Autophagy and cell growth – the yin and yang of nutrient ......Autophagy and cell growth – the yin and yang of nutrient responses Thomas P. Neufeld Department of Genetics, Cell

Autophagy and cell growth – the yin and yang ofnutrient responses

Thomas P. NeufeldDepartment of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN 55455, USA

[email protected]

Journal of Cell Science 125, 2359–2368� 2012. Published by The Company of Biologists Ltddoi: 10.1242/jcs.103333

SummaryAs a response to nutrient deprivation and other cell stresses, autophagy is often induced in the context of reduced or arrested cell growth.

A plethora of signaling molecules and pathways have been shown to have opposing effects on cell growth and autophagy, and results ofrecent functional screens on a genomic scale support the idea that these processes might represent mutually exclusive cell fates.Understanding the ways in which autophagy and cell growth relate to one another is becoming increasingly important, as new roles for

autophagy in tumorigenesis and other growth-related phenomena are uncovered. This Commentary highlights recent findings that linkautophagy and cell growth, and explores the mechanisms underlying these connections and their implications for cell physiology andsurvival. Autophagy and cell growth can inhibit one another through a variety of direct and indirect mechanisms, and can beindependently regulated by common signaling pathways. The central role of the mammalian target of rapamycin (mTOR) pathway in

regulating both autophagy and cell growth exemplifies one such mechanism. In addition, mTOR-independent signaling and other moredirect connections between autophagy and cell growth will also be discussed.

This article is part of a Minifocus on Autophagy. For further reading, please see related articles: ‘Ubiquitin-like proteins and autophagy at a glance’ by Tomer Shpilka et al.(J. Cell Sci. 125, 2343-2348) and ‘Autophagy and cancer – issues we need to digest’ by Emma Liu and Kevin Ryan (J. Cell Sci. 125, 2349-2358).

Key words: Autophagy, Cell growth, Mammalian target of rapamycin (mTOR), Protein synthesis, Lysosome, Cell cycle

IntroductionCells have an intrinsic drive to increase their mass, which is

illustrated by the ravenous growth of embryos and juveniles

during development, and the logarithmic proliferation of cells in

culture. Even in adult organisms, whose size has reached a steady

state, continued growth and proliferation of differentiated and

stem cells allows replacement of damaged and senescent cells,

and many cells and organs are capable of considerable growth

through hypertrophy. Cell growth can thus be considered a

default state for many cell types, requiring only the presence of

permissive factors such as nutrients and appropriate hormonal

signals. The process of cell growth, however, has enormous

energetic requirements and is rapidly abandoned when conditions

become unfavorable. In response to nutrient limitation, DNA

damage, excessive oxidation, viral infection and other cell

stresses, the ATP-consuming processes that underlie cell

growth are rapidly turned off, allowing the cell to conserve or

marshal its resources to deal with the stressor.

In addition to switching off energetically demanding growth

processes, cells induce a variety of responses to stress that enable

them to survive in suboptimal conditions. Central among these is

macroautophagy (herein referred to as autophagy), whereby

portions of cytoplasm are sequestered into vesicles known as

autophagosomes and degraded by hydrolytic enzymes following

fusion of autophagosomes with the lysosome. This process

supports cell survival by eliminating damaged and potentially

harmful cellular structures, and by releasing the breakdown

products as nutrients that can be re-used by the cell or exported

for use by other cells.

On a fundamental level, autophagy and cell growth are mirror

images of one another. If cell growth is defined as the process of

mass accumulation through the net uptake and conversion of

nutrients into macromolecules, autophagy can be considered to

act in opposition to these biosynthetic processes through the

catabolic breakdown of biomolecules. Thus, under conditions

conducive to cell growth, the coupling of high rates of

biosynthesis with low rates of autophagy allows cellular

resources to be channeled towards growth with maximal

efficiency. This synthetic flow is reversed in response to

nutrient limitation or other stresses that halt cell growth and

induce autophagy. This inverse correlation between autophagy

and growth is widely observed under a variety of environmental

conditions. For example, growth inhibition and autophagy

induction are coordinated responses to nutrient starvation,

growth factor withdrawal, cellular stresses such as oxidative

damage, protein misfolding, viral infection, and substrate

detachment or contact inhibition of cultured cells (Fig. 1)

(reviewed by Neufeld, 2004).

Although the coupling of autophagy and growth might appear

intuitive and logical, the potential cause-and-effect relationships

between these two processes and the underlying mechanisms that

link them are just beginning to be unraveled. In this Commentary,

I highlight key regulatory steps and signaling pathways involved

in autophagy and growth control, and discuss the regulatory

relationships by which these processes are coordinated in the cell.

Understanding the physiological benefits of this coordination and

the consequences of its disruption should provide insight into

potential autophagy-based therapeutic approaches.

