This document summarizes recent research on Chlamydia's type III secretion system (T3SS) and effector proteins. It discusses three key findings: 1) A cryo-electron tomography study revealed that Chlamydia elementary bodies are polarized with T3SS arrays oriented towards the host cell membrane during entry. The arrays redistribute as the bacteria differentiate within cells. 2) A novel effector protein, TepP, was identified that is secreted early in infection and interacts with host cell signaling proteins. Infection with TepP-deficient bacteria altered host gene expression of immune response genes. 3) Chlamydia downregulate MHC-I expression on infected and uninfected cells through

1. New evidence for an archaic secretion system: Recent insights on Chlamydia
entry and immune evasion mediated through the T3SS and effector proteins
Connor Ratycz
Department of Biological Science,
University of Notre Dame, Indiana
Highlights
 Chlamydia EBs are polarized, with
increased periplasmic space and
unique T3SS arrays contacting host
cell membrane
 TepP is a novel T3SS effector protein
with innate immune gene regulation
properties
 Chlamydia downregulate MHC-I
expression in infected and uninfected
host cells through unidentified,
soluble factors
Summary
Chlamydia spp. are obligate,
intracellular pathogens of a wide variety of
eukaryotic hosts. Primarily, the human
Chlamydia pathogens are C. trachomatis, the
agent of sexually transmitted disease and
blindness, the respiratory pathogen C.
pneumoniae, and C. psittaci, the zoonotic
agent of an uncommon and often fatal
pneumonia. In order to efficiently infect host
cells and maintain infection, Chlamydia have
developed an arsenal of methods to subvert
and evade the host defenses. One of these
weapons, the type III secretion system, is
found in all chlamydial genomes and appears
to be an important contributor to chlamydial
virulence and infection. The rise of new
findings may be hurdled due to the difficulty
in genetic mutagenesis of Chlamydia and the
struggle to isolate the chlamydial T3SS. This
review highlights the recent advances made
by three studies that reveal how the T3SS is
organized during entry of elementary bodies
into host cells, and the role of specific T3SS
effector proteins in maintain chlamydial
infection through disrupting the immune
response.
Introduction
Originally classified as viruses,
members of the family Chlamydiaceae are
obligate intracellular, Gram-negative
bacteria that are intracellular parasites of
humans and animals throughout the world.
Chlamydia trachomatis, C. pneumonia, and
C. psittaci are three species of the
pathogenic bacteria that are associated with
human disease. Specifically, infections with
C. trachomatis serovars A-C cause ocular
infections, while serovars D-K/L1-L3 cause
genital infection which can have been shown
to lead to blindness and sexually transmitted
disease, respectively (Brunham and Rey-
Ladino, 2005). Chronic infection and
inflammation from sexually transmitted C.
trachomatis can lead to pelvic inflammatory
disease, eventual tissue scarring, and
infertility. In addition, C. pneumonia is a
ubiquitous respiratory bacteria which has
been shown to cause mild pneumonia, while
C. psittaci is acquired rarely through avian
reservoirs/vectors which can lead to fatal,
uncommon pneumonia (Kuo et al., 1995).
The diversity of Chlamydia host infections
and seemingly widespread distribution of
Chlamydia-mediated human disease
illustrate that Chlamydia spp. represent a
successful group of intracellular pathogens
which have evolved to adapt to eukaryotic
host systems. As obligate intracellular
pathogens with a minimal genome, it is
believed that many distinct Chlamydia
factors interact to manipulate host cell
biology, mediate entry into host cells,
subvert host defenses, and create a suitable

2. 2 Connor Ratycz
intracellular environment to support the
bacteria’s harsh lifestyle (Stephens et al.,
1998).
