Week 13 Flashcards
Why do Bmems exit the GC reaction before PCs?
This allows the Bmems to be slightly less mutated so that they may retain more plasticity for related (or further mutated) subsequent infections.
What transcription factors are expressed by PCs?
IRF4, Blimp-1
What transcription factor is expressed by Bmems?
Bach2
What is the order of mouse heavy chain loci?
Cu, Cd, Cg3, Cg1, Cg2b, Cg2a, Ce, Ca
What is the only conserved element between switch region DNA sequences?
The ‘top’ strand is always G-rich
What is AID structurally related to?
APOBEC1, which catalyzes C-> U deamination in the RNA transcript for Apolipoprotein B (a fat emulsifying protein)
What is K0 for antibodies?
The average affinity of an. antibody in serum.
What positions GCs in the Dark zone?
CXCR4
What is the light zone marker for GC B cells?
CD83
What are the general functions of the DZ and the LZ in GCs?
DZ divides and mutates, LZ selects
What is one of the ‘most important contributions of the mathematical modeling crowd” to immunology?
They proposed that ti would be impossible for GC cells to simply mutate and proliferate in the DZ and head to the LZ. They showed with models that GCs would have to re-enter the DZ after selection for a useful antibody maturation to occur.
What is the net flow of cells in a GC reaction?
There is a net flow from the dark to the light zone.
Why do B cells undergo apoptosis in the dark zone?
Because they put a stop codon or had a frameshift mutation in their BCR and no longer have a functional BCR.
CD59
Complement inhibitory receptor that prevents the formation of MAC attack complex
Function of IFNg produced by Th1 cells
Enhance antigen presentation and facilitate bactericidal functions of macrophages.
What are the two STATs for Th1 and Th2 and to what signature cytokine genes do each bind?
Th1 - STAT4 - ifng
Th2 - STAT6 - il4
EBI2
Also known as GPR183, it is a receptor for 7a,25-dihydroxycholesterol and positions B cells within the B cell follicle into inner and outer zones
Cathelicidin
antimicrobial peptide existing as a propeptides stored in secondary granules of neutrophils. Upon fusion with a phagosome, it is cleaved by neutrophil elastase stored in primary grnaules. The carboxy terminal is amphipathic and disrupts membranes.
What does the thioester bond of C3 react with when available?
Hydroxyl or amino groups
Factor D
Present in plasma and is able to cleave Factor B when Factor B is bound to C3b, creating C3bBb. One of the only constitutively active enzymes in the complement cascade, but can only recognize C3b bound to Factor B.
CD55
Also known as Decay-Accelerating Factor (DAF). Competes with Factor B for binding to C3b on cell surface and can displace Bb from a convertase that has already formed.
Factor I
Cleaves C3b to an inactive form iC3b, in conjunction with membrane cofactor of proteolysis (MCP/CD46).
CD35
Also known as complement receptor 1. Inhibits C3 convertase formation and promotes catabolism of C3b to inactive products.
Factor H
Another complement inhibitory protein that competes with Factor B for binding to C3b, but also acts as a cofactor for Factor I. Binds preferentially to C3b on vertebrate cells as it has an affinity for sialic acids.
C5 convertases of the classical/lectin pathway and the alternative pathway of complement
classical/lectin - C4b2a3b
alternative - (C3b)2Bb
What do C3a and C5a induce ?
Contrqaction of smooth muscle, vascular permeability, upregulation of qadhesion molecules on endothelium, activation of mast cells leading to TNF and histamine production.
UNG
uracil DNA glycosylase that recognizes uracils created by AID in the DNA
MutSa
heterodimer enzyme of MSH2 and MSH6 enzymes that recognizes U:G mispairing
Which polymerase does AID associate with?
RNA polymerase II complex
What transcriptional process is thought to allow for AID function once it is assocaited with the polymerase?
Transcriptionall stalling, which allows for AID to have the time needed to exert its enzymatic function.
What is AID activated by, andto what does it bind after phosphorylation?
AID is phosphorylated by protein Kinase A (PKA), and subsequently binds to replication protein A (RPA).
topoisomerase I
Releases strain in unwound DNA for transcription - inhibited by camptothecin
How is AID activity controlled for CSR?
Each switch region contains a specific promoter/enhancer element that only drives transcription and thereby AID recruitment under the appropriate cytokine environment.
Where is AID phosphorylated by PKA?
On serine 38. Overexpressing PKA enhances CSR and SHM, while mutating S38 in AID greatly reduces btoh.
What recognizes uracil lesions made by AID?
Either nuclear isoform of UNG or MutSa
What are the enzymes involved in typical DNA uracil removal?
removal of uracil by UNG, incision at the abasic site by APE1, processing of the abasic sites by DNA polymerase Beta, followed by sealing of the final nick by DNA ligase 3.
Which DNA polymerases are likely involved in CSR and SHM, leading to mutations?
DNA polymerase η and REV1
MOlecules involved in NHEJ
DNAPKcs, Ku70/80, Artemis, Cerunnos, XRCC4/Ligase IV
Transition vs Transversion mutations
Transition is the substitution of a purine from another purine base or pyrimidine from another pyrimidine ( (C ↔T or A↔ G). Transversion is the substitution of a purine from a pyrimidine or pyrimidine from a purine.
Which repair mechanism is A:T biased?
