Regulatory Circuits That Enable Proliferation of the
Fungus Candida albicans in a Mammalian Host
J. Christian Pe ´rez*, Alexander D. Johnson
Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, United States of America
A Rich Fungal Microbiome within Us
The human body harbors trillions of microorganisms—a rich
and diverse microbiota that plays key roles in human health and
disease. All three domains of life—eukaryotes, archaea, and
bacteria—are represented in this large assembly of microbes.
Among eukaryotes, fungi are particularly prominent residents of
the human body. For example, 101 species belonging to 85 fungal
genera have been found in the oral cavity of healthy people .
Similarly, .200 fungal species (half of them novel or unnamed)
representing at least 50 genera have been found in the murine gut
. By comparison, there are ,150 bacterial species (or
phylotypes) inhabiting the mouths of healthy individuals  and
,500–1000 bacterial species in their intestines [4,5]. Although the
methodologies differ, as do the classification schemes, it seems that
the taxonomical diversity of the fungal component of the
microbiota may not be so different from its bacterial counterpart,
even though the latter has been much more heavily catalogued.
With the exception of a handful of species, however, very little is
known about the biology of the members of the human
‘‘mycobiome’’ (i.e., fungal microbiome) and even less about the
interactions that they establish with the human host.
In this review we focus on the most widely studied fungus that
inhabits the human body, Candida albicans. Most, if not all, healthy
adults carry this species asymptomatically in their gastrointestinal
(GI) tract. Despite its status as a commensal microorganism, C.
albicans is also a leading cause of mucosal disease in healthy hosts
and systemic, life-threatening infections in individuals with
debilitated immune systems, such as AIDS patients or people
receiving chemotherapy. Not surprisingly, it is this ‘‘virulent’’ or
‘‘pathogenic’’ facet of C. albicans that has traditionally received the
most attention from researchers. More recently, however, several
laboratories have begun to explore the tactics that the fungus uses
to proliferate in its more common niche, the mammalian gut.
These studies have uncovered unexpected connections between
the commensal and pathogenic lifestyles. We highlight some of
these findings here.
Regulation of Nutrient Acquisition Is Pivotal for
Colonizing the Mammalian Gut
The gut is a crowded environment. In the colon alone, C.
albicans cohabits with ,1011microbial cells per milliliter of
intestinal content . Food resources may be plentiful but
competition is obviously high (reviewed in ). The ability of C.
albicans to colonize and proliferate in the GI tract has been studied
in mice receiving antibiotics orally; while these animals are not
natural hosts of C. albicans, they likely serve as reasonable proxies.
Because transcription regulators are central elements within the
gene network of any organism, the use of them as entry points to
the dissection of this trait has proved an effective strategy. A recent
screen carried with C. albicans in a mouse model of GI tract
colonization  evaluated 77 transcription regulator mutants for
their ability to endure in the intestine for several weeks after oral
inoculation. This group of mutants was chosen because none of
them showed overt defects under a wide variety of conditions in
vitro , hence they would be candidates for regulating circuits
needed specifically in vivo. The screen identified six transcription
regulators required for C. albicans to colonize the murine gut, four
of which (RTG1, RTG3, TYE7, and LYS144) controlled the
expression of genes responsible for the acquisition and metabolism
of nutrients, particularly carbon and nitrogen sources. A
significant fraction of the target genes of these regulators (identified
by full-genome chromatin immunoprecipitation experiments) are
indeed upregulated in C. albicans cells growing in the mouse
intestine . It is noteworthy that none of the four regulators is
required for the species to grow under standard laboratory
conditions , which reinforces the notion that significant
resources are devoted to simply obtain food in the GI tract. It is
plausible that these stringent conditions are set, at least in part, by
the presence of a competing gut microbiota; consistent with this
idea, genes that enable murine gut colonization by intestinal
microbes such as Citrobacter rodentium—a natural mouse pathogen—
are not required to colonize the intestines of germ-free mice .
