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Opinion
Bacterial autophagy: restriction or
promotion of bacterial replication?
Serge Mostowy1,2,3,4 and Pascale Cossart1,2,3
1
Institut Pasteur, Unité des Interactions Bactéries-Cellules, Département de Biologie Cellulaire et Infection, F-75015 Paris, France
Inserm, U604, F-75015 Paris, France
3
INRA, USC2020, F-75015 Paris, France
2
In order to survive inside the host cell, bacterial pathogens have evolved a variety of mechanisms to avoid or
interfere with innate immune defenses. Several reports
have shown that bacterial pathogens are targeted by the
autophagy pathway, and autophagy has been increasingly recognized as an important defense mechanism to
clear intracellular microbes. However, it now appears
that some bacterial pathogens have evolved mechanisms to evade autophagic recognition or even co-opt
the autophagy machinery for their own benefit as a
replicative niche. A complete understanding of bacterial
autophagy in vivo shall be critical to exploit autophagy
and its therapeutic potential.
Autophagy: bacterial friend or foe?
Autophagy is an intracellular degradation process by
which cytosolic materials are delivered to a lysosomal
compartment (Figure 1). The ‘canonical’ autophagy pathway involves the initiation and elongation of double-membrane phagophores that close upon themselves to form
autophagosomes — vacuoles typically 0.3–1.0 mm in diameter — to sequester cargo; this process requires a group of
35 autophagy-related (ATG) proteins conserved from yeast
to humans [1–3] (Box 1). Many studies have revealed the
diverse functions of autophagy in important cellular processes such as aging, development and inflammation [4].
Autophagy is also linked to a wide range of disease states,
including microbial infection [5,6]. Autophagosomes were
first regarded to sequester cytosolic material nonspecifically; however, the recently discovered paradigm of ‘selective’ autophagy, where autophagosomes can degrade
cytosolic material in a selective manner as a result of
receptor–ligand interactions, has highlighted the recognition of specific cargo, such as intracellular bacteria, by
autophagy receptors for targeted lysosomal destruction.
By binding to both ubiquitin and ATG8 family proteins (i.e.
LC3s and GABARAPs), autophagy receptors can mediate
targeting of ubiquitinated cargo to autophagy [7]. p62
(sequestosome 1 or SQSTM1) [8], NBR1 (neighbor of
BRCA1 gene 1) [9], NDP52 (nuclear dot protein, 52 kDa)
[10] and OPTN (optineurin) [11] are well-characterized
autophagy receptors, and together represent an emerging
Corresponding authors: Mostowy, S. ([email protected]);
Cossart, P. ([email protected])
Keywords: autophagy; cytoskeleton; ubiquitination; Listeria; Shigella; Salmonella;
mycobacteria.
4
Present address: Section of Microbiology, Centre for Molecular Microbiology and
Infection, Imperial College London, Armstrong Road, London SW7 2AZ, UK.
category of pattern recognition receptors, called sequestosome 1/p62-like receptors (SLRs), linking autophagy to
innate immunity [12,13] (Table 1).
Some pathogenic bacteria, in order to circumvent extracellular host immune responses, establish an intracellular
niche to live inside host cells and replicate. Internalized
bacteria first localize within a vacuolar compartment. This
residence is sometimes very transient, and some pathogens, such as Listeria or Shigella, have evolved mechanisms to escape from their internalization vacuole to the
cytosol and avoid destruction in phagolysosomes. Other
pathogens, such as Salmonella or mycobacteria, interfere
with the normal biogenesis of phagolysosomes to form
replicative vacuoles. Discovered almost 10 years ago, bacterial autophagy has been highlighted as a fundamental
host cell response to bacterial invasion in vitro by degrading intracellular pathogens located both in the cytosol and
inside an internalization vacuole, including Listeria monocytogenes [14], Shigella flexneri [15], Salmonella Typhimurium [16] and Mycobacterium tuberculosis [17]. Since
then, research in the field has exploded, revealing that
some pathogens may avoid autophagy-mediated degradation, whereas others may exploit the autophagy machinery
for intracellular survival. As a result, the in vivo consequence of bacterial autophagy remains unclear, and probably varies for different bacterial species.
This review will focus on the recognition of pathogenic
bacteria by the autophagy machinery to illustrate the
emerging roles of autophagy during infection (Figure 2).
In addition, we highlight the mechanisms evolved by
pathogenic bacteria to avoid or co-opt the autophagy machinery, strongly suggesting that autophagy should not be
strictly considered as antibacterial.
Pathogens that escape to the cytosol
Escape from the internalization vacuole is a bacterially
driven process, and the survival of pathogens in the cytosol
relies on their ability to avoid recognition and degradation
by autophagy.
L. monocytogenes: escape from autophagic destruction
L. monocytogenes is a Gram-positive bacterium responsible
for foodborne infections. The intracellular lifestyle of this
pathogen has been well studied [18]. Listeria survives
intracellularly by escaping from phagosomes using a combination of effectors including LLO, a pore-forming cytotoxin. Once in the cytosol, L. monocytogenes uses ActA,
0962-8924/$ – see front matter ß 2012 Elsevier Ltd. All rights reserved. http://dx.doi.org/10.1016/j.tcb.2012.03.006 Trends in Cell Biology xx (2012) 1–9
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Phagophore
Autolysosome
Autophagosome
Lyso
Lyso
Initiation
Membrane
elongation
Completion
Maturation
Degradation
TRENDS in Cell Biology
Figure 1. Cellular events of the autophagy process. Cytoplasmic material, in this case a bacterium (gray), is enclosed by an isolation membrane, called a phagophore (blue),
which elongates to form an autophagosome. The autophagosome fuses with the lysosome (Lyso), and the enclosed material is degraded in the autolysosome.
which is expressed on the surface of the bacteria, to assemble the actin polymerization machinery and form actin
tails for intra- and intercellular motility [19]. Strikingly,
autophagic markers do not accumulate around intracytosolic L. monocytogenes polymerizing actin [20–22]. This
situation results from the fact that ActA disguises Listeria
from ubiquitination and autophagic recognition [23,24].
Therefore, ActA-expressing Listeria are not targeted to
autophagic degradation. These findings suggest that host
Box 1. Canonical autophagy versus non-canonical
autophagy
Canonical autophagy includes three different pathways: macroautophagy (herein referred to as autophagy) [1–3]; microautophagy
(the engulfment of cytoplasmic material by invagination of the
lysosomal membrane) [79]; and chaperone-mediated autophagy
(the delivery of cytoplasmic proteins to the lysosome through
interaction with chaperone proteins) [80]. Here, we focus on
autophagy, which is:
A degradation process that targets cytoplasmic material to double
membrane vacuoles that fuse with lysosomes for destruction.
