yeast: endocytosis from the cell-surface, two distinct
biosynthetic pathways, the carboxypeptidase Y (CPY)
and alkaline phosphatase (ALP) from the Golgi,
multivesicular body (MVB) sorting, the cytoplasm to
vacuole pathway (Cvt), macro-autophagy, micro-auto-
phagy, and vacuole inheritance during cell division
(Figure 3A). The endocytic pathway is essential for
regulating levels of cell-surface proteins and intersects
with the CPY pathway at a late endosomal compart-
ment. Components of the CPY-sorting pathway are
directly involved in vacuolar biogenesis, morphology,
and function, as discussed here in greater detail. ALP
travels from the Golgi to the vacuole along a pathway
that is independent of the CPY and endocytic pathways.
Proteins such as aminopeptidase I (API) are delivered
from the cytoplasm to the vacuole through pathways
involving products of the CVT and APG (autophagy)
genes. In micro-autophagy, the vacuole membrane
invaginates to engulf cytoplasmic material, including
entire organelles such as peroxisomes. Vacuolar segre-
gation into dividing daughter cells of budding yeast
requires VAC (vacuolar inheritance) genes, some of
which also participate in the CPY pathway. Previous
studies have also identified several distinct factors
involved in vacuolar inheritance.
THE CPY PATHWAY
CPY is the prototype of a subset of proteins that
traffics from the Golgi to the vacuole via an endosomal
intermediate. This pathway depends on the function of
over 60 VPS gene products, mutations in which result
in the mis-sorting of CPY to the secretory pathway,
abnormal vacuole morphology, and in some cases,
abnormal endosome morphology. In a manner analo-
gous to receptor-mediated sorting in mammalian cells,
the CPY receptor Vps10 binds CPY at the Golgi via a
targeting signal. Sorting of this receptor–ligand com-
plex into vesicles bound to endosomes requires
proteins such as clathrin and accessory factors such
as the AP-1 clathrin adaptor complex and the Gga
proteins. Next, the class D Vps proteins are involved in
CPY vesicle targeting and fusion with endosomes, such
as Vps21 (Rab5 homologue), Vps9 (Rab GEF), Vac1
(EEA1), Vps45 (Sec1 homologue), Pep12 (t-SNARE),
and Sec18 (NSF). At the endosome, Vps10 dissociates
from CPY and recycles to the Golgi in a process
requiring the retromer complex (consisting of Vps29,
Vps26, Vps35, Vps5, and Vps17). Mutants defective in
retromer function mis-localize Vps10 to the vacuole
membrane and secrete CPY, as Vps10 becomes limiting
for subsequent sorting reactions at the Golgi.
Another set of Vps proteins (the class E Vps proteins)
is necessary for efficient sorting at the endosome. Class E
Vps mutant cells accumulate abnormal/aberrant endo-
somes containing both biosynthetic cargo such as CPY
and endocytosed proteins. The class E proteins are also
involved in the formation of multivesicular bodies
(MVBs) at late endosomes. The abnormal/exaggerated
endosomes observed in these mutant cells form in part
due to impaired MVB vesicle budding into the lumen of
the endosome.
Finally, fusion of late endosomes/MVBs with the
vacuole requires another set of proteins including Ypt7
(Rab7 homologue) and SNARE proteins (Vti1, Ykt6,
Nyv1, Vam7, and Vam3). The class C Vps protein
complex (also termed HOPS) consisting of Vps18,
Vps11, Vps16, and Vps33 (Sec1 homologue), Vps41,
and Vps39 (Rab GEF) is required for this final fusion
step as well (Figure 3B). The Vps34 PI 3-kinase also
contributes to this fusion step by the generation of
PI(3)P that recruits effector proteins such as the PX
domain-containing protein Vam7. Mutants with defects
in these gene products accumulate numerous endoso-
mal intermediates and MVBs that fail to fuse with the
vacuole. Accordingly, mutants defective in components
of the vacuolar fusion machinery display highly
fragmented vacuoles and can sometimes even lack
vacuoles entirely.
THE ALP PATHWAY
ALP is an integral membrane protein that travels from
the Golgi to the vacuole independently of endosomal
compartments that transport CPYand endocytic cargoes
(Figure 3A). A specific adaptor complex, termed AP-3,
mediates sorting of ALP into vesicles at the Golgi.
However, following formation, fusion of ALP cargo
vesicles with the vacuole is dependent on the class C Vps
complex, Ypt7, Vam7, and Vam3. Thus, the ALP and
CPY pathways converge upon common docking/fusion
machinery at the vacuole (Figure 3B).
CYTOPLASM TO VACUOLE TRANSPORT
AND
MACRO-AUTOPHAGY
Autophagy is a trafficking pathway to vacuoles
regulated by changes in nutrient availability.
In macro-autophagy, induced during starvation, cyto-
plasmic material is first sequestered in double-mem-
brane vesicles called autophagosomes and then
subsequently delivered to the vacuole (Figure 3A).
While autophagy is induced, the Cvt pathway con-
stitutively packages the hydrolases aminopeptidase I
(API) and
a
-mannosidase into autophagosomes for
delivery to vacuoles. Autophagosomes are targeted to,
and fuse with, the vacuole by the same machinery that
mediates endosome-vacuole fusion (Figure 3B). Inside
the vacuole, the lipase Cvt17 is responsible for auto-
phagosome turnover (Figure 2).
VACUOLES 333