A var gene promoter controls allelic exclusion of virulence genes in Plasmodium falciparum malaria

Abstract

Mono-allelic expression of gene families is used by many organisms to mediate phenotypic variation of surface proteins. In the apicomplexan parasite Plasmodium falciparum, responsible for the severe form of malaria in humans, this is exemplified by antigenic variation of the highly polymorphic P. falciparum erythrocyte membrane protein 1 (PfEMP1). PfEMP1, encoded by the 60-member var gene family, represents a major virulence factor due to its central role in immune evasion and intravascular parasite sequestration. Mutually exclusive expression of PfEMP1 is controlled by epigenetic mechanisms involving chromatin modification and perinuclear var locus repositioning. Here we show that a var promoter mediates the nucleation and spreading of stably inherited silenced chromatin. Transcriptional activation of this promoter occurs at the nuclear periphery in association with chromosome-end clusters. Additionally, the var promoter sequence is sufficient to infiltrate a transgene into the allelic exclusion programme of var gene expression, as transcriptional activation of this transgene results in silencing of endogenous var gene transcription. These results show that a var promoter is sufficient for epigenetic silencing and mono-allelic transcription of this virulence gene family, and are fundamental for our understanding of antigenic variation in P. falciparum. Furthermore, the PfEMP1 knockdown parasites obtained in this study will be important tools to increase our understanding of P. falciparum-mediated virulence and immune evasion.

Full text

© 2006 Nature Publishing Group
Avar gene promoter controls allelic exclusion of
virulence genes in Plasmodium falciparum malaria
Till S. Voss
1
, Julie Healer
1
, Allison J. Marty
1,2
, Michael F. Duffy
3
, Jennifer K. Thompson
1
, James G. Beeson
1
,
John C. Reeder
4
, Brendan S. Crabb
1
& Alan F. Cowman
1
Mono-allelic expression of gene families is used by many organ-
isms to mediate phenotypic variation of surface proteins. In the
apicomplexan parasite Plasmodium falciparum, responsible for
the severe form of malaria in humans, this is exemplified by
antigenic variation of the highly polymorphic P. falciparum
erythrocyte membrane protein 1 (PfEMP1)
1,2
. PfEMP1, encoded
by the 60-member var gene family
3–6
, represents a major virulence
factor due to its central role in immune evasion and intravascular
parasite sequestration. Mutually exclusive expression of PfEMP1
is controlled by epigenetic mechanisms involving chromatin
modification and perinuclear var locus repositioning
7,8
. Here we
show that a var promoter mediates the nucleation and spreading
of stably inherited silenced chromatin. Transcriptional activation
of this promoter occurs at the nuclear periphery in association
with chromosome-end clusters. Additionally, the var promoter
sequence is sufficient to infiltrate a transgene into the allelic
exclusion programme of var gene expression, as transcriptional
activation of this transgene results in silencing of endogenous
var gene transcription. These results show that a var promoter
is sufficient for epigenetic silencing and mono-allelic transcrip-
tion of this virulence gene family, and are fundamental for our
understanding of antigenic variation in P. falciparum. Further-
more, the PfEMP1 knockdown parasites obtained in this study
will be important tools to increase our understanding of
P. falciparum-mediated virulence and immune evasion.
In individual P. falciparum parasites one var gene is expressed and
switching to an alternative occurs by in situ transcriptional acti-
vation
9,10
.var genes are flanked by one of three upstream sequences
(upsA,upsB and upsC)
6
, and differential expression of these subtypes
is linked to disease
11
.UpsA- and upsB-type var genes are located
subtelomerically, whereas upsC-type var genes are in chromosome-
internal clusters. UpsB and upsC sequences display promoter activi-
ties
12,13
and interact with DNA-binding proteins
14
. Cooperative
interactions in cis between upsC and the var intron have been
implicated in silencing
15–17
. A role for silent information regulator
2 (PfSIR2) in var silencing has been demonstrated
7,8
. These findings
suggest a vital function of var promoters in epigenetic regulation of
this family.
To test this hypothesis we transfected P. falciparum strain 3D7 with
plasmids pHBupsC, pHBupsC
R
and pHBupsC
RI
, each containing
blasticidin deaminase (bsd) and human dihydrofolate reductase
(hdhfr), to encode resistance to blasticidin-S and WR99210
(WR), respectively (Fig. 1a). Transfected parasites were grown on
blasticidin-S to obtain 3D7/upsC, 3D7/upsC
R
and 3D7/upsC
RI
carrying episomes. The hdhfr gene represented a tool to analyse var
promoter function, uncoupled from its chromosomal context, in its
natural (WR
2
) and activated (WR
þ
) state.