Dependent on the systematic recruitment of ATG proteins to the
phagophore (i.e. the autophagosome initiation site) to form and
elongate an autophagosome that will fuse with the lysosomal
compartment (Figure 1).
Originally viewed as a random, non-selective degradation process. However, the involvement of specificity factors, such as
ubiquitin [81], for selective autophagy is increasingly recognized.
Classically activated in vitro by treating cells with rapamycin.
Rapamycin is an inhibitor of mTOR, a serine/threonine protein
kinase that is a suppressor of autophagy [82].
A mechanism to target bacteria to lysosomal degradation and
therefore a critical component of innate immunity. Autophagy
receptors act as cytosolic sensors and recruit ATG proteins at
different steps of the invasion process.
Non-canonical autophagy is a new and developing concept, and
can be characterized by features that are different from those in
canonical autophagy [3]. In particular, non-canonical autophagy is:
A mechanism in which the double-membraned autophagosome
does not require all of the ATG proteins to form, and may
elongate from multiple sources of membrane.
A process in which a subset of ATG proteins can be recruited to an
already-existing and probably damaged membrane (e.g. a
phagocytic vacuole containing Salmonella or mycobacteria) that
is different from a phagophore.
Potentially favorable in some cases of infection. Certain bacteria
may replicate inside autophagosome-like structures (i.e. vacuoles
with a double membrane and a subset of ATG proteins that will
not fuse with the lysosomal compartment) generated by noncanonical autophagy.
Bacterial species apparently benefitting from non-canonical
autophagy includes Brucella and Staphylococcus.
2
proteins that interact with ActA on the surface of Listeria
may disguise the bacteria to prevent autophagic recognition, or that ActA itself prevents recruitment of proteins
normally involved in autophagy. Indeed, bacteria lacking
ActA are ubiquitinated and targeted to autophagy. InlK is
another Listeria surface protein that contributes to escape
from autophagy [25]. This protein is poorly expressed in
vitro, but when expressed it can protect bacteria from
autophagy in the absence of ActA. Instead of recruiting
the actin polymerization machinery, Listeria expressing
InlK recruits the major vault protein (MVP) to evade
ubiquitination and autophagic recognition.
Several reports have shown that L. monocytogenes lacking LLO production fail to induce autophagy [14,21,26],
suggesting that autophagy induction by Listeria is LLO
dependent. Indeed, purified LLO triggers formation of
aggregates associated with ubiquitin, p62 and LC3 [27],
all of which are hallmarks of autophagosomes [28]. Cytosolic lectins (e.g. Galectin 3, 8 and 9) are also recruited to
vesicles damaged by LLO and probably other factors
[29,30], and this recruitment may trigger autophagy (see
Salmonella below). However, work in bone marrowderived macrophages has shown that autophagy triggered
by host-cell membrane remnants, created by rupture of
phagosomal vacuoles by LLO, does not control intracytosolic Listeria replication [31]. By contrast, work in Drosophila has shown that LLO-dependent autophagy,
triggered by the pattern-recognition receptor PGRP-LE,
may control Listeria replication [32]. Further studies are
therefore required to clarify the role of LLO-mediated
autophagy induction during bacterial infection.
Together, L. monocytogenes can avoid autophagic destruction, at least in vitro, by preventing the accumulation
of ubiquitinated substrates at the bacterial cell surface;
however, it triggers autophagy by LLO-mediated membrane
rupture. The precise, and probably multiple, roles of autophagy in Listeria pathogenesis thus remain to be established.
S. flexneri: a target of autophagic destruction
S. flexneri is a Gram-negative, foodborne pathogen that
invades the colonic mucosa, causing inflammation and diarrhea. The infectious process at the cellular level is similar
to that of L. monocytogenes, but the mechanisms that Shigella uses to escape from the vacuole are less understood.
Once in the cytosol, the actin-based motility of Shigella is
mediated by its surface expressed IcsA protein [19].
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Table 1. Autophagy receptors implicated in bacterial autophagy and the bacteria they recognize, and bacterial effectors that
prevent autophagy recognition*
Autophagy receptor
p62
OPTN
Targeted bacteria
L. monocytogenes,
S. flexneri,
S. Typhimurium,
M. marinum,
M. tuberculosis
S. flexneri
L. monocytogenes,
S. flexneri,
S. Typhimurium
S. Typhimurium
Effector protein
ActA
Bacteria
L. monocytogenes
InlK
L. monocytogenes
IcsB
S. flexneri
NBR1
NDP52
Mode of action
Self-oligomerization; binds ubiquitin and ATG8 family proteins
References
[24,35,51,60,89]
Interacts with p62 via PB1 domains; binds ubiquitin and ATG8 family proteins
Binds ubiquitin and ATG8 family proteins; binds ubiquitinated bacteria in the
cytosol and binds Galectin 8 at vesicle damage; NDP52 and p62 form
non-overlapping subdomains around ubiquitinated bacteria
Binds ubiquitin and ATG8 family proteins; OPTN and NDP52 localize to
common subdomains around ubiquitinated bacteria separate from p62;
phosphorylation of OPTN promotes selective autophagy
[24,90]
[10,24,29,53]
Role
Recruits Arp2/3 for actin-based motility; masks from ubiquitination and
autophagy recognition by p62, NDP52
Recruits MVP; masks from ubiquitination and autophagy recognition by p62
before ActA
Prevents ATG5 recognition of IcsA; masks from ubiquitination and autophagy
recognition by septin cage, p62, NDP52; prevents recognition byTECPR1
[11]
References
[23,24]
[25]
[15,24,35,36]
*
Aside from bacterial effectors listed here, there are likely to be others that have not yet been discovered.
At the Shigella-entry site, NOD1 and NOD2, key pathogen recognition receptors, are recruited together with
ATG16L1, a protein required for phagophore formation
(Box 1) and associated with Crohn’s disease, beneath the
plasma membrane [26]. NOD proteins sense the bacterial
invasion process as danger signals, and this sensing
triggers autophagy in the infected cell cytosol. At the
same time, membrane remnants, generated by Shigella-mediated membrane damage, are ubiquitinated and
recognized by autophagy receptors, thereby helping to
control inflammatory signaling [33]. Indeed, inflammasome components have been localized to damaged membranes, and their ubiquitination and degradation by
p62-mediated autophagy leads to a dampened inflammatory response [34]. Cytosolic lectins may also detect vesicle damage by Shigella and trigger autophagy [29,30].
Thus, membrane damage is considered to alert the host
cell to subsequent bacterial invasion; however, further
studies are required to determine whether induction
of autophagy by membrane damage can limit Shigella
replication.
