Lecture 15 - Linking Innate & Adaptive Immunity (Antigen Processing)

Question 1

True or False?:

MHCI antigen presentation requires cytosolic or endogenous processing while MHCII presentation requires exogenous processing.

Answer 1

True

Question 2

Where are cytosolic pathogens degraded, what do peptides bind to, what are they presented to, and what is the effect on the presenting cell?

Answer 2

Cytosolic pathogens are degraded in the cytosol. The peptides bind to MHCI and are presented to CD8+ T-cells. This causes the presenting cell to undergo cell death.

Question 3

Where are intravesicular pathogens degraded, what do peptides bind to, what are they presented to, and what is the effect on the presenting cell?

Answer 3

Intravesicular pathogens are degraded in endocytic vesicles via low pH conditions. The peptides bind to MHCII and are presented to CD4+ T-cells. This activates the killing of intravesicular bacteria and parasites.

Question 4

Where are extracellular pathogens and toxins degraded, what do peptides bind to, what are they presented to, and what is the effect on the presenting cell?

Answer 4

Extracellular pathogens and toxins are degraded in endocytic vesicles via low pH. The peptides bind to MHCII and are presented to CD4+ T-cells. This activates B-cells to secrete Ig to eliminate extracellular bacteria/toxins.

Question 5

How are proteins prepared in the endogenous antigen processing pathway?

Answer 5

Proteins are tagged via ubiquitin and fed into proteasomes where they are broken down into peptides.

Question 6

What does TAP do?

Answer 6

TAP delivers peptides from the cytosol to the endoplasmic reticulum.

Question 7

Where are peptides loaded onto MHCI?

Answer 7

ER

Question 8

What are partly folded MHCI α chains held in place by?

Answer 8

Calnexin (A Chaperone)

Question 9

What triggers the release of MCHI from calnexin?

Answer 9

MHCI is released from calnexin when the β₂-microglobulin binds.

Question 10

What does tapasin in the endogenous antigen processing pathway do?

Answer 10

Tapasin binds partly folded MHCI (along with additional chaperones) to TAP.

Question 11

When is the folding of MHCI complete?

Answer 11

The folding of MHCI is complete when the peptide binds to the peptide binding groove.

Question 12

When is MHCI released from TAP? What does it do once released?

Answer 12

MHCI is released from TAP upon binding its peptide. The pMHCI is targeted to the cell membrane.

Question 13

How would you briefly describe the endogenous antigen processing pathway?

Answer 13

In the ER, MHCI α subunits are bound to calnexin and released upon β₂ binding. They bind to TAP and other chaperones in a partially folded state. Meanwhile, cytosolic proteins are ubiquinitied and broken down into peptide fragments by a proteasome. These fragments are passed into the ER by TAP and bind to MHCI. The pMHCI is released from TAP and targeted to the cell membrane.

Question 14

You are a scientist studying macrophage biology. You generated a mutant macrophage cell line that is unable to present antigen to CD8+ T-cells. Your experimental data fails to detect MHC molecules in proximity to TAP. What defect could explain this finding?

Answer 14

This could be explained by a defect in tapasin that stops it from interacting with TAP or the partially folded MHCI. (Note: I think Claire gave another possible answer for this in class but I couldn’t make it out over her laughing at her kids watching videos in the front.)

Question 15

How are peptides generated in the exogenous antigen processing pathway?

Answer 15

Peptides are generated from internalized antigens in endocytic vesicles. The particles are taken in by endosomes that fuse with lysosomes where they are degraded.

Question 16

How are endosomal proteases activated to break down proteins in the exogenous antigen processing pathway?

Answer 16

The proteases are activated by the acidification of the protein-containing vesicles.

Question 17

Where are MHCII produced?

Answer 17

MHCII is formed in the ER.

Question 18

What does the invariant chain (Ii) do?

Answer 18

The invariant chain binds to the peptide groove of MHCII. It guids transport of MHCII molecules to endocytic vesicles and prevents peptides from binding to the groove too early in the ER. It also uses sorting signals in its cytoplasmic tail to direct MHCII-containing vesicles to peptide-containing endocytic compartments.

Question 19

In what way is Ii cleaved? What does this result in?

Answer 19

Ii is initially cleaved to leave a fragment bound to the MHCIi and to the membrane. It is later cleaved to leave just a short peptide fragment in the peptide binding groove called a CLIP (Class II-Associated Invariant Chain).

Question 20

How and when is CLIP released from MHCII?

Answer 20

CLIP is released upon HLA-DM binding MHCII. This happens when MHCII is in an acidified endosome containing pathogenic peptides.

Question 21

What happens when MHCII bind peptide?

Answer 21

It is targeted to the cell surface.

Question 22

Where do peptides come from in the endogenous and exogenous antigen processing pathways?

Answer 22

Endogenous - They come from inside the cell (viruses, nuclear-encoded antigen).

Exogenous - They come from outside the cell (bacterial toxins, phagocytosed bacteria).

Question 23

What processes antigen in the endogenous and exogenous antigen processing pathways?

Answer 23

Endogenous - They are processed by a proteasome.

Exogenous - They are processed by proteases in acidified vesicles.

Question 24

What molecules help load peptide onto MHC in the endogenous and exogenous antigen processing pathways?

Answer 24

Endogenous - TAP loads the peptides (in the cytosol) onto MHC (in the ER).

Exogenous - HLA-DM loads the peptides onto MHC (while removing the CLIP).

Question 25

Which molecules chaperones are involved with the endogenous and exogenous antigen processing pathways?

Answer 25

Endogenous - Calnexin, Tapasin

Exogenous - Invariant Chain (Ii)

Question 26

What is the loading compartment in the endogenous and exogenous antigen processing pathways?

Answer 26

Endogenous - Endoplasmic Reticulum

Exogenous - MHCII Loading Compartment