator in the cytoplasm is a DNA-binding protein for transcription control
• A feedback loop with phosphatase removes phosphate to reset the system
• Examples in E. coli include phosphate assimilation, nitrogen metabolism, and osmotic pressure (OmpC and OmpF)

Quorum Sensing

• Cell-to-cell communication for population density assessment
• Autoinducers are the signaling molecules produced by bacteria

Types of autoinducers

• AHL (Acyl homoserine lactone) was the first autoinducer discovered
• AI-2 is common in many Gram-negative bacteria
• Short peptides are used by Gram-positive bacteria
• Example: Aliivibrio fischeri produces bioluminescence via the lux operon

Virulence Factors

• E. coli O157:H7, AHL and AI-3 induce virulence genes
• Staphylococcus aureus, AIP triggers virulence protein production
• Quorum sensing inhibitors are potential drugs to disrupt biofilm formation and virulence

Heat Shock Response

• Heat shock proteins protect cells from stress like heat, UV, and ethanol
• Major classes include Hsp70 (DnaK in E. coli), Hsp60 (GroEL in E. coli), and Hsp10 (GroES in E. coli)
• Controlled by alternative sigma factor RpoH

General Stress Response

• Controlled by sigma factor RpoS (stationary phase sigma factor)
• Allows survival under stress such as extreme pH and oxidative stress
• RpoS* regulon includes 400+ genes for nutrient limitation, DNA damage resistance, and biofilm formation

Feedback Inhibition

• Temporarily halts biosynthetic pathways when the end product is abundant
• The end product binds the first enzyme's allosteric site
• Binding alters enzyme shape, blocking substrate binding
• Reversible: Enzyme activity resumes when product levels drop

Post-Translational Regulation

• Modification of proteins after synthesis to regulate activity
• Common modifications include adenosine monophosphate (AMP), adenosine diphosphate (ADP), inorganic phosphate (PO₄³⁻), and methyl groups (CH₃)
• Modifications activate or deactivate enzymes by changing their structure

Explore how DNA-binding proteins regulate transcription by interacting with DNA at specific sites. Learn about key structures like inverted repeats and helix-turn-helix motifs. Discover how negative and positive regulation control gene expression.