Overall, much research has been
performed to elucidate the molecular
mechanisms that contribute to the overall
success of these virulent pathogens to live
within host cells. First identified by Hsia et
al. (1997) in C. caviae GPIC, the type III
secretion system (T3SS) has since been
discovered in all Clamydia spp. genomes
(Stephens et al. 1998; Read et al., 2000;
Read et al., 2003; Thomson et al., 2005;
Azuma et al., 2006) and has shown to be a
crucial mechanism in the Chlamydia arsenal
for promoting virulence during infection
(Wolf et al., 2006).
Although I will describe the T3SS in
brief, the purpose of this review is to
illustrate recent scientific findings made to
further understand the role of the
Chlamydia-T3SS in the context of
Chlamyida spp. infections, therefore I refer
readers to excellent, detailed reviews
regarding the assembly, structure, and
mechanics of the T3SS (Burkinshaw and
Strynadka, 2014; Galan et al., 2014). The
first T3SS was discovered in Yersinia spp.
by Hueck (1998) through genomic analysis
followed by characterization of the virulent
Ysc-Yop system. It was the Ysc-Yop system
that allowed researchers to discover a
mechanism utilized by bacteria to hijack
host cells. Found in a wide variety of Gram-
negative bacterial species, the T3SS is
primarily a virulence determinant that acts
as a “specialized nanomachine” with a
needle to deliver antihost effector proteins
from the pathogen into the host cell
cytoplasm to modify cellular processes
(Galan et al., 2014). In short, the T3SS
structure requires four main components that
are necessary for the delivery of effector
proteins (ancillary components, multipartite
core secretory apparatus, needle and tip
complexes, and translocon proteins). In
addition, the activity of the fully assembled
system is often regulated through contact of
bacterial-host target molecules (Ghosh,
2004).
Due to the intracellular lifecycle of
Chlamydia spp. which make in vitro culture
difficult, and the lack of a routine method
for mutagenesis, understanding the role of
the T3SS during infection and lifecycle
development have been difficult. In this
review, I will focus recent findings which
have been made in the last few years
regarding the chlamydial T3SS and
pathogenesis during Chlamydia infection.
Chlamydia entry into host cells: insight
into the distribution and architecture of
T3SS in EBs
All Chlamydia species have a
unique, biphasic developmental cycle during
infection. Early on, infection occurs when
host cells are invaded by highly infectious
Chlamydia particles known as elementary
bodies (EBs). Once inside, the EBs
differentiate into reticulate bodies (RBs) and
manipulate the intracellular environment of
the cell to form a parasitophorous,
membrane bound vacuole referred to as an
inclusion. The RBs undergo a number of cell
divisions before they differentiate back to
EBs, which are then released upon cell lysis
for the subsequent infections (AbdelRhaman
and Belland, 2005). The entry of Chlamydia
into nonphagocytic epithelial cells occurs
via attachment of the pathogen to the cell
surface followed by alterations of the host
cell membrane to engulf the pathogen. Early
experiments provide evidence that the T3SS

3. 3 Connor Ratycz
is involved in Chlamydia entry by detecting
invasion-related effector proteins in the host
cell cytoplasm such as the transolcated
actin-recruiting phosphoprotein (TarP) and
CT694 (Clifton et al., 2004). TarP and
CT694 are secreted almost immediately
upon bacterial contact with host cells and
the administration of anti-TarP antibodies
inhibits successful invasion of Chlamydia
(Clifton et al., 2004). Although it is believed
the T3SSs mediate bacterial entry, it was not
known, until recently, how T3SSs are
organized spatially within EBs and how the
arrangement of T3SSs differ in RBs.
