[Autophagy 2:2, 146-148, April/May/June 2006]; ©2006 Landes Bioscience
The Regulation of Autophagy in Eukaryotic Cells
Addenda
Do All Roads Pass Through Atg1?
ABSTRACT
KEY WORDS
autophagy, cAMP-dependent protein kinase, Tor
proteins, Snf1 protein kinase, Atg1, macroautophagy,
pre-autophagosomal structure
ACKNOWLEDGEMENTS
.
UT
E
RIB
Macroautophagy (hereafter referred to as autophagy) is a highly conserved, degradative
pathway that was originally identified as a cellular response to nutrient deprivation.1,2
More recent work has implicated autophagy in a wide variety of processes, including
programmed cell death, innate immunity and organismal aging.3-5 During autophagy,
bulk portions of the cytoplasm, including whole organelles, are engulfed in vesicular
structures, known as autophagosomes.6 In S. cerevisiae, these intermediates originate from
a poorly-defined organelle, the preautophagosomal structure (PAS), and are targeted to the
vacuole/lysosome for degradation.7 The amount of flux through this pathway can be
rather high and may in fact be incompatible with cell growth. Thus, it is imperative that
the induction of autophagy be tightly regulated.
This control is arguably best-understood in the budding yeast, S. cerevisiae, where three
signaling pathways important for growth control have been implicated in the regulation
of autophagy. In this organism, autophagy is generally triggered by starvation and is
required for the survival of these nutrient-deprived cells.8 Two of these signaling pathways,
containing the Tor and Ras proteins, respectively, are growth-stimulatory and both inhibit
autophagy in dividing cells.9-11 The Tor proteins are highly conserved protein kinases that
are responsible for coordinating eukaryotic cell growth with nutrient availability.12 The
Ras proteins are small GTP-binding proteins that, in S. cerevisiae, control the activity of
the cAMP-dependent protein kinase (PKA).13,14 The inactivation of either of these
pathways results in a G0-like growth arrest and in the full induction of the autophagy
pathway. Finally, autophagy also appears to be controlled by the Snf1 protein, the S. cerevisiae analog of the AMP-activated protein kinase.15 Snf1 activity increases in response to
particular environmental insults, including starvation, and, in contrast to the above pathways,
Snf1 activity is required for the induction of the autophagy process.15,16
Interestingly, all of these pathways appear to converge upon Atg1, a conserved serine/
threonine-specific protein kinase that is, itself, a key regulator of autophagy.17 Upon
nutrient deprivation, Atg1 protein kinase activity increases and this protein is rapidly
recruited from the cytosol to the PAS.10,18,19 Recent work from our lab indicates that this
relocalization of Atg1 is regulated by Ras/PKA signaling activity.20 PKA directly phosphorylates Atg1 and thereby prevents its association with the PAS. However, this PKA
phosphorylation had no effect on Atg1 protein kinase activity. Instead, previous work has
suggested a role for the Tor pathway in the regulation of this Atg1 activity. The Tor pathway
appears to regulate the phosphorylation state of Atg13, a protein important for autophagy
that is associated with Atg1 specifically in nutrient-deprived cells.10 Atg13 is heavily
IEN
We thank Dr. Stephen Deminoff for valuable
discussions and comments on this manuscript.
This work is supported by a grant from the
National Institutes of Health (GM65227) to
P.K.H.
IST
Previously published online as a Autophagy E-publication:
http://www.landesbioscience.com/journals/autophagy/abstract.php?id=2485
OT
D
Received 01/01/06; Accepted 01/07/06
ON
*Correspondence to: Paul K. Herman; Department of Molecular Genetics; The Ohio
State University; 484 West Twelfth Avenue, Room 984; Columbus, Ohio 43210 USA;
Tel.: 614.688.5581; Fax: 614.292.4466; Email: [email protected]
.D
Department of Molecular Genetics; The Ohio State University; Columbus, Ohio USA
The induction of autophagy appears to be tightly controlled in all eukaryotic cells. This
highly conserved, degradative process is induced by a variety of signals, including nutrient
deprivation, and is generally thought to be incompatible with rapid cell growth. Recent
work in the budding yeast, Saccharomyces cerevisiae, has suggested that the Atg1
protein kinase is at the center of this control. Atg1, and its associated proteins, appear
to be directly targeted by multiple signaling pathways important for the control of both
autophagy and cell growth. These pathways involve the small GTP-binding Ras proteins,
the Tor protein kinases and the AMP-activated protein kinase, Snf1, respectively. A key
question that remains is whether this regulatory paradigm has been evolutionarily
conserved. In other words, is Atg1 the primary target of those signaling pathways responsible for coordinating growth with environmental influences in other eukaryotes? Here,
we suggest that Atg1 is very likely to fulfill this role but that a truly definitive answer will
require that we develop a better understanding of this protein kinase and its targets in all
eukaryotes.
