# A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum.

Karine G Le Roch, Jeffrey R Johnson, Hugues Ahiboh, Duk-Won D Chung, Jacques Prudhomme, David Plouffe, Kerstin Henson, Yingyao Zhou, William Witola, John R Yates, et al.

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Karine G Le Roch, Jeffrey R Johnson, Hugues Ahiboh, Duk-Won D Chung, Jacques Prudhomme, et al. A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, Plasmodium falciparum. BMC Genomics, 2008, 9, pp.513. 10.1186/1471-2164-9-513. [hal-00374517](https://hal.science/hal-00374517v1)

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# A systematic approach to understand the mechanism of action of the bisthiazolium compound T4 on the human malaria parasite, *Plasmodium falciparum*

Karine G Le Roch*¹, Jeffrey R Johnson², Hugues Ahiboh³, Duk-Won D Chung¹, Jacques Prudhomme¹, David Plouffe⁴, Kerstin Henson², Yingyao Zhou⁴, William Witola⁵, John R Yates², Choukri Ben Mamoun⁵, Elizabeth A Winzeler²,⁴ and Henri Vial³

Address: ¹Department of Cell Biology and Neuroscience, University of California, Riverside, 900 University Avenue, Riverside, CA, 92521 USA, ²Department of Cell Biology ICND202, the Scripps Research Institute, 10550 North Torrey Pines Rd, La Jolla, CA, 92037, USA, ³Dynamique des Interactions Membranaires Normales et Pathologiques, CNRS UMR 5235, Université Montpellier II, Place Eugène Bataillon, 34095 Montpellier Cedex 05, France, ⁴Genomics Institute of the Novartis Research Foundation, 10675 John Jay Hopkins Drive, San Diego, CA, 92121, USA and ⁵Department of Genetics and Developmental Biology, University of Connecticut Health Center, 263 Farmington Avenue, Farmington, CT, 06030-3301, USA

Email: Karine G Le Roch* - karine.leroch@ucr.edu; Jeffrey R Johnson - jjohnson@scripps.edu; Hugues Ahiboh - vial-h@univ-montp2.fr; Duk-Won D Chung - dchun003@ucr.edu; Jacques Prudhomme - jacques@ucr.edu; David Plouffe - dplouffe@gnf.org; Kerstin Henson - khenson@gnf.org; Yingyao Zhou - yzhou@gnf.org; William Witola - witola@up.uchc.edu; John R Yates - jyates@scripps.edu; Choukri Ben Mamoun - choukri@up.uchc.edu; Elizabeth A Winzeler - winzeler@scripps.edu; Henri Vial - vial@univ-montp2.fr

Published: 30 October 2008

Received: 3 May 2008

BMC Genomics 2008, 9:513 doi:10.1186/1471-2164-9-513

Accepted: 30 October 2008

This article is available from: http://www.biomedcentral.com/1471-2164/9/513

© 2008 Le Roch et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

## Abstract

**Background:** In recent years, a major increase in the occurrence of drug resistant falciparum malaria has been reported. Choline analogs, such as the bisthiazolium T4, represent a novel class of compounds with strong potency against drug sensitive and resistant *P. falciparum* clones. Although T4 and its analogs are presumed to target the parasite's lipid metabolism, their exact mechanism of action remains unknown. Here we have employed transcriptome and proteome profiling analyses to characterize the global response of *P. falciparum* to T4 during the intraerythrocytic cycle of this parasite.

**Results:** No significant transcriptional changes were detected immediately after addition of T4 despite the drug's effect on the parasite metabolism. Using the Ontology-based Pattern Identification (OPI) algorithm with an increased T4 incubation time, we demonstrated cell cycle arrest and a general induction of genes involved in gametocytogenesis. Proteomic analysis revealed a significant decrease in the level of the choline/ethanolamine-phosphotransferase (PfCEPT), a key enzyme involved in the final step of synthesis of phosphatidylcholine (PC). This effect was further supported by metabolic studies, which showed a major alteration in the synthesis of PC from choline and ethanolamine by the compound.

**Conclusion:** Our studies demonstrate that the bisthiazolium compound T4 inhibits the pathways of synthesis of phosphatidylcholine from choline and ethanolamine in *P. falciparum*, and provide evidence for post-transcriptional regulations of parasite metabolism in response to external stimuli.

<footnote>* Corresponding author</footnote>
**Introduction**

Malaria remains a major public health problem in many
parts of the world. Emergence and spread of resistance to
widely accessible and inexpensive antimalarials make the
development of novel therapeutic approaches an urgent
task [1,2]. *Plasmodium falciparum* causes the most severe
form of the disease and has a devastating effect on the
lives of millions. Intensive asexual multiplication of the
parasite occurs in human erythrocytes and is responsible
for the symptoms associated with human malaria. During
its 48-hour intraerythrocytic life cycle, the parasite under-
goes major morphological and metabolic changes fol-
lowed by nuclear division, cytokinesis and merogony to
generate up to 36 new daughter parasites. Accordingly, the
parasite produces and transports large amounts of lipid
precursors and actively uses them to synthesize the mem-
brane components needed during its rapid development
and multiplication. Phosphatidylcholine (PC) is the

major phospholipid in *P. falciparum* membranes and its
content increases by approximately six-fold during the
parasite's intraerythrocytic life cycle [3,4]. Because of its
essential function in parasite development, multiplication
and survival, its synthesis has long been viewed as an ideal
target for the development of new antimalarial drugs [5].
Cell biological studies revealed that the synthesis of this
phospholipid occurs via two major metabolic pathways:
the *de novo* choline pathway and the serine decarboxyla-
tion-phospho-ethanolamine methylation (SDPM) path-
way (Figure 1). The *de novo* choline pathway is initiated by
the transport of choline from host plasma followed by
three enzymatic reactions that lead to the incorporation of
this precursor into PC. The SDPM pathway initiates from
serine either transported from the host plasma or present
within infected erythrocytes as a result of active degrada-
tion of the erythrocyte proteins by parasite specific pro-
teases [6]. Serine is then subjected to five enzymatic

