Specific DNA-binding by Apicomplexan AP2
Erandi K. De Silva*, Andrew R. Gehrke†, Kellen Olszewski*, Ilsa Leo ´n*, Jasdave S. Chahal*, Martha L. Bulyk†‡§,
and Manuel Llina ´s*¶
*Department of Molecular Biology and Lewis–Sigler Institute for Integrative Genomics, Princeton University, 246 Carl Icahn Laboratory, Princeton, NJ 08544;
†Division of Genetics, Department of Medicine, and‡Department of Pathology, Brigham and Women’s Hospital and Harvard Medical School, Boston, MA
02115; and§Harvard/Massachusetts Institute of Technology Division of Health Sciences and Technology, Harvard Medical School, Boston, MA 02115
Edited by Thomas E. Wellems, National Institutes of Health, Bethesda, MD, and approved April 1, 2008 (received for review March 3, 2008)
Malaria remains one of the most prevalent infectious diseases
worldwide, affecting more than half a billion people annually.
Despite many years of research, the mechanisms underlying tran-
scriptional regulation in the malaria-causing Plasmodium spp., and
in Apicomplexan parasites generally, remain poorly understood. In
Plasmodium, few regulatory elements sufficient to drive gene
expression have been characterized, and their cognate DNA-
binding proteins remain unknown. This study characterizes the
DNA-binding specificities of two members of the recently identi-
fied Apicomplexan AP2 (ApiAP2) family of putative transcriptional
regulators from Plasmodium falciparum. The ApiAP2 proteins con-
tain AP2 domains homologous to the well characterized plant AP2
family of transcriptional regulators, which play key roles in devel-
opment and environmental stress response pathways. We assayed
ApiAP2 protein–DNA interactions using protein-binding microar-
rays and combined these results with computational predictions of
coexpressed target genes to couple these putative trans factors to
corresponding cis-regulatory motifs in Plasmodium. Furthermore,
we show that protein–DNA sequence specificity is conserved
inorthologous proteins between
Apicomplexan species. The identification of the DNA-binding spec-
ificities for ApiAP2 proteins lays the foundation for the exploration
of their role as transcriptional regulators during all stages of
parasite development. Because of their origin in the plant lineage,
ApiAP2 proteins have no homologues in the human host and may
prove to be ideal antimalarial targets.
gene expression ? malaria ? Plasmodium ? protein-DNA interaction ?
tually all clinical symptoms are confined to the 48-hour asexual
stage of development, during which the parasite matures and
undergoes major morphological changes within the host red
blood cell. Although the apparent complexity of parasite devel-
transcriptional network, remarkably little is known regarding
gene regulation in Plasmodium spp. and related parasites of the
class Apicomplexa. This knowledge void is surprising, given the
wealth of recent whole-genome gene expression data analyzing
virtually all stages of development (2–5). Bioinformatic analysis
of the Plasmodium falciparum genome demonstrates a dearth of
identifiable specific transcription factors (6, 7). This observation
has led to speculation that gene expression in Plasmodium spp.
is preferentially regulated posttranscriptionally through a com-
bination of mRNA degradation, translational repression, and
epigenetic mechanisms (8–10). In accordance with this, the
genome reveals a near-complete set of chromatin remodeling
machinery and an abundance of proteins containing RNA-
binding domains (7). However, there is compelling evidence that
the mechanisms of transcriptional regulation in Plasmodium spp.
are more similar to other eukaryotic systems.
alaria is caused by the Plasmodium parasite and is respon-
sible for ?1.5 million annual deaths worldwide (1). Vir-
Transcription in Plasmodium uses minimal promoter regions
that produce monocistronic mRNAs, including both 5? and 3?
untranslated regions, and which often contain introns (11, 12).
