CMB2001/L05 Transcriptional Responses to Stress & Infection I Flashcards
What 3 factors are required for adaptation to environmental challenge?
Sensors
Signalling pathway
Effector
What is the common role of the NF-kB, p53 and HIF pathways?
Allow the cell/organism to respond to environmental threats
Give 3 roles of the NF-kB family of transcription factors.
Regulating inflammation
DNA damage
Cell death
Cell adhesion
Proliferation
What does the Rel Homology Domain of mammalian NF-kB encode?
DNA bin and dimerisation functions of NF-kB
What precursor proteins are p50 and p52 proteolytically processed from?
p105 and p100 respectively
What allows p100 and p105 to function as lkB-like inhibitors?
They contain ankyrin repeats in C-termini
Name 2 non-conserved transcriptional activation domains in NF-kB.
TA1/TA2
TAD
SD1
SDII
What form do NF-kB take to bind DNA?
Dimers
What is the function of E3 Ubiquitin ligase?
Facilitates attachment of ubiquitin chains to target protein
Describe the Ubiquitin-proteasome pathway of protein degradation. (6)
Ub conjugated to proteins for degradation by ATP-dependent process
5-Ub chain attached to substrate
Recognition by 26S proteasome
UB removed and protein linearised
Injected into proteasome core
Digested to peptides then amino acids by peptidases or used for antigen presentation
What can induce NF-kB? (3)
Inflammatory cytokines
Bacterial products
Viral proteins & infection
DNA-damage
Cell stress
Describe activation of NF-kB. (8)
Ligand binding
Activated IKK Kinase
IkB kinase complex
NF-kB in inactive cytoplasmic complex
IkB is phosphorylated
IkB is ubiquinated
IkB is proteolytically degraded
NF-kB translocates to nucleus
Give the 3 core subunits of the IkB complex.
IKKa
IKKB
IKKy (NEMO)
Give the 3 inhibitors of NF-kB.
IkBa
IkBB
Bcl-3
How are ikB proteins similar to p105 and p100? (3)
Contain ankyrin repeat motifs (ANK) in C termini
PEST
Domain rich in proline, glutamate, serine and threonine
Using NF-kB, give the sensor, signalling pathway and effector response of the body to an environmental challenge.
TNF receptor
IkB complex
NF-kB transcription factors
What 2 pathways can lead to activation of NF-kB?
Classical/ canonical pathway
Non-canonical (alternative) pathway
How are many NF-kB genes shared?
Between subunits
Which part of NF-kB dimer faces in the 3’ and 5’ direction?
5’ - p50
3’ - RelA
Describe the regulation of NF-kB function. (4)
Translocation to nucleus
Transcriptional repression, transcriptional activation, promoter targeting and selectivity
What is Swi/Snf?
ATP-dependent chromatin remodeller (can move/remove nucleosomes)
What is the role of the beta-interferon enhancer?
Regulates expression of the beta interferon gene, particularly in response to viral infections
What complex is formed by the beta-interferon enhancer and what is its purpose?
Enhanceosome
High affinity platform for recruitment of transcriptional coactivators like p300/CBP
Which complex works at the IFNB enhancer?
p50/RelA complex
Resulting from varying ability with other transcription factors and conformation adopted when binding IFNB kB element
Why are coactivators often required? (3)
Interaction interface (higher affinity than normal activators)
Weak interactions
Chromatin remodelling
Facilitating transcription initiation
Explain how NF-kB combines multiple levels of regulation to give transcriptional specificity.
Phosphorylation and degradation of IkB a, B or e
Translocation of NF-kB to nucleus
Modification of NF-kB subunits
DNA binding and gaining access to promoter/enhancer
Transactivation - interaction with the basal transcription complex and coactivators
Specific transcriptional response
How can NF-kB directly induce transcription after chromatin remodelling?
Helping to recruit the basal transcription machinery (BTM)
How many members of the NF-kB family form a range of homodimers and heterodimers?
5
What targets proteins for degradation by the proteasome?
Ubiquitination
Describe the inactive form of NF-kB complex.
Held in cytoplasm bound to inhibitory protein
What does phosphorylation of the p100 subunit lead to in the alternative pathway?
Processing to p52
Describe the first step of how NF-kB induces a transcriptional response.
Degradation of different IkB proteins, leading to activation of different NF-kB dimers
Why is activation of gene transcription compared to a combination lock?
Each number of the combination lock is a different TF, or specifically modified TF or chromatin remodelling factor
When all numbers are entered correctly, lock is opened (all TFs recruited to gene promoter/enhancer and transcription occurs)
