write detailed notes on DNA supercoiling as a mechanism of global gene regulation

intro What is DNA Supercoiling?

DNA supercoiling refers to the over-winding (positive supercoiling) or under-winding (negative supercoiling) of the DNA double helix upon itself.

It is a critical topological feature of DNA in all cells and is maintained in a supercoiled state in vivo.

Supercoiling contributes to DNA compaction and directly influences transcription, replication, and recombination by altering the accessibility and structural configuration of DNA.

In bacteria, DNA supercoiling functions as a global regulatory mechanism.

A global regulator is typically a protein that modulates the expression of many genes;

however, in this context, supercoiling—a physical property of DNA—plays a similar regulatory role by affecting the transcription of numerous genes across the genome.

In organisms with reduced genomes and limited repertoires of classical regulatory proteins, such as Mycoplasma genitalium and Campylobacter jejuni, DNA supercoiling can represent a primary or apex-level form of gene control.

Introduction: What is DNA Supercoiling?

DNA supercoiling refers to

the over-winding (positive supercoiling) or under-winding (negative supercoiling) of the DNA double helix upon itself.

Introduction: What is DNA Supercoiling?

It is

a critical topological feature of DNA in all cells

maintained in a supercoiled state in vivo.

Introduction: What is DNA Supercoiling?

Supercoiling contributes to

DNA compaction

directly influences transcription, replication, and recombination

by altering the accessibility and structural configuration of DNA.

Introduction: What is DNA Supercoiling?

In bacteria, DNA supercoiling functions as

a global regulatory mechanism.

Introduction: What is DNA Supercoiling?

A global regulator is typically

a protein that modulates the expression of many genes

Introduction: What is DNA Supercoiling?

A global regulator is typically a protein that modulates the expression of many genes;

however, in this context,

supercoiling—a physical property of DNA—plays

a similar regulatory role

by affecting the transcription of numerous genes across the genome.

Introduction: What is DNA Supercoiling?

In organisms with reduced genomes and limited repertoires of classical regulatory proteins,

such as Mycoplasma genitalium and Campylobacter jejuni,

DNA supercoiling can represent a primary or apex-level form of gene control.

main points listed

maintenance and alteration of supercoiling

sensitivity to environmental factors

Mechanism of Regulation

DNA Supercoiling as a Global Regulator

Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Experimental Approaches to Study DNA Supercoiling

2. Maintenance and Alteration of Supercoiling lsited

The level of supercoiling in bacterial cells is tightly regulated by the opposing actions of two enzyme families:

• DNA Gyrase (GyrA/GyrB):

• Topoisomerase I (TopA):

This balance is part of a homeostatic feedback loop.

2. Maintenance and Alteration of Supercoiling

The level of supercoiling in bacterial cells is tightly regulated by

the opposing actions of two enzyme families:

• DNA Gyrase (GyrA/GyrB):

• Topoisomerase I (TopA):

2. Maintenance and Alteration of Supercoiling

DNA Gyrase (GyrA/GyrB):

Introduces negative supercoils into DNA using energy from ATP.

This enzyme is central to maintaining global negative supercoiling, especially in bacteria like C. jejuni.

2. Maintenance and Alteration of Supercoiling

Topoisomerase I (TopA):

Relieves negative supercoiling by inducing single-stranded nicks that relax the DNA

2. Maintenance and Alteration of Supercoiling

This balance is part of a homeostatic feedback loop. For example,

transcription of the gyrB gene in E. coli

is upregulated when DNA becomes more relaxed,

allowing the cell to restore its optimal supercoiling level.

2. Maintenance and Alteration of Supercoiling

This balance is part of

a homeostatic feedback loop.

