Basics of protein degradation

There are two major, fundamentally different mechanisms by which animal cells degrade
proteins: the lysosome and the proteasome.
Both of these are thought to be involved in the degradation of PrP.

Lysosome
The lysosome is a membrane-bound intracellular compartment full of nonspecific proteases
that will cleave into individual amino acids any protein they come into contact with. Proton
pumps fill the lysosome with H+ from the cytosol, making it acidic (pH 4.8) — the proteases
function optimally at this pH and not at all at cytosolic pH (7.2), thus minimizing the risk to
the cell in the event of lysosome rupture. The lysosome is formed by budding off from a
compartment of the late Golgi – it represents an alternate endpoint for some proteins in the
secretory pathway that neither stay in the ER or Golgi nor undergo exocytosis to the cell
surface.
Proteins destined for lysosomal degradation can reach the lysosome by a variety of
means. Following receptor-mediated endocytosis, endocytic vesicles from the cell surface
can fuse with the lysosome; this is a mechanism for degradation of cell surface receptors and
thus the downregulation of incoming signals.
In phagocytosis, the cell engulfs foreign bodies – say, invading bacteria, or apoptotic bodies
from other cells – and delivers them to the lysosome. The membrane of the lysosome itself
can invaginate, creating exosome-like vesicles full of cytosolic proteins to be degraded. In
“canonical”, starvation-induced autophagy, double membrane forms around material (such as
unneeded organelles) in the cytosol and delivers them to the lysosome. The degradation of
proteins in the lysosomes is catabolic – it releases energy – so this response to nutrient
starvation recovers some of the energy originally put into synthesizing proteins and other
cellular components. But autophagy isn’t induced only by starvation – unfolded protein
stress in the endoplasmic reticulum can cause chunks of ER to be degraded by autophagy.
Cooper 2000 defines autophagy narrowly, as “the degradation of cytoplasmic proteins and
organelles by their enclosure in vesicles from the endoplasmic reticulum that fuse with
lysosomes”. But others use autophagy interchangeably with lysosomal degradation – for
instance, “The major pathways for degradation of cellular constituents are autophagy and
cytosolic turnover by the proteasome”. The only lysosomal degradation pathway
I haven’t ever seen called autophagy is phagocytosis, perhaps since the engulfment and
degradation of foreign bodies doesn’t match the auto in autophagy.

Proteasome
The proteasome is a cylindrical protein complex found in the cytosol which cleaves up
proteins tagged with ubiquitin. To accomplish this, an E1 enzyme activates a ubiquitin
molecule, transfers it to an E2 enzyme, and finally an E3 ubiquitin ligase covalently attaches
ubiquitin to a lysine (K) on the protein to be degraded. There are a huge variety of different
E3 ubiquitin ligases, reflecting the many different regulatory pathways by which the cell
selects and recognizes proteins it wants to flag for degradation.
The proteasome itself weighs in at 26S, and is composed of a 19S gate and a 20S core. The
19S gate recognizes and binds ubiquitinated proteins, powered by ATP – unlike the
lysosome, the proteasome is an energy-losing operation. Once recognized, these proteins
must be de-ubiquitinated and unfold in order to pass through the narrow channel of the 19S
and enter the 20S core, a cylindrical complex which does the actual chopping up of
proteins. Unlike the lysosome, where proteases shear proteins up into individual amino acids,
the proteasome just chops proteins into small peptides, usually of 7 – 9 amino acids
each. These are later broken into amino acids by cytosolic proteases.
Since it’s located in the cytosol, the proteasome has immediate access to degrade cytosolic
proteins. However, its action is not limited to cytosolic substrates. Just as proteins can be
translocated into the secretory pathway, they can also be retro-translocated back out in order
to be degraded by the proteasome. This process is called ER-associated degradation or
ERAD. As of today it is not actually known what the channel is that allows for
retrotranslocation across the ER membrane.