Managing Iron Toxicity in the Mammalian Gut
Iron is an essential nutrient for microorganisms but at high
levels it can become extremely toxic. The abundance and
availability of iron vary greatly in different locales of the human
body: relatively high levels (,1024M) are found in the GI tract
as the majority of dietary iron is not absorbed , whereas the
concentration in the bloodstream is orders of magnitude lower
(,10224M free Fe3+) . C. albicans, an organism that typically
inhabits the gut but that can also cross into the bloodstream,
harbors a regulatory circuit composed of three transcription
regulators (SFU1, SEF1, and HAP43) that controls the expression
of iron uptake genes and iron utilization genes . SFU1 is
required to persist in the GI tract  and for resistance to iron
Citation: Pe ´rez JC, Johnson AD (2013) Regulatory Circuits That Enable
Proliferation of the Fungus Candida albicans in a Mammalian Host. PLoS
Pathog 9(12): e1003780. doi:10.1371/journal.ppat.1003780
Editor: William E. Goldman, The University of North Carolina at Chapel Hill,
United States of America
Published December 19, 2013
Copyright: ? 2013 Pe ´rez, Johnson. This is an open-access article distributed
under the terms of the Creative Commons Attribution License, which permits
unrestricted use, distribution, and reproduction in any medium, provided the
original author and source are credited.
Funding: JCP was supported by a Postdoctoral Fellowship from the American
Heart Association and a Postdoctoral Research Award from the UCSF’s Program
for Breakthrough Biomedical Research (PBBR). C. albicans work in the Johnson
laboratory is supported by US National Institute of Allergy and Infectious Diseases
grant RO1 AI049187 (ADJ). The funders had no role in study design, data
collection and analysis, decision to publish, or preparation of the manuscript.
Competing Interests: The authors have declared that no competing interests
* E-mail: firstname.lastname@example.org, email@example.com (JCP)
PLOS Pathogens | www.plospathogens.org1December 2013 | Volume 9 | Issue 12 | e1003780
toxicity in vitro , suggesting that the primary role of this circuit
in the gut is to protect C. albicans from iron’s noxious effects.
SEF1, on the other hand, is required not only for the fungus to
endure in the intestine but also for full virulence after
bloodstream infection . Thus, C. albicans uses a common
circuitry to balance its need to uptake iron in one niche (i.e., in
the bloodstream) and protect itself from its toxic effects in other
locale (i.e., the GI tract).
In addition to circuits that govern carbon, nitrogen, and iron
acquisition, gene products that function as adherence molecules
 and in the detoxification of reactive oxygen species  have
also been shown to play roles in gut colonization. In fact, ECE1
and SOD5, which influence adhesion and protection against
reactive oxygen species, respectively, are among the most highly
upregulated genes when C. albicans is growing in the GI tract
compared to standard laboratory conditions [15,16]. Host cells
such as macrophages and neutrophils produce reactive oxygen
species, raising the possibility that SOD5’s role may be to defend
the fungus from these molecules  during colonization of the GI
tract. Other transcription regulators reported to play roles in gut
colonization have been shown to be rather pleiotropic (e.g., EFG1
, CPH2 , and EFH1 ).
A Molecular Basis for the Interplay of
Commensalism and Pathogenicity
Many systemic, life-threatening infections in humans are
caused by the very same bacteria or fungi that compose their
microbiota. That is, these opportunistic pathogens reside in the
host as harmless commensals (typically on mucosal surfaces) but
can cross the host’s protective barriers and colonize internal
organs causing serious disease. The GI tract, for instance, appears
to be the ultimate source of the majority of deep-seated C. albicans
infections [18,19]. Do entirely different gene sets account for the
seemingly disparate behaviors of C. albicans as commensal versus
Observing phenotypes on a gene-by-gene basis provides a
mixed answer. On the one hand, transcription regulators such as
EFG1 [16,17], SEF1 , RTG1, RTG3, and HMS1  are
necessary for full virulence in mouse models of systemic infection
(i.e., as a pathogen) as well as for GI tract colonization (i.e., as a
commensal). On the other hand, mutant strains lacking the
regulators TEC1 or LYS14 show reduced virulence in models of
systemic infection but display no obvious defect in colonizing the
murine GI tract [8,10,20]. The converse is true for C. albicans
strains lacking TYE7 or SFU1 or ectopically expressing EFH1
[8,14,15]. However, genes do not function in isolation, and a
clearer picture emerges by considering the existing links among
some of these regulators.