3. Sensitivity to Environmental Factors listed

DNA supercoiling is dynamically responsive to external stimuli,

• High Salt (e.g., Salmonella enterica):

• Macrophage Environment:

• Mucus Exposure (e.g., C. jejuni):

These changes in supercoiling serve as signal transduction mechanisms,

3. Sensitivity to Environmental Factors

DNA supercoiling is dynamically responsive to external stimuli, which allows bacteria to

adjust gene expression rapidly in response to changing environmental conditions:

Sensitivity to Environmental Factors

DNA supercoiling is ? to external stimuli, which allows bacteria to adjust gene expression rapidly in response to changing environmental conditions:

dynamically responsive

Sensitivity to Environmental Factors

DNA supercoiling is dynamically responsive to external stimuli, which allows bacteria to adjust gene expression rapidly in response to changing environmental conditions:

• High Salt (e.g., Salmonella enterica)

• Macrophage Environment

• Mucus Exposure (e.g., C. jejuni)

Sensitivity to Environmental Factors

DNA supercoiling is dynamically responsive to external stimuli, which allows bacteria to adjust gene expression rapidly in response to changing environmental conditions:

High Salt

(e.g., Salmonella enterica)

Induces increased negative supercoiling

and upregulates the virulence gene invA

from the SPI-1 pathogenicity island.

Sensitivity to Environmental Factors

DNA supercoiling is dynamically responsive to external stimuli, which allows bacteria to adjust gene expression rapidly in response to changing environmental conditions:

Macrophage Environment:

Causes DNA relaxation,

leading to increased expression of genes

that protect against oxidative stress.

Sensitivity to Environmental Factors

DNA supercoiling is dynamically responsive to external stimuli, which allows bacteria to adjust gene expression rapidly in response to changing environmental conditions:

Mucus Exposure

(e.g., C. jejuni)

Supercoiling levels shift depending on the origin of gastrointestinal mucus.

Porcine mucin induces increased negative supercoiling and alters gene expression accordingly.

Sensitivity to Environmental Factors

These changes in supercoiling serve as

signal transduction mechanisms,

integrating environmental cues

directly into transcriptional responses.

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple molecular mechanisms:

• DNA Structural Changes and Protein Binding:

• Promoter Sensitivity:

• Strand Separation and Duplex Destabilization (SIDD):

• Phenotypic Shifts:

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple

molecular mechanisms

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple molecular mechanisms:

• DNA Structural Changes and Protein Binding:

• Supercoiling alters DNA helical tension,

• affecting the binding affinity of transcription factors and RNA polymerase.

• For instance, LysR-type regulators like CbbR in Xanthobacter flavus require a specific DNA bend for effective transcriptional activation.

• Supercoiling can influence the formation, stability, or resolution of such bends.

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple molecular mechanisms:

Promoter Sensitivity:

Some promoters are inherently supercoiling-sensitive.

Negative supercoiling lowers the energy barrier for local DNA unwinding, promoting transcription initiation.

Relaxation can inhibit transcription by stabilizing double-stranded DNA structure.

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple molecular mechanisms:

Strand Separation and Duplex Destabilization (SIDD):

Supercoiling can promote local melting at promoter regions, facilitating the assembly of the transcriptional machinery.

4. Mechanism of Regulation

DNA supercoiling affects gene expression through multiple molecular mechanisms:

• Phenotypic Shifts:

• In C. jejuni, relaxed DNA topology is associated with decreased motility and increased invasiveness, showing that DNA supercoiling states modulate cellular phenotypes.

DNA Supercoiling as a Global Regulator

Supercoiling qualifies as a global regulatory mechanism because it influences the transcription of numerous, often unrelated, genes simultaneously.

This broad effect is especially evident in bacteria with fewer canonical regulators.

In C. jejuni and M. genitalium, DNA supercoiling may represent the dominant mechanism guiding physiological transitions such as virulence expression, stress adaptation, and metabolic switching.

DNA Supercoiling as a Global Regulator

Supercoiling qualifies as a global regulatory mechanism because

it influences the transcription of numerous, often unrelated, genes simultaneously.

DNA Supercoiling as a Global Regulator

Supercoiling qualifies as a

global regulatory mechanism

DNA Supercoiling as a Global Regulator

Supercoiling qualifies as a global regulatory mechanism because it influences the transcription of numerous, often unrelated, genes simultaneously.

This broad effect is especially evident in

bacteria with fewer canonical regulators.