Growth assays showed that all three transfectants were sensitive to
WR (Fig. 1b). Parasites transfected with control constructs, where the
upsC promoter was replaced with the calmodulin (cam) promoter,
were WR resistant. After selection of 3D7/upsC, 3D7/upsC
R
and
3D7/upsC
RI
with WR, resistant populations were established after
six, four and ten generations, respectively. Similarly, the half-
maximal inhibitory concentration (IC
50
) for unselected populations
was the same as for the WR-sensitive parent 3D7, whereas after
selection they were resistant (Fig. 1c). This suggested that the
upsC-hdhfr cassette was silenced and WR challenge selected for
rare parasites where upsC was activated. To confirm this we mon-
itored hDHFR expression by immunofluorescence (Fig. 1d). A total
of 0.6% of parasites expressed hDHFR in WR-untreated parasites
whereas 80% showed detectable levels after selection. When the
WR-resistant population was maintained without WR for 40 genera-
tions the percentage of hDHFR-expressing cells dropped to 61%.
This demonstrated that upsC-mediated expression was variegated
and stably inherited with the same dynamics as var switching rates
18
.
In WR-untreated 3D7/upsC, 3D7/upsC
R
and 3D7/upsC
RI
parasites no hdhfr transcripts were observed, consistent with tran-
scriptional silencing (Fig. 2a and Supplementary Fig. 2). High hdhfr
transcript levels were present after WR selection, and the activated
episomal upsC promoter displayed temporal transcription similar to
endogenous counterparts
14
. Therefore the episomal promoter con-
tained sufficient regulatory information for upsC-mediated control
and was unaffected by the intron and/or the subtelomeric repeat
element rep20 (see below). Furthermore, the silencing emanating
from upsC had regional effects in cis because transcription of the bsd
gene was substantially reduced on all silenced episomes compared
to activated forms and the control plasmid pHBcam (Fig. 2a, c).
Alterations in transcriptional activity were specific to upsC as no
differences in hdhfr or bsd transcript abundance was evident in
3D7/cam parasites before and after WR selection (Fig. 2b). The var
intron and rep20 played no direct role in silencing because cam
promoter activity was unaffected by these elements (Supplementary
Fig. 3). Our analysis shows that the upsC promoter provides
sufficient information for epigenetic control to establish a silenced
or activated state.
We demonstrated that the P. falciparum nuclear periphery was
associated with transcriptional silencing
7
, and we expected that
targeting of pHBupsC
R
to chromosome-end clusters by inclusion
of rep20 (ref. 19) would result in increased silencing. However, rep20
had no effect on upsC-mediated silencing (Fig. 2a). In contrast, the
intron in 3D7/upsC
RI
antagonized epigenetic activation and spread-
ing of chromatin activation into the bsd locus (Fig. 2a). This agrees
with previous results suggesting that the upsC–intron interaction has
boundary function to protect var genes in chromosome-central
LETTERS
1
The Walter and Eliza Hall Institute of Medical Research, Parkville 3050, Australia.
2
Department of Microbiology, Monash University, Clayton 3800, Australia.
3
Department of
Medicine, The University of Melbourne, The Royal Melbourne Hospital, Parkville 3050, Australia.
4
Papua New Guinea Institute of Medical Research, Goroka EHP 441, Papua
New Guinea.
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1004

© 2006 Nature Publishing Group
clusters from activation through nearby euchromatic regions and
neighbouring var genes
17
. In addition, the delayed resistance of
3D7/upsC
RI
parasites compared to 3D7/upsC and 3D7/upsC
R
para-
sites (Fig. 1b) indicated that activation of upsC paired with the intron
occurred less frequently than activation of the upsC promoter alone.
This is consistent with the role of the var intron in silencing
15–17
and
suggests that interplay between these elements provokes a solid
and stably inherited silenced chromatin environment. However, in
contrast to a recent study
16
we did not find that deletion of the var
intron was required to activate the upsC promoter (Supplementary
Discussion).