Commentary 2359

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mailto:[email protected]://dx.doi.org/10.1242/jcs.093757

Autophagy and the cell growth machineryFormation of autophagosomes and their fusion with lysosomes

are the defining events of autophagy. Whereas autophagosome–

lysosome fusion largely exploits general factors of the endocytic

pathway, autophagosome formation is driven by the coordinated

activity of distinct sets of components that are dedicated to this

process. Many of these components were first identified through

pioneering genetic screens in yeast, and have clear homologs in

metazoan cells. These include: (1) two ubiquitin-like molecules,

Atg12 and Atg8 [microtubule-associated protein 1 light chain 3

alpha (LC3) and additional family members in mammals], and

the E1-, E2- and E3-like processing machinery that regulates

their conjugation to control autophagosome formation and size;

(2) a multi-component protein complex containing the class III

phosphatidylinositol 3-kinase Vps34 (PIK3C3 in mammals),

which promotes autophagosome nucleation from cytosolic

membranes; and (3) a complex containing the serine/threonine

protein kinase Atg1 (ULK1 and ULK2 in mammals), which

integrates signals from multiple upstream regulators to control

the localization or activity of Vps34 and other autophagy

components. One such regulator, the protein kinase target of

rapamycin [Tor1 and Tor2 in yeast; mammalian TOR (mTOR) in

mammals], has a central role in controlling Atg1 and ULK1

activity in response to nutrients and growth conditions. Together,

these three systems act in concert, along with a number of

accessory proteins, to form autophagosomes at a rate that is

appropriate for specific environmental conditions (reviewed by

Mizushima et al., 2011).

The biosynthetic pathways that promote the accumulation of

mass to drive cell growth are also highly coordinated. The best

understood of these processes is the control of protein synthesis,

which is generally rate limiting for cell growth and sufficient to

drive cell transformation (reviewed by Proud, 2007). The activity

of translation initiation and elongation factors [e.g. eukaryotic

translation initiation factors (eIF) 2, 3 and 4 and eukaryotic

translation elongation factor 2 (eEF2)] are tightly regulated by

protein kinases such as mTOR and Gcn2 (for general control non-

repressed 2, also known as EIF2AK4) in response to nutrient and

growth factor levels. The production of ribosomes is similarly

sensitive to growth conditions, and this regulation encompasses all

three RNA polymerases, as well as post-transcriptional controls, to

ensure a balanced production of ribosomal proteins and RNAs.

More recently, we have begun to define the signals that link

cell growth to lipid synthesis and organelle biogenesis, and

these appear to involve a complex interplay of transcriptional,

translational and post-translational control (reviewed by Zoncu

et al., 2011b). It is crucial that the synthesis rates of proteins, lipids

and other biomolecules are regulated in parallel, and that these, in

turn, are linked to the rates of nutrient uptake and, finally, to the

overall growth and division rates of the cell and its organelles.

Together, these regulatory steps represent nodes of control at

which interactions between cell growth and autophagy can occur.

A

B

C

Fig. 1. Correlation between cell size and autophagy.

(A) Bax2/2, Bak2/2 mouse bone marrow-derived cells that were

cultured in the presence (left) or absence (right) of the growth

factor interleukin 3 for six weeks. Of note are the reduced

cytoplasmic volume and abundant autophagosomes (arrows).

Image reprinted from Lum et al., 2005 with permission from

Elsevier (Lum et al., 2005). (B) Camera lucida drawings of

sectioned larval fat body cells from fed (left) or three-day starved

(right) Drosophila larvae. Dark circular structures represent lipid

droplets. Image reprinted from Butterworth et al., 1965 with

permission from John Wiley and Sons (Butterworth et al., 1965).

(C) Histogram indicating cell size (forward light scatter) of

Atg52/2 mouse embryonic fibroblasts carrying a doxycycline-

repressible Atg5 transgene. Cells were starved (ST+, right) in

amino-acid-free DMEM or incubated in normal cell culture media

(ST-, left), in the presence or absence of doxycycline (DOX).

Repression of Atg5 leads to increased cell size under starvation

conditions. Image reprinted from Hosokawa et al., 2006 with

permission from Elsevier (Hosokawa et al., 2006).

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Coordination of these processes can thus be achieved either

through common signaling pathways that intersect at multiple

independent control points, or through autophagy- or growth-

dependent effects and signals (Fig. 2). Here, each of these models

is considered in turn.

Coordinated regulation of growth and autophagyby common signalsAn efficient means of achieving coordination between autophagy

and cell growth rates is through the joint regulation of these

processes by shared upstream signaling pathways. Although the

molecules that act directly on autophagy and biosynthesis are

distinct, a number of regulators have been shown to control both

processes in parallel (Fig. 3).

mTOR-dependent regulation of autophagy and growth

As alluded to above, the kinase mTOR has a central role in

controlling both cell growth and autophagy. mTOR controls the

translation initiation step through direct phosphorylation of two

key targets, EIF4E-binding protein 1 (EIF4EBP1) and S6 kinase

(S6K, also known as RPS6KB1), which, in turn, regulate eIF3-

and eIF4-dependent interactions between the mRNA 59 cap, thepoly(A)-tail and the 40S and 60S ribosomal subunits (Zoncu et al.,

2011b). mTOR also has a major impact on protein synthesis and

cell growth by promoting ribosome biogenesis. In yeast, this

involves inhibitory phosphorylation of three transcription factors,

Stb3, Dot6 and Tod6, which act as repressors of ribosome

biogenesis (RiBi) and ribosomal protein (RP) gene expression

(Huber et al., 2011). This phosphorylation is mediated by the

protein kinase Sch9, a yeast homolog of S6K and AKT, and a

direct TOR substrate. mTOR also contributes to ribosome

biogenesis by promoting expression of ribosomal RNA. Recent

studies indicate that there is a nucleolar role for mTOR

complexes directly at the promoters of rRNA and tRNA genes,

and have identified the RNA polymerase I and III factors TIF1A

(also known as TRIM24), TFIIIC (also known as GTF3) and

MAF1 as downstream targets (Kantidakis et al., 2010; Mayer

et al., 2004; Vazquez-Martin et al., 2011).

