Putative DNA G-quadruplex formation within the promoters of Plasmodium falciparum var genes
- Nicolas Smargiasso†1Email author,
- Valérie Gabelica1,
- Christian Damblon2,
- Frédéric Rosu1,
- Edwin De Pauw1,
- Marie-Paule Teulade-Fichou3,
- J Alexandra Rowe4 and
- Antoine Claessens†4
© Smargiasso et al; licensee BioMed Central Ltd. 2009
Received: 28 July 2008
Accepted: 6 August 2009
Published: 6 August 2009
Guanine-rich nucleic acid sequences are capable of folding into an intramolecular four-stranded structure called a G-quadruplex. When found in gene promoter regions, G-quadruplexes can downregulate gene expression, possibly by blocking the transcriptional machinery. Here we have used a genome-wide bioinformatic approach to identify Putative G-Quadruplex Sequences (PQS) in the Plasmodium falciparum genome, along with biophysical techniques to examine the physiological stability of P. falciparum PQS in vitro.
We identified 63 PQS in the non-telomeric regions of the P. falciparum clone 3D7. Interestingly, 16 of these PQS occurred in the upstream region of a subset of the P. falciparum var genes (group B var genes). The var gene family encodes PfEMP1, the parasite's major variant antigen and adhesin expressed at the surface of infected erythrocytes, that plays a key role in malaria pathogenesis and immune evasion. The ability of the PQS found in the upstream regions of group B var genes (UpsB-Q) to form stable G-quadruplex structures in vitro was confirmed using 1H NMR, circular dichroism, UV spectroscopy, and thermal denaturation experiments. Moreover, the synthetic compound BOQ1 that shows a higher affinity for DNA forming quadruplex rather than duplex structures was found to bind with high affinity to the UpsB-Q.
This is the first demonstration of non-telomeric PQS in the genome of P. falciparum that form stable G-quadruplexes under physiological conditions in vitro. These results allow the generation of a novel hypothesis that the G-quadruplex sequences in the upstream regions of var genes have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family.
Plasmodium falciparum is responsible for the majority of malaria cases worldwide and is the cause of an estimated 300–500 million infections and 1–2 million deaths per year . The parasite invades circulating red blood cells and causes them to adhere to microvascular endothelial cells and sequester in blood microvessels, leading to vascular obstruction. The only proteins known to be responsible for this cytoadherence are members of the P. falciparum erythrocyte membrane protein one (PfEMP1) family (reviewed in ). These highly polymorphic parasite-derived erythrocyte surface proteins are encoded by a repertoire of 50 to 60 var genes. Crucially, each parasite expresses only one var gene at a time, with transcription sometimes being switched to a different var gene in subsequent generations, so allowing antigenic variation and immune evasion .
Despite their extreme sequence variability in the coding regions, var genes can be divided into 3 major groups (A, B and C) according to the presence of one of three conserved 5' upstream (Ups) sequences (UpsA, UpsB and UpsC) . Their chromosomal position further subdivides them into centromeric (C) or telomeric (T) locations . Var gene groups have functional and clinical significance. For example, group B and C var genes are known to bind to the endothelial receptor CD36 , whereas group A var genes have been linked to the most severe clinical forms of malaria [5, 6].
The mechanisms regulating var gene transcription are not well understood and are currently the subject of intensive investigations. Var gene expression is thought to be regulated at the level of transcription initiation . Many mechanisms have been suggested as being involved in the silencing of non-transcribed var genes including var intron sequences  and SPE and CPE motifs located in UpsB and UpsC sequences respectively [9, 10]. The histone deacetylase PfSir2 is thought to be required for chromatin silencing in the subtelomeric regions , and histone methylation in the 5' Ups region has been shown to regulate transcription of the var2csa gene . Finally, a var-specific subnuclear expression site has been proposed recently . How these pieces of evidence fit together is still unclear, and other mechanisms may be discovered before the full picture of var gene transcriptional control is obtained.
G-quadruplexes are also stabilized by interactions with cations located between the tetrads, at the center of the structure. Potassium and sodium are the most commonly described G-quadruplex stabilizing cations, although ammonium and strontium can also assume this function [19–22]. It was previously reported that there are about 376,000 potential G-quadruplex structures in the human genome [17, 18], and about 40% of human genes contain a putative G-quadruplex in their promoter . Initial reports indicate a possible role for G-quadruplex sequences in the regulation of telomere length [24, 25] and the transcriptional regulation of several genes such as c-MYC, c-kit, or KRAS [23, 26–32]. For example, in the case of the c-MYC proto-oncogene, a single nucleotide mutation that destabilizes the G-quadruplex structure in the promoter region leads to a three-fold increase in basal transcription levels, suggesting that the G-quadruplex acts as a transcriptional repressor element . Furthermore, a small ligand that binds to and stabilizes the G-quadruplex structure was shown to suppress further c-MYC transcriptional activity .
