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Eat, kill or die: when amoeba meets bacteria


Pierre Cosson1 and Thierry Soldati2

The core function of the innate immune response, human proteomes [2]. The basic tools and strategies of
phagocytosis, did not evolve first in metazoans but rather in phagocytic cells, invented in primitive protozoan, are still
primitive unicellular eukaryotes. Thus, though amoebae used in both amoebae and mammalian phagocytic cells.
separated from the tree leading to metazoan shortly after the In strictly practical terms, Dictyostelium is a primitive
divergence of plants, they share many specific functions with macrophage.
mammalian phagocytic cells. Dictyostelium discoideum is by
far the most studied amoeba, and it is proving useful to analyze Besides the evolutionary interest of studying this long-
phagocytosis and intracellular killing of bacteria. Since the lost cousin, there are many experimental advantages in
basic the basic mechanisms involved appear extremely working with Dictyostelium amoebae. They grow at room
conserved, Dictyostelium provides novel insights into the temperature in a simple and cheap medium or in the
function of many new gene products. Bacterial pathogenicity presence of bacteria, with no need for a CO2-enriched
was certainly largely developed to resist predatory amoebae in atmosphere. They can be grown in a shaken suspension,
the environment, and this accounts for the fact that a large allowing large-scale cultures and biochemical analysis.
number of bacterial virulence traits can be studied using Their small, haploid, sequenced, and annotated genome
Dictyostelium as a host. This provides a particularly powerful [2] makes them so easily amenable to genetic analysis that
system to analyze the complex interactions between functional analysis of any given gene product most often
pathogenic bacteria and host cells, where both the includes characterization of the knockout mutant. Here,
Dictyostelium host and the bacteria can be manipulated we review two aspects of phagocyte biology for which the
genetically with relative ease. study of Dictyostelium has proven particularly useful: pha-
Addresses gocytosis and related cellular processes, and the complex
1
University of Geneva, Faculty of Medicine, Centre Médical relationships with pathogenic bacteria.
Universitaire, Dpt de Physiologie Cellulaire et Métabolisme, 1 rue Michel
Servet, CH1211 Geneva 4, Switzerland
2
Department of Biochemistry, University of Geneva, 30 quai Ernest
Born to kill: the professional phagocyte
Ansermet, Sciences II, CH1211 Genève 4, Switzerland It is classical in metazoan organisms to distinguish pro-
fessional from occasional, nonprofessional phagocytes,
Corresponding author: Cosson, Pierre but both pale in front of amoebae, which throughout
(Pierre.Cosson@medecine.unige.ch) and Soldati, Thierry
their life ingest, kill, and digest microorganisms at a rate
(thierry.soldati@biochem.unige.ch)
of at least one per minute. Initial studies of phagocytosis
focused on the dynamics of the actin cytoskeleton, a
Current Opinion in Microbiology 2008, 11:271–276 crucial parameter during cell locomotion and phagocytic
This review comes from a themed issue on
engulfment. Acanthamoeaba and Dictyostelium played a
Techniques pioneering role in establishing the function of the actin
Edited by Fred Ausubel and Bruno Lemaitre cytoskeleton in various cellular processes [3–5]. One
example is the discovery of the actin-binding protein
Available online 10th June 2008
coronin [6]. Its role in phagocytosis was established
1369-5274/$ – see front matter initially in Dictyostelium primarily on the basis of analysis
# 2008 Elsevier Ltd. All rights reserved. of knockout mutants [7], and later in mammalian cells [8].
More recently, other facets of phagocytosis have been
DOI 10.1016/j.mib.2008.05.005
studied in Dictyostelium, in particular cellular adhesion
during phagocytosis, phagosome maturation, and intra-
cellular killing.
For researchers studying immune functions, considering
Dictyostelium as a model system may seem inappropriate. Phagocytosis and adhesion: integrins in
After all, this unicellular soil amoeba diverged from the amoebae?
path leading to metazoans shortly after the plant–animal Adhesion to a particle is the first step of the phagocytic
split, and before fungi divergence. Yet, starting with the process. At least three membrane proteins (Phg1, SadA,
seminal observations of Metschnikoff [1], it has been and SibA) [9–11] are essential for cell adhesion and
evident that amoebae and human phagocytic cells share phagocytosis, and SibA is probably the main adhesion
several unique functions, such as the ability to crawl on a receptor [11]. Interestingly, SibA presents features of
substrate or to ingest microorganisms by phagocytosis. integrin b chains, notably an extracellular VWA domain
This resemblance is also supported by the particularly and a conserved cytoplasmic domain. On the cytoplasmic
high degree of conservation between the Dictyostelium and side, like integrins, SibA binds to a complex between

