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MAJOR ARTICLE

Common Surface-Antigen var Genes of


Limited Diversity Expressed by Plasmodium
falciparum Placental Isolates Separated
by Time and Space
Ayman Khattab,1 Peter G. Kremsner,1,2 and Mo-Quen Klinkert1
1
Institute for Tropical Medicine, University of Tübingen, Tübingen, Germany; 2Medical Research Unit, Albert Schweitzer Hospital,
Lambaréné, Gabon

Plasmodium falciparum placental parasites from Cameroon have been shown to express surface variant var
genes encoding Duffy binding–like (DBL)–g domains that bind chondroitin sulfate A. All 5 domains exhibited
sequences with 39%–55% amino acid (aa) identities and appear sufficiently conserved to function in receptor
binding. Transcripts of 2 samples showed complete conservation over 4 kb, demonstrating for the first time
distinct conserved placental var genes. Four placental isolates from Gabon collected 4 years later expressed
DBL-g sequences with 85%–99% aa identities to those from Cameroon, confirming the conserved nature of
placental variants separated by time and location. Five peripheral parasites from children also displayed DBL-
g sequences with 75%–97% homologies. From this, it can be concluded that P. falciparum parasites expressing
unique var DBL-g genes can cause placental malaria, referred to as varPAM genes. This demonstration of
structurally/functionally constrained DBL-g chondroitin sulfate A–binding domains is relevant to understand-
ing pregnancy-associated malaria pathogenesis and to vaccine development.

Pregnancy-associated malaria (PAM) is a major cause of ularly more vulnerable to infection and can present
infant morbidity and mortality and anemia and death clinical manifestations of the disease. Plasmodium falci-
in the mother [1]. Although adults in areas where malaria parum–infected erythrocytes (IEs) are preferentially
is endemic are normally clinically immune to the disease, sequestered in the placenta by interacting with a gly-
women experiencing their first pregnancies are partic- cosaminoglycan, chondroitin sulfate A (CSA), on syn-
cytiotrophoblast cells lining the placenta [2]. CSA acts
as a receptor molecule for P. falciparum erythrocyte
membrane protein 1 (PfEMP-1), which is expressed by
Received 25 July 2002; revised 3 October 2002; electronically published 24
January 2003. the parasites on the surface of IEs [3–5]. Other receptor
Study participants gave written informed consent, and, in the case of children, molecules such as hyaluronic acid and IgG also have been
consent was obtained from their parents or guardians. Ethical clearance was implicated in the adhesion of IEs in placentas [6, 7].
obtained from the ethics committee of the International Foundation of the Albert
Schweitzer Hospital (Lambaréné, Gabon). Antibodies from secundigravid and multigravid
Financial support: European Commission (grants QLK2-CT-1999-01293 and QLK2- women living in areas where malaria is endemic can
CT-2001-01302). block the binding of placental parasites to CSA [8] and
Nucleotide sequence data are available in the GenBank database (accession are thought to be generated in a strain-independent
nos. AF547098–AF547163).
Reprints or correspondence: Dr. Mo-Quen Klinkert, Institute for Tropical
manner, with the capacity of recognizing parasites from
Medicine, University of Tübingen, Wilhelmstrasse 27, 72074 Tübingen, Germany different geographic locations. The panreactive anti-
(mo.klinkert@uni-tuebingen.de).
CSA binding antibodies also react with the surface of
The Journal of Infectious Diseases 2003; 187:477–83
 2003 by the Infectious Diseases Society of America. All rights reserved.
IEs in a sex-specific manner, such that serum samples
0022-1899/2003/18703-0016$15.00 from malaria-exposed men do not show any reactivities