<figure><img src="image_2.png" /><figcaption>**Figure 1**</figcaption></figure>

**Phosphatidylcholine biosynthesis pathways in P. falciparum.** The figure includes relevant steps presented in the results and discussion. Enzyme and lipid abbreviations described in the figures are as followed: **PC**: Phosphatidylcholine; **PE**: Phosphatidylethanolamine; **PS**: phosphatidylserine; **PI**: Phosphatidylinositol; DAG: Diacylglycerol; **SDPM pathway**: Serine Decarboxylation-Phospho-ethanolamine Methylation; **PfSD**: Serine-decarboxylase; **PfEK**: Ethanolamine kinase; **PfPMT**: phosphoethanolamine N-methyltransferase; **PfCK**: Choline kinase; **PfCCT**: CTP-phosphocholine cytidylyltransferase; **PfCEPT**: CDP choline-choline/ethanolamine phosphotransferase protein.
reactions, two of which, serine decarboxylation and phos-
phoethanolamine transmethylation (phosphoeth-
anolamine N-methyltransferase, PfPMT), are plant-like,
while the last two steps are shared with the CDP-choline
pathway (Figure 1) [6-8]. Because of the predicted essen-
tial role of phospholipids in the parasite's intraerythro-
cytic development and multiplication, several efforts have
been made to synthesize lipid-based inhibitors as an alter-
native arsenal to fight malaria. Bisquaternary ammonium
salts that mimic the structure of the phospholipid precur-
sor choline have been shown to target membrane biogen-
esis in *P. falciparum* by blocking the biosynthesis of PC.
The first generation of these compounds consisted of
mono- and bis-quaternary ammonium salts [9,10], and
their lead compound G25 efficiently inhibited the growth
of drug-resistant strains of *P. falciparum* *in vitro*, [11], and
eliminated *Plasmodium* infection without recrudescence in
rodent [12] and primate models [13] at very low doses.
Further structural optimization of this first generation of
compounds produced the bis-thiazolium compounds T3
and T4, which, at very low doses, exerted a very rapid cyto-
toxic effect against malaria parasites *in vitro*. These com-
pounds cleared malaria infection in murine and primate
models with no recrudescence [14]. A clinical candidate,
T3/SAR97276, has recently been advanced to clinical
development in humans for treatment of severe malaria
(Vial, unpublished data). To elucidate the mode of action
of this promising class of compounds, we have analyzed
the global effect of T4 on the parasite's transcriptome and
proteome during the *P. falciparum* intraerythrocytic life
cycle. No significant transcriptional changes were
observed in the genes encoding those enzymes involved
in PC biosynthesis. However, using a proteomic approach
(MS/MS) we detected a down regulation of the choline/
ethanolamine-phosphotransferase protein (MAL6P1.145,
PfCEPT). Metabolic studies further confirmed the specific
action of the compound on the synthesis of PC.

**Methods**

Parasite cultures, treatments and RNA extraction

P. falciparum parasites (3D7 strain) were cultured in
human O+ erythrocytes as previously described [15].
When necessary, cultures were synchronized (twice within
a 6 hour interval) using sorbitol [16]. T4 was added 48
hours after the first synchronization treatment. Parasites
incubated in complete medium at 8% parasitaemia and
2.5 - 3% haematocrit were treated with varying concentra-
tions of T4. The drug was added to 25 ml cultures at 40 nM
or 125 nM and the parasites were further incubated for 5,
24, 30 and 36 hours, and harvested. Total RNA was pre-
pared as previously described [17]. Parasite synchrony
and morphology were monitored by microscopic analysis
of Giemsa-stained blood smears.

Microarray analyses

The custom high-density oligonucleotide array used in
this study was based on the *P. falciparum* sequence data
released in July 2001 [17]. The array includes 260,596 25-
mer probes corresponding to 5159 *P. falciparum* gene
sequences. Probes were synthesized by Affymetrix, Inc.
(Santa Clara, CA) using photosensitive oligonucleotide
chemistry and photolithography. Microarray analysis was
performed as previously described [17]. Briefly, eight
micrograms of total RNA was used for cDNA synthesis. An
oligo-dT primer containing a phage T7 promoter at its 5'
end was used to prime the cDNA synthesis reaction. A sec-
ond strand of cDNA was synthesized and used as a tem-
plate for *in vitro* transcription in the presence of
biotinylated ribonucleotide following the manufacturer
instructions (Enzo). RNA hybridizations were carried out
with 15 µg of fragmented cRNA at 45°C for 16 hour. The
hybridization solution was removed and the arrays were
stained and washed following Affymetrix protocols.
Arrays were scanned with an emission wavelength of 560
nm at 3 µm resolution using a confocal scanner (Affyme-
trix), and the signal intensity for each sequence feature on
the array was determined using Microarray Suite 5
(Affymetrix).