We showed previously that gene expression at the nuclear periph-
ery is restricted to a perinuclear region and activation and silencing
of var genes is linked to locus repositioning
7
. We determined the
nuclear position of episomal and integrated versions of active and
Figure 1 |WR sensitivity of upsC promoter transfectants. a, Vector maps.
hsp86 50, heat-shock protein 86 promoter; Pb T, P. berghei dhfr-thymidilate
synthase terminator; upsC,upsC upstream sequence
13
;PfT,P. falciparum
hrp2 30terminator; rep20, 0.5-kb rep20 repeats; intron, 0.6-kb var intron
sequence
17
. Scale bar, 1kb. b, Growth assay. Parasites were challenged with
WR at day 0. Assays were repeated twice with the same result. c,WR
sensitivities before (open) and after (filled) WR selection. d, hDHFR
expression visualized by indirect immunofluorescence assay. Percentage of
hDHFR-expressing parasites before (2WR, 2 of 361) and after (þWR, 125
of 157) WR treatment, and in WR-selected parasites maintained without
WR for 40 generations (þ/2WR, 269 of 422). Error bars are 95% confidence
intervals (P,0.001). Similar results were obtained for 3D7/upsC and
3D7/upsC
RI
(data not shown).
Figure 2 |Epigenetic regulation of upsC.a, Silencing and activation of
upsC-regulated transcription. Northern blots showing episomal hdhfr and
bsd transcription. Transcription of cam is a stage-specific loading control.
Densitometry compares relative hdhfr and bsd transcript per promoter
before and after selection on WR (see Supplementary Methods). b,hdhfr
and bsd transcription in 3D7/cam. c, Spreading of upsC-mediated silencing.
bsd transcription in WR-untreated 3D7/upsC and 3D7/cam parasites. The
densitometry chart compares relative bsd transcript production per hsp86
promoter. 1, 0–12h post-infection (h.p.i.); 2, 12–24 h.p.i.; 3, 24–36 h.p.i.;
4, 32–44 h.p.i.
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silenced hdhfr transgenes by fluorescent in situ hybridization (FISH)
(Fig. 3 and Supplementary Fig. 4). In agreement with a previous
report
20
we found silenced and active chromosome-internal var loci
at the nuclear periphery. We also demonstrate that a chromosome-
central var locus preferentially co-localizes with telomeric clusters,
irrespective of upsC transcriptional state. This was not observed for
episomally maintained pHBcam, which, as expected for episomes
devoid of rep20 in P. falciparum
19
, showed no preferential co-
localization with telomere clusters (38 ^2.4% co-localization).
Therefore, as the parasites constitutively transcribed bsd,the
telomeric clusters identified by co-localization with integrated
pHBupsC probably represent the previously identified active
perinuclear zone
7
. Surprisingly, the activated pHBupsC episome
co-localized with chromosome-end clusters as frequently as
integrated versions, in contrast to the silenced episomes that
displayed no preferential co-localization (P¼0.01, paired one-tailed
t-test) (Fig. 3b). This indicates that activation of upsC is restricted to
a specific site associated with the active perinuclear zone. Addition-
ally, these findings may explain why targeting of pHBupsC
R
to
telomeric clusters resulted in faster acquisition of WR resistance
(Fig. 1b).
The above results suggested that upsC activation interferes with
endogenous var transcription. To test this we analysed var transcrip-
tion using three universal var probes and one probe specific to var
PFL1960w where integration of pHBupsC occurred (see Supplemen-
tary Methods and Supplementary Fig. 4). 3D7/upsC parasites
showed a var messenger RNA pattern similar to 3D7 when the
plasmid-encoded upsC promoter was silenced (Fig. 4a). Interestingly,
PFL1960w was highly transcribed in these parasites, probably due to
sequestration of this locus to the transcriptionally active perinuclear
zone as a result of bsd transcription. After activation of upsC none
of the probes detected any significant var transcription, but the
upsC-controlled hdhfr was transcribed. The observation that
Figure 3 |Nuclear localization of silenced and activated upsC loci.
a, Nuclear localization of plasmids in 3D7/upsC and 3D7/cam by FISH.
Epifluorescence images of nuclei (DAPI) and nuclei hybridized with TARE4
(red) and pGEM (green) to identify chromosome-end cluster and plasmid
positions, respectively. b, Quantification of co-localization. n, average
number of nuclei scored. Error bars are 95% confidence intervals. P-values
were generated using a paired one-tailed t-test comparing the per cent
co-localization in each of the 3D7/upsC lines to the control 3D7/cam.
S, silenced upsC promoter; A, activated upsC promoter.