Common DBL-g Subtypes in P. falciparum • JID 2003:187 (1 February) • 477


toward IE surface [8, 9]. Taken together, the results suggest the of participants included schoolchildren who presented at the
unusual conserved nature of these placental-sequestering var- Medical Research Unit of the Albert Schweitzer Hospital with
iants (varCSA) of the PfEMP-1 gene. uncomplicated malaria—their parasite counts were 10,000–
In several independent experiments, a polypeptide domain 30,000 parasites/mL. All patients were treated with quinine.
of the var-encoded protein PfEMP-1, the Duffy binding–like Collection of parasites. Placental blood was extracted by
(DBL)–g domain, was shown to be associated with the cyto- squeezing a piece of placenta tissue into 0.9% NaCl that con-
adherence phenomenon involving CSA [3–5]. The CSA-bind- tained 10 U/mL heparin [12] and was examined for the pres-
ing DBL-g domains characterized in our laboratory from clin- ence of malaria parasites in thick blood smears using the Lam-
ical isolates from malaria-infected placentas exhibited 39%– baréné method [13]. The parasites collected in this way were
55% aa sequence identities with each other, and this unique also shown to have the CSA-binding phenotype. Packed eryth-
region is thought to maintain functional integrity through a rocytes (100-mL aliquots) were collected from infected blood
conserved conformational structure [5]. Of interest, we also by centrifugation through ficoll-hypaque to separate the cell
found DBL-g sequences from 2 different parasite isolates, 485 pellet from the plasma, stored at ⫺80C, and subsequently used
and 701, to be nearly identical to each other, as were 2 other for DNA preparation, polymerase chain reaction (PCR) am-
isolates, 720 and 734. In part, these results provide the molec- plification, and genotyping experiments. Peripheral blood was
ular basis to support the immunoepidemiological data that collected in a monovette, parasite densities were determined,
suggest that the CSA-binding ligand is antigenically conserved and packed erythrocytes were collected as described above.
and that women who are infected with parasites expressing this PCR cloning of expressed varPAM genes. PCR amplifi-
varPAM variant during pregnancies can gain lifelong immunity cations were carried out to amplify longer var gene sequences
against PAM. that partially corresponded to 2 identical DBL-g sequences pre-
Recently, a unique regulatory element located at the 5 un- viously isolated by reverse-transcriptase (RT)–PCR on parasite
translated region of the varCSA gene was correlated with the isolates from Cameroonian patients (nos. 720 and 734) [5].
expression of this gene involved in placental malaria. This find- The var sequences amplified were ∼4 kb in length. Genomic
ing provided a plausible explanation for the relative conser- DNA from patients 720 and 734 were isolated from 100 mL of
vation of the varCSA gene in genetically diverse parasites [10]. packed erythrocytes, using the blood DNA mini kit (Qiagen)
Because one of the central issues of PAM research concerns according to the manufacturer’s instructions. DNA was eluted
structure, function, and amino acid sequence conservation in in 50 mL of 10 mM Tris buffer (pH 8.5), and 5 mL was used
DBL-g mediating the cytoadherence of IEs to the placenta, we in a PCR in the presence of the expand amplification enzyme
have extended the scope of our earlier study of Cameroonian (Roche Molecular Biology). Primer AF served as a forward
placental parasites to look specifically at the expression of this
primer and has been shown elsewhere [14] to universally am-
var gene segment in placental parasites collected from a dif-
plify DBL-a sequences; 720/734-R (5-ATC ATT ATC TGC TGT
ferent study site (Gabon). There was a 4-year gap between our
GTG TGT TGC) was used as a reverse primer, designed around
2 studies. The present study also focused on DBL-g domains
a highly variable region on the 720/734 DBL-g sequences. The
amplified from placental, as well as peripheral, parasites, to
resulting PCR products were cloned into pCR-XL-TOPO plas-
examine the occurrence in different parasite populations of the
mid from the TOPO XL PCR cloning kit (Invitrogen). Positive
var gene fragments encoding DBL-g domains that bind CSA
clones were verified by DNA sequencing.
and cause malaria pathogenesis in pregnant women.
RT-PCR amplification of DBL-g domains. Total RNA was
prepared from placental parasites Gb21 and Gb35 using the
QIAamp RNA blood mini kit (Qiagen), as described elsewhere
SUBJECTS, MATERIALS, AND METHODS
[5, 12]. Placental packed erythrocytes (100 mL) were mixed with
Study site and participants. Study participants were resi- 500 mL of the RLT buffer provided. The extraction steps thereafter
dents of Lambaréné, which is situated on the equator in a were conducted according to the manufacturer’s instructions.
typical Central African rainforest area in Gabon. The prevalence The RNA was pretreated on column with RNAse-free DNAse.
of plasmodial infection shows a hyperendemic pattern, and After first-strand cDNA synthesis with random primers (Roche
transmission is intense and perennial [11]. Placental blood sam- first-strand cDNA kit) and RT-PCR amplification using degen-
ples that tested positive for P. falciparum in thick blood smears erate primers UNIEBP5 and UNIEBP3 [16], the products were
were collected from women who presented at the maternity excised from the agarose gels and sequenced directly or cloned
ward of the Albert Schweitzer Hospital for delivery, and 5 sam- into the TA cloning vector pCR2.1 (Invitrogen).
ples were randomly chosen for the study (parasitemia counts Preparation and amplification of genomic DNA. Parasite
of 1000–140,000 parasites/mL). These individuals were asymp- DNA was extracted from pellets of packed erythrocytes collected
tomatic carriers, and parity varied from 1 to 6. Another group from the peripheral blood of P. falciparum–infected children