Semi quantitative RT-PCR

Total RNA was extracted from synchronized untreated and
treated parasites cultures after 24, 30 and 36 hours incu-
bations with T4. RT-PCR was performed as previously
described [18]. Briefly, the RNA was first incubated with
Dnase I (Ambion) at 37°C for 30 min, cleaned using
RNAeasy kit (Qiagen), and quantified. Double strand
cDNA was synthesized using Invitogen superscript RNA
amplification kit. 15 ng of cDNA were loaded into each
RT-PCR reaction using the Gotaq polymerase (Promega).
PCR reactions consisted of 20-35 cycles of amplification
using primers chosen from the 5' coding region of each
selected gene. The following primers were used:
PF14_0708: forward primer 5'- cactgatgatgatattcctc,
reverse primer 3' - attgtgctttaagatgatctc; PF11_0509: for-
ward primer 5' - caagggagtcaatccact, reverse primer 3'-
tcttcttgtgcatcttttgc; Mal7P1.100: forward primer 5' - gaag-
gggatacacttagaat, reverse primer 3' - gttctcgtattaacatgctc;
Mal13P1.129: forward primer 5'- gtggttgtgatattcttctc,
reverse primer 3'- atataccctacacaacgaag; Mal7P1.6: for-
ward primer 5'- cagatgaaacaaatcctactt, reverse primer 3'-
ctaatcattggatggtcttc; Mal13p1.86 (PF13_0092): forward
primer 5'- gagaatcaagatgtagatcc, reverse primer 3'- tctg-
tagttgatacacttc; PFF1375c (Mal6P1.145): forward primer
5'- atgtgtcttaagcgtaacca reverse primer 3'- gtatggttgta-
caataagcc. Gel images were quantified for relative band
intensity using the NIH ImageJ software.
## OPI algorithm

The Ontology-based Pattern Identification (OPI) algorithm was introduced by Zhou et al. and has been previously applied to the full life cycle transcriptome data set [19]. Briefly we applied the OPI analysis to six T4 transcription hybridizations along with previous 38 life cycle hybridizations. For each gene ontology group, OPI identifies a list of genes that not only share a similar expression profile, but also show functional enrichment in the target GO category. A total of 290 clusters were retained after 100 permutation runs (with estimated P ≤ 0.05). The representative expression patterns of each OPI clusters were hierarchically clustered as previously described [20]. This enabled us to visualize drug-related global expression changes side-by-side with the transcriptome expression variation in *P. falciparum* life cycle.

## Protein preparation and MudPIT

Equal amounts of untreated or T4-treated parasites were analyzed using MudPIT as previously described [21,22]. Briefly, parasite pellets were lysed by osmotic shock in 10 mM Tris-HCl (pH 8.5) and incubated in ice for one hour. After centrifugation at 18,000 g for 30 min, supernatants were saved and the pellet was solubilized in 0.1 M sodium carbonate (pH 11.5) and incubated on ice for an hour. Solubilized proteins were extracted after centrifugation and the pellet was resuspended one more time in 0.1 M sodium carbonate (pH 11.5). The three protein fractions were denatured in 8 M urea, reduced in 5 mM Tris (2-carboxyethyl)phosphine hydrochloride (TCEP, Roche); alkylated by 20 mM iodoacetamide (IAM), and digested with proteinase K (Roche) for 4 hours at 37°C, in 0.1 M Sodium Carbonate (pH 11.5) as described in Wu et al. 2003 [23]. Peptide mixture was analyzed as previously described [24].

## Targeted MS/MS approach

Nine proteins involved in key phospholipid biosynthesis were selected (PFL0620c; MAL13P1.214; PF11_0257; PF13_0253; PF14_0020; PF13_0092; MAL6P1.145; PF11370c; and MAL8P1.58). Ten peptides uniquely matching these proteins were targeted for quantitation in a directed MS/MS experiment. Treated and untreated parasites were lysed with 0.1 M Na₂CO₃, centrifuged for 30 minutes at 4°C, and fractionated into soluble and pellet fractions. After adjusting the pH to 8.5, fractions were denatured, reduced, alkylated and digested with endoproteinase Lys-C and trypsin as described previously [21].

The chromatography method entailed a six-step MudPIT approach, and a custom MS method collecting MS/MS spectra for each of the 10 targeted ions repeatedly. To estimate the rate of false positives in the protein identification analysis, MS/MS data were searched using SEQUEST against a combined database containing *P. falciparum* and

Human/Mouse/Rat amino acid sequences as well as an identical database where each protein sequence was randomized. The length and amino acid composition of each protein sequence remained the same, but the positions of amino acids were altered. Thus any hits to the scrambled protein sequences indicate false positives, and the overall rate can be determined. Protein identification parameters were adjusted to achieve a 5% false positive rate.

For the *P. falciparum* phosphoethanolamine methyltransferase, PfPMT, peptides derived from untreated and T4-treated samples eluted in the same MudPIT cycle with retention times that correlated with each other – eluting at 54 and 58 minutes for untreated and treated samples, respectively. Extracted ion chromatograms (XICs) for the y6, y8, y10, and y15 fragment ions of PfPMT peptide were generated for the cycle in which they were identified using a retention time window of two minutes (Data not shown). Each individual XIC was smoothed using adjacent averaging, and the area under each was calculated. The average ratio was 1.03 (untreated:treated) with a standard deviation of 0.08.

For PfCEPT, 45 spectra were identified as PfCEPT peptide in untreated sample and 1 spectra in T4-treated samples. The single peptide identified in the treated sample had a significantly different retention time (0.43 minutes) from those identified in the untreated sample, which eluted consistently near the end of the organic gradient (~113 minutes). An inconsistent retention time and manual inspection of the MS/MS spectrum led us to believe the peptide detected in the treated sample was a false positive. XICs were generated for the y5, y6, y13, and y14 fragment ions, which clearly indicate that this peptide elutes near 113 minutes in the untreated sample, whereas no signal was detected for any of these fragment ions in the treated sample near this retention time (Data not shown).

## T4 effects on *P. falciparum* phospholipid biosynthesis

*P. falciparum*-infected erythrocytes (3D7 strain) (5–7% parasitemia, 5% hematocrit) were incubated in 150 µl of choline-free RPMI 1640 supplemented with 25 mM Hepes (pH 7.6) in the presence or absence of T4 at the indicated concentration. After 30 minutes, 50 µl of medium containing [³H]-choline (5 µM final concentration in 200 µl, 2 µCi/well), [³H]-ethanolamine (2 µM, 1 µCi/well) or [³H] hypoxanthine (1 µCi/well) were added. Suspensions were incubated for 4 hours at 37°C in a 5% CO₂ incubator. Reactions were stopped at 4°C and cell suspension washed 3 times with 0.9% NaCl. Phospholipids were extracted according to a modified Folch protocol [25,26] and the organic phase was fractionated by silica gel thin-layer chromatography (TLC) with chloroform/methanol/acetic acid/0.1 M sodium borate (75/45/12/
4.5) [26]. Identified phospholipids were scraped off and radioactivity was measured by scintillation counting.