Given the increasing evidence for the importance of G-quadruplex sequences in gene regulation, we decided to investigate whether G-quadruplexes could be discovered in the genome of P. falciparum, and in particular to determine whether there are any G-quadruplex sequences in the upstream regions of var genes that have the potential to play a role in the transcriptional control of this major virulence-associated multi-gene family. In addition, the ability of potential G-quadruplex sequences from P. falciparum to form stable G-quadruplex structures under physiological conditions was examined using biophysical techniques.
Results and discussion
Identification of putative G-quadruplex forming sequences in the P. falciparum genome
The genome of P. falciparum clone 3D7 was searched for Putative Quadruplex Sequences (PQS) using QGRS-Mapper  on both the positive and negative strands. We set up the QGRS-mapper software to identify all PQS with four repeats of at least three guanines interrupted by loops of a maximum length of 11 nucleotides. As expected, most PQS were found in the telomeres (828 out of 891) due to their repetitive sequence: GGGTT(T/C)A (see Additional file 1). These telomeric G-quadruplexes of P. falciparum have recently been described by De Cian et al . Here we focused on the non-telomeric PQS because of their potential role in gene transcriptional regulation. We identified 63 non-telomeric PQS (listed in full in Additional file 2). This is an average of one PQS per 380 kb, which is a much lower ratio than that seen in the human genome (1 PQS per ~8 kb) . This was expected due to the extreme AT-richness (80.6%) of the P. falciparum genome . 37 of the 63 PQS are in intergenic regions, and of the 26 PQS within genes, 9 are on the coding strand and 17 on the non-coding strand.
PQS in the upstreamB region of var genes
Predicted G-quadruplex sequences in the upstream regions of Group B var genes from P. falciparum clones 3D7 and HB3
P. falciparum clone 3D7
P. falciparum clone HB3
Sequence of the PQS from the var gene upstream B regions of P. falciparum
CAGGG TTAAGGG TATAACTTTAGGGG TTAGGG TT
TAGGG TTAAGGG TATAACGTTAAGGG TTAGGG TT
CAGGG TTAAGGG TATACATTTAGGGG TTAGGG TT
CAGGG TTTAGGG TATAACTTTAGGGG TTAGGG TT
Evidence of G-quadruplex formation by PQS in the upstream B region of var genes
The stoichiometries of the G-quadruplexes formed by the UpsB-Q were also examined to determine whether these structures are likely to form intra-molecular bonds (unimolecular structures) or inter-molecular bonds (multimolecular structures) . Mass spectrometry showed only monomeric DNA (Additional file 3), indicating that the UpsB-Q form intra-molecular G quadruplex structures (inter-molecular structures would have been indicated by the presence of multimers by mass spectrometry).
Stability of G-quadruplexes formed by PQS in the upstreamB region of var genes
Melting temperature (T m ) of G-quadruplex sequences from the upstream B regions of var genes and the equilibrium dissociation constant of the PQS with the G-quadruplex ligand BOQ 1 (shown in the Kd column)
T m 1
47.2 ± 0.6
35.1 ± 1.2
31.6 ± 0.7
2.6 ± 0.5
49 ± 0.5
36.1 ± 2
27.7 ± 0.5
1.4 ± 0.4
50 ± 1.2
36.9 ± 1.1
34.2 ± 1.1
1.7 ± 0.7
49.3 ± 1.4
39.4 ± 0.9
32.3 ± 0.3
2.7 ± 1.1
Interactions of UpsB-Q G-quadruplexes with a ligand
In addition to the potential transcriptional repressor activity of G-quadruplex sequences themselves , it has been shown previously that G-quadruplex ligands can further suppress transcription of genes containing potential G-quadruplexes in their promoters, by impeding the binding of proteins needed for initiation of transcriptional activity on DNA [50, 51]. Moreover, these molecules are also able to interfere with telomere structure and to indirectly induce their shortening [52–55]. These molecules are thus promising weapons in the fight against cancer, since this disease needs both a high expression of oncogenes and stable telomere length to develop and survive [56–62]. With the discovery of G-quadruplex forming sequences in the genome of P. falciparum, it can be hypothesized that these ligands may also have the potential to affect parasite gene expression by stabilizing G-quadruplexes located in gene promoter regions.
The equilibrium dissociation constants of all UpsB-Q with BOQ 1 were deduced from the relative intensity of peaks of free DNA and complexes, as described previously . For the four sequences, the values are around 2 μM (Table 3). They are lower than those obtained by mass spectrometry for the binding of BOQ1 to telomeric G-quadruplex (5.7 μM) or to model duplex sequences (57 μM) (unpublished data). These results confirm the ability of the PQS in the upstream B regions of the var genes to fold in G-quadruplexes, and show that G-quadruplex ligands are likely to bind to these structures within the P. falciparum genome, and could therefore be tested for biological activity against the parasite.
