Chapter 16 (Lecture 20&21)

• Bacteria are nutritional opportunists
• Bacteria can metabolize/synthesize sugars, amino acids, and nucleotides if needed, but it is efficient to use them from the environment
• Bacteria need to recognize and respond to environmental conditions
• Bacteria switch transcription on and off for genes required for synthesis or metabolism of specific nutrients
• Structural genes


  Code for products that play some important metabolic or structural role for the cell

  
• Regulatory genes


  Code for products that play a role in regulating expression of other genes

  
• Regulatory elements


  Non-coding DNA sequences that affect expression of nearby genes

  
• Regulatory proteins


  Products of regulatory genes that often have DNA-binding domains to help them bind to specific regulatory elements

  
• DNA-binding domains of regulatory proteins have common motifs that can bind DNA sequences through hydrogen bonding with bases in the major groove

  
• Regulatory proteins


  • They can act as environmental sensors through allosteric effectors
  • Some bind to DNA and stimulate gene expression (activators)
  • Others bind to DNA and repress gene expression (repressors)

  
• Constitutive genes


  Genes that are always expressed, like housekeeping genes
• Inducible genes


  Genes that increase expression in response to a signal

  
• Repressible genes


  Genes that decrease expression in response to a signal
• Genes can have combinations of both inducible and repressible regulation, in response to many different signals

  
• Transcription


  1. RNA polymerase binds to promoter

  2. Elongation stops at terminator

  
• Translation


  1. Ribosome binds to mRNA

  2. Blocks initiation by proteins, riboswitches, or antisense RNA

  3. Affects mRNA stability

  
• Bacterial operons have a regulatory element usually overlapping the promoter, and a separate regulator gene with its own promoter

  
• Positive transcriptional control


  An activator protein promotes transcription when bound to the DNA

  
• Negative transcriptional control


  A repressor protein inhibits transcription when bound to the DNA

  
• The lac operon in E. coli requires two proteins to digest lactose: beta-galactosidase and galactoside permease

  
• Regulation of the lac operon

  1. Transcription is repressed in the absence of lactose

  2. Transcription is induced in the presence of lactose

  
• Catabolite repression


  Glucose is the preferred energy source, so the lac operon is repressed when glucose is present

  
• Catabolite activator protein (CAP)


  Required for full transcription of catabolite operons when glucose is depleted

  
• Glucose depletion


  Activates CAP, which induces transcription of the lac operon

  
• The lac operon is an example of both inducible and repressible regulation

  
• The trp operon uses transcription attenuation to regulate expression in response to tryptophan abundance

  
• Transcription attenuation of the trp operon

  1. 5' UTR contains a short peptide sequence and a premature transcription terminator

  2. Stops transcription when tryptophan is abundant

  3. Transcription and translation occur simultaneously

  
• Transcription attenuation gives an 8-10 fold change in expression, combined with negative transcriptional control for over 600 fold effect

  
• Antisense RNA


  Can block translation of mRNA by binding to it
• Riboswitches


  RNA sequences that regulate their own expression by taking on different conformations
• Mutations in the lac operon can affect structural genes, regulatory genes, or regulatory DNA elements

  
• Cis elements


  Genetic elements that affect genes on the same piece of DNA
• Trans elements


  Genetic elements that affect genes on different pieces of DNA
• lacOc is a cis-acting mutation that constitutively activates transcription of the structural genes on the same chromosome

  
• lacI+ is a trans-acting mutation that can induce transcription of genes in cis or in trans

  
• lacIS is a dominant trans-acting mutation that constitutively activates structural genes in cis and trans

  
• Control of gene expression in bacteria

  
• Repression: gene expression decreases in response to a signal or small molecule

  
• Induction: gene expression increases in response to a signal or small molecule

  
• Positive control


  Expression is turned up by an activator protein