## T4 effects on aqueous-soluble metabolites

P. falciparum-infected erythrocytes were incubated at 20 – 22% hematocrit and 5–10% parasitemia in a final volume of 200 µl of choline-free RPMI 1640 supplemented with 25 mM Hepes (pH 7.6) in the presence or absence of T4. [³H]-choline (20 µM) and [³H]-ethanolamine (2 µM) were added at time 30 min. Suspensions were incubated for 2.5 hours at 37°C in a 5% CO₂ incubator. Water-soluble metabolites were obtained from the aqueous supernatant according to the Folch protocol and were fractionated by a silica gel TLC with methanol/water/30% NH₄OH (70/29/1) (Retention Factor Cho:0.02; P-Cho:0.18; P-Etn:0.44; CDP-Cho and CDP-Etn:0.78). Spots were identified by comparison to co-migrating standards. All spots were scraped off and amounts of radioactivity were determined by liquid scintillation counting. Results are expressed as percents of control test without T4.

## Results

### Global transcriptional analysis of T4-treated P. falciparum

Consistent with those results reported previously for various P. falciparum clones [14], T4 inhibited growth of the 3D7 strain with an IC₅₀ of 1 nM. We were interested in the biological effect of this drug at early stages of the lifecycle, and over longer time periods. As such, highly synchronized cultures were harvested 6, 12, 18, 24, 30, 36, 43, 48 and 71 hours after the addition of 0 or 40 nM T4 (> IC₈₀ value), to allow morphological analysis, RNA isolation and protein extraction (Figure 2). Short exposures (4 hours incubation time) with 40 nM T4 have been shown to inhibit growth of ring and trophozoite stages by 99% and 85%, respectively [14]. Despite the fact that short drug exposure shows a potent non-reversible cytotoxic effect [14], parasites were maintained in the presence of the drug to avoid additional culture handling, parasite stress (due to temperature changes) and loss of potential transcriptional effects after washes. Whereas no morphological differences could be detected between untreated and T4-treated parasites during the first 24 hours, significant morphological abnormalities and arrest of the cell cycle progression were observed between 30 and 71 hours following addition of 40 nM T4. In these cultures, small and dense trophozoites appeared and parasites failed to enter schizogony (Figure 2). Parasitemia of treated cultures decreased dramatically at 48 (3–4% parasitemia versus 10–12%) and 71 hours (0.5–1% parasitemia versus 10 – 12%). RNA extraction was performed on each sample in order to monitor global transcriptional profiles. RNA samples were labeled and hybridized to the custom malaria oligonucleotide array as previously described [17]. No significant differences were detected between untreated and T4-treated parasites during the first 18

hours of incubation at low drug concentration (2 nM and 20 nM (The correlation coefficient of the transcript expression values between untreated and T4-treated cultures was 0.99) – Data not shown). No significant changes after 5 hours of incubation with a high drug concentration (125 nM – Figure 3A and Additional file 2) were detected. Hybridization studies performed with parasites incubated with 40 nM of T4 for 24 hours resulted in a correlation coefficient of 0.98 with a total of 137 genes showing greater than 2-fold differential expression between untreated and T4-treated parasites (P<0.05 values for these genes were lower than 0.05 (Additional file 3 and Figure 3B). Of the 137 genes, 99 were known to be expressed in gametocytes, 21 were known to display strong variations in the level of expression throughout the erythrocytic life cycle and 17 showed a transcript level close to background in treated and untreated parasites. None of these genes were known or predicted to be involved in phospholipid metabolism in P. falciparum (Figure 1). T4 treatment for 30 and 36 hours resulted in increased transcriptional changes with 1140 and 1825 genes differentially expressed, respectively (See Additional file 3). The correlation coefficient of the expression values between untreated and treated parasites at these time points decreased significantly (r = 0.87 and 0.72 at 30 and 36 hours, respectively) (Figure 3C and 3D). However the correlation coefficients observed between transcripts at different stages of the P. falciparum cell cycle without treatment also changed significantly (i.e., 24 hours/30 hours, r = 0.64; 30 hours/36 hours, r = 0.95 and 24 hours/36 hours, r = 0.95). To further understand these complex transcriptional changes, data obtained from studies involving T4 treatment were compared to those previously reported for the parasite intraerythrocytic life cycle [17,19] using the ontology based pattern identification algorithm (OPI) [20]. As illustrated in Figure 4, three main categories of gene behavior emerged. The first category includes genes already known to be expressed during gametocytogenesis [19] (pattern A). These genes were defined by the gene ontology groups GNF0004 (sexual development), GO:0006633 (fatty acid biosynthesis in apicoplast) or GO:0015630 (microtubule cytoskeleton). The second category includes genes whose expression was not significantly altered following treatment with T4 (pattern B and D Figure 4). These include the following representative GO clusters: GO:0030260 (cell invasion), GO:0020008 (rhoptry), GO:0045177 (apical part of cell) and GO:0030383 (host-pathogen interaction). The third category (pattern C Figure 4) encompassed genes involved in cell cycle and metabolism such as GO:0006006 (glucose metabolism), GO:0019538 (protein metabolism), GO:00063396 (RNA processing), GO:0007049 (cell cycle) and GO:0006260 (DNA replication). The expression profile of the genes in this category in untreated parasites decreased during the trophozoite/schizont
<figure><img src="image_3.png" /><figcaption>**Figure 2**</figcaption></figure>