Figure 4 |Effect of upsC activation on mono-allelic var transcription.
a, Northern blot analysis. var transcription was monitored by hybridization
with specific and universal var probes (Supplementary Methods). The short
transcripts above 2.37 kb detected with var exon 2 and varC represent
‘sterile’ exon 2 transcripts
3
.kahrp, knob-associated histidine-rich protein;
msp8, merozoite surface protein 8; S, silenced upsC; A, activated upsC;R,
ring stage; T, trophozoite stage; 2WR, WR-unselected parasites; 2/þWR,
WR-selected parasites grown in the absence of drug for 70 generations.
b, Binding of iRBCs to CD36. Graph showing iRBC binding to CD36 for
WR-selected parasites (þWR) and WR-selected parasites maintained
without drug for 70 generations (2/þWR) compared to WR-unselected
parasites (2WR). Values for WR-unselected and selected parasites are
means (^s.e.m.) of six experiments in duplicate with three independent
transfectants (3D7/upsC, 3D7/upsC
R
, 3D7/upsC
RI
); values for the 2/þWR
parasites are means of two experiments performed in duplicate with the
3D7/upsC transfectant. c, Binding of serum IgG to iRBCs. Bar graph shows
flow cytometry of IgG median binding for sera of 20 malaria-exposed adults,
and five non-exposed controls, to the surface of iRBCs for WR-unselected
(black) and WR-selected (white) 3D7/upsC parasites. Error bars are 95%
confidence intervals.
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PFL1960w transcripts were absent in this population demonstrates
allelic exclusion and promoter switching within a chromosome-
internal var cluster. This knockdown of var transcription occurred
in rings and trophozoites and was observed with 3D7/upsC
R
and
3D7/upsC
RI
carrying episomal or integrated plasmids (Fig. 4a,
Supplementary Fig. 5). var transcripts reappeared in WR-resistant
parasites after removal of WR, indicating that a subpopulation had
switched from transcribing hdhfr to endogenous var genes (Fig. 4a).
Therefore, var promoter activation is a crucial step in control of
allelic var exclusion because transcriptional activation of one var
promoter-associated locus inhibits transcription of the remaining
var loci.
To confirm these observations we tested the PfEMP1-mediated
binding of infected red blood cells (iRBCs) to CD36 and chondroitin
sulphate A (CSA). In WR-selected parasites binding of iRBCs
to CD36 was reduced to 14% of WR-untreated parasites, and
WR-resistant parasites cultured in the absence of WR had inter-
mediate binding, showing that var activation and PfEMP1
expression was returning as hdhfr was silenced (Fig. 4b). None of
the parasites tested bound to CSA (not shown). In addition, IgG
binding to the surface of infected erythrocytes in sera from malaria-
exposed donors was significantly higher for WR-unselected com-
pared to WR-selected 3D7/upsC parasites (median ^s.d. fluores-
cence 26.4 ^20.3 versus 9.0 ^7.2, respectively; P,0.00001,
Wilcoxon’s signed-rank sum test), and there was little binding of
IgG among samples from non-exposed donors (median fluorescence
0.9 ^0.9 versus 0 ^0.3) (Fig. 4c and Supplementary Fig. 6). These
findings are consistent with a substantial reduction or absence of
PfEMP1 on the iRBC surface due to silencing of endogenous var
transcription.
We have identified two important features of var promoters in
epigenetic regulation and mono-allelic expression. First, the upsC var
promoter mediates nucleation and spreading of stably inherited
silenced chromatin through interactions between unidentified
cis-acting promoter motifs and the P. falciparum silencing machin-
ery. We conclude that the upsC promoter is required to maintain
chromosome-internal var genes in their silenced default state, and
preliminary data indicate that upsB promoters have a similar role in
subtelomeric var silencing (T.S.V. et al., unpublished data). Second,
the information provided by the upsC promoter is sufficient to insert
a locus into the allelic exclusion programme of var transcription
independent of chromosomal context (Supplementary Discussion).
On the basis of our findings, the simplest model for mechanisms
underlying mono-allelic var expression is a unique perinuclear
compartment, associated with the active chromosome-end cluster,
responsible for transcription of a single var locus (Supplementary
Fig. 1). Switching in var transcription, and thus antigenic variation of
PfEMP1, would occur by competition of silenced var promoters for
occupancy of this compartment. A similar mechanism has been
identified to control mono-allelic expression of vsg genes in African
trypanosomes
21
, and has been proposed to control mono-allelic
transcription of the mammalian odorant receptor gene family
22
.
The results presented here are, to our knowledge, the first description
of transcriptional repression of a gene family and are fundamental
to understanding antigenic variation and epigenetic regulation in
P. falciparum and mono-allelic transcription and phenotypic varia-
tion in other systems. The var knockdown parasites obtained in this
study provide an invaluable tool to understand the role of PfEMP1
in parasite-mediated virulence, protective immunity and cyto-
adherence.
METHODS
Parasites, drug sensitivity and cyto-adherence. P. falciparum 3D7 and trans-
fected parasites were cultured as described previously
23
. Growth synchronization
was achieved using sorbitol. A total of 250
m
l of packed iRBCs (5–10% ring
parasites) were transfected by electroporation of 100
m
g of plasmid. Selection on
blasticidin-S (2
m
gml
21
) was 4–6 h after transfection. Selection on WR99210
was at 4 nM. Drug sensitivity assays were performed with standard techniques.