Autophagy is also induced by the presence of cytosolic
Shigella. In epithelial cells infected with Shigella, autophagy is triggered by the recognition of IcsA by ATG5 [15], a
protein critical for autophagosome elongation and completion (Figure 1). However, Shigella can evade autophagy by
expressing IcsB, a type III secretion system (T3SS) effector, which competitively binds IcsA to block ATG5 binding.
Thus, IcsB enables Shigella to evade autophagic recognition [15,24,26,35]. Recent work has identified a Tectonin
domain-containing protein, TECPR1, as a receptor for
ATG5 in Shigella-infected cells [36]. Via binding to
ATG5, and not to ubiquitinated substrate, TECPR1 activity promotes autophagosome–lysosome fusion and mediates bacterial autophagy [37].
Strikingly, septin cage-like structures target Shigella to
autophagy, and are required for this process [24,35] (Box
2). Septins are GTP-binding proteins that assemble as
filaments and approximately 0.6-mm diameter rings, and
accumulate at bacterial entry sites and around intracytosolic bacteria [38]. In the cytosol, septin rings assemble at
sites of IcsA-induced actin polymerization and form cages
surrounding the bacterium to restrict cell-to-cell spreading
[35]. The precise role of septins in autophagy is unknown,
yet work has shown that septins help to scaffold ubiquitinated proteins and autophagy receptors around actin-polymerizing bacteria [24,35]. Whether septin cages and
autophagy serve to clear intracytosolic Shigella in vivo
has yet to be tested.
Mycobacterium marinum: recruitment of canonical and
non-canonical autophagy
M. marinum causes a systemic tuberculosis-like disease in
fishes and frogs, and a localized disease in humans, and
has been widely used as an alternative model to study M.
tuberculosis. Like most pathogenic mycobacteria, M. marinum survives within host macrophages by preventing
phagolysosome fusion [39]. However, M. marinum can also
escape from the phagosome to the cytosol and, unlike other
mycobacteria, initiate actin-based motility [19,39]. Mutations in ESX-1, a specialized secretion pathway in mycobacteria that encodes for genes with membrane lysing
activity, attenuates the virulence of M. marinum by abrogating phagosomal escape.
Recent work has shown that phagosomes containing
M. marinum recruit the autophagic marker LC3, and this
recruitment depends on ESX-1 activity [40]. M. marinum
can temporarily reside in a LC3-decorated compartment,
characterized as a late endosome lacking the degradative
properties of a lysosome. By contrast, when autophagy is
stimulated by rapamycin, there is increased LC3 recruitment to the M. marinum-containing compartment, and this
leads to its fusion with the lysosome. This suggests that
autophagy can help to eliminate mycobacterial-containing
phagosomes, in agreement with studies using M. tuberculosis (see below).
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Bacterial invasion
Autophagy of
bacteria inside a phagosome
Autophagy of
membrane remnants
Ub
3
LC
3
LC
AR
AR
Bacteria inside
a damaged phagosome
Cytosolic bacteria
Ub
Ub
3
3
3
LC
LC
LC
Autophagy of
bacteria and septin
cage formation
AR
AR
AR
Autophagy of
cytosolic bacteria
Autophagy of bacteria
inside a damaged phagosome
TRENDS in Cell Biology
Figure 2. Different autophagy pathways triggered by bacterial invasion. Ub, ubiquitin; AR, autophagy receptor (see Table 1 for examples); LC3, ATG8.
In the cytosol, ubiquitinated M. marinum can be found
within organelles that resemble autophagosomes (i.e. they
have a double membrane) albeit lacking canonical autophagy markers ATG5 and LC3 [41]. In close proximity to
cytosolic bacteria, a mixture of host membrane remnants
and shed M. marinum cell walls are also ubiquitinated
[41]. From these observations, it has been proposed that
ubiquitinated M. marinum cell walls are sequestered into
autophagy-like organelles by a non-canonical autophagy
pathway, and cell wall shedding may enable bacterial
escape from this process. Indeed, similarly to Listeria
[23,24,35] and Shigella [15,24,35], M. marinum that polymerize actin tails are not recognized by ubiquitin. By
contrast, ubiquitin, p62, LC3 and septin caging have been
observed around cytosolic M. marinum at the onset of
actin tail formation [24,35,41]. Considering the role of
septin caging during Shigella infection, it is likely that
septin caging also helps the targeting of M. marinum to
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autophagy (Box 2). A major issue is now to determine the
respective roles of canonical and non-canonical pathways in
the autophagy of M marinum.
Francisella tularensis: autophagic restriction of cytosolic
replication
F. tularensis is a Gram-negative, facultative intracellular
bacterium that causes tularemia, a human infection that
starts through contact with infected animal tissues or
spread through an arthropod vector. Following entry into
cells, F. tularensis is localized within a phagosome, but
escapes to the cytosol to avoid destruction in phagolysosomes [42]. In the cytosol, Francisella does not exhibit
actin-based motility, and instead replicates rapidly until
the cell undergoes apoptosis and the bacteria are released
to continue infection. However, an infected host cell can
restrict cytosolic replication by sequestering Francisella
into a compartment called the Francisella-containing
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Box 2. Autophagy and the cytoskeleton
Proteins involved in actin-based motility are also connected to
bacterial autophagy. Septins, increasingly well-characterized cytoskeleton components [38], are recruited with autophagy proteins to some
intracytosolic bacteria and form cage-like structures to counteract
actin tail formation and restrict bacterial dissemination [35] (Figure I).
These observations have linked septin caging and autophagy as
interdependent host defense processes, and suggest that a more
comprehensive understanding of septins and autophagy will have
important consequences for the understanding of bacterial pathophysiology and its control.
In the cytosol, Listeria, Shigella and M. marinum all share the ability
to polymerize actin tails. However, septin caging has been observed
for Shigella and M. marinum, but not for Listeria [35]. In this case,
caging does not occur because Listeria ActA masks the bacteria from
autophagic recognition so that septin caging is also avoided [24,35].
Comparative investigation of these different intracellular bacteria has
highlighted the role for actin and septins in selective autophagy, and
has revealed that Shigella and Listeria are recognized by different
pathways of autophagy [24,35] (Figure 2). Septin-mediated bacterial
autophagy will have to be studied in vivo across a panel of pathogens
to fully understand its role in host defense.
