Lecture 9 - Repressors and activators Flashcards
Describe the S+F of the DNA binding domain (DBD) in 1 component systems
- Conserved helix-turn-helix dimer
- Alpha helix binds inverted repeat in DNA = consensus/operator sequence
Describe the S+F of the effector binding domain (EBD) in 1 component systems
- Variable to bind ligands = change DBD conformation = where DBD binds DNA
- More EBDs if complex life
Describe how 1 component systems function
- Simple feedback loop = high substrate conc binds EBD = changes DBD to free promoter = transcription of pump gene to lower conc
What are the 2 types of functions of 1 component systems
- Specialised = recog 1
- Generalist = recog multiple related
How are both 1 and 2 component systems versatile despite having specific ligand binding domains?
1+ EBD linked to 1 DBD = 1 broad response to multiple related signals + more sensitive
Describe the S+F of the 3 domains of the histidine kinase (HK) in 2 component systems
- Periplasmic = sense ligand, activate by conformation change
- In PM = dimerises, conseved histidine for signal transduction
- Cytoplasmic = HK + ATP to phosphorylate histidine = signal transduction to RR
Describe the S+F of the 2 domains in the response regulator of 2 component systems
- DBD
- EBD with conserved aspartate to receive phosphate from HK
Describe the 4 steps to transcription initiation
- Sigma factor binds promoter = closed RNAP
- Sigma factor separates dsDNA = open RNAP
- mRNA initiation
- Sigma factor dissociates = elongation
Describe the 4 ways 1 component systems interact with RNAP as activators of transcription
- Class 1 = bind far upstream of promoter, interact with alpha domain = closed RNAP = better binding
- Class 2 = bind close upstream of promoter, enhance dsDNA melting = open RNAP = more initiation
- Conformational change = activator binds -10 -35 spacer = higher sigma factor affinity = better RNAP binding
- Activate sigma54 promoters = bend DNA = closed RNAP -> sigma factor conformational change = open RNAP = better elongation
How do 1 component systems derepress transcription?
DBD-EBD as repressor then either no/ligand means derepression
Describe the 4 ways 1 component systems repress transcription
- Steric hindrance = bind promoter = block sigma factor
- Roadblock = bind +1 site = stop initiation
- Deformation = bind to form loop = blocks RNAP
- Anti-activation = prevent dsDNA separation and bind RNAP alpha subunit = block closed-open RNAP and sigma factor not released
Describe E coli’s 2 component systems that enables it to switch to a human pathogen?
- PmrA (RR) and PmrB (HK) responding to high Fe in humans
- PmrA phosphorylated = activator for transferases AnT and EptA = add arabinose and phosphoethanolamine to lipid A = -ve to +ve = defensins can’t bind and lyse
What are the components involved in E. coli’s conserved stress response?
- DnaK/DnaJ/GrpE or GroEs/L systems for protein folding
- RpoH and E gene regulation for misfolded proteins
Describe E. coli in terms of habitat, genome size, and no. of component systems and no. of sigma factors
- Habitat = environ/human gut epithelia
- Genome size = 4 Mb
- 230x 1 component, 30x 2 component, 7 sigma factors
Describe N. gonorrhoeae in terms of habitat, genome size, and no. of component systems and no. of sigma factors
- Habitat = obligate human genital pathogen
- Genome size = 2 Mb
- 30x 1 component, 3x 2 component, 3 sigma factors
Compare E. coli and N. gonorrhoeae in terms of no. of RpoH regulated genes. Why is there a difference?
- E coli has 30 vs N gonorrhoeae has 12
- Conserved stress regulator but E coli has changing environment vs N gonorrhoeae has stable