Cyto-adherence of parasitized erythrocytes to CD36 and CSA were as
described
24
.
Transfection constructs. The puromycin resistance cassette in pHH1/pac
25
was
excised with NotI/BglII. After ligation of adaptors the cassette was cloned into
SacII/NotI-digested pHHMC*/R0.5 (ref. 19) to generate pHH_VP, where a
0.5-kilobase (kb) rep20 fragment separates the head-to-tail expression cassettes.
The vector pHBcam
R
was obtained by replacing the puromycin resistance gene
with bsd amplified from pCBM
26
. pHBcam
RI
was generated by ligation of a
0.6-kb var intron fragment
17
into the EcoRI site of pHBcam
R
. pHBupsC
R
was
generated by replacing the BglII/BamHI cam promoter with the upsC promoter
(PFL1960w) amplified from pCAT5B1 (ref. 13). pHBupsC
RI
was derived in
thesamewayfrompHBcam
RI
. The 0.5-kb rep20 sequence in pHBcam
R
and pHBupsC
R
was deleted by digestion with PstI/BglII, end-polishing and
re-ligation to yield pHBcam and pHBupsC, respectively.
Southern and northern analysis. gDNA was digested with EcoRV and PvuII.
Southern blots were probed with hdhfr and pfsir2 fragments. Copy number was
determined by densitometry comparing signal intensities of EcoRV/PvuII frag-
ments representing hdhfr to the EcoRV fragment from the single copy pfsir2.
Plasmid integration was mapped by hybridization with hdhfr and a 735-base pair
fragment derived from the 5 0end of PFL1960w. Pulsed-field gel electrophoresis
(PFGE) was carried out as described
27
. Northern experiments are described in
detail in Supplementary Methods.
Indirect immunofluorescence assay and FISH. Indirect immunofluorescence
assays to detect hDHFR expression were performed as described
28
using a
monoclonal mouse anti-bovine dihydrofolate reductase antibody (BD
Biosciences) and anti-mouse Alexa-Fluor 488-nm (Molecular Probes). Parasite
DNA was visualized using DAPI and cells were counted for DAPI and hDHFR
positivity. FISH analysis was performed as presented elsewhere
7
using telomere-
associated repeat element 4 (TARE4) and pGEM probes for the detection of
telomere clusters and the plasmid backbone, respectively. Images were counted
by three independent scorers in a blinded design in two to three independent
FISH experiments.
Fluorescence-activated cell sorting. Serum samples were tested for IgG bound
to the surface of mature trophozoite-infected erythrocytes using flow cytome-
try
29
. Cells were sequentially incubated with test serum or plasma diluted 1/10,
rabbit anti-human IgG (Fc-specific, Dako; 1:100), Alexa-Fluor 488-conjugated
anti-rabbit Ig (Molecular Probes; 1:750) and ethidium bromide (10
m
gml
21
).
Samples were analysed using a FACSCalibur flow cytometer (Becton-Dickinson)
and Flowjo software (TreeStar). For each sample the mean fluorescence of
uninfected erythrocytes was deducted from the mean fluorescence of infected
erythrocytes. All samples were tested in duplicate. Serum samples were obtained
from malaria-exposed adults from Madang, Papua New Guinea (ten men, five
non-pregnant women, five pregnant women) following informed consent. Five
samples from non-exposed Australian residents were included as controls.
Ethical clearance was obtained from the Medical Research Advisory Committee,
Department of Health, Papua New Guinea.
Received 1 September; accepted 4 November 2005.
Published online 28 December 2005.
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Supplementary Information is linked to the online version of the paper at
www.nature.com/nature. A summary figure is also included.
Acknowledgements We are grateful to A. Gemmill and J. Baum for statistical
advice. This work was supported by the National Health and Medical Research
Council and the Wellcome Trust. A.F.C. and B.S.C. are International Fellows of
the Howard Hughes Medical Institute. T.S.V. is supported by fellowships from
the Swiss National Science Foundation and the Roche Research Foundation.
A.J.M. is supported by an Australian Postgraduate Award. J.G.B. was supported
by the NHMRC and the Miller Fellowship of WEHI. We also thank G. Kelly and
A. Raiko for sample collection and processing in Papua New Guinea.
Author Information Reprints and permissions information is available at
npg.nature.com/reprintsandpermissions. The authors declare no competing
financial interests. Correspondence and requests for materials should be
addressed to A.F.C. (cowman@wehi.edu.au).
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