CE
Joseph S. Stephan
Paul K. Herman*
Addendum to:
BIO
SC
An Evolutionary Proteomics Approach Identifies Substrates
of the cAMP-Dependent Protein Kinase.
©
20
05
LA
ND
ES
Y.V. Budovskaya, J.S. Stephan, S.J. Deminoff and
P.K. Herman
Proc Natl Acad Sci USA 2005; 102:13933-8
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The Regulation of Autophagy in Eukaryotic Cells
component of this regulation. However, it should be pointed out
that several of the important regulators of this protein kinase,
including Atg13, do not have clear orthologs in animals.28
Therefore, it is imperative that we begin to define the proteins associated with Atg1 in other organisms and to examine whether these
partners might also be targets of the signaling pathways controlling
growth. For example, are there functional homologs of Atg13 that
are not recognizable with simple sequence comparisons?29 Clearly,
these experiments will be guided by the studies already done in yeast,
but we expect that the results will provide some interesting new
twists into the multilayered regulation of this degradative process.
References
Figure 1. The Atg1 protein kinase complex is targeted by both the Ras/PKA
and Tor signaling pathways in S. cerevisiae. Potential roles for the Ras/PKA
and Tor pathways in the regulation of the Atg1-PAS and Atg1-Atg13 associations are shown, respectively. See the text for more details. The other
proteins known to be associated with Atg1 are not shown for the sake of
simplicity.3 PAS, preautophagosomal structure.
phosphorylated in dividing cells and is rapidly dephosphorylated
upon either nutrient deprivation or the inactivation of the Tor
pathway.10,21 Atg1 specifically associates with the hypophosphorylated form of Atg13.10,22 Although it is not known whether this
regulation by Tor is direct or indirect, recent work has indicated that
this Atg13 phosphorylation is not the result of PKA activity.20
Therefore, in the simplest sense, the Ras/PKA pathway appears to
influence the subcellular localization of Atg1 while the Tor pathway
may be regulating Atg1 protein kinase activity (Fig. 1).
Unfortunately, this simple model does not fully account for all of
the present experimental data. For example, the inactivation of the
Tor pathway also causes Atg1 to relocalize to the PAS.18 This could
be either because the Tor pathway independently regulates Atg1
localization or that this pathway, directly or indirectly, influences
Ras/PKA activities. This latter point is important as the precise
relationship between the Ras and Tor pathways is not yet clear in
S. cerevisiae.14,23,24 In fact, we think that autophagy may serve as a
useful readout in future attempts to resolve this regulatory relationship. The ability to specifically assess the phosphorylation of Atg1
and Atg13 may allow us to determine precisely how the Ras/PKA
and Tor signaling pathways have an impact upon one another.
We would be remiss if we failed to point out that to truly
understand the role of Atg1 in autophagy, we will need to identify
the substrates of this enzyme. Although substrate identification has
historically been a difficult task, there are a number of emerging
technologies that should facilitate this endeavor for Atg1.20,25 Of
particular interest is the protein chip technology that allows you to
query specific biochemical properties of an entire library of proteins
that are fixed to a solid substrate. A study using this approach recently
identified a number of potential Atg1 substrates in S. cerevisiae.26
Although more than 180 proteins were identified in this report, at
least two, Atg8 and Atg18, are of particular interest because of their
previously-described roles in the autophagy process.
The final but perhaps most important question here is whether
Atg1 also has a central role in the regulation of autophagy in other
organisms. Although a number of signaling pathways have been
implicated in the control of autophagy in metazoans, the target of
this control has for the most part not been established.4,27 Based on
the above results with yeast, we propose that Atg1 will be a key
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