MSH2/6
Role of gamma/delta T cells in repairing keratinocytes
produce IGF1, keratinocyte growth factor (KGF) and KGF2, at the wound edge, which all facilitate keratinocyte proliferation and timely wound closure
Four important properties of PAMPs
1) Produced only by pathogens and not host (self:non-self discrimination)
2) Represent conserved molecular patterns essential for survival f the pathogen
3) Shared by large groups of microbes
4) Represent a microbial class
How do MAL, MyD88 and TLR4 all interact?
Through TIR domains. MAL assocaites with cell membrane by binding to PIP2
Sorting adaptors
MyD88 - TIRAP (MAL)
TRIF - TRAM
Transcription factors generally activated by C-type lectin receptor signaling
AP-1, NFAT, NFkB.
Characteristic domain s of NLR
NLRs are characterized by the combined presence of a NACHT domain and a variable number of LRRs. Most NLRs further contain either a CARD or PYD motif in their amino-terminus
Three steps of NLRP3 activation
1) Potassium influx induces chaperones that keep NLRP3 in an inactive state
2) NLRP3 forms oligomers with ASC causing proteolytic cleavage of pro-caspase 1
3) Caspase 1 releases mature inflammatory cytokines such as IL-1 nd IL-18 from their proproteins
factor H binding protein (fHbp)
produced by neisseria meningitidis; recruits factor H to the bacterial membrane to inactivate complement.
PorA
produced by neisseria meningitidis; recruits C4-binding protein to the bacterial membrane to inactivate complement.
Staphylcoccal protein A
(Spa) Binds to the Fc portion of Igs and interferes with the recruitment and activation of C1 protein. Used to purify IgG.
staphylokinase
Produced by staphylococcus aureus and cleaves bound antibodies, thereby preventing pahgocytosis
CD21
Complement receptor that is expressed on B cells, binds to CD3dg and augments antibody responses when ligated.
Dectin-1 ligand
B-1,3 linked glucans (polymers of glucose) expressed by fungal cells
fMet-Leu-Phe (fMLF) receptor
Recognizes N-formylmethionine residues on bacterial peptides. Ligation promotes chemotaxis towards the source and production of ROS in the phagolysosome.
Two chemotactic G-protein-coupled receptors for monocytes and neutrophils
fMET-Leu-Phe receptor and C5a receptor
heterotrimeric G proteins
intracellulat GTP-binding proteins downstream of GPCRs.
Two MyD88 domains
TIR domain and death domain (DD)
What does the death domain interact with and activate in MyD88?
Two serine threonine kinases - IRAK4 and IRAK-1, which form a signaling complex
What does the IRAK complex recruit after MyD88 activation?
TRAF6, UBC13, Uve1A
what does NOD stand for in NOD-like receptors?
nucleotide-binding domain
What does CARD stand for?
Caspase recruitment domain
What does ‘caspase’ mean?
cysteine-aspartic acid protease
Proteins with TIR domains
MyD88, MAL, TRIF, TRAM, all TLRs
PRoteins with CARD domains
Caspase 1, RIP2, RIG-1, MDA5, MAVs, NODS, NLRC4/p1, ASC
PRoteines with pyrin domains
AIM2, ASC, NLRP1-14
Difference between NLRPs and NLRCs
NLRPs have a PYRIN domain, and NLRCs have a CARD domain
ASC
Adaptor protein for NLRP3 (and others) that has a carboxy-terminal CARD and an amino-terminal PYRIN domain and links NLRP3 to caspase 1
HDAC6
dynein adaptor histone deacetylase 6. Required for inflammasome formation at the MTOC of cells in NLRP3- and pyrin-mediated inflammasome, by retrograde transport of NLRP3 to aggresome
domains of canonical inflammasomes
upstream sensor, adaptor, and downstream caspase-1
non-canonical inflammasomes
caspase 4/5 (humans) caspase 11 (mice)
Activation and downstream mediators of NLRP3
Activated by diverse stimuli (bacterial pore forming toxins, EC ATP, monosodium urate (MSU) crystals, alum, silica) that increase potassium efflux. Recruits ASC, which recruits caspase-1, which autoprocesses and makes the inflammasome.
Activation and downstream mediators of NLRC4
forms inflammasome with or without ASC upon complex formation with NAIP, directly senses bacterial flagellin or TIIISS.
Where do NLRP3 and pyrin inflammasomes form (but not AIM2)?
The inflammasome puncta perinuclear and associating with the MTOC.
What have been shown to be essential for the localization of the NLRP3 inflammasome?
the dynein-microtubule pathway and the HDAC6.
Which domain of HDAC6 is required for the inflammasome formation of NLRP3?
THe uqibuitin-binding domain, but not the deacetylase domain
How was it shown that NLRP3 inflammasome formation is mediated by autophagy?
The colocalization of the inflammasome and the aggresome, and the accumulation of autophagosomal markers around the inflammasome.
Which inflammasomes form at the MTOC?
NLRP3 and pyrin
Which inflammasomes do NOT form at the MTOC?
AIM2 and NLRC4.
APOL3
IFNg-stimulated potent antimicrobial capable of killing intracytosolic bacteria and produed in epithelial cells.
minD
a bacterial cell division protein that loses its lateral membrane oscillatory behavior when IM potential is perturbed
GBP1
IFNg-inducible GTPase that disrupts the outer membrane of cytosolic bacteria so that APOL3 can disrupt the inner membrane.
How does APOL3 discriminate and permea- bilize bacterial membranes?
APOL3 targets anionic lipids that are highly enriched in bacterial membranes (35). In contrast, cho- lesterol, which is present exclusively in eukary- otic membranes, inhibits APOL3 membranolytic activity.
