PfeIK1, a eukaryotic initiation factor 2α kinase of the human malaria parasite Plasmodium falciparum, regulates stress-response to amino-acid starvation
- Clare Fennell†1, 2,
- Shalon Babbitt†3,
- Ilaria Russo3,
- Jonathan Wilkes4,
- Lisa Ranford-Cartwright5,
- Daniel E Goldberg3Email author and
- Christian Doerig1, 6Email author
© Fennell et al; licensee BioMed Central Ltd. 2009
Received: 05 December 2008
Accepted: 12 May 2009
Published: 12 May 2009
Post-transcriptional control of gene expression is suspected to play an important role in malaria parasites. In yeast and metazoans, part of the stress response is mediated through phosphorylation of eukaryotic translation initiation factor 2α (eIF2α), which results in the selective translation of mRNAs encoding stress-response proteins.
The impact of starvation on the phosphorylation state of PfeIF2α was examined. Bioinformatic methods were used to identify plasmodial eIF2α kinases. The activity of one of these, PfeIK1, was investigated using recombinant protein with non-physiological substrates and recombinant PfeIF2α. Reverse genetic techniques were used to disrupt the pfeik1 gene.
The data demonstrate that the Plasmodium falciparum eIF2α orthologue is phosphorylated in response to starvation, and provide bioinformatic evidence for the presence of three eIF2α kinases in P. falciparum, only one of which (PfPK4) had been described previously. Evidence is provided that one of the novel eIF2α kinases, PfeIK1, is able to phosphorylate the P. falciparum eIF2α orthologue in vitro. PfeIK1 is not required for asexual or sexual development of the parasite, as shown by the ability of pfeik1- parasites to develop into sporozoites. However, eIF2α phosphorylation in response to starvation is abolished in pfeik1- asexual parasites
This study strongly suggests that a mechanism for versatile regulation of translation by several kinases with a similar catalytic domain but distinct regulatory domains, is conserved in P. falciparum.
Human malaria is caused by infection with intracellular protozoan parasites of the genus Plasmodium that are transmitted by Anopheles mosquitoes. Of four species that infect humans, Plasmodium falciparum is responsible for the most virulent form of the disease. The transition from one stage of the life cycle to the next must be tightly regulated, to ensure proliferation and differentiation occur when and where appropriate; this is undoubtedly linked to differential gene expression. Analysis of the P. falciparum transcriptome during the erythrocytic asexual cycle reveals an ordered cascade of gene expression , and the various developmental stages display distinct transcriptomes; how this is orchestrated remains obscure. Initial investigation of the P. falciparum genome revealed a paucity of transcriptional regulators , although this picture has recently been challenged by the recent identification of the ApiAP2 transcription factor family . There is nevertheless a large body of evidence suggesting that post-transcriptional control is an important means of gene regulation in P. falciparum. Examples include the relatively small number of identifiable transcription-associated proteins, abundance of CCCH-type zinc finger proteins commonly involved in modulating mRNA decay and translation rates  and translational repression during gametocytogenesis [4–6].
In mammalian cells, regulation of gene expression is a key mechanism in the mediation of stress responses, which may be achieved by influencing transcription or translation. The Stress Activated Protein kinases (SAPKs), specifically JNKs and p38 kinases, are subfamilies of mitogen activated protein kinases (MAPK) that are expressed in most eukaryotic cells, and respond to a variety of stress conditions . Although the parasite kinome includes two MAPK homologues, none of these are members of the SAPK subfamily [8–10]. In contrast, the P. falciparum kinome contains a phylogenetic cluster of three kinases with homology to eukaryotic Initiation Factor 2α (eIF2α kinases, which in other organisms regulate translation in response to stress . Interestingly, the related apicomplexan parasite Toxoplasma gondii has been shown to differentiate from tachyzoites to bradyzoites on exposure to a number of cellular stresses, concomitant with an increase in phosphorylation of TgeIF2α, indicating a possible role for this mechanism in parasite differentiation .
Phosphorylation of eukaryotic initiation factor 2α at residue Ser51 in response to stress is a well-characterized mechanism of post-transcriptional control that regulates initiation of translation [12–17]. In mammalian cells this phosphorylation event is mediated by four distinct protein kinases, called the eIF2α kinases: general control non-derepressible-2 (GCN2), haem-regulated inhibitor kinase (HRI), RNA-dependent protein kinase (PKR), and PKR-like endoplasmic reticulum kinase (PERK). These enzymes contain a similar catalytic domain allowing them to phosphorylate the same substrate, but have different accessory domains that regulate kinase activation in response to different signals. In GCN2 the functional kinase domain is followed by a histidyl-tRNA synthetase (HisRS)-like domain , which is the major motif for sensing amino acid starvation and triggering kinase activation; PERK has a transmembrane domain allowing it to reside in the endoplasmic reticulum membrane; the N-terminal domain can protrude into the lumen of the ER to sense unfolded proteins, while the catalytic domain extends into the cytoplasm where its substrate and effector mechanism lie; human PKR contains an RNA binding domain and responds to viral infection; and HRI contains haem binding sites to modulate translation of globin chains according to the availability of haem. In this way the eIF2α kinases can integrate diverse stress signals into a common pathway [12–14, 19].
