week 3 - global regulation Flashcards
local vs global regulation
- considered single operons
o lac operon
o trp operon - encode only a few genes
o all that is needed to a very specific purpose - respond to a simple signal (usually a small molecule)
- examples of local regulation
sometimes multiple genes are needed to change expression
o this enables e.g. e. coli to survive in many different environments
- shift from aerobic to anaerobic growth
- change in external pH
- osmotic shock DNA damage
- change in temperature
- change in level of available glucose
o glucose levels drop, cAMP levels rise (this activates CRP protein)
o CRP protein binds cAMP
o Can bind and activate many different operons (not just lac)
o CRP Is acting as a global regulator
Regulates many different operons
operon
- Set of genes, transcribed as a single mRNA
- Adjacent on DNA
regulon
- Set of genes and operons regulated by the same protein
- May be scattered across whole genome
Regulon example
LexA
- Genes of the LexA regulon are for repair of DNA damage
- All are normally repressed by LexA protein
Regulon example
LexA
what does it do
- Damaged DNA forms a complex with RecA proteins and activates it
o RecA: Binds single stranded RN, Changed shape, Now RecA binds to LexA - Activated RecA cleaves LexA
- Genes which are normally repressed by LexA are now expressed
- Genes of the LexA regulon are for repair of DNA damage
- All are normally repressed by LexA protein
Regulon example
LexA
What will happen to the LexA regulon if recA is deleted?
- Mutation recA strain cannot respond to UV radiation
The cell can’t mount an SOS response.
It becomes hypersensitive to DNA damage (e.g., UV light, certain antibiotics).
DNA damage will accumulate, potentially leading to cell death
GLOBAL REGULATION
How widespread?
- About 10% of genes in e. coli are regulators
- 50% of all genes in e coli are controlled directly or indirectly by one or more of seven global regulators
GLOBAL REGULATION
Why does it occur?
- Requires fewer regulators
o More efficient use of resources - Enables co-ordinated response to major changes in growth conditions
- Enables different combinations of key operons to be expressed under different conditions
GLOBAL REGULATION
How does it happen?
- Many mechanisms, but all have in common
o Something has to detect the signal or change in conditions
o This has to be linked somehow to altered gene expression
GLOBAL REGULATION
examples
aerobic/anaerobic switch
heat shock
GLOBAL REGULATION
Aerobic/anaerobic switch
- E coli can grow aerobically or anaerobically (facultative anaerobe)
- If switch to anaerobic growth need to:
o Repress expression of genes involved in aerobic pathways (e.g. TCA cycle, FA oxidation)
o Repress expression of genes involved in protection against oxygen and its biproducts
o Repress expression of expensive genes where proteins require large amounts of ATP
GLOBAL REGULATION
Aerobic/anaerobic switch
what is responsible for the switch
o ArcAB system is an example of a two-component system
sensor kinase senses changes in conditions
(autoposphorylates itself and passes phosphate onto a response regulator)
ArcB stimulated to become active by lactate, pryuvate, acetate. ArcA is then phosphorylated
represses a wide range of genes (TAC cycle; cirtrate synthase, operons involved in fatty acid oxidation)
also activates some genes
this represses aerobic respiration
GLOBAL REGULATION
Aerobic/anaerobic switch
What phenotype would you predict for an arc ArcA or arcB deletion?
- No repression of aerobic respiration
GLOBAL REGULATION
Aerobic/anaerobic switch
ArcB
Sensor kinase (membrane-bound) that detects low oxygen (reducing conditions)
GLOBAL REGULATION
Aerobic/anaerobic switch
ArcA
Response regulator (cytoplasmic); when phosphorylated, it represses or activates gene expression
GLOBAL REGULATION
Aerobic/anaerobic switch
Aerobic conditions
ArcB is inactive → no phosphorylation of ArcA.
ArcA remains unphosphorylated.
Genes for aerobic respiration stay on (e.g., TCA cycle, cytochrome oxidases).
Anaerobic genes are not repressed by ArcA.
GLOBAL REGULATION
Aerobic/anaerobic switch
anaerobic conditions
ArcB senses reducing conditions and autophosphorylates.
ArcB transfers the phosphate to ArcA → ArcA~P (phosphorylated form).
ArcA~P acts as a transcriptional regulator:
Represses genes for aerobic respiration (e.g., sdh, cyo).
Activates genes for anaerobic pathways (e.g., cyd, fermentation genes).
GLOBAL REGULATION
heat shock
- For e coli: going from 37 degrees to 43
o To do with folded protein structures (on the edge of stability) most organisms have evolved to grow at a restricted temperature range - Nearly all organisms show heat shock
o Temperature depends on their normal growth temperature - Major consequence of heat shock is that proteins begin to unfold and to aggregate
GLOBAL REGULATION
heat shock
genes of heat shock response
Assist proteins to refold (molecular chaperones)
Old unfolded proteins in stable, non-aggregating state until heat shock ends (molecular chaperones)
Degrade proteins that cannot be refolded (proteases)
GLOBAL REGULATION
heat shock
how is heat shock response regulated in e. coli
Do cells detect increase in temperature or presence of unfolded proteins
o Key feature: alteration of a component of RNA polymerase
GLOBAL REGULATION
heat shock
RNA polymerase composition
- Alpha2betabeta
o core enzyme contains enzymatic machinery for mRNA synthesis
change the RNA polymerase
o to recognise promoters and transcribe DNA, needs another factor
sigma factor
o e coli has several different sigma factors
GLOBAL REGULATION
heat shock
how are heat shock genes turned on
heat shock genes can be turned ON by increasing levels of sigma 32
GLOBAL REGULATION
heat shock
how is sigma 32 regulated
- post-transcriptionally
Heat shock causes more efficient translation of rpoH mRNA to make more sigma 32
- Sigma 32 can be regulated by its own RNA
- RNA’s Secondary structure keeps protein from being translated
- If increase temp break down the secondary structure
- Therefore more expression of Sigma 32
GLOBAL REGULATION
heat shock
how is sigma 32 regulated
- post-transcriptionally
regulation is..