478 • JID 2003:187 (1 February) • Khattab et al.


the present study have different genotypes (data not shown)
argues against the possibility that the 2 individuals from whom
the parasites have been isolated had been infected with the
same strain. The results presented here provide clear evidence
for the existence of var genes of genetically diverse placental
isolates that are almost identical, at least in their N-termi-
nal–deduced amino acid sequences.
Comparison of varPAM sequences of placental isolates
and laboratory clones. To determine the extent of similari-
ties between well-characterized var genes (FCR3varCSA,
Figure 1. Alignment of sequences from Plasmodium falciparum pla- CS2varCSA, and 3D7chr5var) known to bind CSA and those
cental isolates 720/734 with laboratory clones FCR3var chondroitin sulfate placental parasites that cause disease during pregnancy, we
A (CSA), CS2varCSA, and 3D7chr5var. The total length of the varPAM aligned each of the sequences in the form of a diagram (figure
sequences being compared is ∼4 kb each and spans N-terminal var
1). The alignment of ∼4 kb of nucleotides covers the N-terminal
domains from Duffy binding–like (DBL)–a to DBL-g. Percentages in the
boxes refer to the degree of amino acid conservation of the laboratory half of the var domains, namely DBL-a, CIDR-a, DBL-b, and
clones in comparison to sequence 720. Sequence 734 was erroneously DBL-g. The levels of amino acid conservation in each of these
labeled in a previous study [5] as being identical to 732. CIDR, cysteine- blocks are shown as percentages in figure 1. For simplification,
rich interspersed domain region. the comparison was made on sequence 720.
Frequency of expressed DBL-g domains of placental isolates
(Gb53, Gb54, Gb55, Gb56, and Gb59) or from blood samples from Gabon. Next, we examined placental parasite isolates
from infected placentas (Gb35, Gb170, Gb172, and Gb174) using from Lambaréné, with a focus on their expressed DBL-g se-
the QIAmp DNA mini blood kit (Qiagen), according to the quences. RT-PCR products amplified on cDNA prepared from
manufacturer’s instructions. Universal UNIEBP5 and UNIEBP3 2 different placental parasites (Gb21 and Gb35) were cloned and
primers were used to randomly amplify genomic DBL-g se-
quences, and PCR products were analyzed by cloning into
pCR2.1 and nucleotide sequencing. Approximately 25 positive Table 1. Frequency of expressed conserved var Duffy bind-
ing–like (DBL)–g domains from 2 Gabonese placental isolates.
clones from each PCR fragment were examined.
Parasite isolate, Total no.
var DBL-g domain Identity sequenced
RESULTS
Gb21
Analysis of expressed placental var genes. In the present study, 498-like variant 85% to sequence 498 5
we sought to examine the extent to which var genes expressed 701-like variant 42% to sequence 701/485 3
by placental isolates are conserved, on the basis of immuno- 732-like variant 99% to sequence 732 1
epidemiological data that appear to point to a functional and Gb35
structural conservation of the CSA-binding ligand. Because nu- 498-like variant 80% to sequence 498 5
cleotide sequencing provides the best answer for determining the 701-like variant 1 97% to sequence 701/485 2
degree of polymorphism in a gene, we proceeded to clone and 701-like variant 2 43% to sequence 701/485 1
sequence the expressed var genes of interest. 732-like variant 98% to sequence 732 1
For this purpose, we concentrated on a previously published
NOTE. In the Gb21 sequence analysis, 5 of 9 clones exhibited 85% aa
DBL-g sequence named 720 (GenBank accession no. AF334806), sequence identity to the previously published Cameroonian sequence 498, 3
which was ∼600 bp in length and was unexpectedly found to be clones could be attributed to a novel sequence with 42% homologies to the
701/485 sequence (first hit in the BLAST search), and 1 clone had 99% aa
98% identical to sequence 734 at the nucleotide and deduced sequence identity to sequence 732. The 498 sequence of the Cameroonian
amino acid sequence levels. The analysis of these 2 expressed and the Gabonese strains differed from each other by a 19-aa deletion in the
latter sequence. The analysis of Gb35 sequences indicated that 5 of 9 DBL-
var genes was extended into the 5 upstream sequences encoding
g isoforms had 80% aa sequence identity to sequence 498 (with the exception
the DBL-a/cysteine-rich interspersed domain region (CIDR) of the 19-aa deletion). Two clones exhibited 97% conservation to sequence
head structure regions. Clones of ∼4 kb each of the 720- and 701/485, whereas 1 was 98% identical to sequence 732. Another sequence
in this set was a novel sequence but showed sequence conservation at 43%
734-related sequences (GenBank accession nos. AF547158 and with 701/485 (first hit in the BLAST search). Additional sequences of 8 clones
AF547159, respectively) were isolated and sequenced. The de- each were obtained from the products of independent reverse-transcriptase–
polymerase chain reaction (PCR) amplification reactions using Gb21 and Gb35
duced amino acid sequence analysis demonstrated that the 2 cDNA and were found to be identical to those of the first amplifications. PCR-
var genes extending from the DBL-a to the DBL-g regions based genotyping experiments using merozoite surface antigen (MSA)–1– and
MSA-2–specific primers [12, 15] indicated that 2 different parasite genotypes
shared almost complete conservation with each other, on the were detected in isolate Gb21, whereas 3 different genotypes were deter-
order of 96%. The fact that parasites 720 and 734 analyzed in mined in isolate Gb35.

