Advanced Microbiology Lecture 13 - Gene Regulation

Advanced Microbiology: Lecture 13 - Gene Regulation

• Gene regulation is how cells control which genes are expressed in response to their environment.
• Negative regulation - genes are expressed unless a repressor protein turns them off.
• Positive regulation - genes are not expressed unless an activator protein turns them on.
• Regulation can be both inducible (activated by an inducer) and repressible (inhibited by a corepressor).
• Inducers increase gene expression, activating activators or inactivating repressors.
• Corepressors decrease gene expression, activating repressors or inactivating activators.
• Apo- v. holo-proteins: Apoproteins are inactive, holoproteins are active proteins.

Negative Regulation

• Negative Inducible System (Lac Operon):

  • In the absence of lactose, the lac repressor protein binds to the operator, preventing transcription.
  • In the presence of lactose and allolactose, the lac repressor protein changes shape and cannot bind to the operator, allowing transcription.

• Negative Repressible System (Trp Operon):

  • In the absence of tryptophan, the trp repressor protein is inactive and cannot bind to the operator, allowing transcription.
  • In the presence of tryptophan, tryptophan binds to the trp repressor, activating it so it can bind to the operator, preventing transcription.

Positive Regulation

• Positive Inducible System (Ara Operon):
  • In the absence of arabinose, the activator protein AraC is inactive and cannot bind to the operator. Thus, transcription does not occur.
  • In the presence of arabinose, arabinose binds to AraC, activating it, causing it to bind to the operator and allowing transcription of the ara operon.

Riboswitches

• RNA elements within mRNA leaders that sense metabolites (small molecules
• Conformational change in the RNA structure in response to ligand binding leads to either terminator or anti-terminator alterations, which in turn regulate access to ribosomal binding sites.

tRNA Sensing (T Box Mechanism)

• tRNA molecules can bind to RNA leader sequences and affect gene expression of aminoacyl-tRNA synthetases in B. subtilis.
• Unpaired regions in leader sequences allow for RNA base pairing that can create anti-terminator forms, leading to increased expression.
• Presence of aminoacyl-tRNA leads to terminator forms that reduce expression.

Metabolite-binding Riboswitches

• Small molecules can bind directly to leader RNAs in response to metabolic pathways, thus altering gene expression
• Common types include amino acids, vitamins, nucleic acids, and cofactors.
• Binding of small molecules can lead to transcription attenuation or blocking of transcription initiation regions.

Regulation of mRNA Degradation

• mRNA half-life is the time it takes for half of a particular mRNA template to be degraded.
• Longer half-lives mean more protein production, while shorter half-lives reduce production.
• RNase E is involved in degrading mRNAs, and its activity may be regulated to affect protein production levels.

Regulation by sRNAs

• Small RNAs (sRNAs) are non-coding RNAs involved in posttranscriptional regulation.
• sRNAs can affect the translation rate of their target mRNA by interacting with the ribosome binding site (RBS).
• They can down-regulate or up-regulate target mRNA levels by interfering or assisting with the stability and translation of the target mRNAs

Regulation of Translation

• Translation initiation is sensitive to mRNA structure.
• Proteins and sRNAs can bind and block translation initiation regions, preventing ribosome binding
• This can lead to either decreased or increased translation depending on how mRNA's secondary structure and ribosome binding site is altered.

Posttranslational Regulation

• Proteins may need modification to be fully active.
• Common modifications include phosphorylation, acetylation, and methylation.
• Phosphorylation is a crucial signal in transduction systems, like two-component systems.

Feedback Inhibition

• End products of a pathway bind to the first enzyme of that pathway.
• The binding inhibits further activity in the pathway.
• Feedback inhibition is a common method to precisely regulate the production of end products in biosynthetic pathways, making the process faster and more sensitive.

Global Regulation (Regulons & Stimulons)

• Regulon: A set of operons controlled by a single regulatory protein.
• Several operons can be coordinated to respond to environmental changes.
• Examples: Trpr regulon, LexA regulon, AdcR regulon.
• Stimulon: A collection of regulons that respond to the same environmental condition.

Catabolite-sensitive Operons

• Catabolites are smaller molecules resulting from larger molecule breakdown.
• Catabolite repression ensures cells preferentially use the best energy source.
• Glucose often represses operons used for other carbon sources (glucose effect).

Stress Responses in Bacteria

• Bacterial cells have global mechanisms to adapt to stress conditions (osmolarity, pH, temperature, etc.)
• Heat shock proteins (Hsps) are produced in response to temperature increase.
• Dnak protein is a cellular thermometer that helps other proteins to fold correctly under both normal and heat shock conditions.

Signal Transduction Systems (STSs)

• Bacteria adapt to external stimuli with sensor proteins and response proteins.
• Two-component systems involve a histidine kinase (in the cell membrane) that senses environmental signals and a response regulator (an intracellular protein) that transmits the signal to regulate gene expression.