Furthermore, the basal eukaryotic transcription factors are
RNA polymerase II-dependent messenger RNA production (6,
7). In addition, the Plasmodium transcriptome follows a dynamic
cascade of periodic gene expression initiated upon invasion of
only once in a ‘‘just-in-time’’ fashion, suggesting an important
role for stage-specific regulation of gene expression. Despite a
number of previous studies suggesting the presence of stage-
specific nuclear factors (13–15), the identification of factors that
might modulate this expression cascade has remained elusive in
A recent bioinformatic search for DNA-binding domains
identified the Apicomplexan AP2 (ApiAP2) family of proteins
parasites sequenced to date (16). ApiAP2 proteins exhibit weak
homology to a family of transcription factors in plants called the
AP2/ERF DNA-binding proteins. In the plant Arabidopsis thali-
ana, this family comprises the second largest class of regulators,
with ?145 members (17). The plant AP2/ERF domain is ?60 aa
in size and can be found either as a single module or in a tandem
arrangement (18). In plants, the architecture of these proteins is
correlated with their function: single-domain AP2 genes are
involved in environmental stress responses from thermotoler-
ance to dehydration and ethylene response, whereas proteins
with tandem domains have been implicated in plant develop-
There are 26 members of the P. falciparum ApiAP2 protein
family, all currently annotated as conserved hypothetical pro-
teins (19). Subsets of Plasmodium ApiAP2 proteins are ex-
pressed throughout the four stages of the intraerythrocytic
development cycle (IDC): the ring, trophozoite, early schizont,
and late schizont stages (2, 16). As in plants, the predicted AP2
domains in Plasmodium are ?60 aa in size and can be found as
both single and tandem domain architectures, although there is
an additional architecture containing three AP2 domains in a
single protein. Within the Plasmodium spp., there is virtually
100% identity between orthologous AP2 domains, and often
homologues of lower sequence similarity can be identified in
Author contributions: E.K.D.S. and M.L. designed research; E.K.D.S., A.R.G., K.O., I.L., and
J.S.C. performed research; M.L.B. contributed new reagents/analytic tools; E.K.D.S., A.R.G.,
K.O., and M.L. analyzed data; and E.K.D.S., A.R.G., K.O., and M.L. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Freely available online through the PNAS open access option.
¶To whom correspondence should be addressed. E-mail: email@example.com.
This article contains supporting information online at www.pnas.org/cgi/content/full/
© 2008 by The National Academy of Sciences of the USA
www.pnas.org?cgi?doi?10.1073?pnas.0801993105 PNAS ?
June 17, 2008 ?
vol. 105 ?
no. 24 ?
The AP2 domains in P. falciparum are located within the context
of much larger proteins ranging in size from 200 to ?4,000 aa,
although there is generally very low homology in regions outside
of the AP2 domains themselves.
In this study, we demonstrate the DNA-binding specificities of
two ApiAP2 proteins representing different classes of AP2
domain architectures from P. falciparum using protein-binding
microarrays (PBMs) (20, 21). We report that these AP2 domains
have a high specificity for unique DNA sequence motifs found
in the upstream regions of distinct sets of genes that are
coregulated during asexual development. We also show that
from distantly related Apicomplexan species (P. falciparum and
Cryptosporidium parvum), the DNA-binding specificities of or-
thologous pairs of AP2 domains are fundamentally conserved,
although their downstream targets are not. This demonstrates a
previously undescribed interaction between Plasmodium trans
factors and their putative target sequences. These results, along
with computational predictions of genome-wide motif enrich-
ment, allow us to begin constructing a network of regulatory
interactions in Plasmodium.
ApiAP2 Proteins of Differing Domain Architecture. We selected two
different architectures of P. falciparum AP2 domains that re-
semble the single and tandem domain plant architectures. The
first gene, pf14?0633, encodes an 813-aa protein, is maximally
expressed during the ring stage of development (2) and contains
a single 60-aa AP2 domain and an adjacent AT-hook DNA-
binding domain (16). PF14?0633 not only has orthologues in all
other sequenced Plasmodium genomes but also in all of the other
sequenced Apicomplexan genomes (Fig. 1). Although the AT-
hook is conserved only in Plasmodium spp., residues within the
AP2 domain are well conserved in all Apicomplexa.
The second ApiAP2 gene examined, pff0200c, shows maximal
expression in late-stage parasites and encodes a 1,979-aa protein
possessing two AP2 domains in tandem, linked by a conserved
17-aa sequence. In Plasmodium spp., the amino acid sequence
identity across the orthologous tandem AP2 domains of
PFF0200c approaches 95% [supporting information (SI) Fig.
S1]. In contrast, the individual AP2 domains of PFF0200c share
only 35% identity with each other. In plants, it has been shown
that the two tandem AP2 domains of AINTEGUMENTA in A.
thaliana, which share 43% identity, bind two different DNA
between tandem domains in P. falciparum remains unknown.