Common DBL-g Subtypes in P. falciparum • JID 2003:187 (1 February) • 479


Figure 2. Comparison of Duffy binding–like (DBL)–g genomic sequences from placental and children’s parasites. Sequences identified in the present
study are labeled varX and are preceded by the number of the clinical isolate (e.g., Gb170var5). Percentages given in each box refer to the percentage
of amino acid conservation to known sequences in the database, provided in the form of their accession nos. Names of clinical isolates from Cameroon,
whose DBL-g domains have been demonstrated elsewhere to bind chondroitin sulfate A (CSA) [3–5], are included in some boxes and, for comparison
purposes, also the 2 laboratory strains FCR3varCSA and CS2varCSA. Boxes are shaded in 3 different gray intensities. Dark gray, sequences that have
at least 75% conservation to the clinical isolates; medium gray, sequences with at least 40% conservation; and light gray, sequences with similarities
to the laboratory strains. White boxes, sequences that have not been implicated in CSA binding. Sequences encoding DBL-g domains that are capable
of binding CSA were detected with similar frequencies in parasites from both pregnant and nonpregnant donors. There were 9 of 28 Cameroon-
specific DBL-g sequences in the placental parasite population, vs. 9 of 29 sequences in the peripheral parasite population. Five additional placental
sequences showed sequence similarities with FCR3varCSA and CS2varCSA, whereas 3 FCR3- and CS2-related sequences were found among the
peripheral parasites.