Five transcription regulators that displayed a significant
phenotype ‘‘exclusively’’ in association with the host  form a
tightly knit circuit (Figure 1). In this circuit, the regulators are
connected with one another irrespective of whether they are
required for GI-tract colonization, systemic infection, or both.
This observation implies that significant portions of the ‘‘patho-
genic’’ and ‘‘commensal’’ lifestyles are coupled and controlled by
the same core circuitry. Thus, from a gene network perspective,
commensalism and pathogenicity do not appear to represent fully
independent traits but rather are intertwined. The close links
between these two traits may reflect the natural history of C.
albicans: its association with mammals is ancient  and the
selection pressure on the fungus has likely been as a commensal
organism. Thus, it is plausible that the functions employed by C.
albicans to spread from the human gut into systemic infections rely
on the same regulatory circuitry that evolved to enable growth in
the host as a commensal organism. Consistent with this idea, some
Figure 1. Gene regulatory network directing C. albicans proliferation in a mammalian host. (A) Gene network composed of the
transcription regulators RTG1/3, HMS1, ZCF21, and TYE7 (orange circles) and their target genes (black circles) as determined by full-genome chromatin
immunoprecipitation. Thin lines indicate binding of the specified regulator to a target gene. About a quarter of the genes in the network (those in the
middle) are targets shared by two or more regulators. (B) Relationships among the ‘‘master’’ regulators at the core of the network. Arrows represent
protein-DNA interactions. Notice that the circuit displays multiple autoregulatory, feed-forward, and feedback loops. Adapted from .
PLOS Pathogens | www.plospathogens.org2December 2013 | Volume 9 | Issue 12 | e1003780
impairment in the host immune system is typically required for C. Download full-text
albicans to be fully pathogenic.
Circuit in C. albicans Has Structure in Common
with Circuits Underlying Cell Differentiation
It has been shown that at the heart of the ability of C. albicans to
proliferate in the mammalian host lies a highly interconnected
transcriptional circuit composed of five transcription regulators
(Figure 1). The distinctive feature of this circuit is the existence of
multiple connections among all its components; that is the
‘‘master’’ regulators control one another (in addition to their
target genes), and the target genes are typically bound by multiple
master regulators. Thus, the circuit has many feed-forward and
feedback loops. By contrast, many ‘‘textbook’’ genetic circuits—
those that most scientists have grown used to—consist of simple,
unidirectional relationships among their components, making their
behavior more predictable. Because of the distinctly interwoven
appearance of the C. albicans circuit, it is difficult to predict its
behavior without extensive knowledge of the parameters (e.g.,
concentration of proteins, affinity constants, and the like). It is
noteworthy that the overall topology resembles other circuits
known to direct well-established cell differentiation processes such
as white-opaque switching  and biofilm development  in
C. albicans, filamentation in S. cerevisiae , and embryonic
development in metazoans (e.g., see ). The fact that disparate
functions in divergent organisms rely on a similar network
architecture suggests that these transcriptional circuits may share
common, underlying features. It is possible, for example, that the
network structure enables the integration of multiple internal and
external cues to then specify the precise pattern of target gene
The study of opportunistic pathogens such as the fungus C.
albicans, which can proliferate in disparate niches of the host either
as a commensal or a pathogenic organism, allows us to genetically
dissect the features of these two ways of life as well as to reveal the
links between them. The results thus far suggest that there may be
no clear distinction between the genetic circuitries employed
during ‘‘harmless’’ proliferation in the gut or ‘‘disease-causing’’
growth after bloodstream infection. Rather, a single highly
interconnected transcriptional circuit (one whose structure resem-
bles others that orchestrate cell differentiation) may govern
proliferation in all niches of the mammalian host.
We thank an anonymous reviewer for valuable comments on the
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