P. falciparum AP2 Domains Bind Specific DNA Motifs. To elucidate
whether isolated AP2 domains from P. falciparum bind DNA,
and if so, to determine the specificity of binding, we assayed
purified AP2 domains using PBMs. PBMs are a methodology
used to determine the specificity of protein–DNA interactions
and have been extensively used to characterize transcription
factors from yeast to human (20). The array is not organism-
specific but contains all possible 10-mer DNA sequences spread
across 44,000 double-stranded DNA 60-mers, providing exten-
sive negative and positive specificity controls across the array
(20). As a proof of principle, we first measured the binding of a
63-aa A. thaliana ERF1 AP2 domain (residues 144–206) and
(data not shown) (23).
Using PBMs, we obtained distinct and highly specific DNA
sequence motifs for the single AP2 domain from PF14?0633 and
for the double AP2 domain from PFF0200c. As is common for
transcription factor-binding sites, these motifs are palindromic,
with PF14?0633 binding the TGCATGCA consensus sequence
and PFF0200c-binding GTGCAC (Fig. 2, Dataset S1). The
motifs for the P. falciparum AP2 domains were noticeably more
AT-rich than the canonical GCC-box motifs that are bound by
plant AP2 domains. This is consistent with predictions that the
regulatory motifs would be more AT-rich than other eukaryotic
cis-acting motifs, given that the AT-content in the intergenic
region of P. falciparum approaches 90% (16, 19).
Of the 26 ApiAP2 proteins in P. falciparum, all are conserved
in the other sequenced Plasmodium spp., whereas only a small
subset span all Apicomplexan genomes. The AP2 domain from
the C. parvum gene cgd2?3490 has 47% identity (68% similarity)
to the plasmodial PF14?0633 (Fig. 1). To determine whether the
conserved residues between evolutionarily distant orthologues
were sufficient to confer similar DNA-binding specificity, we
tested the cgd2?3490 AP2 domain by PBM. Remarkably, our
results show that the C. parvum AP2 domain and its PF14?0633
Plasmodium orthologues have highly similar DNA-binding spec-
ificities (Fig. 2). This unexpected result demonstrates that the
Apicomplexan parasites have conserved not only the AP2 DNA-
binding domain architecture, but also the sequence specificity.
Although the AP2 region for PF14?0633 is conserved between
Apicomplexa, the AT-hook DNA-binding motif is found only in
the Plasmodium spp. (Fig. 1). We tested the possible contribu-
tion of this additional domain to DNA-binding using a GST-
fusion protein containing both the AT-hook and the AP2
domain from PF14?0633 and found no change in the DNA-
binding motif recognized (data not shown). This suggests that
DNA binding by the AP2 domain is sufficient for specific
The AP2 domain (boxed) is highly conserved across all species. Conservation of residues is most significant in the three ?-strands (shaded yellow) of the AP2
black line). Absolutely conserved residues likely to be involved in DNA binding are highlighted in red. Secondary structure predictions were made by using Jnet
(39). PF, P. falciparum; PVX, Plasmodium vivax; PKH, Plasmodium knowlesi; PB, Plasmodium berghei; PY, Plasmodium yoelii; PC, Plasmodium chabaudi; 583, T.
gondii; TP, Theileria parvum; TA, Theileria annulata; BBOV, Babesia bovis; Chro, Cryptosporidium hominis; cgd2, Cryptosporidium parvum.
Alignment of the AP2 domain from PF14?0633 (amino acids 63–123) to orthologues in five additional Plasmodium spp. and six Apicomplexan species.
www.pnas.org?cgi?doi?10.1073?pnas.0801993105 De Silva et al.
binding, although it is possible that the AT-hook region may
increase affinity through nonspecific interactions with the DNA.
In plants, it has been demonstrated that proteins with tandem
AP2 domain architectures absolutely require both domains for
specific DNA binding (22). To explore the relative contribution
of each AP2 domain in the PFF0200c tandem AP2 architecture,
we dissected the protein and tested each domain separately using
PBMs. Surprisingly, domain 1 of PFF0200c was sufficient for
specific DNA binding and bound the identical GTGCAC motif
as the full-length tandem double domain of PFF0200c (Fig. 2).
The isolated PFF0200c domain 2 did not demonstrate any
specific protein–DNA interaction. These results suggest that, in
contrast to plants, the second AP2 domain in PFF0200c may not
contribute to the protein’s DNA-binding specificity.