Potential for G-quadruplexes to be involved in gene transcriptional regulation in P. falciparum
Increasing evidence suggests that G-quadruplexes play a role in gene transcriptional regulation in humans and other organisms. We identified 63 potential G-quadruplex sequences in the non-telomeric regions of the genome of P. falciparum clone 3D7. 16 of these PQS occurred in the upstream region of group B var genes. The var gene-related PQS were shown to form stable G-quadruplex structures in vitro under physiological conditions and bind with high affinity to a known G-quadruplex ligand. It is noteworthy that the most prevalent sequence UpsB-Q-1 (dCAGGGTTAAGGGTATAACTTTAGGGGTTAGGGTT) adopts a single structure which is stable in physiological conditions (37°C and 150 mM K+). This discovery allows us to generate a new hypothesis concerning var gene regulation mechanisms in P. falciparum, in which a helicase such as PFI0910w could be involved in G-quadruplex unwinding and thus facilitate RNA polymerase transcriptional activity. The role of G-quadruplexes in Plasmodium gene regulation, the structure of these G-quadruplexes, and their use as potential drug targets merits further research.
Both strands of each chromosome of the P. falciparum 3D7 clone (PlasmoDB_5.4 ) were analyzed using QGRS-Mapper . The parameters used were: Max length: 33; Min G-group: 3; loop size: 0 to 11. The P. falciparum HB3 genome was downloaded from the Broad Institute http://www.broad.mit.edu. Upstream sequences of var genes were analyzed using QGRS-Mapper with the same parameters.
All oligonucleotides were ordered from Eurogentec (Seraing, Belgium) with Oligold quality. The oligonucleotide sequences used are shown in the Table 2. Oligonucleotides were received lyophilized and stock solutions were prepared in bi-distilled water with 300 μM total strand concentration. For all experiments, the stock solution was heated at 80°C for 5 minutes, diluted using a cold aqueous solution containing either KCl, NaCl or NH4OAc to reach the desired DNA concentration in 150 mM cation, and then cooled rapidly on ice. 10 mM lithium cacodylate, pH 7.4 was added in thermal denaturation and circular dichroism experiments. The molecule BOQ1 was synthesized as described previously 
Experiments were performed on a Jasco J-810 spectropolarimeter using 1-cm path length cells (Hellma, type No. 114-QS, France). The final concentration of oligonucleotide was 5 μM in a buffer containing 150 mM salt and 10 mM lithium cacodylate, pH 7.4. For each sample, five spectra were recorded from 220 nm to 350 nm with a scan rate of 100 nm/min.
NMR samples were prepared by dissolving the oligonucleotides in H2O/D2O 90/10, lithium cacodylate 10 mM, pH 7.4 to get a oligonucleotide final concentration of 270 μM. Ammonium acetate or potassium chloride were progressively titrated in to a final cation concentration of 150 mM. NMR data were collected at 500 MHz on a Bruker Avance spectrometer (fitted with a TXI triple resonance probe with z-axis gradient). 1D 1H spectra were recorded at a temperature of 25°C using a WATERGATE sequence with a water flip-back pulse [75, 76].
Thermal denaturation experiments were carried out on a Uvikon XS spectrophotometer (Secomam), using 1-cm path length quartz cells (Hellma, type No. 115B-QS, France). The final oligonucleotide concentration was 5 μM in 150 mM salt and 10 mM lithium cacodylate, pH = 7.4. Absorbance was monitored as a function of the temperature at 295, 240, 260 nm for the determination of the melting temperature (Tm)  and at 405 nm as control wavelength. Gradient was 0.2°C/min between 10 and 90°C. Melting temperatures were determined using the method described by Marky and Breslauer . Before heating and after the cooling, spectra were recorded from 220 to 440 nm, to allow thermal difference spectra (TDS) to be obtained. TDS were obtained by subtracting the low temperature curve from the high temperature curve and normalization, as described previously by Mergny et al. .
Electrospray mass spectrometry
All measurements were carried out on a Q-TOF Ultima Global mass spectrometer (Micromass, now Waters, Manchester, U.K.), using the electrospray ionization (ESI) source in negative mode, as described previously . Source conditions were optimized to avoid in-source fragmentation: capillary voltage = -2.2 kV, cone voltage = 50 V, RF, source block temperature = 80°C, and desolvation gas temperature = 100°C. Source backing pressure was set to 3.5 mbar. Oligonucleotide samples were first prepared at 50 μM final concentration in NH4OAc 150 mM. Just before injection in the mass spectrometer, they were further diluted to 10 μM in 150 mM NH4OAc and 20% methanol. The role of methanol is to increase ion signals.
We thank Prof. Pierre Colson for UV experiments, Dr Pascal De Tullio for NMR experiments and Dr. Andre Matagne for CD experiments. We acknowledge the FNRS and FRIA (VG is a FNRS research associate, FR is a FNRS postdoctoral researcher, and NS is a FRIA doctoral fellow) and the financial contributions of the Fonds de la Recherche Scientifique-FNRS (FRFC 2.4.623.05 to EDP; CC 1.5.096.08 to VG) and the University of Liège (Starting Grant D-08/10 to VG). JAR is funded by a Wellcome Trust Senior Research Fellowship in Basic Biomedical Science (grant no. 067431) and AC is funded by a Wellcome 4 year PhD studentship.
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