Independent of these effects on protein synthesis, mTOR

regulates the autophagic machinery and suppresses

autophagosome formation under conditions that are favorable

for growth. Autophagy inhibition by mTOR largely occurs

independently of the targets known to be involved in growth

regulation, such as EIF4EBP1 or S6K. Instead, mTOR directlyinteracts with and phosphorylates components of the Atg1 protein

kinase complex, including Atg1 (ULK1), Atg13 and FIP200 (alsoknown as RB1CC1) (reviewed by Mizushima, 2010). In yeast,Atg13 is phosphorylated on multiple serine and threonineresidues under growth conditions, and this disrupts its

association with Atg1. Ohsumi and co-workers recently foundthat Atg13 is phosphorylated directly by TOR in vitro, andshowed that Atg13 lacking these phosphorylation sites stably

associates with, and activates, Atg1 and is sufficient to promoteautophagy under growth conditions, independent of TOR activity(Kamada et al., 2010). This ability of non-phosphorylatable

Atg13 to bypass TOR signaling highlights the Atg1 complex asthe crucial downstream target mediating the effects of TOR onautophagy.

How TOR-dependent phosphorylation of Atg13 promotes

Atg1 activation and induction of autophagy remains poorlyunderstood. Interestingly, Herman and colleagues havedemonstrated that Atg1 forms dimers or oligomers under

conditions that favor autophagy, and that this self-association ispromoted by Atg13 (Yeh et al., 2011). Forced dimerizationof Atg1 increases its kinase activity and the level of

autophosphorylation, which is a prerequisite for inducingautophagy (Kijanska et al., 2010; Yeh et al., 2010). However,this is not sufficient to induce autophagy, suggesting that Atg13

has additional functions. Regulation of metazoan Atg1 (ULK1)appears to differ from that in yeast, as mTOR inhibits ULK1without affecting its interaction with Atg13. A functional rolefor Atg13 phosphorylation has not yet been demonstrated

in mammals, and mTOR-mediated phosphorylation of othercomponents of the ULK1 complex might have important roles.Recently, Ser757 of ULK1 was identified as an mTOR-

dependent phosphorylation site that influences the associationof ULK1 with the AMP-activated protein kinase (AMPK), whichis an important activator of autophagy in response to cellular

energy levels (Kim et al., 2011a; Shang et al., 2011) (see below).

The potential role of mTOR to regulate later steps ofautophagosome maturation, movement and lysosomal fusion isless well characterized. At least in some cell types, mTOR

activation can promote autophagosome–lysosome fusion, in partby facilitating the interaction of Rab7 with its lysosomal effectorRab-interacting lysosomal protein (RILP) (Bains et al., 2009;

Bains et al., 2011; Yamamoto et al., 2006). Furthermore,reactivation of mTOR during sustained nutrient starvation isrequired to allow re-formation and recycling of lysosomes

following the massive delivery of autophagic membrane andcargo. This recovery of mTOR activity and lysosomal integrity isdependent on autophagic degradation and efflux, suggesting that

nutrients derived from the autolysosome are able to promotemTOR activation (Rong et al., 2011; Shin and Huh, 2011; Yuet al., 2010). Nutrient efflux from autolysosomes also appearsto promote TOR signaling required for secretory activity in

senescent cells (Narita et al., 2011).

Recent investigations into the nutrient-dependent regulationand localization of mTOR are consistent with this model. In

response to an increase in nutrient levels, mTOR is recruited tothe surface of lysosomes by members of the Rag family ofheterodimeric GTPases (Sancak et al., 2010). The lysosomal

translocation of mTOR requires nutrient-dependent GTP loadingof the Rag complex, and this recruitment is sufficient to bypassthe nutrient input to mTOR activation. Interestingly, nucleotide

A Signal

Autophagy

Integrator

Cell growth

Signal

Autophagy

Cell growth

Signal

Cell growth

Autophagy

B C

Fig. 2. Potential signaling relationships between autophagy and cell

growth. The inverse correlation between rates of cell growth and autophagy

can be accomplished through several distinct mechanisms. Common upstream

signaling pathways (A) can provide a coordinated effect on autophagy and

cell growth. Such pathways bifurcate at integration points that independently

control the autophagy and growth machinery downstream. Inhibitory effects

of autophagy on cell growth (B) and of cell growth on autophagy (C) can

provide a direct mechanism for linking these processes. Please refer to the text

for additional details.

Cell growth and autophagy 2361

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loading of Rag GTPases is sensitive to the amino acid

concentrations within the lysosome, and subunits of the

vacuolar ATPase protein pump are required for this signaling

(Zoncu et al., 2011a). The microtubule-dependent positioning of

lysosomes within the cell has also been shown to influence

mTOR activity, and this appears to be mediated by nutrient-

dependent changes in intracellular pH (Korolchuk et al., 2011).