Prediction and Validation of AP2 Target Genes. Ultimately, we are
in Plasmodium. The two binding sites identified biochemically in
this study are highly similar to two motifs predicted indepen-
dently by Elemento et al. (24) using the Finding Informative
Regulatory Elements (FIRE) algorithm (Fig. 2). The FIRE
algorithm compiles a list of candidate target genes associated
with each predicted motif (Dataset S2). These target genes share
two characteristics: (i) at least one instance of the considered
motif in their promoter regions and (ii) peak mRNA abundance
levels within a particular phase of the IDC transcriptome that is
significantly enriched in genes whose promoters contain the
motif (2). We compared the expression profile of PFF0200c to
target genes, Dataset S2) containing the GTGCA motif (Fig. 3).
The highly positive Pearson correlation (0.97) between
PFF0200c, and its putative targets suggests that it functions to
activate this set of genes (Fig. 3). We also note that the induction
of gene expression (20–35 h postinvasion) for PFF0200c pre-
cedes the average expression profile of the putative target genes
by 1–2 h. The mean profile from the top cluster (34 genes)
containing the PF14?0633 consensus motif, however, is not
strongly correlated with the PF14?0633 expression profile (Pear-
son correlation ? 0.25) (Fig. S2, Dataset S2) and may suggest
that other auxiliary regulatory factors are involved for expres-
sion timing. The striking and independent convergence of these
computational motif predictions with our biochemical DNA-
binding specificity results strongly suggests that these motifs are
of significant biological importance.
From the FIRE-predicted gene sets, we selected candidate
genes to be tested for specific DNA–protein interactions by
EMSA. A radiolabeled 40-bp sequence (Table S1), found up-
stream of the putative target gene pfi0540w and containing the
TGCATGCA motif, could be specifically shifted using the
purified AP2 domain from PF14?0633 (Fig. 4). This interaction
could be competed by an unlabeled oligonucleotide of identical
sequence, but a 50-fold excess of a related, mutant oligonucle-
otide (AT to GC change in the motif) did not disrupt binding.
We also confirmed the PFF0200c-binding interaction using an
oligonucleotide sequence from the upstream region of a candi-
date target gene mal7p1.119 containing the GTGCAC DNA
motif (Fig. 4). These results validate our PBM data and extend
this analysis by demonstrating that ApiAP2 domains can bind
specifically to sequences present upstream of putative target
genes in the Plasmodium genome.
Analysis of Putative Regulons. The FIRE algorithm predicts a total
associated with PFF0200c, of which 115 (59.3%) are annotated as
hypothetical. Gene Ontology (GO) analysis reveals significant
enrichment for genes involved in protein modification (P value ?
9.85e-5), particularly protein phosphorylation (P ? 3.83e-4) and
cysteine peptidase activity (P ? 1.30e-3), and in genes associated
with the rhoptry organelle (P ? 4.12e-5) and apical complex (P ?
targets include the rhoptry-associated proteins RAP1, RAP2, and
RAP3; the merozoite surface proteins MSP1, MSP7, and MSP9;
and the cytoadherence-linked asexual proteins CLAG2, CLAG3.1,
CLAG3.2, and CLAG9. This suggests that PFF0200c regulates
late-stage genes involved in the critical process of preparing the
parasite for host cell rupture and reinvasion.
the motif specifically bound by the P. falciparum AP2 domain of PF14?0633 are
highly similar to those bound by its C. parvum orthologue cgd2?3490 (Top and
using the FIRE algorithm (Bottom, Predicted) (24). (B) The PBM-derived motif
bound by the first domain alone (Middle). Domain 2 of PFF0200c did not bind a
specific DNA motif (data not shown). Both PBM-derived motifs for PFF0200c
match the computationally predicted motif (Bottom).
DNA motifs specifically bound by AP2 domains predicted using PBMs
compared with the averaged expression profiles of putative FIRE-predicted
target genes. The 48-hour gene expression profiles are positively correlated
with a Pearson correlation coefficient of 0.97.
Blood-stage gene expression profile of the PFF0200c ApiAP2 protein
De Silva et al.
June 17, 2008 ?
vol. 105 ?
no. 24 ?