Given that septin assembly [38] and autophagy [1,2] are processes
well-conserved from yeast to humans, their interdependence may not
be limited to bacterial autophagy. In uninfected cells, levels of
autophagy critical components are reduced upon septin depletion
[24,35], consistent with the hypothesis that multiple autophagic
activities benefit from septin assembly. It is now critical to investigate
the role of septin assemblies in various autophagic processes,
including starvation-induced autophagy [83], microautophagy [79],
chaperone-mediated autophagy [80], and other processes of selective
autophagy such as clearance of the midbody ring [84], entotic cell
death [85], mitophagy [86] and virophagy [87,88].
TRENDS in Cell Biology
Figure I. The Shigella-septin cage. Recruitment of septin (SEPT9, red) to actin (green)-polymerizing S. flexneri (blue) devoid of actin tails. Scale bar, 1 mm. Reproduced,
with permission, from [35].
vacuole (FCV), which shares several hallmarks of canonical autophagosomes, including a double membrane and
LC3 labeling [43]. The precise role of FCV compartmentalization remains unknown, yet the expression of type
IV pili (Tfp) [44] may help F. tularensis to avoid this
compartmentalization. In agreement with this, microarray analysis of cells infected with F. tularensis has shown
that several canonical autophagy markers are down-regulated during infection [45]. However, the potential
subversion of autophagy by F. tularensis awaits further
characterization.
Streptococcus pyogenes: degradation by non-canonical
autophagy
S. pyogenes [Group A Streptococcus (GAS)] is a Grampositive bacterium responsible for a variety of infectious
diseases associated with significant morbidity and mortality worldwide. It is noninvasive, but once taken up by
phagocytic cells, GAS escapes from phagosomes using
streptolysin O (SLO), a cholesterol-dependent cytolysin
[46]. SLO induces autophagy, and cytosolic GAS are contained within an LC3-positive, membrane-bound structure
called GAS-containing autophagosome-like vacuoles
(GcAVs) [47]. Unlike canonical autophagosome formation
(Box 1), GcAV formation requires the small GTPases Rab7,
Rab9a and Rab23 [48,49]; otherwise, the molecules responsible for GcAV formation – and not for canonical autophagosome formation – are largely unknown. GAS are
degraded upon fusion of GcAVs with lysosomes, and in
autophagy-deficient cells, GAS survive and replicate [50].
Thus, non-canonical autophagy may represent a critical
defense against GAS infection.
Pathogens that survive inside the phagosome
Several pathogens can survive inside the vacuole and avoid
destruction upon fusion, or by preventing fusion, with the
lysosome. For these pathogens, escape to the cytosol is
considered to be accidental. Remarkably, these bacteria
can be recognized by autophagy both in the phagosome and
in the cytosol, and their survival may be critically linked to
their ability to co-opt the autophagy machinery.
Salmonella Typhimurium: a paradigm of selective
autophagy
S. Typhimurium is a Gram-negative intracellular foodborne pathogen with a broad host range. Following Salmonella invasion of host cells, most bacteria reside and
replicate within a modified endosomal compartment called
the Salmonella-containing vacuole (SCV) [51]. However,
approximately 25% of S. Typhimurium become cytosolic,
and Salmonella in the cytosol can be surrounded by ubiquitin [20]. The first autophagy receptor discovered to
target ubiquitinated Salmonella to autophagic destruction
was p62 [52]. Shortly thereafter, NDP52 was also shown to
act as an autophagy receptor that restricts the replication
of ubiquitinated Salmonella in the cytosol [10]. The unique
features of NDP52 important for bacterial autophagy are
unknown, although p62 and NDP52 may be recruited to
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distinct membrane domains surrounding bacteria [53].
Interestingly, post-translational modification may be critical for autophagy receptor function [11]. The autophagy
receptor OPTN, which seems to function more closely with
NDP52 than p62, is phosphorylated to efficiently detect
and eliminate ubiquitinated, cytosolic Salmonella [11].
The role of OPTN in other autophagy pathways, and the
general role of post-translational modifications in autophagy receptor function, remain relatively unexplored.
Independent of ubiquitin-mediated autophagy recognition, a diacylglycerol (DAG)-dependent signaling pathway
also contributes to anti-Salmonella autophagy [54]. Salmonella targeted to autophagy are indeed labeled with
either ubiquitin or DAG, suggesting that at least two
autophagy pathways independently promote bacterial
clearance. A major issue is now to investigate what other
non-ubiquitin signals may target bacteria to autophagy.
Recent work has revealed that NDP52 can be recruited to
the damaged vacuoles by Galectin 8 (LGALS8) [29]. Strikingly, this recruitment occurs independently of ubiquitin,
which is critical for NDP52 recruitment to cytosolic bacteria [10]. This suggests a temporal pattern of autophagy
recruitment (i.e. Galectin 8-mediated recruitment of
NDP52 occurs first and is followed by a ubiquitin-dependent recruitment of NDP52) and highlights the emerging
concept that different pathways of bacterial autophagy
may act at distinct steps of the infectious process, an
issue that now deserves careful characterization using
other invasive bacteria. Considering work showing that
autophagosome-like (i.e. double-membrane, LC3-positive)
structures can surround bacteria still residing within the
SCV independent of canonical phagophore generation
[55,56] (Box 1), future studies should also investigate
whether bacteria targeted by autophagy have only compromised the SCV, or have fully escaped from the SCV.
M. tuberculosis: delivery of the phagosome to the
lysosome by autophagy
The pathogenicity of M. tuberculosis, the causative agent of
human tuberculosis, is largely attributed to its ability to
survive within macrophages by arresting phagosomal maturation toward an acidified phagolysosome, and thus residing in a phagosomal compartment that maintains many
characteristics of an early endosome [57]. However, recent
studies using cryo-immunogold electron microscopy and
single-cell fluorescence resonance energy transfer (FRET)based methods have reported an ESX-1-dependent mechanism of phagosomal escape of M. tuberculosis into the
cytosol [58,59], which may lead to necrotic death of the
infected host cell [59]. Whereas M. tuberculosis can clearly
escape to the cytosol, the role of autophagy in recognizing
cytosolic M. tuberculosis and in delaying host cell necrosis
caused by cytosolic entry of M. tuberculosis has not been
investigated.
In contrast to the well-documented ability of M. tuberculosis to prevent phagosome maturation and allow bacterial survival, several studies have shown that autophagy
can help to efficiently eliminate phagosomal M. tuberculosis [60]. Indeed, the induction of autophagy by starvation,
mTOR (mammalian target of rapamycin) inhibition, vitamin D and interferon-gamma (IFNg) is reported to
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contribute to phagosome maturation and M. tuberculosis
elimination [60,61]. How mycobacteria can survive in phagosomes, but not in phagosomes having recruited the
autophagy machinery, is a key issue. It has been suggested
that cytosolic components, such as ubiquitin, p62 and
ribosomal proteins [62], may equip mycobacterial autophagolysosomes (i.e. phagosomes surrounded by a doublemembrane decorated with LC3) with potent antimicrobial
properties to abrogate M. tuberculosis survival [12]. In
agreement with this proposal, recent work has shown that
vitamin D is required for IFNg-mediated induction of
autophagy, the maturation of phagosomes and the production of cathelicidin to result in antimicrobial activity
against M. tuberculosis [63].