Importantly, lysosome-mediated regulation of mTOR influences

multiple, if not all, aspects of mTOR function, including its effects

on targets involved in cell growth and autophagy. This implies that

mTOR might retain its activation state for some time after its

departure from the lysosomal surface and diffusion or transport to

other cellular compartments. Indeed, activation of mTOR might be

required for its release from the lysosome (Ohsaki et al., 2010).

Compartmentalization of mTOR from its targets, such as ULK1,

has been suggested to promote autophagy during senescence, but

the extent to which similar mechanisms contribute more generally

to mTOR signaling is unclear (Narita et al., 2011). Live imaging

and fluorescence recovery after photobleaching (FRAP)-based

analysis of mTOR complexes might help to clarify this issue. This

centralized control of mTOR activation status probably makes a

substantial contribution to coordinating its diverse functions in

autophagy and cell growth.

mTOR-independent control of autophagy and growth

Despite the multiple inputs to mTOR signaling and its pervasive

effects on autophagy and cell growth, a surprisingly large number

of signaling pathways and regulators have been shown to affect

these processes independently of changes in mTOR activity.

Small-molecule screens have identified several compounds that

induce autophagy without affecting mTOR. These chemicals

inhibit a variety of intracellular targets and processes, including

ion channels, Ca2+ homeostasis and G-protein signaling

(Williams et al., 2008; Zhang et al., 2007). A strong correlation

has been observed between the ability of these compounds to

promote long-lived protein degradation and to increase cellular

levels of phosphatidylinositol 3-phosphate [PtdIns(3)P], the

product of Vps34, thus implicating this kinase as an ultimate

autophagic effector. Despite some reports linking Vps34 to

mTOR activation (Byfield et al., 2005; Nobukuni et al., 2005), no

effect on the phosphorylation of mTOR substrates has been found

for these compounds (Williams et al., 2008; Zhang et al., 2007).

Similarly, a genomic siRNA screen for autophagy regulatory

genes has found little correlation between autophagy induction

and mTOR activity, whereas nearly half of the 236 identified hits

had a substantial effect on PtdIns(3)P levels (Lipinski et al.,

2010). Gene ontology analysis of these hits has revealed a

Gcn2

Amino acids

Lysosome

Gcn4

Vps34

CDKs

Atg1

TOR

Glucose Gl

AMPK

Energy

CKIs

E2F pRb

Autophagy gene expression

Δψ, Π, pH

tRNAs

Actively translatingribosome

Endoplasmic reticulum

Fig. 3. Effects of cell growth on autophagy. Growth-dependent import of nutrients, such as amino acids and glucose, generates multiple signals that influence

the induction of autophagy through their effects on pH, osmotic pressure (P) and the electrochemical gradient (DY), as well as through several key signaling

molecules such as Gcn2 (EIF2AK4 in mammals), TOR (or mTOR) and AMPK. The eIF2a kinase Gcn2 senses reduced amino acid levels through the

accumulation of uncharged tRNAs, and activates autophagy-related gene expression through the transcription factor Gcn4 (ATG4 in mammals). Amino acids

activate the mTOR pathway, in part, by recruiting mTOR complexes to the lysosomal surface through factors such as the Rag GTPases and p62, and through

effects on intracellular lysosomal positioning. The AMP-activated protein kinase (AMPK) responds to glucose uptake, and regulates multiple downstream targets

that have effects on autophagy, including mTOR, Atg1 (ULK1 in mammals) and CDKs (through cyclin kinase inhibitors; CKIs). The induction of autophagy can

also be suppressed by the presence of actively translating ribosomes on the surface of the endoplasmic reticulum, which might limit the availability of sites for

autophagosome nucleation. Additional components of TOR, Atg1 and Vps34 complexes are indicated. Please refer to the text for details.


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substantial enrichment in signaling molecules and transcriptionfactors, including multiple genes involved in growth factor and

cytokine signaling that have well-characterized effects on cellgrowth. Taken together, these results indicate that the ability ofsignaling pathways to regulate autophagy and cell growth inparallel is not confined to the mTOR pathway and might be

widespread.

The oncogenic Ras–RAF–MAPK cascade stimulates cellgrowth through multiple transcription factors including MYC,

JUN (also known as transcription factor AP-1) and ETS1, whichtarget genes that regulate cell cycle progression, ribosomebiogenesis and cytokine signaling (McCubrey et al., 2007).

Ballabio and colleagues recently identified the mammaliantranscription factor EB (TFEB) as a master regulator of a largenumber of autophagy and lysosomal genes that facilitatethe coordination of autophagosome formation, fusion and

degradation (Settembre et al., 2011). Furthermore, this groupshowed that TFEB can be negatively regulated through directphosphorylation by extracellular-signal-regulated kinase 2

(ERK2), which is independent of mTOR activity. Similarly inyeast, Ras and its downstream target cAMP-dependent proteinkinase (PKA) inhibit the starvation-induced expression of

autophagy genes, such as ATG8, independently of TOR, andPKA promotes expression of growth gene networks such as theRiBi regulon through inactivation of the repressor Tod6 (Graef

and Nunnari, 2011; Lippman and Broach, 2009). Thus bothmammalian and yeast Ras signaling pathways use a coordinatedtranscriptional mechanism to link growth stimulation andautophagy inhibition in response to nutrients.