the expressed DBL-g CSA-binding domains were analyzed. The DBL-g–specific sequences in the natural parasite population in
complete sequences from 9 clones from each isolate were avail- Gabon, their presence in the genome of P. falciparum placental,
able for comparison, and the results are summarized in table 1. as well as peripheral, parasites was further investigated. A com-
We show here for the first time, to our knowledge, that the parative analysis of a total of 57 sequences taken from parasites
placental parasites collected 4 years apart originating from areas from the placentas of 4 women and from the peripheral blood
where malaria is endemic in 2 different African countries, Cam- of 5 children indicated that DBL-g sequences were found in every
eroon and Gabon, are constrained in having a limited and tested parasite sample, with a frequency ranging from 4 to 9
uniquely conserved DBL-g repertoire. It is conceivable that dis- different sequences, independently of the source of the isolate
tinct sets of DBL-g sequences, such as those described here, are (figure 2). However, the possibility cannot be entirely ruled out
specifically induced and proliferate during placental sequestra- that additional DBL-g sequences with greater diversity could also
tion. Because these are similar sequences with 39%–55% aa iden- be identified through the use of primer sets distinct from the
tities, these domains can still retain sufficient structural homology ones selected here. Of interest, all samples, with the exception
to function as CSA-binding cytoadherence molecules. of parasites taken from one child, harbored at least 1 of 5 DBL-
Analysis of genomic DBL-g sequences in placental and pe- g sequences previously isolated from infected placentas from
ripheral isolates. To determine the array and frequency of Cameroonian subjects and characterized for CSA binding. The

480 • JID 2003:187 (1 February) • Khattab et al.


DISCUSSION

In the present study, we have carried out a further analysis of


placental P. falciparum parasites that have been shown elsewhere
[5] to express distinct subtypes of DBL-g domains that were
capable of binding the glycosaminoglycan CSA. In considering
the likelihood that var gene conservation extends beyond the
DBL-g domains, we analyzed the 5 extensions of 2 expressed
var genes of the parasites 720 and 734. The most striking result
was the finding that the entire 4 kb of their deduced amino
acid sequences were 96% indistinguishable from each other.
Thus, contrary to the belief that var genes are extensively di-
verse, evidence is provided in the present study that some
varPAM genes expressed by placental parasites isolated from
different individuals are unique to the extent that they are
almost totally conserved in their amino acid sequences.
Using the previously described RT-PCR methodology, we
analyzed more closely the DBL-g domains of placental parasites
from a different malaria-endemic area. The samples from the
first study were collected in Yaounde in Cameroon, whereas
those of the second study originated from Lambaréné in Gabon,
and the time lapse between sample collections was 4 years. The
novel and significant result of our var gene analysis is the dem-
onstration of a limited number of distinct highly homologous
varDBL-g sequences that are commonly expressed in parasites
from geographically separated study areas and were collected
at different time intervals.
Most interesting, the 720/734 pair of identical varPAM genes
Figure 3. Phylogenetic analysis of unique Duffy binding–like (DBL)–g is ∼98% homologous at the amino acid level to a 3D7 chro-
sequences from placental and peripheral isolates found in the natural mosome 5 var gene (3D7chr5var). The 3D7 DBL-g domain was
population of Gabon. Alignment was made with the CLUSTAL program expressed in a heterologous expression system and has been
(available at http://inn-prot.weizmann.ac.il/software/ClustalX.html), and
shown to bind CSA [10]. Furthermore, this 3D7varCSA gene
the tree was created by the CLUSTREE program (part of the CLUSTAL
suite). Bootstrap values (1000 resamplings) are shown along the branch has been shown to be expressed by many placental isolates from
lines. Sequences are labeled as in figure 2. Sequences that show sig- Malawi [18], despite the fact that the N-terminal half of the gene
nificant identities to previously published DBL-g domains are boxed, as (DBL-1a–DBL-4e) exhibits low homology to the FCR3varCSA
are those of the laboratory-selected clones. gene, which has been implicated to have a role in placental ma-
laria. This allows us to conclude that 3D7chr5var-like (and by
extension, also 720/734-like) sequences belong to a pool of com-
finding of DBL-g–specific sequences in var genes from peripheral monly expressed DBL-g varPAM genes set among placental iso-
parasites would also explain why some peripheral P. falciparum lates capable of infecting pregnant women. It is also noteworthy
isolates have been reported to bind CSA [17]. The presence of that other workers, using a different degenerate set of primers,
DBL-g sequences in the natural population with the potential were able to detect the Cameroonian-type of varDBL-g sequences
to bind CSA ensures that these tightly controlled varDBL-g genes from placental isolates from Kenya [19]. Even though these se-
do not get lost in the population in the absence of a selection quences have an overall amino acid sequence homology only on
pressure, namely the placenta. the order of 39%–55%, it is very likely that this unique set of
A phylogenetic analysis of the 57 DBL-g domains together sequences is structurally and conformationally conserved in na-
with the 2 DBL-g sequences of the laboratory strains [3, 4] ture, which is crucial for determining an interaction with CSA.
was made (figure 3). The comparison showed that sequences In fact, the earlier study showed that these DBL-g domains that
with highest homologies to some of the Cameroonian DBL-g were expressed on the surface of COS-7L cells and capable of
sequences (701/485 and 720/734) were found in one cluster binding CSA were predicted to exhibit specific structural features,
(boxed data), whereas others with homologies with sequences such as conserved a-helical stretches. Such conservation of the
498 and 732 were found in another cluster (boxed data). CSA-binding ligand can clearly explain how antibodies from