**Giemsa-stained smears of T4-treated and untreated cultures.** T4 was added at 40 nM at the early ring stage. The morphology of parasites in treated and untreated cultures is shown (early trophozoites, T0+24 h; late trophozoites, T0+30 h; schizonts, T0+36 h; early ring stage, T0+43 h; late ring stage, T0+48 h; and trophozoites, T0+71 h). Morphological changes are clearly observed at 36 hours with absence of schizont formation (T0+36 h). Between 43 and 48 hours surviving parasites are blocked at the trophozoite stages. At 71 hours parasitemia falls to negligible level.
<figure><img src="image_4.png" /><figcaption>**Figure 3**
Logarithm-transformed expression values of untreated versus treated *P. falciparum* cultures. A- The logarithm-transformed expression values of untreated and treated (T4 = 125 nM) mixed population after 5 hours of incubation. B – C – D – The logarithm-transformed expression values of untreated and treated (T4 = 40 nM) synchronized population for 24, 30 and 36 hours of incubation respectively (drug added at the ring stage).</figcaption></figure>

transition (30 and 36 hours), consistent with previous
reports. In contrast, in treated parasites, these genes exhib-
ited stable transcript levels at 30 and 36 hours. Impor-
tantly, although T4 and its analogs are known to interfere
with the synthesis of PC, no specific effect on the expres-
sion of the genes encoding enzymes of the CDP-choline
and SDPM pathways could be detected in response to the
drug (Additional file 4). RT-PCR analysis performed on
RNA isolated from untreated and T4-treated parasites con-
firmed the results of the microarray analyses (See Addi-
tional File 1). The complete cluster analysis as well as
various statistical parameters can be accessed from our
web page http://carrier.gnf.org/publications/T4/ or from
the PlasmoDB database http://plasmodb.org/.

**Proteomic profiling**

The lack of specific transcriptional regulation of the genes
involved in phospholipid metabolism following T4 treat-
ment led us to investigate the global effect of this com-
pound on the proteome. To estimate relative changes in
protein levels following treatment with T4, proteins were
extracted from cultures 24 hours after the addition of T4
at a concentration of 40 nM to ring-stage parasites. Protein
abundance was estimated by mass spectrometry analysis
{Zybailov, 2005 #341; Le Roch, 2004 #203; Florens, 2002
#112}. Protein identification was carried out in six exper-
iments, each consisting of three replicate analyses of
treated and untreated parasites. A total of 889 proteins
were identified, with 560 and 571 proteins identified
from T4 treated and untreated parasites, respectively
(Additional file 5). The Pearson correlation coefficient
was high (r = 0.932) compared to the Pearson correlation
<figure><img src="image_5.png" /><figcaption>**Figure 4**</figcaption></figure>

**Hierarchical clustering of all 290 OPI clusters.** Genes in each cluster share a similar expression pattern represented as a row in the heat map. The right panel is the zoom-in view of selected heat map sections with the six T4 data set further horizontally expanded for ease of visual inspection. Bright red indicates highest expression; bright green indicates lowest expression (gene-wise normalized). Asexual S, T refers to the erythrocytic cycle expression profile analysis of malaria parasite synchronized using Sorbitol chemical treatment (S) or the thermo-cycling incubation (T) describes in Le Roch et al, 2003. Gene behaviors of T4-treatment can be characterized into three categories: Pattern A shows an induction in gametocytogenesis; Pattern B and D shows no change in expression before and after T4 treatment; Pattern C shows an up regulation most likely due to DNA replication, metabolism and cell cycle progression. Some representative GO groups are shown next to the pattern.
coefficient observed between independent proteome
datasets of different stages of the *P. falciparum* life cycle
(i.e., ring/trophozoite, r = 0.534; trophozoite/schizont, r =
0.389 and schizont/ring, r = 0.506) [22]. The high corre-
lation coefficient observed between untreated and T4-
treated parasites correlates with the lack of observable
transcriptional changes at 24 hours post drug treatment.
Nevertheless, a small number of proteins showed subtle
differences in their relative abundance. Proteins predicted
to play a role in biological processes occurring in the food
vacuole, such as plasmepsin or falcipain, were enriched
amongst those proteins showing the most significant
increases. Four of the seven annotated food vacuole pro-
teins were among the top 64 of those that showed
increased peptide abundance in the T4 treated sample.
Conversely, with the exception of MSP1, many know
invasion proteins such as rhoptry proteins (RAP1, CLAG1,
and CLAG2) were found to be less abundant following
treatment with T4 (P = 8.47e-7). By focusing our analysis
on proteins significantly up-regulated in response to drug
treatment, 53 proteins were found to exhibit a 3-fold or
greater increase in expression level (as measured by the
ratio of spectral counts) or were detected only in the drug
treated samples. Of these 'over-expressed' proteins, nine
were proteins from surface antigen families. Their modu-
lation may represent an overall stress response of the par-
asite [28]. The glycerol-3-phosphate acyltransferase
(PFL0620c, PfGAT) and the acyl carrier protein homolog
(PFB0385w) were detected in the drug treated samples
only. In addition, the PfPMT, a key enzyme in the SDPM
pathway as well as the S-adenosylmethionine synthetase
(PFI1090w, which provides the PfPMT essential cofactor
S-adenosylmethionine), showed an increase in treated
versus untreated spectral counts (17 versus 5 spectra
counts for PfPMT and 7 versus 2 spectral counts for
PFI1090w in T4 treated and untreated parasites, respec-
tively). Using a semi quantitative MudPIT analysis, slight
differences in spectral counts are not always significant
and enzymes expressed at low levels are often difficult to
detect. To improve our analysis and perform a quantita-
tive proteomic analysis, we used a labeled isoleucine strat-
egy [29]. Unfortunately, this method proved unsuccessful
due to an irregular distribution of labeling efficiency for
all proteins even after two cell cycles (Data not shown).
This is most likely attributed to the incorporation of non-
labeled isoleucine from the human serum. To gain further
insight into the expression pattern of proteins involved in
phospholipid metabolism in the absence or presence of
T4, a targeted MS/MS approach was used. Ten peptides
derived from nine phospholipid metabolic enzymes were
selected (Additional file 6). PfPMT, and choline/eth-
anolamine-phosphotransferase (PfCEPT, MAL6P1.145;
involved in the final step of synthesis of PC via the choline
and SDPM pathways), were successfully detected [7]. The
difference in the levels of PfPMT peptides detected in