This transcriptional response is probably shared by many otherfactors that regulate growth in response to multiple stimuli.Botstein and colleagues found that 25% of all yeast genes

display a similar transcriptional response to changes in nutrientconditions regardless of carbon source, a pattern they termed a‘universal’ growth rate response (GRR) (Slavov and Botstein,

2011). Growth-related genes involved in ribosome biogenesis andtranslation display a positive universal GRR (i.e. increasedtranscription in rich medium), whereas autophagy- and vacuolar-associated genes have a negative GRR. Although such

widespread responses certainly reflect the activity of multipletranscriptional regulators, individual transcription factors canalso generate coordinated effects on growth and autophagy. For

example, the yeast transcriptional regulator Gcn4 responds toamino acid starvation by promoting expression of autophagygenes and repressing genes encoding ribosome proteins and

translation factors (Natarajan et al., 2001). The synthesis of Gcn4protein itself increases under conditions of general translationinhibition, providing an additional layer of connection between

autophagy and cell growth (Hinnebusch, 1997).

In metazoans, the FOXO family of transcription factorssuppresses cell growth through the expression of inhibitors oftranslation and proliferation (Jünger et al., 2003; Stahl et al.,

2002). Concurrently to this, they stimulate autophagy byactivating the expression of a large number of autophagy-associated genes (Mammucari et al., 2007; Zhao et al., 2007).

Interestingly, FOXO1 also has a transcription-independentcapacity to promote autophagy. This process involvesdeacetylation of cytoplasmic FOXO1 in response to starvation

or oxidative stress, which promotes its association with ATG7and leads to autophagy through an, as yet, unclear mechanism(Zhao et al., 2010). Dual nuclear and cytoplasmic effects have

also been described for p53, which induces autophagy in

response to DNA damage through the activation of target genes

such as those encoding the lysosomal protein DNA-damage

regulated autophagy modulator 1 (DRAM1) and ULK1, as well

as factors, such as sestrin 2, phosphatase and tensin homolog

(PTEN) and tuberous sclerosis 2 (TSC2), that inhibit mTOR

signaling (Crighton et al., 2006; Feng et al., 2005; Gao et al.,

2011; Maiuri et al., 2009). These inductive effects on autophagy

through p53-mediated transcription are opposed by a cytoplasmic

function of p53, which increases mTOR activity and suppresses

autophagy under basal conditions (Tasdemir et al., 2008).

Other factors also regulate cell growth and autophagy

through a combination of mTOR-dependent and -independent

mechanisms. For example, in addition to its transcriptional

effects noted above, PKA also inhibits autophagy in yeast by

directly phosphorylating Atg1 and Atg13, which prevents their

localization to the sites of autophagosome assembly (Stephan

et al., 2009). At the same time, PKA activation increases the

sensitivity of cells to rapamycin and exacerbates the growth

defects of tor mutants, which indicates that PKA has antagonistic

effects on TOR (Ramachandran and Herman, 2011). Taken

together, these results suggest that PKA sends both positive and

negative signals to the autophagy network, and that the inhibitory

effect is dominant under most conditions. Similarly, the energy-

sensing AMPK regulates autophagy both upstream and

downstream of mTOR. By inhibiting mTOR activity under

conditions of low energy, AMPK indirectly promotes activation

of the ULK1 complex. In addition, AMPK can directly

phosphorylate ULK1, in this case leading to further activation

and induction of autophagy (Egan et al., 2011; Kim et al., 2011b;

Shang et al., 2011).

Regulation of autophagy by cell growthAs discussed above, the inverse relationship between cell growth

and autophagy can result in part from their co-regulation.

However, this close correlation is also consistent with a cause-

and-effect connection between these processes, and suggests

that autophagy and cell growth might inhibit each other

independently of shared upstream signaling components.

We can examine this issue from the viewpoint of protein

synthesis and cell cycle progression, two processes that are

central to cell growth and proliferation. The first obligate step in

increasing cellular protein mass is the import of amino acids. The

regulation of this process in metazoan cells is poorly defined, but

it is clear that growth factor signaling promotes the expression of

a variety of nutrient transporters on the cell surface, in part by

blocking their endocytic degradation (Edinger, 2007; Edinger and

Thompson, 2002; Hennig et al., 2006). Amino acid uptake in

growing cells might directly lead to mTOR activation and hence

suppression of autophagy. However, rapid incorporation of

amino acids into growing peptide chains might limit their free

intracellular concentration and thus mTOR activation. Transport

of amino acids into the cell can also have secondary

consequences, such as changes in osmolarity and cell

membrane polarization, which have been shown to influence

autophagic signaling (Häussinger et al., 1990). In addition, there

is evidence that some amino acid transporters might act as

‘transceptors’ with dual transport and signaling functions, and

mTOR and PKA have been implicated as targets of such

molecules (Taylor, 2009).


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Subsequent steps in protein synthesis can also have substantialregulatory effects on autophagy. Following their transport into

the cell, amino acids are ligated to their cognate tRNAs byaminoacyl-tRNA synthetases. Disruption of this process causesaccumulation of uncharged tRNAs, which directly activates theeIF2a kinase Gcn2 (also known as EIF2AK4 in mammals),leading to translation arrest, upregulation of GCN4 and increasedexpression of autophagy genes (Hinnebusch, 1994). In addition,export of tRNA from the nucleus is inhibited by starvation, and

depletion of the tRNA nuclear exporter XPOT can activateautophagy in the presence of abundant nutrients (Huynh et al.,2010). In this case, autophagy correlates with reduced mTOR

activity, which indicates that tRNAs can influence multiplesignaling pathways.