Despite convincing evidence obtained in vitro, a role for
autophagy in control of M. tuberculosis in vivo has yet to be
shown. This will be a critical issue, considering that clinical
isolates of M. tuberculosis have been suggested to manipulate autophagy for their own survival [64].
Legionella pneumophila: inhibition of autophagosome
maturation and exploitation of the autophagy
machinery
L. pneumophila, a Gram-negative bacterium, is the causative agent of a form of pneumonia called Legionnaires’
disease. The natural hosts of L. pneumophila are different
species of protozoa abundant in aquatic environments, and
the capacity to grow intracellularly in protozoa has selected for virulence traits that allow Legionella to also infect
humans [65].
Inside mammalian phagocytic cells, L. pneumophila
recruits vesicles emerging from the endoplasmic reticulum
(ER), and remodels Legionella-containing vacuoles (LCVs)
to evade the phagocytic pathway and support bacterial
replication [66]. LCVs in macrophages from mice resistant
to Legionella infection (e.g. C57BL/6) rapidly fuse with
lysosomes, resulting in bacterial degradation. However,
in macrophages from mice permissive to Legionella infection (e.g. A/J, which are deficient in Naip5, a NOD-like
receptor), bacteria can replicate within LCVs that do not
fuse with lysosomes. Studies have shown that these bacteria persist in LCVs that also recruit LC3 and resemble
autophagosomes, and the ability of Legionella to inhibit
maturation of these vacuoles is considered to promote
bacterial survival [67]. The precise role of Legionella effector proteins and autophagy in Legionella survival now
requires further dissection using host genotypes that are
permissive and resistant to infection.
Coxiella burnetii: exploitation of the autophagy
machinery
C. burnetii, a highly infectious Gram-negative bacterium,
is the causative agent of Q fever. An obligate intracellular
pathogen, C. burnetii enters a phagocytic pathway and
interacts with the autophagy machinery shortly after internalization [68,69]. In this case, the autophagy marker
LC3 is recruited to the Coxiella-containing vacuole. This
interaction delays fusion with lysosomes and enables bacteria to replicate [68,70]. Strikingly, the number of infected
cells, the size of the vacuoles and the bacterial load all
increase when autophagy is stimulated by rapamycin,
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highlighting the benefit of autophagy for Coxiella survival.
Similarly to L. pneumophila, C. burnetii also encodes a
functional type IV secretion system (T4SS), and C. burnetii
is likely to secrete T4SS effectors which co-opt the autophagic machinery and create a replicative niche. How Coxiella exploits the autophagy machinery for better
replication awaits investigation.
Yersinia pseudotuberculosis: promotion of bacterial
replication by autophagy
Y. pseudotuberculosis is an enteric pathogen and Y. pestis
is the causative agent of plague; both of these species
possess T3SS and deliver effectors called Yersinia outer
proteins (Yops). After internalization into host cells,
Y. pseudotuberculosis replicates inside Yersinia-containing
vacuoles (YCVs) that display markers of autophagy (i.e. a
double membrane and LC3 recruitment) [71]. When autophagy is stimulated by rapamycin, YCVs increase in size
with more replicating bacteria. When autophagy is inhibited by 3-methyladenine (3-MA), an inhibitor of phosphoinositide 3-kinases (PI3Ks), YCVs mature into an acidic
bactericidal compartment. Together, these results strongly
suggest that autophagy can promote Y. pseudotuberculosis
replication.
YCVs containing Y. pestis are also recognized by autophagy [72]. However, unlike Y. pseudotuberculosis, Y. pestis-containing YCVs may colocalize with markers of acidic
lysosomes in the absence of autophagy inhibition. This
suggests that autophagy is not involved in promoting
Y. pestis survival, in agreement with observations that
Y. pestis does not require autophagy for intracellular replication [72] and instead proliferates by suppressing innate
immune responses [73]. Together, the role of autophagy in
Yersinia intracellular survival is different between the two
species. Future work should exploit interspecies differences to investigate the autophagy of Yersinia, and a
potential role for Yops in modifying this process.
Brucella abortus: subversion of the autophagy
machinery
B. abortus is a Gram-negative, intracellular pathogen
which causes brucellosis, a zoonosis which can result in
spontaneous abortion and infertility in a wide variety of
animals. Shortly after Brucella entry into host cells in a
lipid raft-dependent manner, Brucella-containing
vacuoles (BCVs) transiently interact with endosomes,
acquire early endosomal markers, become acidified and
fuse with ER-derived membrane to establish a replicative
compartment [74]. Recent work has shown that bacteria
convert their ER-derived replicative vacuole into an
autophagosome-like compartment, called autophagic
BCVs (aBCVs) [75]. Indeed, Brucella generate aBCVs
by co-opting autophagosome initiation factors ATG1
(ULK1), Beclin1 (ATG6) and ATG14. By contrast, autophagosome elongation factors ATG4B, ATG5, ATG7, LC3B
and ATG16L1 are not required for aBCV formation. Although the mechanism by which B. abortus manipulates
this non-canonical autophagy pathway has yet to be fully
defined, the Brucella T4SS may be required for biogenesis
of aBCVs, as has previously been shown for biogenesis of
replicative BCVs [74].
Trends in Cell Biology xxx xxxx, Vol. xxx, No. x
Interestingly, the formation of aBCVs from ER-derived
BCVs is similar to the formation of autophagosomal, ERderived LCVs in the case of Legionella (see above). This
suggests that Brucella and Legionella exploit similar components of the autophagy machinery for replication and
survival [75]. The ability of pathogenic bacteria to subvert
the autophagy machinery and promote their infection
process in vivo has yet to be shown.
Staphylococcus aureus: replication in an
autophagosomal niche
S. aureus is a Gram-positive bacterium that causes a wide
range of infectious diseases and can lead to septic and toxic
shock. Classically considered an extracellular pathogen, S.
aureus has been increasingly recognized to invade cells and
replicate intracellularly [76]. After invasion of epithelial
cells, S. aureus can be found in autophagosome-like
vacuoles, characterized by double membrane and colocalization with LC3 [77]. This process is dependent on agr, a
global regulator of S. aureus virulence. S. aureus-containing autophagosomes do not fuse with lysosomes, creating a
niche for bacteria to replicate. After replication, S. aureus
eventually escape from autophagosomes into the cytoplasm and induce apoptosis-like cell death. Therefore, in
the case of S. aureus, the autophagy machinery is essential
for bacterial replication and host cell killing.