untreated (2 spectra) and T4-treated (6 spectra) parasites
was not highly significant. In the case of PfCEPT, however,
45 peptides were detected in the absence of T4 compared
whereas in the presence of the compound no peptide
spectra could be detected. This result suggests that the
expression of PfCEPT is severely reduced following treat-
ment with T4. Using the global proteomic approach as
well as the targeted MS/MS approach, no additional
known or predicted phospholipid metabolic enzymes
were detected. The abundance of these proteins may be
below the levels that can be detected using mass spec-
trometry.

To validate T4 specific effects on PC metabolism, the
incorporation of radiolabeled choline (Cho) and eth-
anolamine (Etn) into PC and phosphatidylethanolamine
(PE), and their intermediary water-soluble metabolites,
phosphocholine (P-Cho), phosphoethanolamine (P-
Etn), cytidine-diphospho-choline (CDP-Cho) and cyti-
dine-diphospho-ethanolamine (CDP-Etn) was moni-
tored in the absence or presence of the compound. As
shown in Figure 5A, choline-derived PC levels were
decreased by 50% in the presence of 0.8 µM T4. At this
concentration, the synthesis of PC from ethanolamine
was unaffected. Higher concentrations of T4, however,
resulted in a decrease in PC biosynthesis from eth-
anolamine. On the other hand, T4 had no affect on the
biosynthesis of PE or nucleic acid from ethanolamine or
hypoxanthine, respectively. Together these data suggest
that T4 treatment elicits a rapid and specific inhibition of
the synthesis of PC via the two main biosynthetic path-
ways. Analysis of the water-soluble intermediary metabo-
lites of PC biosynthesis following labelling with
[^14C]choline showed that T4 treatment caused a major
decrease in the intracellular levels of radiolabeled choline
and of the downstream metabolites phosphocholine and
CDP-choline (Fig. 5B and 5C). This suggests that T4 may
have an effect on the transport of choline into the parasite
and may also inhibit the first two steps of the CDP-
choline pathway catalyzed by the choline kinase,
PfCK1 and the phosphocholine citidylyltransferase,
PfCCT. The inhibition of choline transport is consistent
with previous studies that showed inhibition of choline
transport into *P. falciparum*-infected erythrocytes and yeast
by quaternary ammonium compounds [22,27]. The met-
abolic studies also showed that at T4 concentrations
above 1 µM the incorporation of radiolabeled eth-
anolamine into phosphocholine was significantly
decreased whereas ethanolamine phosphorylation was
not affected, suggesting an inhibition of at least one
enzyme downstream P-Etn i.e. PfPMT, CTP-phospho-
choline cytidylyltrasnferase (PfCCT) or PfCEPT.
<figure><img src="image_6.png" /></figure>

<figure><img src="image_7.png" /></figure>

<figure><img src="image_8.png" /><figcaption>**Figure 5** (see legend on next page)</figcaption></figure>
**Figure 5** (see previous page)

**Biochemical effect of the bisthiazoliums T4.** A- Effect of T4 on the biosynthesis of phospholipids and nucleic acids. *P. falciparum* trophozoite-infected erythrocytes were incubated in the presence of the indicated concentrations of T4 at time 0 and radioactive choline (5 µM), ethanolamine (2 µM) and hypoxanthine were added at time 30 min. Incorporation of the radioactive precursors into their corresponding macromolecules at time 4 h are expressed as percentage of those measured in infected erythrocytes incubated without T4 and are means of 4 experiments ± SEM. In the absence of drugs, choline incorporation into PC was 4.71 ± 0.26 nmol/10¹⁰ cells/hour, and ethanolamine incorporation into phosphatidylethanolamine PE and into PC (indicated as PC*) was 14.3 ± 0.33 and 1.97 ± 0.16 nmol/10¹⁰ cells/hour. Effects of T4 on choline (B) and ethanolamine (C) water-soluble metabolites. *P. falciparum*-infected erythrocytes were incubated in the presence of the indicated concentrations of T4 at time 0. Radioactive choline (20 uM) and ethanolamine (2 uM) were added at time 30 min and reactions were stopped at time 2.5 hours. Incorporation of the radioactive precursors into their corresponding metabolites is expressed as percentage of those measures in infected cells incubated without T4 and are means of 4 experiments ± SEM. In the absence of drugs, intracellular choline, phosphocholine and CDP-choline were respectively 1.1 ± 0.1, 23.7 ± 0.5 and 0.30 ± 0.01 nmol/10¹⁰ cells/hour. In C, phosphorylethanolamine and phosphocholine and the sum CDP-choline + CDP ethanolamine were respectively 4.90 ± 0.25 and 1.86 ± 0.07 and 0.77 ± 0.06 nmol/10¹⁰ cells/hour. Incorporation of Eth into P-ETn is not affected by T4.