In rapidly growing cells, the elongation of polypeptide chainsmight also inhibit autophagosome formation. Recent studies have

implied that PtdIns(3)P-rich domains of the rough endoplasmicreticulum (ER) are central staging areas of autophagosomeinitiation (Axe et al., 2008). The tight juxtaposition of the

growing autophagic membrane with the ER surface (Hayashi-Nishino et al., 2009; Ylä-Anttila et al., 2009) suggests thatengagement of active ribosomes with the ER translocon might be

incompatible with this initiation process. In rapidly growingcells, high occupancy of the surface of the ER with translatingribosomes might therefore limit its availability as a platform for

autophagosome formation (Blommaart et al., 1995).

The cell division cycle of proliferating cells provides anotherstage for the interaction between autophagy and growth control.It has been known for some time that cells in mitosis are resistant

to a variety of autophagic stimuli, including starvation andmTOR inhibition (Eskelinen et al., 2002), and this mightprovide a crucial barrier to autophagic degradation of spindle

components, genetic material and other exposed cellularstructures. A study using multiple cell cycle markers and avariety of autophagy inducers found that each stimulus had

maximal effects in the G1 and S phases of the cell cycle, withlittle activity in the G2 and M phases (Tasdemir et al., 2007).This autophagy timecourse corresponds inversely with activity ofthe mitotic protein cyclin-dependent kinase 1 (CDK1). Yuan and

colleagues recently identified Vps34 as a substrate of CDK1–cyclin-B during mitosis in human cells (Furuya et al., 2010). Thatstudy found that CDK1-mediated phosphorylation of Vps34 on

Thr159 disrupts its association with beclin 1, an essential corecomponent of Vps34 complexes, thereby reducing the lipid kinaseactivity of Vps34. Thr159 phosphorylation of Vps34 increases

during mitosis, correlating with a reduction in autophagy. Thesefindings suggest that suppression of autophagy during mitosis canresult from CDK1-dependent inhibition of Vps34 activity. By

contrast, yeast Cdk1 appears to have a positive function inautophagy because loss of Cdk1 activity leads to G1 arrest andautophagy inhibition (Yang et al., 2010). The region of Vps34that surrounds Thr159 is not well conserved in yeast, which

indicates that other Cdk1 substrates probably mediate its effectson autophagy.

Regulation of autophagy by CDKs might be a general

phenomenon. The CDKN1B (also known as p27 and KIP1) andCDKN2A (also known as p16 and INK4) families of G1 CDKinhibitors are important regulators of cell cycle and growth in

response to stress, hormonal and developmental signals. Recentstudies have revealed that these factors have a similarly crucialrole in regulating autophagy by integrating signals from multiple

upstream pathways. Liang and co-workers have shown that

autophagy is inhibited in mouse embryonic fibroblasts that lackp27, and that overexpression of p27 or depletion of CDK2 orCDK4 induces autophagy in breast adenocarcinoma cells (Liang

et al., 2007). Both p27 and p16 are linked to autophagy throughthe tumor suppressor retinoblastoma 1 (RB1, also known as pRb),which is a central downstream target of CDK4 in cell cycleregulation. RB1 is required for the induction of autophagy by p27

and p16, and can trigger autophagy when overexpressed (Jianget al., 2010). RB1 controls cell cycle progression, cell growth andsurvival by binding to the transcription factor E2F and inhibiting

expression of E2F target genes. Similarly, induction of autophagyby RB1 requires binding of RB1 to E2F, and this process can beantagonized by overexpression of E2F. The effects of RB1 and

E2F are complex, however, and might be influenced by cell typeand stress conditions. For example, E2F is required for autophagyinduction by DNA-damaging agents in U2OS cells, and

overexpression or activation of E2F can promote autophagyand increase expression of Atg1 (ULK1), ATG5, LC3 andDRAM1 in these cells (Polager et al., 2008). In addition, RB1–E2F complexes have a negative effect on autophagy in response

to hypoxia, in this case by inhibiting expression of BNIP3 (forBCL2/adenovirus E1B 19kDa interacting protein 3), an activatorof VPS34–beclin-1 complexes and inhibitor of mTOR (Tracy

et al., 2007).

Even a single CDK can have both positive and negative effectson autophagy. Klionsky and co-workers have found that the yeastCDK Pho85 has both positive and negative effects on autophagy

induction, depending on the cyclin partner it is associated with(Yang et al., 2010). The relative expression levels of these cyclinsvary with cell cycle phase and in response to environmental

signals, and each phase probably directs Pho85 to differentcellular compartments or downstream targets, thereby allowingPho85 to provide an integrated autophagic response to multiple

growth and cell cycle cues.

In addition to these molecular links, processes that are intrinsicto cell growth and proliferation might themselves be incompatiblewith autophagy. For example, periodic reorganization of

microtubules into a mitotic spindle in dividing cells would beexpected to disrupt transport of autophagic vesicles or ofcomponents required for their formation. Similarly, dedicating

vesicular trafficking pathways towards active synthesis andsecretion might preclude their use in autophagy. Growth andautophagy might also compete for raw materials, such as

membrane lipids, or for regulators that function in bothprocesses. For example, Vps34 can assemble into at least threecomplexes with distinct subunits and functions, but only one them(which is defined by the presence of Atg14) is dedicated to

autophagosome formation (Simonsen and Tooze, 2009). Suchcompetition-based mechanisms could prevent autophagy fromcausing damage during vulnerable cell cycle phases.