cis
- The regulatory element in the mRNA regulates the downstream gene(s) and ONLY the downstream gene(s)
- How might you test whether a different gene is regulated by a similar mechanism
GLOBAL REGULATION
heat shock
how is sigma 32 regulated
- post-translationally
o Stability of sigma 32 is regulated by molecular chaperone DnaK and protease FtsH
It is unstable in conditions where it is not needed
GLOBAL REGULATION
heat shock
how is sigma 32 regulated
- post-translationally
UNDER NORMAL GROWTH CONDITIONS
very low levels of sigma32
DnaK: a molecular chaperone that helps proteins fold bound to sigma 32
DnaK delivers sigma 32 to FtsH (a protease) that degrades sigma 32
GLOBAL REGULATION
heat shock
how is sigma 32 regulated
- post-translationally
EXPOSED TO HEAT SHOCK
heat shock causes proteins to unfold and DnaK bind to them (to help them refold)
this competes with sigma 32
more free sigma 32
high levels of sigma 32, high transcription of heat shock genes
- Sigma 32 stable and can bind to RNA polymerase
- Get high levels of transcription
GLOBAL REGULATION
heat shock
how is heat shock regulated
- Cells detect both the increase in temp and presence of unfolded proteins
GLOBAL REGULATION
heat shock
how is heat shock regulated
- raised temp.
o Increases translatability of rpoH mRNA
More sigma 32 made
o Post transcriptional regulation
GLOBAL REGULATION
heat shock
how is heat shock regulated
increased unfolded protein
o Reduced DnaK binding to sigma 32
o Reduced degradation of sigma 32 by FtsH
o Post translational regulation
GLOBAL REGULATION
heat shock
predicted phenotypes of deletion mutations
- rpoH
no increase in sigma 32, no post-transcriptional regulation
Without σ32, the heat shock regulon cannot be activated. Consequently, heat shock proteins (like DnaK, GroEL, etc.) will not be expressed in response to temperature stress, making the strain highly sensitive to heat and other stresses that would normally activate the heat shock response.
the mutant would show increased sensitivity to heat shock and poor recovery from stress because heat shock proteins cannot be synthesized.
GLOBAL REGULATION
heat shock
predicted phenotypes of deletion mutations
FtsH
Increased sigma 32 (no degredation)
Normally, FtsH helps regulate σ32 levels by degrading excess σ32, ensuring that it doesn’t accumulate unnecessarily. In the absence of FtsH, σ32 levels would remain abnormally high, leading to excessive transcription of heat shock genes even under normal conditions.
The mutant would show elevated basal levels of heat shock proteins (due to increased σ32), which could lead to growth defects or stress response imbalances in non-stressful conditions. Under heat shock, it might show some overreaction to stress, leading to an inefficient stress response.
GLOBAL REGULATION
heat shock
predicted phenotypes of deletion mutations
DnaK
Increased sigma 32 (as reduced binding to sigma 32 so less competition)
Without DnaK, less σ32 would be bound, reducing competition for binding to RNA polymerase. This would result in an increase in free σ32 available for transcription activation, leading to increased transcription of heat shock genes.
The mutant would show increased levels of heat shock proteins (due to increased free σ32), similar to the FtsH deletion, but the mechanism is different. This could also lead to growth defects or an inefficient stress response.
what is global regulation
chatgpt
Global regulation refers to the coordinated control of multiple genes or operons across the genome by a single regulator or regulatory system. These genes may be involved in unrelated processes but are activated or repressed together in response to a shared environmental or internal signal.
🔹 Example: The LexA regulon, which controls DNA damage repair genes scattered across the chromosome.
🔹 Example: CRP, which regulates many catabolic operons in response to glucose availability.
why does global regulation occur
chatgpt
It allows bacteria to quickly adapt to major environmental changes (e.g., oxygen levels, temperature, nutrient availability).
It’s efficient: instead of regulating each gene individually, a single regulator can control many genes.
Ensures a coordinated physiological response, so related pathways are turned on or off together.
Saves resources by avoiding unnecessary gene expression.
🔹 Example: In oxygen-poor conditions, E. coli represses energy-expensive aerobic pathways and activates anaerobic ones via ArcAB.
how does global regulation occur
chatgpt
Global regulation typically involves:
Sensing a signal or environmental change.
Transducing that signal to a regulator protein.
Regulator acts (often a transcription factor or sigma factor) to alter transcription of multiple genes.
common mechanisms of global regulation
Two-component systems
chatgpt
A sensor kinase detects a signal and phosphorylates a response regulator
ArcB/ArcA (O₂ switch)
common mechanisms of global regulation
Sigma factor switching
chatgpt
Changing RNA polymerase’s sigma factor to recognize different promoters
σ32 (heat shock)
common mechanisms of global regulation
Allosteric activation
chatgpt
A small molecule activates a transcription factor
CRP-cAMP (glucose starvation)
common mechanisms of global regulation
Protein cleavage
chatgpt
Signal leads to cleavage of a repressor
LexA-RecA (DNA damage)
what makes a good global regulator
chatgpt
A global regulator is typically:
Responsive to a key environmental cue
Capable of binding multiple promoters
Often able to coordinate opposing pathways (turning one on, another off)