**Discussion**

In the recent years, large-scale transcriptional profiling has been used, with varying degrees of success, to gain a better understanding of the mechanism of action of small molecules [30-35]. Whereas this approach has sometimes been challenging [36], in large part it has proven successful in bacteria and the yeast *Saccharomyces cerevisiae*. In multicellular organisms, large-scale transcriptional profiling analyzed under different stress conditions have proven more difficult due to multiple cell types or tissues as well as complex transcriptional regulations. In addition to transcriptional profiling, proteomic approaches are also gaining wide use as molecular tools to help unravel the mode of action of various compounds [37-39]. In this study, we have combined both approaches to study the response of the human malaria parasite, *P. falciparum*, to exposure to the bisthiazolium choline analog T4. Following exposure to low concentrations (2, 20 nM, (data not shown) or short incubations at 125 nM (30 minutes and 5 hours – data not shown), no specific transcriptional changes were observed, nor after a 5 hour treatment at a higher dose (T4 = 125 nM; Figure 2 and Additional File 2). Following a longer incubation with 40 nM T4 (24, 30 and 36 hours) no specific changes could be observed in the transcription of genes involved in phospholipid metabolism. However, changes due to an arrest of the cell cycle were significantly detected after 30 and 36 hours of incubation with the drug. To subtract the transcriptional changes due to cell cycle effect, we analyzed the transcription profile obtained at 24, 30 and 36 hours with previously published life cycle data set [19,22] using the OPI algorithm [20]. A transcriptional profile reminiscent of a global drug-induced stress response was detected when compared to untreated cultures (Figure 4). This profile is characterized by an apparent arrest of the cell cycle and a significant induction of genes known to be expressed in gametocytes [17,19]. This cell cycle arrest could signify a major shift of the parasite from asexual development to sexual differentiation.

Although more than 5,000 infected red blood cells were analyzed, no gametocytes could be observed in the treated cultures, suggesting a specific induction of expression of genes involved in sexual differentiation and development rather than production of gametocytes in the culture following drug treatment. Gametocytogenesis can be induced by various external factors both *in vitro* and *in vivo*, most of which are conditions that cause physiological stress on the parasite, such as treatment with antimalarial drugs [40-45]. Thus, the changes in gene expression observed as a result of T4 treatment might indicate an attempt by the parasite to commit to sexual differentiation. The lack of gametocytes following treatment with T4 could, however, be due to the potent activity of quaternary ammonium compounds against this stage of the parasite's life cycle or the time taken to produce gametocytes post commitment to gametocytogenesis. However, G25, the first generation lead compound [13] was shown to prevent *P. falciparum* sexual differentiation and to prevent parasite transmission by altering gametocyte maturation, exflagellation and sporogony (H. Vial, personal communication). Using the OPI algorithm, our data showed that, once changes due to the cell cycle and stress related (gametocytogenesis) genes were subtracted, T4 treatment led to no specific or compensating changes in transcription under the experimental conditions described herein. It is possible, however, that a longer exposure to a lower drug concentration could reveal a parasite specific response. Using such a condition, Dahl et al [46] were successful in their use of transcriptome analysis to identify the effects of tetracycline on the *P. falciparum* apicoplast after more than 48 hours of treatment.

Global proteomic profiles of untreated and T4-treated parasites after 24 hours suggested that T4 treatment leads to an induction of those proteins localized to the food vacuole. As choline analogs have been shown to accumulate within the parasite digestive vacuole and possibly
interact with heme [47], detection of an increased level of these enzymes potentially validate this interaction. A decrease in the levels of invasion proteins such as those localized to the rhoptry or the peripheral surface of the parasites was also detected. This could suggest a cell cycle arrest at the protein level even thought no significant transcriptional changes were detected for such proteins. To assess the effect of T4 on the expression of enzymes involved in phospholipid metabolism, changes in protein levels using a targeted MS/MS approach was applied. The proteomic data indicated a significant decrease in the abundance of PfCEPT, a protein involved in the final step of phosphatidylcholine synthesis. Nonetheless, no PfCEPT transcriptional changes could be detected at 24 hours using RT-PCR analysis (data not shown). Previous studies have shown a significant discrepancy between mRNA and protein levels, suggesting a major role for post-transcriptional events within the parasite life cycle [22,48,49]. One possible explanation for the effect of T4 on PfCEPT is that the expression of PfCEPT could be directly controlled by the amounts of CDP-choline available.

Metabolic studies showed that T4 inhibits the biosynthesis of PC but not that of PE or DNA. This finding is consistent with previous reports that showed a specific inhibition of PC biosynthesis by quaternary ammonium compounds [11,14,50-52]. Previous studies have shown that T4 accumulates to 200 to 300-fold in *Plasmodium*-infected erythrocytes within two hours [14]. This suggests that the concentrations used in the metabolic studies are within the range of the intracellular concentration of the compound, and that the pathways for synthesis of PC from both choline and ethanolamine are the targets of the compound. These biochemical analyses showed that T4 treated parasites had low levels of intracellular choline, phosphocholine and CDP-choline. This suggests that T4 inhibits choline transport and may also act by inhibiting the steps of the CDP-choline pathway catalyzed by the choline kinase PfCK and the phosphocholine cytidylyltransferase, PfCCT. The inhibition of choline entry into the parasite is consistent with previous findings that showed that this class of compounds are potent inhibitors of choline transport into Plasmodium-infected erythrocytes and into the parasite [52,53]. The metabolic studies also showed that at a slightly higher concentration T4 inhibited the synthesis of phosphocholine from ethanolamine with no effect on the synthesis of phosphoethanolamine or CDP ethanolamine. This point out an additional effect of T4 that also inhibiting PC biosynthesis from ethanolamine through an action on one step downstream P-Etn, i.e. PfPMT, CTP-phosphocholine cytidylyltransferase (PfCCT) or PfCEPT. In vitro studies indicated that millimolar concentrations of the bisthiazolium are required to dose-dependently inhibit the PfCCT and

PfCEPT (unpublished). Thus, the very high accumulation of the choline analogues into the blood stage of the malarial parasite [13,14], can lead to *in situe* concentration able to interfere with parasite choline uptake and PC biosynthetic enzymes. The specificity of inhibition by T4 towards enzymes of the CDP-choline pathway and eventually PfPMT whose substrates or products contain a choline moiety could thus be directly linked to its structural properties. Future structural studies aimed to characterize the interaction between T4 and these enzymes are warranted.