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272 Techniques

talin and the FERM-containing myosin VII, both of suggested an alternative killing mechanism: deficiencies
which are essential for adhesion and phagocytosis [12– in the ability of NADPH-oxidase to produce reactive
14]. The emerging picture is remarkably similar to integ- oxygen species (ROS) lead to inefficient intracellular
rin-dependent phagocytosis in mammals (e.g. CR3- bacterial killing. However, it has proven difficult to
mediated phagocytosis) and the parallel might extend distinguish experimentally between the direct bacteri-
further, since Rap1 (Ras-related protein 1) also seems to cidal effects of ROS and their indirect effects through
be involved in both cases [15]. Dictyostelium is thus changes in ionic composition of the phagosome lumen.
bringing a new perspective to our knowledge of integ- Despite rises and falls in the dominance of each theory,
rin-dependent adhesion, a phenomenon so far only stu- the currently prevailing model is that lysosomal enzymes
died in metazoans. It is also offering a number of are the key players, while NADPH-oxidase regulates the
promising leads, since several other genes essential for ionic composition of the phagosomal milieu (see [25] for
adhesion have been identified in Dictyostelium (e.g. TM9 an insightful review).
proteins [9]) that have not yet been studied in mamma-
lian systems. Dictyostelium avidly engulf and kill most bacteria
(Figure 1), offering a simple but genetically tractable
A well-orchestrated maturation program model to investigate intracellular killing. Remarkably,
The endocytic and phagocytic pathways of Dictyostelium Dictyostelium NADPH-oxidase knockout mutants are
exhibit marked similarities with mammalian cells [16], unaffected in their efficiency of Klebsiella pneumoniae
and have been extensively studied [17,18]. A number of killing [26], and they can grow on a wide variety of
studies have defined the exact composition of phago- bacterial strains, suggesting that killing is largely inde-
somes at each step. During the formation of phagosomes pendent of ROS production at least in the experimental
some membrane proteins are selectively excluded [19], conditions used in these studies. What are then the
while others are delivered in the first minutes following superefficient bactericidal strategies of Dictyostelium?
phagosome closure [20]. This is then followed by suc- The characterization of mutants deficient in Klebsiella
cessive maturation steps involving sequential delivery killing identified only two genes so far: KIL1 and
and retrieval of components to and from phagosomes. PHG1 [26]. They encode a sulfotransferase and a TM9
Immunocytochemical profiling of signaling, cytoskeletal, (nine transmembrane domains) protein, respectively, but
and trafficking proteins defined at least three distinct their mode of action in Dictyostelium as well as in mammals
maturation steps [21], while exhaustive proteomic remains to be established. Interestingly, Phg1 and Kil1
analysis established a dynamic record of phagosome are dispensable for the killing of a number of other
protein composition [22]. Today the phagosomal compo-
sition is established with better temporal resolution in
Figure 1
Dictyostelium than in mammals. The major focus of many
laboratories is now to link this extensive knowledge of
phagosome composition to its specific functions. From
that perspective, comparing phagosomal proteomes in
evolutionarily distant organisms might allow to dis-
tinguish the elements linked to its conserved functions
(e.g. bacterial killing) from those dedicated to more
organism-specific functions (e.g. antigen presentation in
mammals). The relative ease with which Dictyostelium
knockout mutants can be generated will certainly be
useful to test the putative role of specific gene products,
as was done for example to establish the role of trimeric G
proteins in phagocytosis [22].

Killing: Dictyostelium likes it raw


For amoebae as well as for mammalian phagocytes, pha-
gocytosis is a prelude to intracellular killing, a still largely
mysterious phenomenon. Lysosomal hydrolases are
delivered to the bacteria-containing phago-lysosomes
and were therefore initially believed to play a key role The various steps of phagocytosis are apparent in this electron
in killing. Cathepsin G and elastase are involved in the micrograph of a Dictyostelium cell in the process of internalizing
intracellular killing of S. aureus and C. albicans, respect- Klebsiella bacteria: adhesion of the amoeba to the bacteria, engulfment
of a bacteria in a phagosome, killing and digestion of internalized
ively [23], and secreted b-hexosaminidase has been bacteria. In Dictyostelium, undigested material is then exocytosed in the
implicated in the killing of mycobacteria [24]. The study extracellular medium. Imperfect fixation of the cytosol is common in
of patients suffering from chronic granulomatous disease Dictyostelium and can be noticed in some regions of the cell.

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Eat, kill or die: when amoeba meets bacteria Cosson and Soldati 273

bacteria, suggesting that different mechanisms are used

Downstream of Gram-peptidoglycans, NF-kappaB insect immune defence pathway


to kill various kinds of bacteria.