As previously mentioned, creating
Chlamydia spp. mutants and isolating the
Chlamydia T3SS are quite difficult. Nans et
al. (2014), using a cryo-electron tomography
analysis, were the first researchers to
examine T3SSs at the EB surface during
host cell invasion in greater detail. The
authors grew HeLa cells on electron
microscopy (EM) grids which were then
infected with C. trachomatis LGV2 post-
egress EBs and then underwent plunge-
freezing (Nans et la., 2014). To assess the
baseline structure of the EBs, the authors
applied the cryo-electron tomography
technique to egressed EBs without HeLa
cells. This revealed that, in the absence of
host cells, the EB structure appears to
maintain a polarization by which one end of
the EB has an increase in periplasmic space
of ~29 nm. In addition, this widened space
was reported to house an array of fifteen to
thirty ~40 nm projections that were
identified as T3SSs (Nans et al., 2014). The
EBs were then cultured in the presence of
host cells to assess how EB-host cell contact
affects T3SS distribution during the early
stages of entry. In presence of HeLA cells,
EBs were found to universally orient their
T3SS array toward the host plasma
membrane, including EBs that were not
directly next to a host cell (Nanes et al.,
2014). This observation suggests orientation
of T3SSs is not exclusively dependent upon
adhesion. Analysis of the early entry process
via cry-electron tomography methods
revealed diverse host structures such as
phagocytic cups, filopodia, and membrane-
ruffling are responsible for internalization of
EBs (Nans et al., 2014). This provides
further evidence for the idea that T3SS
effectors such as TarP, CT166, and CT694
are critical components required for host cell
entry as many of these cellular structures are
mediated by Rac1 GTPase signaling.
Unfortunately, the authors do not suggest
whether the intermediate events of various
host cell internalization events represent
sequential assemblies or independent
mechanisms. Because the RBs are thought
to utilize the T3SS within the inclusion to
hijack the cell and the membrane structure is
different between EBs and RBs, it is likely
that the fate of the T3SS array is altered in
RBs. The authors also attempt to provide
details regarding the morphological
transition that accompany early EB
differentiation within host cells. In the first
few hours after internalization, EBs lose the
periplasmic polarity as both ends of the
particles were associated with a reduction in
the periplasmic widening. Moreover, an
equal distribution of the T3SSs throughout
the membrane was also reported (Nans et
al., 2014). Further work must be done to
fully understand the distribution of T3SSs in
RBs within host cells, however, Nans et al.
(2014) describe the use of a novel system
that uses a more physiological form of C.
trachomatis EBs to capture early stages of
Chlamydia infection.

4. 4 Connor Ratycz
Maintaining the niche: interference of
immune signaling and antigen
presentation
Following Chlamydia invasion into
host cells, the newly formed inclusion
escapes from the trafficking pathways of the
host cell and avoids lysosome fusion via
type III-secreted effector proteins (Fields et
al., 2002). Once Chlamydia have established
this intracellular niche, the inclusion has
been observed to selectively interact with
host organelles which provide crucial
nutrients and factors required for inclusion
support and RB multiplication. Specifically,
the Golgi and exocytic vesicles are primary
targets for chlamydial interaction as sources
of essential lipids including sphingomyelin,
cholesterol, and glycerophospholipids
(Moore et al., 2008). In addition, it has been
reported that Chlamydia interact with the
endoplasmic reticulum and lysosomes to
obtain nutrients (Fields et al., 2002). Many
of the hijacking and nutrient acquisition
occur through a large family of Chlamydia
effector proteins referred to as inclusion
(Inc) proteins (Banantine et al., 1998). It was
not until recently that the chlamydial Inc
proteins were identified as T3SS substrates
and hypothesized to be secreted into the host
cell cytoplasm from the inclusion (Dehoux
et al., 2011). These findings provided
evidence for the idea that T3SSs are active
in chlamydial inclusions and secrete Inc
proteins into the cytoplasm to disrupt host
signaling pathways to evade immune
activation. How Chlamydia employ the
T3SS and effector Inc proteins to modify the
host cell biology remains largely unknown
due to difficulty in functional
characterization of the Inc proteins.
However, some new evidence has emerged
with regards to the regulation of genes
involved in innate immune signaling and
MHC-I antigen presentation in the context
of Chlamydia infection.