The extremely high conservation between the PF14?0633- and
determine whether these proteins regulate similar gene sets. Of the
5,460 P. falciparum genes, 31.5% (1,722) have homologues in C.
parvum. Surprisingly, only 26 of the 127 FIRE-predicted targets of
the PF14?0633 motif (20.4%, P ? 3.43e?3) are conserved between
these organisms, suggesting that, whereas the sequence specificity
of these two AP2 domains is absolutely conserved, a significant
rewiring of the transcriptional network has occurred since these
species diverged. In contrast, there is no significant deviation from
the background frequency homology for the 194 FIRE-predicted
targets of PFF0200c (37.6%, P ? 0.972), as is expected because of
the lack of a PFF0200c homologue in C. parvum.
from every gene in the P. falciparum and C. parvum genomes for
the occurrence of the PF14?0633 and cgd2?3490 AP2 DNA
motif, respectively. The 1,003 C. parvum genes containing at
least one instance of the cgd2?3490 DNA binding motif are most
significantly enriched for transmembrane proteins (P ? 5.40e-9),
whereas the 775 putative PF14?0633 targets are most enriched
for cytoadherence to the microvasculature (P ? 2.51e-12). There
are no common enriched annotations between the two sets,
further indicating that they target very different regulons. In-
terestingly, we found members of the upsB and upsC var gene
subfamilies in the PF14?0633 target set. The var genes in P.
falciparum encode PfEMP1 (erythrocyte membrane protein)
one of the major surface antigens involved in cytoadherence and
host immune evasion (25). Sequence alignments of the upsB
upstream regions revealed an almost perfectly conserved in-
stance of the consensus PF14?0633 motif CATGCA between
1,478 and 1,352 bp of the ATG and another instance between
1,218 and 1,093 bp upstream, which corresponds to the SPE1 site
identified by Voss et al. (15). These data suggest that PF14?0633
may play a role in var gene regulation. In addition, the potential
target set also includes PFF0200c, which contains an exact match
to the sequence TGCATGCA 1,746 bp upstream from the ATG
start. This raises the intriguing possibility that PFF0200c is itself
regulated by PF14?0633, in what may be one link in an ApiAP2
regulatory cascade (Fig. S3).
The majority of the P. falciparum ApiAP2 family of proteins are
expressed throughout asexual development and represent the first
candidate set of transcriptional regulators in this parasite (16). Our
analysis of two Plasmodium asexual-stage ApiAP2 proteins estab-
lishes that these proteins bind highly specific DNA sequences that
are enriched in the upstream regions of subsets of Plasmodium
genes. We have further demonstrated that two representative
up to three AP2 domains are present in plasmodial ApiAP2
proteins. We also examined the significance of the conservation of
AP2 domains across Apicomplexa by characterizing an orthologous
AP2 domain from C. parvum. The conservation of DNA-binding
specificities likely occurs through the highly conserved predicted
?-strand residues (Fig. 1, Fig. S1). However, we provide computa-
tional evidence that the putative target genes are not conserved
between distant Apicomplexa, implying that the regulons in differ-
ent organismal classes are likely to be highly diversified. These
results further caution against the inference of transcriptional
regulatory networks based solely on homology, as was recently
different gene sets in three yeast species (26).
Our results also demonstrate that the AP2 domain from Plas-
modium is sufficient for specific DNA binding and lead us to
question the functional roles of other regions in the ApiAP2
proteins. Outside of the AP2 domains, sequence homology be-
tween orthologous ApiAP2 proteins deteriorates, making the iden-
tification of other relevant domains such as transcriptional activa-
tion domains difficult. The 26 ApiAP2 proteins in P. falciparum
with the exception of PF14?0633, which contains an AT-hook. In
light of this, we examined all P. falciparum ApiAP2 proteins for the
presence of additional informative sequences. We were unable to
detect any motifs for apicoplast targeting, mitochondrial transit,
endoplasmic reticulum trafficking, transmembrane domains, or
host cell surface targeting by the PEXEL/VTS. However, we are
able to identify classical lysine- and arginine-rich nuclear localiza-
PredictNLS (27), supporting the conclusion that this protein family
consists of transcription factors.