Translation initiation requires the assembly of the 80S ribosome on the mRNA, which is mediated by proteins known as eukaryotic initiation factors (eIFs). Formation of the 43S pre-initiation complex depends on binding of the ternary complex that consists of the heterotrimeric G-protein eIF2 (α, β and γ subunits), methionyl-initiator tRNA (met-tRNAi) and GTP . Initiation of translation and release of the initiation factors involves hydrolysis of GTP to GDP, which leaves an inactive eIF2-GDP complex. Before further rounds of translation initiation can occur eIF2 must be reactivated by exchange of GDP for GTP . The presence of a phosphate group on the α subunit of eIF2 inhibits recycling of inactive eIF2-GDP to active eIF2-GTP by limiting the activity of the guanine nucleotide exchange factor, eIF2B . The consequence of activity of the eIF2α kinases therefore is global translation repression, since initiation complexes cannot form. In spite of the generalized reduction in translation, selected mRNAs are translated, whose products shapes the subsequent stress response. Reduced translation conserves energy and nutrients, allowing time for the cell to adapt appropriately to the stress conditions. This mechanism is conserved in the vast majority of eukaryotes. One notable exception is the Microsporidium Encephalitozoon cuniculi, whose kinome does not include eIF2α kinases (or other stress-response kinases), a probable adaptation to its parasitic lifestyle . It is, therefore, of interest to investigate the extent to which malaria parasites may rely on eIF2α phosphorylation for stress-response and/or life cycle progression.
A cluster of three sequences that includes PfPK4, a protein kinase that was previously described as a putative eIF2α kinase , was identified in the P. falciparum kinome on the basis of catalytic domain similarity [10, 23]. Here, evidence is provided that the P. falciparum eIF2α orthologue is phosphorylated in response to amino acid starvation. Bioinformatics analysis reveals that P. falciparum encodes three eIF2α kinases, one of which, P lasmodium f alciparum e ukaryotic I nitiation Factor K inase-1 (PfeIK1), is indeed be able to phosphorylate P. falciparum eIF2α in vitro. Reverse genetics experiments show that inactivation of the pfeik1 gene does not affect asexual growth, gametocytogenesis or further sexual development, since pfeik1- sporozoites can be formed in the mosquito vector; in contrast, pfeik1- parasites are unable to phosphorylate eIF2α in response to amino-acid starvation.
BLASTP analysis was used to identify the closest human and Plasmodium berghei orthologues of the PfeIF2α kinases. Catalytic domains of the putative PfeIF2α kinases as defined by the alignment of P. falciparum kinases  were aligned with the four human eIF2α kinases and other P. falciparum and human sequences that were selected to represent all kinase subfamilies. The sequences were aligned using the HMMER package against a profile generated from our previous kinome analysis . After removal of gaps and positions with a low quality of alignment, alternate phylogenies generated with the neighbour joining method were visualized using NeighbourNet implemented on SplitsTree version 4 .
BLASTP searches of PlasmoDB using metazoan eIF2α sequences as queries identified PF07_0117 as the P. falciparum homologue of eIF2α, which was then confirmed by reciprocal analysis. Alignment of these sequences was performed using ClustalW.
A 1278 bp fragment encoding the catalytic domain of PfeIK1 (PF14_0423) was amplified from a P. falciparum cDNA library using the Phusion polymerase (Finnzymes), using the following primers: forward, GGGGGGATCC ATGGGGAAAAAAAAACATGG, reverse GGGGGTCGAC CGTAAAAAGTACACTTTCGTG. The primers contained Bam HI and Sal I restriction sites, respectively (underlined). The Taq polymerase (Takara) was used to add adenine tails to enable cloning of the product into the pGEM-T Easy vector (Promega) for sequencing. The correct sequence was removed by digestion with Bam HI and Sal I and inserted into the expression vector pGEX-4T3 (Pharmacia). A catalytically inactive mutant was obtained by site directed mutagenesis of Lys458 to Met using the overlap extension PCR method  (forward: CTTATGCATTAATGATTATAAG, reverse: CTTATAATCATTAATGCATAAG).
Oligonucleotide primers were designed to amplify the complete coding sequence of PfeIF2α (PF17_0117) by PCR from a cDNA library of the P. falciparum clone 3D7, using the Phusion polymerase (Finnzymes). The primers used were as follows: forward, GGGGGGATCC ATGACTGAAATGCGAGTAAAAGC and reverse, GGGGGTCGAC TTAATCTTCCTCCTCCTCGTC (restriction sites are underlined). Taq polymerase (Takara) was used to add adenine tails to enable cloning of the 990 bp product into the pGEM-T Easy vector (Promega) for amplification and sequencing. The correct sequence was removed by digestion with Bam HI and Sal I and inserted into the expression vector pGEX-4T3 (Pharmacia). A mutant of PfeIF2α designed to be refractory to phosphorylation was obtained by site directed mutagenesis (Ser59 – Ala) using the overlap extension PCR technique , (primers: forward, CTTATGCATTAATGATTATAAG, reverse, CTTATAATCATTAATGCATAAG).