In C. jejuni and M.genitalium

DNA Supercoiling as a Global Regulator

In C. jejuni and M. genitalium, DNA supercoiling may represent

the dominant mechanism

guiding physiological transitions

such as virulence expression, stress adaptation, and metabolic switching.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis) listed

Campylobacter jejuni:

Salmonella enterica and Shigella:

Other Bacteria:

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

listed

• Motility and Invasion:

• Flagellar Function:

• Biofilm Formation:

• FlgRS System:

• Antibiotic Resistance:

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

Motility and Invasion:

Negative supercoiling enhances motility, whereas relaxation promotes invasion of human epithelial cells.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

Flagellar Function:

DNA relaxation prompts secretion of proteins via the flagellar apparatus, suggesting a switch from motility to secretion.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

Biofilm Formation:

Relaxed DNA increases biofilm formation under aerobic stress.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

FlgRS System:

Relaxation disrupts the expression ratio of FlgR and FlgS, affecting flagellar assembly and motility.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Campylobacter jejuni:

Antibiotic Resistance:

Fluoroquinolone resistance via gyrA mutations causes persistent DNA relaxation, which secondarily enhances biofilm formation and invasiveness.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Salmonella enterica and Shigella: listed

• SPI-1 Activation:

• SPI-2 Activation:

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Salmonella enterica and Shigella:

SPI-1 Activation

: High salt increases negative supercoiling, upregulating invA.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Salmonella enterica and Shigella:

• SPI-2 Activation:

• Relaxed DNA induces ssrA expression, essential for intracellular survival.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Other Bacteria: listed

• Mycoplasma genitalium:

• E. coli:

• Staphylococcus aureus:

• Dickeya dadantii

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Other Bacteria:

Mycoplasma genitalium:

Lacks classical regulators, with supercoiling acting as the primary global control.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Other Bacteria:

E. coli:

Supercoiling regulates major outer membrane protein (MOMP) expression.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Other Bacteria:

Staphylococcus aureus:

Gene expression altered by drugs affecting supercoiling.

6. Examples of Global Regulation by Supercoiling (Focus on Pathogenesis)

Other Bacteria:

Dickeya dadantii:

Supercoiling and PecT regulate pel genes for thermally induced virulence.

7. Experimental Approaches to Study DNA Supercoiling

Key techniques for investigating DNA supercoiling include:

• Chloroquine Gel Electrophoresis

• In Vitro Supercoiling Assays

• Pharmacological Manipulation

7. Experimental Approaches to Study DNA Supercoiling

Key techniques for investigating DNA supercoiling include:

Chloroquine Gel Electrophoresis:

Separates DNA topoisomers based on supercoiling density. More relaxed DNA migrates differently than highly supercoiled forms.

7. Experimental Approaches to Study DNA Supercoiling

Key techniques for investigating DNA supercoiling include:

In Vitro Supercoiling Assays:

Involve treating relaxed plasmid DNA with DNA gyrase and monitoring changes in topology using gel electrophoresis.

7. Experimental Approaches to Study DNA Supercoiling

Key techniques for investigating DNA supercoiling include:

Pharmacological Manipulation:

Subinhibitory concentrations of novobiocin inhibit gyrase, relaxing DNA in vivo and allowing researchers to study downstream transcriptional and phenotypic effects.

Conclusion

DNA supercoiling is a vital structural and regulatory property of bacterial genomes.

It serves not only to compact DNA but also to globally modulate transcription in response to environmental and physiological signals.

Particularly in pathogens, DNA supercoiling orchestrates the expression of virulence genes, influences motility and biofilm formation, and can be affected by antibiotic resistance mutations.

As such, it represents a unique, non-protein-based system of global gene regulation, with especially pronounced roles in organisms lacking complex transcriptional regulatory networks.

Conclusion

DNA supercoiling is

a vital structural and regulatory property of bacterial genomes.

Conclusion dna supercoiling

It serves not only to

compact DNA but also to globally modulate transcription in response to environmental and physiological signals.

Conclusion dna supercoiling

Particularly in pathogens, DNA supercoiling

orchestrates the expression of virulence genes,

influences motility and biofilm formation,

can be affected by antibiotic resistance mutations.

Conclusion dna supercoiling

As such, it represents

a unique, non-protein-based system of global gene regulation,

with especially pronounced roles in organisms lacking complex transcriptional regulatory networks.

