Prokaryote Gene Regulation

• Gene expression


  In a symphony, various instruments play their own parts at different times; the musical score determines which instruments play when. In an organism, different genes are expressed at different times, with a "genetic score," written in regulatory regions of the DNA, determining which genes are active when.

  
• When do cells need to regulate gene expression?

  • Prokaryotes need to respond to their environment (constantly changing – need to adapt). In multicellular organisms, gene expression is critical for directing development and maintaining homeostasis.

  
• Mechanisms for controlling metabolism

  • Regulate enzymes
  • Regulate gene expression

  
• Regulate enzymes


  Competitive and non-competitive inhibition to turn on and off production
• Regulate gene expression


  Activating/deactivating genes using regulatory proteins that switch transcription on or off

  
• Levels of gene expression regulation

  • Transcription
  • Translation
  • Post-translation

  
• Regulatory proteins


  Gene expression is often controlled by regulatory proteins binding to specific DNA sequences

  
• DNA-binding motifs


  • Helix-turn-helix motif
  • Zinc finger motif
  • Leucine zipper motif

  
• Bacteria are frugal and only express a gene if the protein is needed for the cell to survive
• Operon


  In prokaryotic mRNA may contain multiple genes and thus produce multiple proteins at once. Prokaryotic genes are often organized such that genes encoding related functions are clustered together.

  
• Components of an operon

  • Promoter
  • Operator
  • Structural genes

  
• Positive control by activators

  Activators enhance the binding of RNA polymerase to the promoter to increase the frequency of transcription initiation

  
• Negative control by repressors


  Repressors are proteins that bind to operator to prevent or decrease the initiation of transcription
• Regulatory gene


  A gene located upstream of the operon that codes for the regulator protein (e.g. repressor) which will affect the operator

  
• Types of operons


  • Inducible operon (off by default)
  • Repressible operon (on by default)
• Regulatory gene


  Regulator protein
• Prokaryote gene regulation


  • Regulate of Gene expression at the transcription level (Negative control)

  
• Types of operons


  • Inducible operon
  • Repressible operon
• Inducible operon


  Operon is OFF by default, only produces enzymes when inducer (e.g. lactose) is present

  
• Repressible operon


  Operon is ON by default, stops producing enzymes when repressor (e.g. tryptophan) is present

  
• Inducible operons


  • Regulator gene makes a functioning repressor protein
  • Repressor protein binds to operator and prevents RNA polymerase from binding to promoter

  
• Inducible operons


  1. No inducer (e.g. lactose) present

  2. Repressor binds to operator

  3. RNA polymerase cannot bind to promoter

  4. Genes not transcribed

  
• Inducible operons


  1. Inducer (e.g. lactose) present

  2. Inducer inactivates/detaches repressor

  3. RNA polymerase can bind to promoter

  4. Genes transcribed

  
• Repressible operons


  • Regulator gene makes a non-functioning repressor protein
  • RNA polymerase able to bind to promoter and genes transcribed

  
• Repressible operons


  1. No repressor (e.g. tryptophan) present

  2. RNA polymerase able to bind to promoter

  3. Genes transcribed

  
• Repressible operons


  1. Repressor (e.g. tryptophan) present

  2. Repressor binds to operator

  3. RNA polymerase cannot bind to promoter

  4. Genes not transcribed

  
• Tryptophan binding increases distance between repressor recognition helices, allowing repressor to fit into major groove of DNA
• Positive control of gene expression in bacteria

  • Bacteria preferentially use glucose first in presence of other sugars
  • Producing enzymes to degrade other sugars costs energy, so bacteria are frugal
• Promoter for lactose operon is not very efficient at recruiting RNA polymerase, so transcription and production of enzymes is not very high

  
• Presence of lactose alone is not enough, bacteria also need to detect low glucose levels
• Cyclic AMP (cAMP)


  Molecule used for intracellular signaling in bacteria
• Positive control of lac operon

  1. Lactose present (inactivates lac repressor)

  2. Low glucose (high cAMP)

  3. cAMP binds to catabolite activator protein (CAP)

  4. CAP binds to promoter and enhances RNA polymerase initiation, increasing transcription
• Inducer molecules (allolactose) can bind to the repressor protein, causing it to change shape and release from the DNA.
• The lac operon is an example of gene regulation.
• The binding of allolactose causes the repressor protein to dissociate from the operator region, allowing RNA polymerase to initiate transcription of the structural genes.