Kinase, mammalian MAPK pathway, positive regulator of NF-kappaB cascade


Secreted receptor for yeast polymeric beta-(1,3)-glucans, insect TLR pathway
Scavenger and pattern recognition receptor, mammalian co-TLR signaling
Today, in mammalian and in Dictyostelium cells, intra-
cellular killing is still a largely unexplored field. It is too

TNF receptor-associated factor 6, signaling downstream of TLR–NLR


Cytosolic co-chaperone, resistance (R) gene-mediated plant defence
early to know if Dictyostelium will help us understand how

Cytosolic chaperone, resistance (R) gene-mediated plant defence


mammalian phagocytes kill bacteria, or lead us to the
discovery of new mechanisms, unparalleled in mammals.

And then things turned ugly. . .


Imagine a planet populated with the ancestors of pre-
sent-day bacteria, fungi, and plants, all shyly hidden

Function

Transcription factor, plant immune response


within a rigid cell wall. Imagine amoebae irrupting in
this rather peaceful world, capable of engulfing and
killing virtually any other cell. What a feast it must have
been for the predators, and what a terrible fate for cells
ill-equipped to deal with such a situation. All microor-
ganisms must have been under strong selective pressure
to develop the traits needed to survive an encounter with
phagocytic cells. These include not only passive (resist-
ant capsule) or active (toxin secretion) defense mech-
anisms but also the ability to replicate directly within the
predator cell. This might account for one of the most
sinister paradoxes of microbiology, that many environ-
mental microorganisms, though they only exceptionally
infect mammals, have nevertheless apparently evolved
E-value

2E 19
3E 48

1E 17
2E 17

5E 04
sophisticated mechanisms to do so (for a more extensive

6E-63
0.044
review see [27]). One of the clearest examples is the
0

intracellular replication of Legionella. How can a bacter-


NCBI accession

ium that did not infect humans before the invention of


NP_001043620
NP_001063503
NP_001008162

air conditioning present such sophisticated strategies to


number

NP_178433

NP_000063
NP_573394
NP_523986
NP_976226

transform the harmful phagosomal environment into a


cozy replication niche? The answer is clearly related to
the observation that amoebae are the natural host of
Legionella. Indeed, the virulence traits of Legionella (and
D. melanogaster
D. melanogaster

of many other pathogens) were probably initially


Of species

X. tropicalis

selected to fight amoebae long before the appearance


H. sapiens

H. sapiens
A. thaliana
O. sativa
O. sativa

of metazoans. In many cases, amoebae represent the


Has two additional paralogues, DDB0191198 and DB0191189.

natural host of pathogens, and human infections are only


an accidental encounter.
Orthologous

A long list of pathogens


WRKY3

MEKK3
GNBP3
to

Not surprisingly, many pathogens have turned out to use


Hsp90
Traf-6
SGT1

CD36
Imd

similar virulence mechanisms to fight Dictyostelium and


Family greatly expanded in D. discoideum.

