The NF-kB pathway Flashcards
which pathway alls the cell/organism to respond to environmental threats
NF-kB, p53 and HIF
what are the environmental changes that sets off the p53, NF-kB and HIF pathway
DNA damage, Infection, Hypoxia and physical stress
what pathway is set off by p53
DNA damage
what pathway is set off by NF-kB
Infection
what pathway is set off by HIF
Hypoxia
what are the cellular responses to these pathways
Gene expression, repair, programmed death and immune response
what is NF-kB
Nuclear factor of the kappa immunoglobulin light chain in B cells
what is the function Rel homology Domain (RHD)
encodes the DNA binding and dimerisation functions of NF-kB
what are the proteins proteolytically processed from the precursors p105 and p100
p50 and p52
T/F p105 is inducibly activated into p50
false it is generally constitutive where as p100 is inducible
NF-kB needs to _ to bind to DNA
dimerise
how can p100 and p105 function as a IkB-like inhibitor
contain ankyrin repeats in their C-termini
what are the non conserved transcriptional activation domain
TA1/TA2, TAD, SD1, SDII
what is a E3 ubiquitin ligase
a protein that facilitates the attachment of ubiquitin chains to a target protein
what is ubiquination
Ub is conjugated to proteins that are destined for degradation by an ATP-dependent process that involves three enzymes
how is a protein ubiquiniation started
- a chain of 5 Ub molecules attached to the protein substrate is sufficient for the complex to be recognised by the 26S proteasome
when 26S proteasome attaches to the protein, what happens next
after ATP dependent reactions occurs, Ub is removed and the protein is linearised and injected into the central core of the proteasome where it is digested to peptide
what happens to digested proteins after degradation from Ub
The peptides are degraded to amino acids by peptidases in the cytoplasm or used in antigen presentation
NF-kB is induced by
Inflammatory cytokines,
Bacterial products,
Viral proteins & infection, DNA-damage, Cell Stress
NF-kB regulates
The immune and inflammatory responses, Stress responses, Cell survival and cell death, Cell adhesion, Proliferation
how are they induced and how do they regulate all these things
This is accomplished through the
regulation of 100’s (possibly 1000’s) of NF-
κB gene targets - but not all at the same
time, in the same way in all cell types
what are the specific stimuli which binds to the ligand receptors on the cell
ionising radiation, cytokines - inflammatory cytokines tumour necrosis factor a (TNFa) and interleukin 1 (IL-1), growth factors, bacterial lipopolysaccharide (LPS) and hypoxia
when not induced, what is NF-kB form in the cell
in-active cytoplasmic complex, bound to its inhibitor protein IkB
upon cellular stimulation, IkB becomes _
phosphorylated which in most cases results in its ubiquinitnation and degradation from 26S proteasome.
where does NF-kB translocate to after freeing
nucleus
what are the 3 core subunits of the IkB (IKK) complex
IKKa and IKKB and the IKKy (NEMO)
what are the catalytic subunits and which is the regulatory subunit
IKKa and IKKB = catalytic
NEMO = regulatory
both IKKa and IKKB have a _ domain with _
kinase, with an activation loop
NEMO contains CC1 and CC2 which stand for
coiled coil regions 1 and 2
what is the similarities between p105+p100 and IkB
they contain ankyrin repeat motifs in their C termini and PEST domain (rich proline, glutamate, serine and threonine)
what are the two NF-kB activation pathways
Canonical classical pathway and non-canonical (alternative) pathway
which p protein is associated which the classical and which is linked to the alternative
p50 is linked to the classical and p52 is linked to the alternative
how does the alternative pathway occur
NIK causes a dimer of IKKa to remove P100 Ankyrin repeats which causes p52 version of NF-kB to localise to the nucleus
NF-kB/IKK regulates many target genes associated both with normal responses to infection and stress as we as with human diseases (cancer, inflammation etc)
Inflammation, proliferation, survival, angiogenesis, Tumor promotion & metastasis, Cell death & anti-proliferative effects
What is a danger with NF-kB
when control is lost of them, they become nuclear - causing cancer, arthritis, AIDS, Asthma, Diabetes and atherosclerosis
interaction with proteins can be determined by _
orientation
how does diversity and dimerisation affect NF-kB function
- NF-kB family is multi-gene which when two proteins dimerise allows the formation of many different types with different properties/function
hows does NF-kB target different genes
different subunits have subtly different DNA binding specificity, however many NF-kB target genes are shared between subunits
When NF-kB translocates into nucleus, what can happen?
- Kinases, Acetylases and phosphatases can act on NF-kB
- NF-kB can bind to DNA for either, transcriptional repression, activation as well as promoter targeting and selectivity
when NF-kB binds to DNA relating to transcription repression what binds to RelA-TAD subunit
Co-repressor
when NF-kB binds to DNA relating to transcription activation what binds to RelA-TAD subunit
Co-activator
when NF-kB binds to DNA relating to promoter targeting and selectivity, what binds to RelA-RHD
heterologous transcription factors and DNA binding proteins
How can chromatin be remodelled around NF-kB dependent genes
NF-kB can recruit chromatin remodellers
or can rely on other proteins to do this
-HATs and Swi/Snf
P65 =
RelA
what is a beta interferon
a and b interferon (IFN) are produced from viral infection as well as other subsets of genes
What does the expression of a and B interferon cause, as well as why does it need to be controlled
- a and B interferon bind specific cell surface receptors which results in a signalling cascade leading to the activation of over 50 anti-viral genes.
- Needs to be controlled as viral response needs to be activated when infected, not in response to other immunological challenge
what happens if the individual txn factor binding sites in the B IFN enhancer was exploited and multimerised,
they can act as a viral inducible promoter, however they have varying basal levels of activity and can respond to other inducers
what allows the Beta-interferon enhancers to perform its function
- key is the combination and organisation of the enhancer
-spacing and orientation allows appropriate protein:protein contact
The transcription factors binding the B IFN enhancer all interact to form the _
enhanceosome complex
This complex forms a I_ I_ which allows _
- interaction interface
- allow the high affinity recruitment of transcriptional coactivators such as p300/CBP (these proteins can bind more than one transcription factor at one time
Individual transcription factor:coactivator interactions can be described as
generally weak
Instead of Individual
transcription factor: coactivator interactions what is favoured
the formation of coactivator complexes only at the promoters and enhancers
what is created and what is required in coactivator complexes only at the promoter and enhancers
created = appropriate interaction interface
required = coactivator activity
Which NF-kB complex works at the B IFN enhancer
p50/RelA(p65)
After chromatin remodelling NF-kB can directly induce transcription by helping to recruit what ?
Basal transcription machinery