A novel effector protein with potential innate
immune response subversion properties
In a recently published study, Chen
et al. (2014) took a mass spectrometry-based
approach to deal with the difficulty of
characterizing T3SS effectors. By
employing this new technique, the authors
discovered a previously uncharacterized
protein, CT875/TepP, as a new chlamydial
effector protein secreted by the T3SS. Chen
et al. (2014) immunoprecipitated Slc1, a
known T3SS chaperone (Saka et al., 2011),
and identified co-purifying proteins via mass
spectrometry. Although it was originally
hypothesized to bind TarP exclusively, Chen
et al. (2014) identified TarP, CT694, CT695,
and two hypothetical proteins, CT365 and
CT875 (TepP), that also co-precipitated with
Slc1. It is reported that the Slc1-TarP
interactions enhances Tarp secretion in
chlamydial systems. Using a heterologous
secretion system in Yersinia pestis, it was
revealed that TepP secretion is also affected
as secretion was enhanced three-fold when
Slc1 was co-expressed in the system (Chen
et al., 2014). In addition, Chen et al. (2014)
identified TepP to be secreted within 2 hours
post-infection of host HeLa cells, which
suggests the newly identified T3SS effector
protein is translocated into host epithelial
cells early after C. trachomatis entry. After
identifying TepP, the authors performed
several subsequent experiments in an
attempt to further characterize and
determine the function of the effector
protein. A number of effector proteins
secreted by the T3S apparatus, including
TarP, are tyrosine-phosphorylated upon
infection of epithelial cells with C.
trachomatis EBs (Birkelund et al., 1994).

5. 5 Connor Ratycz
The authors performed their
immunoprecipitation-mass spectrometry
technique and determined that TepP
immunoprecipitated from infected HeLa cell
lysates, but not EBs lysates, contained
tyrosine-phosphorylated TepP (Chen et al.,
2014). Analysis of the TepP peptide
sequence indicated the presence of a binding
site for the Crk which is an adaptor protein
responsible for mediating phosphorylation-
mediated regulating of cytoskeletal
dynamics, adhesion and phagocytosis. Chen
et al. (2014) confirmed Crk and TepP
interact with one another during Chlamydia
infection, and observed that as the infection
progressed, increasing amounts of Crk
interacted with TepP. Although the TepP is
phosphorylated upon entry into the host cell
cytoplasm and TepP associated with Crk
during infection, the authors did investigate
whether phosphorylation of TepP is required
for recruitment of Crk to the inclusions.
To further assess the role of TepP,
the authors infected host cells with tepP
mutants or wild type C. trachomatis EBs,
and found the mutants did not impact
overall infection or replication of the
pathogen. However, comparison of global
transcriptional profiles between mock
infected and infected host cells revealed
different results. Chen et al. (2014)
discovered 33 genes displaying fold changes
greater than 2-fold in gene expression levels.
Genes for IL-6, TNF-α, and CXCL3 were
found to be downregulated in host cells
infected in the presence of TepP. To date,
only two effector proteins secreted before
EB entry into host cells have been
characterized and studied, and only a few
more effectors have been identified to be
secreted from the chlamydial inclusion.
Chen et al. (2014) have provided the novel
approach to identify a new effector protein
that is translocated from the inclusion to
recruit Crk and other proteins to the
inclusion to aid in niche maintenance.
Furthermore, preliminary evidence also
suggests that TepP aids in altering host
innate gene products to promote C.
trachomatis survival and dissemination.
An insight into Chlamydia immune evasion
via disruption of MHC-1 antigen
presentation
Chlamydia spp. are equipped with an
arsenal of weapons to combat the host
defense such as regulating transcription
factors in apoptotic signaling pathways,
inhibition of NF-kB transcriptional activity
through effector molecules with protease
ability and deubiquitinating activities
(Cocchiaro and Valdivia, 2009). Evidence of
a new immune evasion strategy for
Chlamydia has emerged in the last decade of
reduced/downregulated antigen presentation
in C. trachomatis-infected epithelial cells
mediated by a protein referred to as
chlamydial protease activity function
(CPAF) (Kawana et al., 2007). It is
important to note that other secreted effector
proteins with similar activity on antigen
presentation may exist in Chlamydia.