Structure

See

Every

Moment

Globally

Play

Experiments

Supercoiling Definition

Enzyme Balance

Environmental Sensitivity

Mechanism of Regulation

Global Control

Pathogenic Examples

Experimental Methods

Supercoiling Definition

Enzyme Balance

Environmental Sensitivity

Mechanism of Regulation

Global Control

Pathogenic Examples

Experimental Methods

DNA is over- or under-wound; affects transcription, replication, and recombination

Supercoiling maintained by Gyrase (adds) and Topo I (removes) negative supercoils

Supercoiling responds to salt, macrophages, mucus to alter gene expression

Affects TF binding, promoter unwinding (SIDD), and phenotypes (e.g. motility)

Supercoiling acts like a global regulator, especially in minimal-genome organisms

C. jejuni, Salmonella, etc. shift gene expression and phenotype via supercoiling

Use gels, in vitro assays, or novobiocin to probe supercoiling and effects

What is DNA supercoiling

,"DNA supercoiling refers to the over- or under-winding of DNA, affecting its compactness and accessibility for processes like transcription, replication, and recombination."

How does DNA supercoiling regulate gene expression in bacteria

,"It alters DNA structure and accessibility, influencing RNA polymerase and transcription factor binding, and thereby modulating transcription globally."

What enzymes maintain DNA supercoiling in bacteria

,"DNA gyrase (introduces negative supercoils) and topoisomerase I (relaxes negative supercoils)."

What is the role of DNA gyrase

,"DNA gyrase introduces negative supercoils using ATP, helping maintain overall supercoiling."

What is the function of topoisomerase I

,"Topoisomerase I relaxes negative supercoils by creating transient single-stranded breaks."

How does the environment affect DNA supercoiling

,"Environmental changes like high salt, oxidative stress, or mucus exposure can alter supercoiling, changing gene expression profiles."

Give an example of an environmental factor influencing supercoiling.

,"High salt increases negative supercoiling and activates invA gene expression in Salmonella enterica."

What is SIDD and how is it related to supercoiling

,"SIDD (Strand Separation and Duplex Destabilization) refers to local DNA melting promoted by negative supercoiling, which aids transcription initiation."

How does supercoiling affect promoter sensitivity

,"Negative supercoiling lowers the energy barrier for promoter unwinding, enhancing transcription; relaxation has the opposite effect."

Why is DNA supercoiling considered a global regulator

,"It affects the transcription of many unrelated genes simultaneously, often in organisms with minimal classical transcription factors."

How does DNA supercoiling affect Campylobacter jejuni

,"Negative supercoiling promotes motility; relaxed DNA enhances invasion, biofilm formation, and disrupts flagellar gene expression."

What is the FlgRS system and its link to supercoiling

,"FlgRS controls flagellar gene expression; DNA relaxation disrupts FlgR/FlgS expression, affecting motility."

How can supercoiling influence antibiotic resistance

,"Mutations in gyrA can relax DNA topology, leading to increased biofilm formation and invasiveness in pathogens like C. jejuni."

What technique separates DNA based on supercoiling density

,"Chloroquine gel electrophoresis."

What experimental approach involves using DNA gyrase to study supercoiling

,"In vitro supercoiling assays with relaxed plasmid DNA treated with gyrase."

How is novobiocin used in studying supercoiling

,"Subinhibitory doses of novobiocin inhibit gyrase, relaxing DNA in vivo and revealing transcriptional/phenotypic changes."

In what organisms does DNA supercoiling serve as a primary regulatory mechanism

,"In minimal-genome bacteria like Mycoplasma genitalium and Campylobacter jejuni."

How does DNA supercoiling affect flagellar function

,"Negative supercoiling supports motility; relaxed DNA switches function toward secretion via the flagellar apparatus."

Name a gene in Salmonella regulated by supercoiling.

,"invA gene in the SPI-1 pathogenicity island."

What is a real-world implication of DNA supercoiling in bacterial pathogenesis

,"It regulates virulence, biofilm formation, and antibiotic resistance, aiding adaptation and survival in host environments