The endogenous pathway of antigen processing and presentation

In this article, I briefly explain the endogenous pathway of antigen processing and presentation.

Table of Contents

The pathways for elimination of pathogens

The immune system applies different strategies to eliminate various pathogens out of our body. There are two pathways for eliminating extracellular and intracellular pathogens. Antigens generated within the cell are known as endogenous antigens are eliminated by the endogenous pathway. The exogenous pathway helps to eliminate exogenous antigens. The endogenous or intracellular antigens are processed by the cytosolic or endogenous pathway. After processing, the antigens are presented on the cell membrane with MHC class-I molecules.

In the endogenous pathway, cytosolic antigens are degraded by the proteasome, a cytosolic proteolytic system present in all cells. Thus, proteins are broken down into smaller peptides. Many proteins are ready for proteolysis with the attachment of a small protein called ubiquitin.

The conjugates of ubiquitin-protein get an entry into the proteasome complex. The cleaving of peptide bonds by the proteasome complex is an ATP dependent process. Within the central core of the proteasome, the degradation of ubiquitin-protein complexes is thought to occur.

The large proteasome and the immunoproteasome

The large (20S) proteasome, which is the standard proteasome present in all cells, is composed of multiple α and β subunits arranged in concentric rings. The top and bottom rings are made up of the α subunits, while the β subunits make the two middle rings.

Our immune system specifically produces small peptides optimized for binding to MHC class I molecules. Professional antigen-presenting cells along with some infected cells, contain a distinct proteasome of the same size as the standard 20S proteasome known as immunoproteasome. The immunoproteasome has the same structure as the standard 20S proteasome except for some unique subunit substitutions.

These unique subunits are not constitutively expressed like the other components of the proteasome. However, when exposed to certain cytokines, like IFN-γ or Tumor necrosis factor (TNF), the subunits can be induced.

Replacement catalytic protein subunits, encoded by LMP2 and LMP7 genes located within the class-II MHC region, convert standard proteasomes into immunoproteasomes. Thus, it increases the efficiency with which cytosolic proteins are degraded into peptide fragments that bind specifically to class-I MHC molecules.

Transportation of peptides from cytosol to rough endoplasmic reticulum

The proteasome degrades proteins into peptides in the cytosol, which are translocated to the rough endoplasmic reticulum by a transporter protein TAP (transporter associated with antigen processing) with the requirement of hydrolysis of ATP.

The peptides with 8-16 amino acids are favored by TAP. The transporter protein TAP is a heterodimer transmembrane protein in the rough endoplasmic reticulum. The TAP consists of two proteins, TAP1 and TAP2.

The TAP 1 and TAP2 proteins have transmembrane segments. Each protein possesses a domain projecting into the lumen of the rough endoplasmic reticulum and cytosol projecting ATP binding domain.

The TAP has an affinity for peptides with hydrophobic or basic carboxyl-terminal amino acids, the anchored residues for MHC class-I molecules. Thus, the TAP transports peptides that interact with MHC class-I molecules.

Chaperones assist peptide association with MHC class-I molecules

Chaperones are proteins that aid in conformational folding or unfolding of large proteins. There are many classes of molecular chaperones which assist large proteins in proper folding during protein synthesis.

Loading and processing of peptide fragments is assisted by chaperone proteins and proteases in the rough endoplasmic reticulum. Ribosomes on the rough endoplasmic reticulum synthesize the α chain and β₂ microglobulin components of the class-I MHC molecule.

Calnexin- the first molecular chaperone in class-I MHC assembly

A resident membrane protein of the endoplasmic reticulum, calnexin is the first molecular chaperone involved in the class-I MHC assembly. Calnexin with ERp57, a protein with enzymatic activity, is associated with the class-I MHC α chain and aids in its folding.

The binding of β₂ microglobulin with the α chain causes the release of the chaperone calnexin. This causes the association of class-I-ERp57 with the chaperones, i.e., calreticulin and tapasin.

The TAP-associated protein

Tapasin is the TAP-associated protein that brings the TAP transporter close to the class-I MHC molecule. Before the peptides are open to the luminal environment of the rough endoplasmic reticulum, the class-I MHC molecule captures the peptide. This is promoted by the TAP protein.

The tapasin-related protein TAPBPR binds the class-I MHC molecules much like tapasin. The over-expression of TAPBPR leads to a decrease in class-I MHC surface expression, unlike the over-expression of tapasin, which causes an increase in class-I MHC surface expression.

Some peptides of the endoplasmic reticulum can not bind efficiently to the class-I MHC molecules because of their long length. Thus, the exoproteases can act on these peptides. The amino-terminal residue from peptides is removed by ERAP1, an endoplasmic reticulum aminopeptidase to get optimum class I binding size.

Due to the productive peptide binding, the class-I MHC shows increased stability. The increased stability makes them dissociate from the peptide-loading complex (calreticulin, tapasin, and ERp57). The class-I MHC molecule then gets an exit from the rough endoplasmic reticulum. Then, they enter into the Golgi complex and exocytic vesicles, finally heading towards the cell surface.

Conclusion

The two types of pathways, the endogenous pathway and the exogenous pathway are used for processing and presenting the antigen. The endogenous pathway of antigen processing and presentation is used to eliminate endogenous antigens. The exogenous pathway is used to eliminate the exogenous antigens.

In the endogenous pathway, cytosolic antigens are degraded by the proteasome, a cytosolic proteolytic system present in all cells. The proteasome degrades proteins into peptides in the cytosol which are translocated to rough endoplasmic reticulum by a transporter protein, TAP (transporter associated with antigen processing) with the requirement of hydrolysis of ATP.

Chaperones are the proteins that aid in conformational folding or unfolding of large proteins. Calnexin, a resident membrane protein of the endoplasmic reticulum, is the first molecular chaperone involved in class-I MHC assembly. Tapasin, the TAP-associated protein brings the TAP transporter close to the class -I MHC molecule.