Although the AP2/ERF proteins are established as transcrip-
tional regulators in plants, there is currently little understanding of
how these proteins interact with the basal transcriptional machin-
ery. We hypothesize that ApiAP2 proteins may mediate specific
protein–protein interactions. A recent Plasmodium-based global
yeast two-hybrid study suggests that ApiAP2 proteins interact with
each other and with chromatin remodeling factors, including the
Plasmodium histone acetyltransferase GCN5 (28). Binding to chro-
matin remodeling factors may serve to recruit these complexes to
specific chromosomal locations and facilitate interaction with the
core transcription machinery. One report in plants has suggested
that the A. thaliana AP2 protein, CBF1, interacts with GCN5 and
two transcriptional adaptor proteins (ADA2 and ADA3) (29).
Alternatively, protein–protein interactions may occur directly
through an AP2 domain, as has been seen for the plant proteins
DORNRO ¨SCHENandDORNRO ¨SCHEN-LIKE(30).Aswegain
further knowledge regarding the DNA-binding specificity of all
to biochemically identify interacting partners to define the full
network of transcriptional regulation.
A similar motif to the GTGCAC motif bound by PFF0200c has
been identified upstream of the upsB-type var genes (SPE2) in P.
falciparum and was found repeated 5–18 times 565–1,035 bp
the tandem AP2 domains from PFF0200c (Lower) were used to shift 40 bp of
a radioactively labeled DNA probe derived from the upstream region of a
computationally predicted target genes (PFI0540w and MAL7P1.119, respec-
tively) (lane 2). Competition experiments show that an unlabeled specific
competitor (SC) can deplete the labeled shifted band (lanes 3–6). An unla-
9) cannot deplete the shift.
EMSA of AP2 domains. The AP2 domain from PF14?0633 (Upper) and
www.pnas.org?cgi?doi?10.1073?pnas.0801993105De Silva et al.
This motif was shown to be specifically bound by a nuclear factor
expressed in late-stage parasites and was further found to induce
late-stage expression from an otherwise minimal promoter (31).
This has been interpreted to suggest a late-stage var gene silencing
role for this nuclear factor. Both the binding activity and reporter
of PFF0200c and its predicted target gene set (Fig. 3). If PFF0200c
is the nuclear factor identified (15), it may serve dual roles as a
However, it is also possible that there are two different DNA-
binding proteins that recognize the GTGCAC motif.
Interestingly, the TGCATGCA sequence bound by the AP2
domains of PF14?0633 and C. parvum cgd2?3490 is the most highly
sequenced Apicomplexan genomes (32). This motif is seven times
overrepresented in P. falciparum, and 11?, 18?, and 18? over-
represented in Toxoplasma gondii, Cryptosporidium parvum, and
unexplored, although it is well established that the presence of a
motif does not necessarily imply that it is functional. Future
chromatin immunoprecipitation experiments will help to decipher
the precise targets for PF14?0633 and PFF0200c.
We note that the FIRE algorithm reveals significant enrichment
for 21 distinct motifs from all phases of the intraerythrocytic
developmental cycle (24). This number is similar to the number of
ApiAP2 proteins, which are actively transcribed during the asexual
stages, supporting the idea put forth by Balaji et al. (16) that gene
expression during the IDC could be controlled by a cascade of
ApiAP2 proteins, each regulating a specific phase of development
genes, suggesting they may regulate one another. In fact, the
upstream region of PFF0200c contains five copies of its own
TGCATGCA motif (?1,746 bp from the ATG) recognized by
This study links specific DNA-binding proteins to sequences
found in putative regulatory regions of Apicomplexan genomes.
The existence of a possible network of ApiAP2 DNA-binding
proteins contributes an important piece to the puzzle of gene
regulation in Plasmodium. Although it remains to be determined
how ApiAP2 proteins function as transcriptional regulators, the
DNA-binding sequence specificity of these proteins, their conser-
vation across Apicomplexa, and the highly coherent expression
role in regulating parasite development. Additionally, several P.
falciparum ApiAP2 proteins show no detectable expression during
the IDC and may prove to be functionally important in the
mosquito or exoerythrocytic liver stages.
Materials and Methods
PBMs. N-terminal GST fusion proteins were made by using the pGEX4-T1 vector
(GE Healthcare) and AP2 domains from PF14?0633 (residues 63–123), AT-hook
plus AP2 domain from PF14?0633 (residues 37–123), cgd2?3490 (residues 340–
domains. Domain boundaries were defined as (16), PCR-amplified and cloned
into BamHI and XhoI restriction sites in pGEX4-T1. Proteins were expressed in
Escherichia coli BL21 (RIL Codon PLUS) (Stratagene) cells at 25°C and purified by
using Uniflow Glutathione Resin (Clontech). Proteins were eluted in 10 mM
reduced glutathione, 50 mM Tris?HCl, pH 8.0. Purity was verified by silver stain
SDS/PAGE and Western blot analysis with an anti-GST antibody (Invitrogen).
