Gene Regulation II : The Ribosome Strikes Back

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Gene Regulation II The Ribosome Strikes Back!
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Mechanisms Covered

• Attenuation Control
• Tryptophan Biosynthesis

• Riboswitches
• Tryptophan Biosynthesis

• Translational Control
• RBS strength
• Mechanisms that prevent translation

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Attenuation Control

• Relies on the fact that in Bacteria transcription
  and translation are coupled.
• They occur at the same time! (Draw Diagram)
• Allows translational machinery to effect
  transcription

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Attenuation Control

• Low Tryptophan Levels
• Slow translation of leader peptide from Domain 1
• This allows hairpin formation between Domains 2
  and 3
• Transcription continues

• High Tryptophan Levels
• Fast translation of leader peptide from Domain 1
• Domain 2 blocked by ribosome
• Hairpin formation between Domains 3 and 4 lead to
  formation of terminator structure!

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Alternative RNA Folding Dictates Termination
Properties
5 Region of trp operon transcript
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Riboswitches

• Riboswitches are structures in mRNA that regulate
  gene expression
• up to now only found in bacteria
• Riboswitches are bound directly by small ligands
• vitamins, such as riboflavin, thiamin and
  cobalamin
• amino acids, such as methionine and lysine
• purine nucleotides (adenine, guanine)
• The binding of such ligands affects the secondary
  structure of mRNA containing the riboswitch and
  thus exerts a regulatory function
• Riboswitches are probably one of the oldest
  regulatory systems

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Riboswitch Structures

• All known riboswitches fold into compact RNA
  secondary structures with a base stem, a central
  multi-loop and several branching hairpins

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Riboswitch Mechanism I

• Riboswitches form a defined three-dimensional
  conformation capable of specifically binding a
  low molecular ligand (such as an amino acid,
  vitamin or nucleotide)
• Binding of the ligand stabilizes one particular
  three-dimensional conformation of the riboswitch
• If no ligand is bound a different
  three-dimensional conformation of the riboswitch
  becomes energetically more favourable and is
  adopted
• The different conformations (i.e., in absence or
  presence of ligand) have different functional
  consequences!

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Riboswitch Mechanism II
Vitreschak et al., (2003). Riboswitches the
oldest mechanism for the regulation of gene
expression? Trends Genet. 20, 44-50.
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Gene Regulation

• Mostly performed at the transcription level in
  bacteria such as E.coli
• IE John Cs lecture on gene regulation

• However it is possible to regulate at higher
  levels
• Eg. Translation (RNA -gt Protein)
• Eg. Post-translational modification (Protein -gt
  Active Protein)

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Translational Control in Bacteria

• Strength of ribosome-binding sites (RBSs) this
  is especially important in bacterial
  polycistronic messages where different amounts of
  proteins need to be synthesized from a single
  mRNA

Note the different lengths and position of the
RBSs!
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Translational Control in Bacteria

• Other examples of translational control
• Translational repression occurs when excess
  ribosomal proteins bind to their own mRNAs to
  represses their translation. If there is
  sufficient rRNA, these proteins will bind to it
  in preference to the mRNA
• The stringent response and attenuation (trp
  operon and other amino acid biosynthetic operons)
  are both negative control mechanisms that operate
  through the ribosome to reduce transcription

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Translational Control in Bacteria

• A final example of translational control
• Riboswitches do not only regulate transcription
  but can also control the translation efficiency
  of an mRNA
• They do this by controlling access to the
  Ribosome Binding (RBS) sequence
• If the RBS is hidden, ribosomes will not be
  recruited at all (or very inefficiently) and thus
  the mRNA will not be effectively translated

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Controlling Ribosome Recruitment through RBS
Accessibility
Ligand
Ribosomes get recruited (via RBS) to mRNA -gt
efficient translation
Ribosomes cannot get recruited to mRNA -gt no
translation