Regulation of cell growth by autophagyBone marrow cells derived from mice that are deficient for theproapoptotic BCL2 family proteins BAX and BAK are able to

survive in culture for several weeks in the absence of growthfactors. This survival is autophagy-dependent and coincides witha dramatic reduction in cell mass (Lum et al., 2005). In vivo,

starvation of Drosophila can result in a 90% decrease in the sizeof larval fat body cells, which is accompanied by a massiveinduction of autophagy (Butterworth et al., 1965). Genetic


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disruption of autophagy in this system suppresses the observed

reduction in growth, and overexpression of Atg1, which induces

autophagy, is sufficient to reduce cell size in the fat body (Scott

et al., 2007; Scott et al., 2004). In starved mice, the intracellular

protein degradation rate of hepatocytes approaches 40% per day in

vivo, and starvation-induced size reduction of mouse embryonic

fibroblasts can be substantially inhibited by disrupting Atg5

(Conde and Scornik, 1976; Hosokawa et al., 2006). Together,

these examples illustrate the intrinsic ability of autophagy to

directly reduce cellular mass through the degradation of bulk

cytoplasm (Fig. 4A).

In addition to these presumably non-selective effects in

growth-arrested cells, autophagy might further reduce the

growth rate of actively growing cells through targeted

elimination of growth-promoting molecules, complexes and

organelles. The protein p62 (also known as sequestosome 1) is

an intriguing candidate for such a factor. p62 is a multifunctional

adapter protein that binds LC3 and other Atg8 family members

through its LC3-interacting region (LIR), and thereby becomes

incorporated into autophagosomes (Bjørkøy et al., 2005). This

results in efficient autophagy-dependent degradation of p62, and,

indeed, p62 protein levels are widely used as indicators of

autophagic flux (Klionsky et al., 2008). Recently, an important

role for p62 in mTOR activation has been described. In cells

where p62 has been depleted or knocked out, mTOR fails to be

activated in response to amino acids, which leads to a decrease in

cell growth. Remarkably, p62 has been shown to stimulate

mTOR signaling by supporting the interaction between Rag

GTPases, the mTOR partner Raptor and the lysosomal surface,

which promotes amino-acid-dependent recruitment of mTOR to

the lysosome and its subsequent activation (Duran et al., 2011).

These results imply that autophagy can impair mTOR-dependent

cell growth through selective degradation of p62. In addition, p62

contains a C-terminal ubiquitin-associated (UBA) domain and

can promote selective autophagy of ubiquitylated soluble or

aggregated proteins (Bjørkøy et al., 2005; Kim et al., 2008),

which potentially include other factors involved in cell growth

regulation. In a proteomic study tracing the progressive

autophagic degradation of proteins in breast cancer cells, it has

been found that proteins involved in translation, including

mTOR, ribosomal protein S6 and tRNA synthetases, are among

the most rapidly depleted factors (Kristensen et al., 2008).

Whether these and other growth-promoting factors are selectively

targeted for autophagy in a p62-dependent manner remains to be

shown.

Autophagy can also be employed by cells to selectively

degrade larger complexes and organelles that are required for cell

growth, such as ribosomes and mitochondria. In yeast, starvation

results in rapid sequestration and digestion of ribosomes in the

vacuole. This process is essential for survival under starvation

conditions, is highly selective and involves the ubiquitin protease

Ubp3, its activator Bre5, and ubiquitylation of specific ribosomal

proteins (Kraft et al., 2008). Interestingly, the mammalian

orthologs of Ubp3 and Bre5 interact with ULK1, which is

required for the clearance of ribosomes from the cytoplasm

of reticulocytes (Behrends et al., 2010; Kundu et al., 2008).

Ribosomal degradation represents a potent mechanism to

directly reduce cellular growth capacity. In addition, large

macromolecular complexes such as P granules in C. elegans

and midbody rings of dividing cell populations can indirectly

promote growth by acting as stem cell factors, and these

complexes have also been shown to be selective autophagy

substrates (Kuo et al., 2011; Pohl and Jentsch, 2009; Zhang et al.,

2009).

Mitochondria can be selectively degraded by autophagy in a

process referred to as mitophagy recently (reviewed in Youle and

Narendra, 2011). Both starvation and mitochondrial damage

can trigger mitophagy, and this requires LIR-motif-containing

proteins [Atg32 in yeast, Nix (also known as BNIP3L) and

possibly p62 in mammalian cells], which are thought to guide

expansion of autophagosomal membranes over the mitochondrial

surface through interaction with Atg8 family members. In yeast,

this interaction is regulated by phosphorylation of Atg32 (Aoki

et al., 2011). It was recently demonstrated that mitochondria can

be protected from starvation-induced mitophagy by a PKA-

dependent process of fusion and elongation, which somehow

spares mitochondria from engulfment into autophagosomes

(Gomes et al., 2011; Rambold et al., 2011). Similarly, in yeast

that are grown under conditions in which mitochondria are

required for metabolism, mitophagy is not induced, not

even by severe starvation (Kanki and Klionsky, 2008). In

starved mammalian cells, degradation of mitochondria occurs

subsequent to degradation of cytosolic proteins and ribosomes

(Kristensen et al., 2008). Thus, mitochondria appear to be the last

-Ub-

-Ub-

WIPI1 ULK1 mTOR

A

B

P-

Bulkautophagy

Mitophagy

Ribophagy

p62-mediatedselective autophagy

KeyMitochondrion

Fig. 4. Negative effects of autophagy on cell growth. (A) Multiple forms of

autophagy can contribute to growth suppression. From left to right: bulk

autophagy of cytoplasmic contents including cytosol and organelles;