The proteomic data indicated that PfCEPT protein levels decreased significantly following treatment with T4. Taken together these findings suggest that PfCEPT expression or stability might be directly regulated by the availability of CDP-choline. Recent studies have provided evidence for the regulation of the expression and stability of PfPMT in response to exogenous choline [54]. It is possible that PfCEPT might also be subjected to posttranslational regulation by its substrate CDP-choline. Low amounts of this substrate due to direct inhibition of PfCCT or other earlier steps of the CDP-choline and SDPM pathways could result in the inhibition of synthesis or increased degradation of PfCEPT.

In conclusion, despite the absence of highly significant transcriptional changes within the metabolic pathways targeted by T4, this analysis validates the existence of a specific transcriptional cascade across the *P. falciparum* cell cycle [17,55]. The malaria parasite, as an obligate intracellular parasite, has evolved within a buffered intracellular environment where evolutionary forces may have induced the loss of specific transcriptional feedback responses. Proteomic and biochemical studies indicate a decreased level of PfCEPT, suggesting a specific mechanism of inhibition of PC biosynthesis. Together, these results emphasize the importance of post-transcriptional regulation in parasite drug response. The nature of such modifications has been largely unexplored in *P. falciparum*. It can involve mRNA stability, phosphorylation, as well as an increase in protein instability and degradation via the ubiquitin/proteasome pathway. Further experiments will be required to characterize the mechanisms involved in such post-transcriptional regulations.

**List of abbreviations**

**MudPIT:** Multidimensional Protein Identification Technology; **OPI:** Ontology-based Pattern Identification algorithm; **PC:** Phosphatidylcholine; **SDPM pathway:** Serine Decarboxylation-Phospho-ethanolamine Methylation; **PfPMT:** phosphoethanolamine N-methyltransferase; **PfCEPT:** choline/ethanolamine-phosphotransferase protein; **Cho:** Choline; **Etn:** Ethanolamine; **PE:** Phosphatidylethanolamine; **P-Cho:** Phosphocholine; **P-Etn:** Phosphorylethanolamine; **CDP-Cho:** Cytidine-diphos-
pho-choline; CDP-Etn: Cytidine-diphospho-eth-
anolamine; PS: Phosphatidylserine; PfSD: Serine-
decarboxylase; PfeK: Ethanolamine kinase; PfeCT: CTP:
Phosphoethanolamine cytidylyltransferase; PfeCK:
Choline kinase; PfcCCT: CTP:phosphocholine cytidylyl-
transferase; XIC: Extracted ion chromatography; TLC:
Thin layer chromatography.

Authors' contributions

KLR conceived the study and the design, carried out
microarray and proteomic studies, participated in bioin-
formatics analyses and wrote the manuscript. JRJ carried
out proteomic studies and conducted proteomic statistical
analyses. HA carried out metabolic studies. DDC and WW
carried out molecular studies. DP and KH carry out para-
site cultures. YZ conducted statistical and bioinformatics
analyses. JRY edited the manuscript. CBM helped in the
design of molecular studies and edited the manuscript.
EAW participated in the microarray design and edited the
manuscript. HV conceived the study, the design and
edited the manuscript. All authors read and approved the
manuscript.

**Additional material**

Additional file 1

Additional Figure 1: RT-PCR validation – RT-PCR experiments were performed to validate the microarray results. Plasmodium RNA was extracted at 24, 30, and 36 hours after 40 nM T4 treatment of synchronized cultures. Untreated RNA was extracted in tandem as a control. cDNA was created from the RNA extractions and quantified using spectrophotometry. 15 ng of cDNA were loaded into each RT-PCR reaction and was subjected to 20–35 cycles of amplification. Semi-quantifications of RT-PCR were done using NIH’s ImageJ and illustrated by a column graph. Another column graph depicting the microarray results for the respective genes is shown for comparison. Pf14_0708, Mal13P1.129 and Mal7P1.100 were selected as genes expressed in gametocytes and showing a significant induction when incubated with T4); PF11_0509 and Mal7P1.6 showed an arrest of the cell cycle progression. Mal13P1.86, a gene involved in the parasite lipidic pathway is expressed and does not show any particular transcriptional change when incubated with the drug.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S1.pdf]

Additional file 2

Additional table 1: Transcriptional intensities at 30 minutes and 5 hours time points for treated and untreated parasite at 125 nM of T4 on a mix parasite population.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S2.xls]

Additional file 3

Additional table 2: Transcriptional intensities at 24, 30 and 36 hours time points for treated and untreated parasite at 40 nM on synchronized parasites.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S3.xls]

Additional file 4

Additional table 3: Known and putative phospholipid and neutral lipid enzymes of P. falciparum.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S4.xls]

Additional file 5

Additional table 4: Protein abundance detected at 24 hours for treated and untreated parasite at 40 nM of T4 on synchronized parasites.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S5.xls]

Additional file 6

Additional table 5: Nine proteins selected for the Targeted MS/MS approach.
Click here for file
[http://www.biomedcentral.com/content/supplementary/1471-2164-9-513-S6.xls]

**Acknowledgements**

Professor M. Calas team is gratefully acknowledged for the synthesis of the compound. We would like to thank Dr. Laurence Florens, Randal Maile and Megan Downie for their critical reading of the manuscript and helpful suggestions and Andrey Santrosyan for his help on the supplementary material web site. This work was supported by a grant to E.A.W. from The Ellison Foundation and the W.M. Keck Foundation and NIH R01 AI059472-01, the European FP6 Network of Excellence BioMalPar and the Integrated Project Antimal.

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