Similarly to what has been described for LLO and SLO
(see above), a-hemolysin (Hla) is a pore-forming toxin
secreted by S. aureus that can trigger autophagy [78].
Work has shown that membrane damage mediated by
Hla is required for the recruitment of autophagy markers
(e.g. LC3 labeling) to S. aureus-containing phagosomes
that do not fuse with lysosomes. Together with the fact
that Hla-induced autophagy requires ATG5 but not
Beclin1 nor PI3Kinase activity [78], this suggests the
involvement of a non-canonical autophagy pathway to
prevent the maturation of S. aureus containing autophagosomes.
Concluding remarks
Autophagy controls the fate of some intracellular bacteria,
such as Listeria, Shigella, Francisella, Salmonella and
mycobacteria, through the ATG protein-dependent machineries required for canonical autophagy (Box 1). As a
result, canonical autophagy deserves recognition as a critical component of innate immunity. By contrast, other
bacterial pathogens, such as Legionella, Coxiella, Yersinia,
Brucella and Staphylococcus, benefit from autophagy pathways, and may subvert the autophagy machinery in favor
of an infection process. These alternative outcomes highlight the molecular complexity that underlies bacterial
autophagy, and suggests possible difficulties in therapeutic modulation of autophagy to resolve bacterial infection.
Is autophagy strictly an antibacterial process in vivo?
Clearly, in vitro data show that more research is required
to answer this question (Box 3). Key molecules, mechanisms and pathways have to be tested across a variety of
cell types and bacterial pathogens. In the future, a detailed
comparative survey of the composition of the various
bacterial autophagosomes will be crucial to elucidate
the molecular features unique to the various autophagic
7
TICB-869; No. of Pages 9
Opinion
Box 3. Outstanding questions
Are there different roles for different autophagy receptors? Under
what circumstance is ubiquitination a prerequisite for autophagy
receptor recruitment?
What are the ubiquitinated proteins that allow recognition by
autophagy receptors? Are they of host or bacterial origin?
DAG and Galectin 8 are examples of non-ubiquitin signals that
may target bacteria to autophagy. What other non-ubiquitin
signals may target bacteria to autophagy? Are they all lipid-based
sensors?
Can autophagy receptors target bacteria to different autophagy
pathways? Can recognition by autophagy receptors be co-opted
for growth by bacterial pathogens?
What are the sources of membrane during bacterial autophagy?
What are the different molecules and mechanisms underlying
bacterial autophagy? Do they overlap with other processes of
autophagy, such as virophagy and/or mitophagy? What is the role
of the cytoskeleton?
Under what circumstance is autophagy antibacterial? Under what
circumstance can bacteria co-opt autophagy? Which bacterial
effectors enable survival inside autophagosomes?
How can bacterial autophagy be exploited for therapeutics and
clinical application?
pathways (Figure 2). It will also be critical to test the role of
cytokines, such as tumor necrosis factor alpha and IFNg,
and other physiological stimuli for their ability to induce
autophagy and/or autophagy receptor activity. Finally, a
major issue will be to validate the molecular and cellular
events analyzed in vitro during bacterial infection in vivo
using relevant animal models including Drosophila, zebrafish and mice. Nevertheless, the results generated from
the study of bacterial autophagy are expected to provide
fundamental advances in understanding the biology of
cellular immunity. They could also suggest the development of new strategies aimed at combating infectious
diseases, and possibly other human diseases arising from
a dysfunctional autophagic response.
Acknowledgments
Work in the Serge Mostowy laboratory is supported by a Wellcome Trust
Research Career Development Fellowship. Work in the Pascale Cossart
laboratory is supported by the Institut Pasteur, INSERM, INRA,
Fondation Louis-Jeantet and a European Research Council Advanced
Grant Award (233348).
References
1 Mizushima, N. et al. (2011) The role of Atg proteins in autophagosome
formation. Annu. Rev. Cell Dev. Biol. 27, 107–132
2 Nakatogawa, H. et al. (2009) Dynamics and diversity in autophagy
mechanisms: lessons from yeast. Nat. Rev. Mol. Cell Biol. 10, 458–467
3 Codogno, P. et al. (2012) Canonical and non-canonical autophagy:
variations on a common theme of self-eating? Nat. Rev. Mol. Cell
Biol. 13, 7–12
4 Mizushima, N. and Komatsu, M. (2011) Autophagy: renovation of cells
and tissues. Cell 147, 728–741
5 Levine, B. et al. (2011) Autophagy in immunity and inflammation.
Nature 469, 323–335
6 Mizushima, N. et al. (2008) Autophagy fights disease through cellular
self-digestion. Nature 451, 1069–1075
7 Johansen, T. and Lamark, T. (2011) Selective autophagy mediated by
autophagic adapter proteins. Autophagy 7, 279–296
8 Pankiv, S. et al. (2007) p62/SQSTM1 binds directly to Atg8/LC3 to
facilitate degradation of ubiquitinated protein aggregates by
autophagy. J. Biol. Chem. 282, 24131–24145
9 Kirkin, V. et al. (2009) A role for NBR1 in autophagosomal degradation
of ubiquitinated substrates. Mol. Cell 33, 505–516
8
Trends in Cell Biology xxx xxxx, Vol. xxx, No. x
10 Thurston, T.L.M. et al. (2009) The TBK1 adaptor and autophagy
receptor NDP52 restricts the proliferation of ubiquitin-coated
bacteria. Nat. Immunol. 10, 1215–1221
11 Wild, P. et al. (2011) Phosphorylation of the autophagy receptor
optineurin restricts Salmonella growth. Science 333, 228–233
12 Deretic, V. (2011) Autophagy as an innate immuntiy paradigm:
expanding the scope and repertoire of pattern recognition receptors.
Curr. Opin. Immunol. 24, 21–31
13 Ogawa, M. et al. (2011) Manipulation of autophagy by bacteria for their
own benefit. Microbiol. Immunol. 55, 459–471
14 Py, B.F. et al. (2007) Autophagy limits Listeria monocytogenes
intracellular growth in the early phase of primary infection.