A minimum of two PBM experiments were performed as described (20, 21)
for each protein tested. Briefly, this methodology utilizes a custom 60-mer
single-stranded Agilent DNA microarray with ?44,000 features covering all
possible 10-mers. Primer extension from a universal 24-mer region on all
60-mers generates a double-stranded DNA microarray platform. Purified
proteins were diluted to a final concentration of 100–500 nM in PBS, 2%
(wt/vol) milk, 51.3 ng/?l salmon testes DNA (Sigma), 0.2 ?g/?l BSA (New
England Biolabs), and incubated for 1 h at 20°C. After washing, specific
DNA–protein interactions were visualized by using a GSI Lumonics ScanArray
5000 scanner to detect fluorescence from an Alexa488-conjugated anti-GST
antibody. After data normalization as described (20, 21), enrichment scores
were calculated for all 8-mers, and the ‘‘Seed-and-Wobble’’ algorithm (20)
PBM-derived DNA-binding specificities, which we represent using the Web-
based tool enoLOGOS (33).
Computational Analysis. Data from the FIRE analysis of the P. falciparum
transcriptome (24) was downloaded from http://tavazoielab.princeton.edu/
FIRE. Genes with highly conserved upstream regions, including the var, rifin,
and stevor subfamilies, are filtered to contain only one randomly selected
member per cluster by the FIRE algorithm, not to bias the sequence analysis.
For our analyses, we defined the putative targets of a given motif as those
region 1 kb upstream from their ATG start and (ii) fall into a phase bin that is
significantly enriched for that motif.
Peptides involved in targeting to various organelles and the host cell surface
and putative transmembrane domain were analyzed by using tools at PlasmoD-
B.org (34). GO analyses were performed in GOLEM (35) with the most recent P.
discovery rate (FDR) of 0.05. Because of the lack of an official GO annotation for
C. parvum, functional enrichment analyses were performed by using the DAVID
Functional Analysis Tool with an FDR threshold of 0.05 (36). To determine or-
thologous gene pairs, conservation analysis was performed by reciprocal best
BLAST by using a lenient E-value cutoff of 1 on the P. falciparum and C. parvum
predicted protein sequences [PlasmoDB 5.4 (34) and CryptoDB 3.7 release (37)].
Deviation from the background level conservation within a subset of genes was
the 2 kb upstream regions of every predicted ORF in the P. falciparum or C.
parvum genomes. We used a significance threshold of 2 standard deviations
below the mean score in the alignment file.
EMSA. Forty-base pair DNA oligonucleotides containing the PBM-derived
motifs were taken from the 5? upstream regions of predicted target genes
PFI0540w and MAL7P1.119 (Table S1).32P radiolabeled double-stranded DNA
EDTA, 50 ng/?l poly dI/dC) for 1 h at 25°C. Competition experiments included
50–500? excess unlabeled probes. Binding reactions were separated on 6%
nondenaturing acrylamide gels run in 0.5? TBE buffer.
ACKNOWLEDGMENTS. We thank J. Kissinger (University of Georgia, Athens)
for the C. parvum genomic DNA, B. Krizek (University of South Carolina,
Columbia) for the A. thaliana genomic DNA, and E. Bush for cloning the C.
parvum cgd2?3490 AP2 domain. We also thank A. Caudy, O. Elemento, J.
Forman, M. Szpara, S. Tavazoie, and members of the Llina ´s lab at Princeton
University; M. Berger at Brigham and Women’s Hospital and Harvard Medical
School; and A. Vaidya at Drexel University College of Medicine for valuable
discussion and critical reading of the manuscript. This work was mainly sup-
ported by the Arnold and Mabel Beckman Foundation (M.L.), National Insti-
tutes of Health Grant P50 GM071508 (to M.L.), and in part by National
Institutes of Health/National Human Genome Research Institute Grant R01
HG003985 (to M.L.B.). K.O. is funded by a National Science Foundation Grad-
uate Research Fellowship.
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