Common DBL-g Subtypes in P. falciparum • JID 2003:187 (1 February) • 481


multigravid women can block the binding to CSA of placental for the interaction, as first steps in the design and development
parasites collected from different continents [8] and also how of a vaccine against placental infection in pregnant women.
serum samples from multigravid women can react with antigens
on the surface of CSA-binding parasites, whereas serum samples
from adult men cannot. Acknowledgments
The next logical question to ask is how CSA-binding var genes We are grateful to the patients of the Albert Schweitzer Hos-
escape frequent recombination and rearrangement events within pital for their cooperation. We thank the scientists and funding
the parasite, processes that form the basis of clonal antigenic agencies comprising the international Malaria Genome Project
variation of var genes known so far. The mechanism controlling for making sequence data from the genome of Plasmodium
the regulation of expression of varCSA genes recently has been falciparum (3D7) public before publication of the completed
shown to involve a unique 1.8-kb 5 varCSA element. The hy- sequence. The Sanger Centre (United Kingdom) provided se-
pothesis was advanced that the FCR3varCSA gene implicated in quence for chromosomes 1, 3–9, and 13, with financial support
PAM has a subtelomeric location in the chromosome and is less from the Wellcome Trust. A consortium composed of the In-
likely to undergo recombination and rearrangement, unlike many stitute for Genome Research, along with the US Naval Medical
other centrally located var genes. Besides gene location, orien- Research Center, sequenced chromosomes 2, 10, 11, and 14,
tation also appeared to play a role, because the FCR3varCSA with support from National Institutes of Allergy and Infectious
gene was found to be transcribed in the opposite sense from the Diseases/National Institutes of Health, the Burroughs Wellcome
more “common” var genes [10]. Moreover, the same unique, Fund, and the Department of Defense. The Stanford Genome
single-copy regulatory element upstream of the initiation codon Technology Center sequenced chromosome 12, with support
was also present in the 3D7varCSA gene as well as in var genes from the Burroughs Wellcome Fund. The Plasmodium Genome
of placental isolates [10]. Database is a collaborative effort of investigators at the Uni-
It is known that the var-encoded PfEMP-1 is surface exposed versity of Pennsylvania and Monash University and is sup-
and undergoes clonal variation as a result of the stress exerted ported by the Burroughs Wellcome Fund
on the parasite by the host immune effector mechanism. In
view of the fact that the majority of the peripheral parasites
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