mammalian hosts (reviewed recently in [28,29]). These


include extracellular pathogens (e.g. Pseudomonas aerugi-
HATPase_c, HSP90

PB1, S_TKc, WD40

nosa), or bacteria capable of intracellular replication like


Conserved

TPR, p23, SGS


domains

Death-domain

Legionella. In several cases, Dictyostelium has been instru-


mental in analyzing bacterial virulence, allowing for
zf-TRAF
WRKY

example the discovery of the role of the type VI secretion


GH16
CD36

system of Vibrio cholera pathogenesis [30,31]. Many key


findings concerning Legionella pathogenicity have been
DDB0191500 b
DDB0252616 a

made in Dictyostelium (reviewed in [32,33]), particularly


Dictyostelium

DDB0220001
DDB0190154
DDB0191163

DDB0189971
DDB0206476
DDB0220118
dictyBase Id
discoideum

when traditional cell culture models had failed to deliver


Table 1

clear answers. For example, the use of Dictyostelium


knockout mutants demonstrated that autophagy is dis-
b
a

pensable for Legionella replication [34]. Dictyostelium has

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274 Techniques

also been instrumental in revealing how Legionella manip- Box 1 Is there a molecular machinery for microbe recognition in
Dictyostelium?
ulates host cell phosphoinositide metabolism [35], and
facilitated the discovery of a nonlytic release mechanism It is now well established that phagocytes of animal innate immune
for spreading the infection [36,37]. The analysis of the systems can recognize commensal and pathogenic microbes with
which they interact. From an evolutionary perspective, it might seem
transcriptional response of Dictyostelium infected with logical for protozoan to be also equipped with the molecular
Legionella also provided new insights into the infectious equipment necessary to recognize microbe-associated molecular
process [38]. patterns in order to distinguish food from pathogens. Surprisingly,
this has virtually not been studied so far in Dictyostelium, but a
number of likely orthologs and weaker homologs to proteins involved
Probably one of the most original approaches has been to
in innate immunity can be recognized. Table 1 lists a few
use amoebae as microbial hosts to identify new pathogens Dictyostelium orthologs of genes that have been involved in
[39], a strategy implicitly assuming that bacteria capable pathogen recognition in plants, insects, or vertebrates. In all these
of surviving within amoebae are also potential human instances, it remains to be seen if these gene products do participate
pathogens. in pathogen recognition in Dictyostelium. In addition, many
Dictyostelium proteins exhibit domains conserved in proteins
involved in immune functions, such as TIR, LysM (involved in
Surviving infection: resistance genes peptidoglycan-binding, e.g. DDB0184330), Saposin B1 and B2
Phagocytic cells are confronted frequently with bacteria, (involved in membrane lysis, e.g. DDB0169339), or C-type lectin
and the result of this encounter largely determines the domains (involved in recognition of fungi and mycobacteria, e.g.
DDB0189466). Finally, proteins with leucine-rich repeats (LRR) such
pathogenic potential of any given bacteria. Little is
as TLRs and NLRs form a large group of innate response genes in
known today about cell-intrinsic resistance mechanisms: various organisms. Among the 163 LRR-containing proteins in the
only a few potential resistance genes are identified, and Dictyostelium genome, 45 have a transmembrane domain, but none
their exact function often remains unclear. One of the of them exhibits a cytoplasmic TIR domain such as found in TLRs.
best studied examples is N-Ramp1, a metal transporter Nevertheless, some have homologies to plant flagellin surface
receptors that bear homologies to mammalian TLR5 (DDB0204296)
present in the phagosomal membrane in mammalian or to other innate immune response receptors (DDB0232377).
cells, whose loss leads to enhanced replication of some
ingested bacteria [40]. An N-Ramp1 knockout Dictyoste-
lium is also more prone to sustain intracellular bacterial
replication [41], providing an additional tool to study N- be used for the study of both host defenses and pathogen
Ramp1 function, and indicating that at least some resist- virulence strategies.
ance mechanisms are conserved from amoebae to
humans. Since not all microorganisms are good to eat, Dictyostelium
would certainly benefit from the ability to recognize patho-
This functional conservation suggests that resistance gens and to modulate its response accordingly, though this
genes could be identified in genetic screens in Dictyoste- is still largely a matter of speculation. At least one recent
lium, then further characterized in mammalian cells. For study points to mechanisms allowing recognition of patho-
example, recent studies of Mycobacterium marinum, a close gens by amoebae [45]. In addition, the Dictyostelium gen-
cousin of M. tuberculosis, indicated that pathogenic myco- ome exhibits a number of putative elements of pathogen
bacteria use similar mechanisms to invade mammalian recognition pathways (see Box 1). The characterization of
macrophages and Dictyostelium [42,43]. Vacuolin (a Dic- mechanisms by which Dictyostelium could recognize diverse
tyostelium flotillin-like protein) was shown to accumulate microorganisms would certainly bring a new dimension to
at the membrane of the mycobacterial replication niche, the study of its encounter with pathogens.
allowing direct observation of the vacuole growth and
rupture and of the release of bacteria into the cytosol [43]. Conclusion
The generality of these findings was confirmed in How many ways are there for a phagocyte to kill bacteria?
infected human blood monocytes where selective How many ways for pathogenic bacteria to escape killing?
accumulation of flotillin-1 around M. marinum vacuole What determines phagocyte resistance to pathogens? In
followed by membrane rupture was also seen. Genetic Dictyostelium, the answer to each of these questions will be a
disruption of the vacuolin gene rendered Dictyostelium long list of gene products. As these lists start growing, we
more immune against infection, indicating that the pre- will begin to discern how many different strategies phago-
sence of vacuolin is important for M. marinum to success- cytes have evolved to survive in the great game of evolution.
fully arrest phagosome maturation. The same study also
revealed a host resistance factor [43], since the absence of
RacH rendered Dictyostelium more susceptible to M. mar- Acknowledgements
We would like to thank members of our research groups for helpful
inum proliferation. The RacH GTPase has been reported discussions, and Bianca Habermann (Bioinformatics, Max Planck Institute
to play a role in the regulation of the actin cytoskeleton, in of Molecular Cell Biology and Genetics, Dresden, Germany) for her help
early phagosomal acidification and in the control of the with protein homology searches. This work was supported by grants from
the Fonds National Suisse pour la Recherche Scientifique (to PC and TS).
morphology and function of vacuolin-positive compart- Both of our laboratories participate in the NEMO network, supported by
ments [44]. These results illustrate how Dictyostelium can the 3R Foundation.

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Eat, kill or die: when amoeba meets bacteria Cosson and Soldati 275

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276 Techniques

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Current Opinion in Microbiology 2008, 11:271–276 www.sciencedirect.com

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