mitophagy, which utilizes adapter molecules such as Atg32, Nix and p62;

ribophagy, which requires the ubiquitin protease Ubp3 and its activator Bre5;

and p62-dependent degradation of ubiquitylated (Ub) signaling molecules and

of p62 itself, which can promote mTOR signaling. (B) Activation of

autophagy factors such as ULK1 and WIPI1 might lead to downregulation of

mTOR through multiple mechanisms, possibly including ULK1-mediated

phosphorylation (P) of Raptor (indicated by the blue oval) and WIPI1-

dependent effects on maturation of endocytic vesicles.


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resort for nutrients, which probably reflects their essential role in

both growing and stationary cells.

Several components of the autophagic machinery have

been shown to have important autophagy-independent roles in

regulating apoptotic cell death, and it is interesting to speculate

that similar dual functions might be at work in controlling cell

growth. One possible example of this is a feedback signaling loop

from ULK1 to mTOR, which involves mTOR inhibition by its

downstream kinase (Fig. 4B). In Drosophila and mammalian

cells, Tor (or mTOR)-dependent phosphorylation of its substrates

S6K and EIF4EBP1 is increased in Atg1 (or ULK1)-depleted

cells, and decreased in response to the overexpression of Atg1

(Lee et al., 2007; Scott et al., 2007). These effects correlate with

changes in the cytoplasmic localization and trafficking of TOR,

and with ULK1-dependent phosphorylation of the TORC1

component Raptor (Chang and Neufeld, 2009; Dunlop et al.,

2011). Feedback signaling from Atg1 to mTOR might help to

amplify weak or variable signals into a stable biphasic switch,

and might allow pathways that regulate ATG1 and autophagy

independently of mTOR to influence growth in an mTOR-

dependent manner. Other autophagy regulators can also affect

mTOR signaling independently of their effects on autophagy. A

recent study identified the Atg18 ortholog WD repeat domain,

phosphoinositide interacting 1 (WIPI1) as an inhibitor of mTOR

in human melanocytes (Ho et al., 2011). WIPI1 has an

autophagy-independent role in the biogenesis of melanosomes,

which are lysosome-related organelles that develop through an

endosome-like maturation process. WIPI1 has been shown to

function in part by suppressing mTOR activity, which negatively

regulates transcription of melanogenic proteins in these cells.

As mTOR activation is sensitive to disruption of endocytic

maturation (Flinn et al., 2010; Li et al., 2010), it will be

interesting to see whether WIPI1 also regulates TOR in other

contexts through its effects on endocytic trafficking.

ConclusionsThe separation of cell growth and autophagy into non-

overlapping states appears to provide several advantages,

including maximal resource efficiency and protection against

cellular damage. However, although autophagy and cell growth

tend to display an inverse response to many stimuli, it should

be noted that this correlation is not absolute. High levels of

autophagy can be observed in some rapidly growing cells, and in

some cases this might actually contribute to cell growth

and biosynthesis. Deeper investigation into these apparent

‘exceptions to the rule’ might prove particularly fruitful. For

example, exercise induces both autophagy and cell growth of

muscle fibers (Ogura et al., 2011), and this might involve a

temporal separation into distinct phases of fiber breakdown and

rebuilding. Similarly, senescent cells display high levels of

autophagy despite showing highly active mTOR signaling and

protein synthesis. In this case, these processes are separated

spatially within the cell, with autophagy components being

insulated within an ‘mTOR–autophagy spatial coupling

compartment’ that protects them from mTOR-mediated

downregulation (Narita et al., 2011). In other cases, such as in

Ras-transformed cells, autophagy might provide intermediate

metabolites that are specifically required to fuel the altered

metabolic pathways of these cells and to facilitate their rapid

growth (Guo et al., 2010; Kim et al., 2011b; Lock et al., 2011).

As new roles of autophagy continue to be revealed, the viewthat emerges is that this ancient process is deeply entwined with

the basic cellular functions of growth, proliferation and survival.Disentangling these connections will be important to ourunderstanding of the molecular regulation of each of theseprocesses. Furthermore, as autophagy-based therapies against a

number of diseases are pursued, it will be important to considerhow potential treatments might impact other processes such ascell growth that are linked to autophagy. This will be aided by a

better understanding of growth-dependent and -independentmechanisms that regulate autophagy.

FundingThe work of our laboratory is supported by the National Institutes ofHealth [grant number GM62509]. Deposited in PMC for releaseafter 12 months.

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Autophagy and cell growth – the yin and yang of nutrient ......Autophagy and cell growth – the yin and yang of nutrient responses Thomas P. Neufeld Department of Genetics, Cell