Antigen Processing and Presentation Lecture: Part Two - Endogenous Pathway

This pathway is utilized by all nucleated cells to present self peptides and to alert the immune system that everything is functioning normally.
The endogenous antigen processing pathway primarily presents antigens to CD8 T cells via MHC Class I molecules.

When a virus infects a nucleated cell:
- It hijacks the host cell's protein synthesis machinery to produce viral proteins.
- Viral proteins can have a half-life of up to 12 hours.
Early detection of viral peptides on MHC Class I can occur as early as 3 to 5 hours post-infection.
Proteins synthesized in the endoplasmic reticulum are not directly accessible to the proteasome for degradation initially.

Defective Ribosomal Products (DRiPs):
- Misfolded, nonfunctional, and partially translated proteins formed during protein synthesis due to inefficiency.
- DRiPs accumulate rapidly in the cytosol after viral infection, providing a source of early peptides for MHC Class I presentation.

To target proteins for degradation, they need a barcode known as ubiquitin, added through ubiquitination:
- Facilitated by a family of enzymes called ubiquitin ligases.
- Ubiquitin Ligase E3: Recognizes and binds to defective proteins, recruiting E2 ligase, which brings a ubiquitin molecule.
- Ubiquitin molecules are transferred to the target protein and repeated until a polyubiquitin tail is formed.

The proteasome is a cytosolic structure resembling a doughnut, comprising stacked ring structures forming a cylindrical channel.
- Cap Structure: Recognizes ubiquitinated proteins and feeds them into the inner channel as linear protein chains.
Catalytic Core: Composed of heptameric rings, specifically:
- Beta Subunits: Beta 1, Beta 2, and Beta 5 are responsible for proteolysis, breaking down proteins into peptide fragments.
Main Role: Recycling unneeded proteins into individual amino acids rather than specifically generating peptides for MHC Class I.
Many peptide fragments generated are further degraded by amino peptidases into single amino acids.
A notable proportion of peptide fragments survive degradation and are transported to the endoplasmic reticulum.

Proteasome cleaves proteins, preferentially at hydrophobic residues, generating peptide fragments mainly at the C-terminus.
Aminopeptidases in the cytosol further trim peptide fragments from the N-terminus, creating varied peptides, allowing about 1% to survive and be transported into the ER.
TAP (Transporter Associated with Antigen Processing): Facilitates peptide entry from cytosol to ER, preferentially allowing peptides of length 9 to 12 amino acids while hydrolyzing ATP to enable transport.

MHC Class I heavy chain and beta-2 microglobulin are synthesized in the ER but do not associate until peptide loading occurs.
The heavy chain is supported by the chaperone protein calnexin until peptide loading.
Upon loading:
- The heavy chain forms a peptide loading complex with:
- Calreticulin: Stabilizes MHC Class I during peptide loading.
- Tapasin: Brings MHC Class I into proximity with TAP.
- ERp57: A thiol reductase; breaks and reforms disulfide bonds.
ERAP (Endoplasmic Reticulum Aminopeptidase): Further processes peptides before loading onto MHC, crucially impacts immunogenicity by optimizing peptides for immune response.
Once peptides bind to the MHC Class I cleft, the stable MHC-peptide complex can be transported via the Golgi in an exocytic vesicle to the cell surface for presentation to CD8 T cells.

Virus hijacks host cell's machinery, producing viral proteins.
DRiPs accumulate as potential early peptide sources.
Ubiquitin tags defective proteins for degradation in the proteasome.
The immunoproteasome, enhanced by interferon-gamma, generates suitable peptides for MHC Class I.
Peptides are transported from the cytosol to the ER via TAP.
MHC Class I molecules are formed, loaded with peptides, and presented on cell surface to activate CD8 T cells.

Join the next part of the lecture covering exogenous antigen processing and presentation on MHC Class II.