Advanced Microbiology Lecture 13

Advanced Microbiology: Lecture 13 - Regulation of Gene Expression: Genes & Operons

• Gene expression is regulated to allow cells to express only necessary genes in specific environments.
• Regulation occurs at various levels: transcriptional, posttranscriptional, translational, and posttranslational.
• Negative regulation: genes are constitutively expressed unless a repressor protein turns them off.
• Positive regulation: genes are not expressed unless an activator protein turns them on.
• Regulation can be inducible or repressible, or both.
• Inducers increase gene expression by activating an activator or inactivating a repressor.
• Co-repressors decrease gene expression by activating a repressor or inactivating an activator.
• Apo- vs. holo-proteins: Apoproteins are inactive forms, while holoproteins are active forms.

Negative Regulation in the Lac Operon

• Negative inducible system: In the absence of lactose, the repressor protein (LacI) binds to the operator, preventing RNA polymerase from transcribing the lac genes.
• In the presence of lactose (as allolactose), allolactose binds to the repressor, causing a conformational change that prevents the repressor from binding to the operator, allowing transcription.

Negative Regulation in the Trp Operon

• Negative repressible system: In the absence of tryptophan, the repressor protein (TrpR) is inactive, allowing transcription of the trp genes.
• In the presence of tryptophan, tryptophan binds to the repressor protein, activating it. The activated repressor then binds to the operator, blocking transcription.

Positive Regulation

• Positive inducible system (e.g., arabinose operon): Presence of arabinose activates arabinose-activating protein, which then binds to the promoter region, increasing transcription.

Riboswitches

• RNA elements in mRNA leaders that sense metabolites.
• 3D structures of RNA bind to metabolites.
• Binding of metabolites leads to conformational changes.
• These changes affect terminator/anti-terminator alteration and access to ribosomal binding sites.
• Can affect the expression of genes.

tRNA Sensing

• This mechanism is responsible for gene expression of aminoacyl-tRNA synthetases.
• Amino acid attachment to tRNA affects expression; without attached amino acids, expression increases, and with attached amino acids, expression decreases.
• Unpaired regions of leader RNA in the absence of the appropriate amino acid allow for antiterminator formation.
• Expression decreased with tRNA with attached amino acids due to terminator formation.

Metabolite-binding Riboswitches

• Small molecules bind directly to leader RNA.
• They are involved in same metabolic pathway.
• Many types of molecules (atoms) bind: amino acids, vitamins, nucleic acid bases, cofactors, and metal ions.
• Binding can lead to transcription attenuation or blocking.

mRNA Degradation Regulation

• Half-life — the time it takes a template to reduce to 50% of the original amount.
• Some transcripts last only minutes.
• Increased half-life correlates to increased protein production.
• RNase E targets its own mRNA.
• Low RNase E leads to increased message, while high RNase E leads to mRNA degradation.

Regulation by sRNAs

• Small RNAs (sRNAs) are non-protein-coding RNAs involved in posttranscriptional regulation.
• sRNAs encoded in intergenic regions or antisense can form secondary stem loop structures.
• May play a role in physiological regulation, metabolism, and virulence.

Mechanisms of sRNA Interactions

• sRNAs can inhibit translation by blocking ribosomal binding sites (RBS).
• sRNAs can destablize target RNA by recruiting RNase.
• sRNAs enhance translation by exposing occluded RBSs.
• sRNAs stabilize target RNA by preventing RNase cleavage.

Regulation of Translation

• Translation initiation is mRNA structure-sensitive.
• Elongation is less sensitive to mRNA structure.
• Proteins and sRNAs can block translation initiation regions preventing 30s binding.
• Proteins/sRNAs can also disrupt secondary structure of mRNA exposing RBSs, activating translation.
• Specific examples include the thermosensor RNA thermometer and how factors like temperature affect translation.

Posttranslational Regulation

• Not all polypeptides are immediately active proteins; some require modification.
• Common modifications include phosphorylation, methylation, and acetylation.
• Phosphorylation serves as a common signal in transducer signals and two-component systems.

Feedback Inhibition

• Products of a pathway bind to the first enzyme in the pathway preventing further reaction.
• This is a common mechanism in biosynthetic pathways.
• It is a fast and sensitive mechanism for modulating the amount of end product.
• Trp operon is a great example.

Global Regulation: Regulons & Stimulons

• Bacteria must adapt quickly to environmental changes in nutrients, moisture, and temperature.
• Global regulatory mechanisms enable simultaneous regulation of numerous operons.
• Regulons: clusters of genes controlled by a single regulatory protein. (TrpR regulon, LexA regulon, and AdcR regulon).
• Stimulons: collections of associated regulons that respond to the same environmental conditions.

Catabolite-sensitive Operons

• Catabolites are smaller molecules produced from larger molecule degradation.
• Energy for catabolism of different carbon sources often requires different enzymes.
• Catabolite repression ensures cells prefer the best energy source.
• Examples include the repressions occurring in glucose or galactose use, and how these preferences affect gene expression.

Stress Responses in Bacteria

• Bacteria have global regulons responding to numerous stress conditions like osmolarity, pH, temperature, metal availability, and nutrient access.
• These responses may influence each other.
• The Heat Shock Response is an example, where heat shock proteins increase after temperature increases.

Signal Transduction Systems (STS) in Bacteria

• Some gene regulation involves sensing external environment.
• Two-component systems are often used for environmental sensing:
• Histidine kinase sits in the membrane, senses the environment, and autophosphorylates.
• Response regulator accepts phosphate from the histidine kinase and regulates gene expression.

This quiz focuses on the regulation of gene expression with an emphasis on genes and operons, particularly the Lac operon. It explores mechanisms of transcriptional, translational, and posttranslational regulation, as well as the roles of inducers and co-repressors in gene control. Understand negative and positive regulation in the context of microbiology.