Transcript Gene Regulation at Higher Levels

Gene Regulation II :
The Ribosome Strikes Back!
Mechanisms Covered
• Attenuation Control
– Tryptophan Biosynthesis
• Riboswitches
– Tryptophan Biosynthesis
• Translational Control
– RBS strength
– Mechanisms that prevent translation
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
Attenuation Control
Low Tryptophan Levels:
1. Slow translation of leader
peptide from Domain 1
2. This allows hairpin formation
between Domains 2 and 3
3. Transcription continues
High Tryptophan Levels:
1. Fast translation of leader peptide from
Domain 1
2. Domain 2 blocked by ribosome
3. Hairpin formation between Domains 3
and 4 lead to formation of terminator
structure!
Alternative RNA Folding Dictates
Termination Properties
5’ Region of trp operon transcript
Riboswitches
• Riboswitches are structures in mRNA that
regulate gene expression
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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
Riboswitch Structures
• All known riboswitches fold into compact RNA secondary structures with a
base stem, a central multi-loop and several branching hairpins
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 threedimensional 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!
Riboswitch Mechanism II
Note the different secondary structures formed by
sequences 1 and 2. When base-paired they become
part of a transcription terminator structure!
Vitreschak et al., (2003). Riboswitches: the oldest mechanism for the regulation of gene expression? Trends Genet. 20,
44-50.
Gene Regulation
• Mostly performed at the transcription level
in bacteria such as E.coli
– IE John C’s lecture on gene regulation
• However it is possible to regulate at higher
levels
– Eg. Translation (RNA -> Protein)
– Eg. Post-translational modification (Protein ->
Active Protein)
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!
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
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
Controlling Ribosome Recruitment
through RBS Accessibility
Ligand
Ribosomes cannot get
recruited to mRNA
-> no translation
Ribosomes get
recruited (via RBS) to
mRNA
-> efficient translation