Unfortunately, much information regarding
the mechanisms of how this antigen
presentation is reduced during chlamydial
infection is unknown, and remains an
important avenue for research. A recent
study by Ibana et al. (2011) provides new
evidence to help elucidate the mechanism of
chlamydial regulation of antigen
presentation.
During in vivo infection, only a
portion of epithelial host cells will become
infected by Chlamydia EBs. In vitro models
of Chlamydia can be modified with harmful

6. 6 Connor Ratycz
toxins for EBs to infect all host cells
exposed. In contrast, systems that lack these
toxins allow for an infection that mimics in
vivo infections with a mixed population of
cells that must be analyzed together. Ibana et
al. (2011) bypass these issues by using an in
vitro system which mimics in vivo infection
proportions, followed by sorting the cells
into C. trachomatis-infected host cells and
bystander cell populations. To distinguish
between infected cells and bystander cells,
the authors labeled C. trachomatis with a
FITC-labeled antibody against the
chlamydial lipopolysaccharide (LPS). To
analyze the expression of MHC-I on
infected and mock-infected host A2EN cells,
Ibana et al. (2011) used a fluorescently-
labeled antibody that recognizes properly
folded MHC-I associating with β2-
microglobulin. Compared to uninfected cells
and non-IFNy exposed C. trachomatis-
infected cells, infected cells exposed to
IFNy showed an intermediate level of MHC-
I expression (Ibana et al., 2011). In addition,
it was also observed that uninfected,
bystander cells within the infected cultures
also showed reduced MHC-I expression
levels. Following exposure of fresh media or
media from C. trachomatis-infected cells, it
was reported that cells treated with
supernatants from noninfected cells
experienced the largest increase in MHC-I
expression while cells treated with
supernatant from infected cells had a greater
reduction in MHC-I expression (Ibana et al.,
2011). This data provides evidence of a
soluble factor responsible for the
downregulation of MHC-I in Chlamydia
infection. Moreover, this process is also
mediated by a factor through direct
mechanisms in the infected host cell, and
through an indirect mechanism in nearby
uninfected cells. Although the authors
provide new evidence of a soluble factor
responsible for the regulating MHC-I, Ibana
et al. (2011) do not identify the factor as
CPAF or any other potential effector protein
so the identity currently remains unknown.
However, the authors do claim their future
directions consist of developing an
experiment to further define the effector
molecule. Despite the unknown identity of
this virulent factor, Ibana et al. (2011)
demonstrate an elegant system which allows
for the separation and analysis of both
infected and uninfected host cell
populations, and provide new insight into
the mechanisms by which C. trachomatis
prevent antigen presentation.
Perspectives
Despite the lack of effective tools for
consistent genetic manipulation of
Chamydia, it appears that an integrative
approach involving cell biology, proteomics,
and biochemistry techniques will continue to
bring new insight of the chlamydial T3SS
and the associated effector molecules (both
known and currently unknown). Moreover,
it seems that many of the older methods of
chlamydial biology such as the heterologous
secretion models of Y. pestis as well as in
vitro approaches will still aid in the
challenge to shed more light on the T3SS. I
have described just a few examples of the
emerging work that is being performed on
understanding how Chlamydia use the T3SS
to establish and sustain infection within host
cells. Specifically, Nans et al. (2014)
demonstrated the polarization of T3SSs in
C. trachomatis EB sand the gradual, equal
distribution of the T3SS array as EBs
differentiate into RBs. Moreover, Chen et al.
(2014) and Ibana et al. (2011) showed the
emerging functions of T3SS effector
proteins by identifying a novel protein is

7. 7 Connor Ratycz
responsible for regulate innate genes and
how unknown molecule is responsible for
disrupting antigen presentation, respectively.
However, much work must be done to
further understand how the host immune
response is subverted and/or dismantled by
the T3SS and its arsenal of effector proteins
with regards to Chlamydia infection.
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