Autophagy 3, 117–125
15 Ogawa, M. et al. (2005) Escape of intracellular Shigella from
autophagy. Science 307, 727–731
16 Birmingham, C.L. et al. (2006) Autophagy controls Salmonella
infection in response to damage to the Salmonella-containing
vacuole. J. Biol. Chem. 281, 11374–11383
17 Gutierrez, M.G. et al. (2004) Autophagy is a defense mechanism
inhibiting BCG and Mycobacterium tuberculosis survival in infected
macrophages. Cell 119, 753–766
18 Cossart, P. (2011) Illuminating the landscape of host–pathogen
interactions with the bacterium Listeria monocytogenes. Proc. Natl.
Acad. Sci. U.S.A. 103, 19484–19491
19 Gouin, E. et al. (2005) Actin-based motility of intracellular pathogens.
Curr. Opin. Microbiol. 8, 35–45
20 Perrin, A.J. et al. (2004) Recognition of bacteria in the cytosol
of mammalian cells by the ubiquitin system. Curr. Biol. 14, 806–
811
21 Birmingham, C.L. et al. (2007) Listeria monocytogenes evades killing by
autophagy during colonization of host cells. Autophagy 3, 442–451
22 Kathryn, A.R. et al. (2003) Cytoplasmic bacteria can be targets for
autophagy. Cell. Microbiol. 5, 455–468
23 Yoshikawa, Y. et al. (2009) Listeria monocytogenes ActA-mediated
escape from autophagic recognition. Nat. Cell Biol. 11, 1233–1240
24 Mostowy, S. et al. (2011) p62 and NDP52 proteins target intracytosolic
Shigella and Listeria to different autophagy pathways. J. Biol. Chem.
286, 26987–26995
25 Dortet, L. et al. (2011) Recruitment of the major vault protein by InlK: a
Listeria monocytogenes strategy to avoid autophagy. PLoS Pathog. 7,
e1002168
26 Travassos, L.H. et al. (2009) Nod1 and Nod2 direct autophagy by
recruiting ATG16L1 to the plasma membrane at the site of bacterial
entry. Nat. Immunol. 11, 55–62
27 Viala, J.P.M. et al. (2008) A bacterial pore-forming toxin forms
aggregates in cells that resemble those associated with
neurodegenerative diseases. Cell. Microbiol. 10, 985–993
28 Mizushima, N. et al. (2010) Methods in mammalian autophagy
research. Cell 140, 313–326
29 Thurston, T.L.M. et al. (2012) Galectin 8 targets damaged vesicles for
autophagy to defend cells against bacterial invasion. Nature 482, 414–
418
30 Paz, I. et al. (2010) Galectin-3, a marker for vacuole lysis by invasive
pathogens. Cell. Microbiol. 12, 530–544
31 Meyer-Morse, N. et al. (2010) Listeriolysin O is necessary and sufficient
to induce autophagy during Listeria monocytogenes infection. PLoS
ONE 5, e8610
32 Yano, T. et al. (2008) Autophagic control of Listeria through
intracellular innate immune recognition in drosophila. Nat.
Immunol. 9, 908–916
33 Dupont, N. et al. (2009) Shigella phagocytic vacuolar membrane
remnants participate in the cellular response to pathogen invasion
and are regulated by autophagy. Cell Host Microbe 6, 137–149
34 Shi, C.S. et al. (2012) Activation of autophagy by inflammatory signals
limits IL-1B production by targeting ubiquitinated inflammasomes for
destruction. Nat. Immunol. 13, 255–263
35 Mostowy, S. et al. (2010) Entrapment of intracytosolic bacteria by
septin cage-like structures. Cell Host Microbe 18, 433–444
36 Ogawa, M. et al. (2011) A Tecpr1-dependent selective autophagy
pathway targets bacterial pathogens. Cell Host Microbe 9, 376–389
37 Chen, D. et al. (2012) A mammalian autophagosome maturation
mechanism mediated by TECPR1 and the Atg12–Atg5 conjugate.
Mol. Cell 45, 629–641
TICB-869; No. of Pages 9
Opinion
38 Mostowy, S. and Cossart, P. (2012) Septins: the fourth component of the
cytoskeleton. Nat. Rev. Mol. Cell Biol. 13, 183–194
39 Stamm, L.M. and Brown, E.J. (2004) Mycobacterium marinum: the
generalization and specialization of a pathogenic mycobacterium.
Microbes Infect. 6, 1418–1428
40 Lerena, M.C. and Colombo, M.I. (2011) Mycobacterium marinum
induces a marked LC3 recruitment to its containing phagosome that
depends on a functional ESX-1 secretion system. Cell. Microbiol. 13,
814–835
41 Collins, C.A. et al. (2009) Atg5-independent sequestration of
ubiquitinated mycobacteria. PLoS Pathog. 5, e1000430
42 Santic, M. et al. (2006) Francisella tularensis travels a novel, twisted
road within macrophages. Trends Microbiol. 14, 37–44
43 Checroun, C. et al. (2006) Autophagy-mediated reentry of Francisella
tularensis into the endocytic compartment after cytoplasmic
replication. Proc. Natl. Acad. Sci. U.S.A. 103, 14578–14583
44 Naslund Salomonsson, E. et al. (2011) Type IV pili in Francisella – a
virulence trait in an intracellular pathogen. Front. Microbiol. 2,
29
45 Butchar, J.P. et al. (2008) Microarray analysis of human monocytes
infected with Francisella tularensis identifies new targets of host
response subversion. PLoS ONE 3, e2924
46 Cole, J.N. et al. (2011) Molecular insight into invasive group A
streptococcal disease. Nat. Rev. Microbiol. 9, 724–736
47 Nakagawa, I. et al. (2004) Autophagy defends cells against invading
group A Streptococcus. Science 306, 1037–1040
48 Yamaguchi, H. et al. (2009) An initial step of GAS-containing
autophagosome-like vacuoles formation requires Rab7. PLoS
Pathog. 5, e1000670
49 Nozawa, T. et al. (2012) The small GTPases Rab9A and Rab23
function at distinct steps in autophagy during Group A
Streptococcus infection. Cell. Microbiol. http://dx.doi.org/10.1111/
j.1462-5822.2012.01792.x
50 Sakurai, A. et al. (2010) Specific behavior of intracellular Streptococcus
pyogenes that has undergone autophagic degradation is associated
with bacterial streptolysin O and host small G proteins Rab5 and
Rab7. J. Biol. Chem. 285, 22666–22675
51 Brumell, J.H. and Grinstein, S. (2004) Salmonella redirects
phagosomal maturation. Curr. Opin. Microbiol. 7, 78–84
52 Zheng, Y.T. et al. (2009) The adaptor protein p62/SQSTM1 targets
invading bacteria to the autophagy pathway. J. Immunol. 183, 5909–
5916
53 Cemma, M. et al. (2010) The ubiquitin-binding adaptor proteins p62/
SQSTM1 and NDP52 are recruited independently to bacteriaassociated microdomains to target Salmonella to the autophagy
pathway. Autophagy 7, 22–26
54 Shahnazari, S. et al. (2010) A diacylglycerol-dependent signaling
pathway contributes to regulation of antibacterial autophagy. Cell
Host Microbe 8, 137–146
55 Kageyama, S. et al. (2011) The LC3 recruitment mechanism is
separate from Atg9L1-dependent membrane formation in the
autophagic response against Salmonella. Mol. Biol. Cell 22, 2290–
2300
56 Noda, T. et al. (2012) Three-axis model for Atg recruitment in
autophagy against Salmonella. Int. J. Cell Biol. 2012, 389562
57 Rohde, K. et al. (2007) Mycobacterium tuberculosis and the
environment within the phagosome. Immunol. Rev. 219, 37–54
58 van der Wel, N. et al. (2007) M. tuberculosis and M. leprae translocate
from the phagolysosome to the cytosol in myeloid cells. Cell 129, 1287–
1298
59 Simeone, R. et al. (2012) Phagosomal rupture by Mycobacterium
tuberculosis results in toxicity and host cell death. PLoS Pathog. 8,
e1002507
60 Deretic, V. et al. (2009) Autophagy in immunity against Mycobacterium
tuberculosis: a model system to dissect immunological roles of
autophagy. Curr. Top. Microbiol. Immunol. 335, 169–188
61 Deretic, V. (2011) Autophagy in immunity and cell-autonomous
defense against intracellular microbes. Immunol. Rev. 240, 92–
104
62 Ponpuak, M. et al. (2010) Delivery of cytosolic components by
autophagic adaptor protein p62 endows autophagosomes with
unique antimicrobial properties. Immunity 32, 329–341
Trends in Cell Biology xxx xxxx, Vol. xxx, No. x
63 Fabri, M. et al. (2011) Vitamin D is required for IFN-g-mediated
antimicrobial activity of human macrophages. Sci. Trans. Med. 12,
104ra102
64 Kumar, D. et al. (2010) Genome-wide analysis of the host intracellular
network that regulates survival of Mycobacterium tuberculosis. Cell
140, 731–743
65 Bruggemann, H. et al. (2006) Adaptation of Legionella pneumophila to
the host environment: role of protein secretion, effectors and
eukaryotic-like proteins. Curr. Opin. Microbiol. 9, 86–94
66 Isberg, R.R. et al. (2009) The Legionella pneumophila replication vacuole:
making a cosy niche inside host cells. Nat. Rev. Microbiol. 7, 13–24
67 Joshi, A.D. and Swanson, M.S. (2011) Secrets of a successful pathogen:
Legionella resistance to progression along the autophagic pathway.
Front. Microbiol. 2, 138
68 Gutierrez, M.G. et al. (2005) Autophagy induction favours the
generation and maturation of the Coxiella-replicative vacuoles. Cell.
Microbiol. 7, 981–993
69 Beron, W. et al. (2002) Coxiella burnetii localizes in a Rab7-labeled
compartment with autophagic characteristics. Infect. Immun. 70,
5816–5821
70 Romano, P.S. et al. (2007) The autophagic pathway is actively
modulated by phase II Coxiella burnetii to efficiently replicate in the
host cell. Cell. Microbiol. 9, 891–909
71 Moreau, K. et al. (2010) Autophagosomes can support Yersinia
pseudotuberculosis replication in macrophages. Cell. Microbiol. 12,
1108–1123
72 Pujol, C. et al. (2009) Yersinia pestis can reside in autophagosomes and
avoid xenophagy in murine macrophages by preventing vacuole
acidification. Infect. Immun. 77, 2251–2261
73 Price, P.A. et al. (2012) Pulmonary infection by Yersinia pestis rapidly
establishes a permissive environment for microbial proliferation. Proc.
Natl. Acad. Sci. U.S.A. 109, 3083–3088
74 Celli, J. and Gorvel, J-P. (2004) Organelle robbery: Brucella interactions
with the endoplasmic reticulum. Curr. Opin. Microbiol. 7, 93–97
75 Starr, T. et al. (2012) Selective subversion of autophagy complexes
facilitates completion of the Brucella intracellular cycle. Cell Host
Microbe 11, 33–45
76 Kim, H.K. et al. (2011) Recurrent infections and immune evasion
strategies of Staphylococcus aureus. Curr. Opin. Microbiol. 15, 92–99
77 Schnaith, A. et al. (2007) Staphylococcus aureus subvert autophagy for
induction of caspase-independent host cell death. J. Biol. Chem. 282,
2695–2706
78 Mestre, M.B. et al. (2010) a-Hemolysin is required for the activation of
the autophagic pathway in Staphylococcus aureus infected cells.
Autophagy 6, 110–125
79 Mijaljica, D. et al. (2011) Microautophagy in mammalian cells:
revisiting a 40-year-old conundrum. Autophagy 7, 673–682
80 Arias, E. and Cuervo, A.M. (2011) Chaperone-mediated autophagy in
protein quality control. Curr. Opin. Cell Biol. 23, 184–189
81 Husnjak, K. and Dikic, I. (2012) Ubiquitin-binding proteins: decoders of
ubiquitin-mediated cellular functions. Annu. Rev. Biochem. (in press)
82 Laplante, M. and Sabatini, D.M. (2012) mTOR signaling in growth
control and disease. Cell 149, 274–293
83 Rabinowitz, J.D. and White, E. (2010) Autophagy and metabolism.
Science 330, 1344–1348
84 Pohl, C. and Jentsch, S. (2009) Midbody ring disposal by autophagy is a
post-abscission event of cytokinesis. Nat. Cell Biol. 11, 65–70
85 Florey, O. et al. (2011) Autophagy machinery mediates macroendocytic
processing and entotic cell death by targeting single membranes. Nat.
Cell Biol. 13, 1335–1343
86 Youle, R.J. and Narendra, D.P. (2011) Mechanisms of mitophagy. Nat.
Rev. Mol. Cell Biol. 12, 9–14
87 Sumpter, R. and Levine, B. (2011) Selective autophagy and viruses.
Autophagy 7, 260–265
88 Orvedahl, A. et al. (2011) Image-based genome-wide siRNA screen
identifies selective autophagy factors. Nature 480, 113–117
89 Itakura, E. and Mizushima, N. (2011) p62 targeting to the
autophagosome formation site requires self-oligomerization but not
LC3 binding. J. Cell Biol. 192, 17–27
90 Lamark, T. et al. (2003) Interaction codes within the family of
mammalian Phox and Bem1p domain-containing proteins. J. Biol.
Chem. 278, 34568–34581
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