All inserts were verified by DNA sequencing (The Sequencing Service, Dundee, UK) prior to expression of recombinant proteins or transfection of P. falciparum.
Recombinant protein expression
Expression of recombinant GST fusion proteins was induced in E. coli (strain BL21, codon plus) with 0.25 mM Isopropyl Thiogalactoside (IPTG). After induction, bacteria were grown at 16°C overnight and the resulting bacterial pellets were stored at -20°C until use. All subsequent work was done on ice, centrifugation steps at 4°C. Protein extraction was performed by digestion of bacterial pellets for 5 min. with lysozyme (Sigma), followed by 10 min. in lysis buffer (1 × PBS, 2 mM ethylenediaminetetraacetic acid (EDTA), 1 mM dithiothreitol (DTT), 0.5% Triton ×100, 1 mM Phenyl Methyl Sulphonate (PMSF), Benzamidine Hydrochloride Hydrate (BHH), 1× complete cocktail protease inhibitors (Roche)). Bacterial lysates were sonicated at 20% amplitude (Bioblock Scientific, Vibracell 72405), 5 × 15 sec. pulses/15 sec. rest, and cleared by centrifugation 13000 g, 15 min. GST-fusion proteins were purified by incubation of cleared lysates on glutathione agarose beads (Sigma) for 2 hours, followed by four washes with lysis buffer and eluted for 20 min. in elution buffer (Tris 40 mM, pH8.7, 75 mM NaCl, 15 mM reduced glutathione). Protein concentration was monitored using the Bradford assay (Biorad reagent). Kinase assays were carried out immediately after purification.
Kinase reactions (30 μl) were carried out in a standard kinase buffer containing 20 mM Tris-HCl, pH 7.5, 20 mM MgCl2, 2 mM MnCl2, phosphatase inhibitors; 10 mM NaF, 10 mM β-glycerophosphate, 10 μM ATP and 0.1 MBq [γ-32P] ATP, using 2 μg recombinant kinase, and 10 μg non-physiological substrate (α-casein, β-casein), or recombinant GST-PfeIF2α. Reactions were allowed to proceed for 30 min. at 30°C and stopped by addition of reducing Laemmli buffer, 3 minutes, 100°C. Samples were separated by SDS-PAGE and phosphorylation of kinase substrates assessed by autoradiography of the dried gels.
Plasmodium falciparum genetic manipulation
A gene disruption plasmid was produced for PF14_0423 in the plasmid pCAM-BSD  that contains the gene conferring resistance to blasticidin. The oligonucleotide pair GGGGGGATCC GTAATGAAAGTAAAAAATAAG/GGGGCGCCGGCG AGGTGAAATATAATGAATTGTTCC, containing Bam HI and NotI sites (underlined) was used to amplify a 789 bp fragment for insertion to pCAM-BSD. Ring stage parasites were electroporated with 50 – 100 μg plasmid DNA, as previously described . Blasticidin (Calbiochem) was added to a final concentration of 2.5 μg/ml 48 hours after transfection to select for transformed parasites. Resistant parasites appeared after 3–4 weeks and were maintained under selection. After verification by PCR that pfeik1- parasites were present, the population was cloned by limiting dilution in 96 well plates (0.25/0.5/1.0 parasite per well). Genotypic analysis enabled selection of independent pfeik1- clones for further phenotypic analysis.
Parasite culture and mosquito infection
Plasmodium falciparum clone 3D7 was cultured as previously described . In brief, asexual cultures were maintained in complete RPMI at a haematocrit of 5%, between 0.5% and 10% parasitaemia. Asexual growth cycle was analyzed by flow cytometric assessment of DNA content as previously described . Gametocytogenesis was induced as described previously ; briefly, gametocyte cultures were set up at 0.5–0.7% parasitaemia in 6% haematocrit (using human blood not more than 7 days after the bleed), in an initial volume of 15 ml in 75 cm2 flasks. Cultures were maintained for 4–5 days until 8–10% parasitaemia was reached and parasites appeared stressed, after which the volume was increased to 25 ml. For each clone a mixture of day 14 and day 17 gametocyte cultures were fed to Anopheles gambiae, through membrane feeders as described . Female mosquitoes were dissected 10 days post-infection and midguts examined by light microscopy for presence of oocysts. Sporozoite invasion of salivary glands was assessed by removal of salivary glands 16 days post-infection and examination by light microscopy. DNA was extracted from oocyst-positive midguts using previously published methods . Fisher's exact test was used to compare infection prevalence between oocyst and sporozoite stages, where appropriate.
Preparation of parasite pellets
Parasite pellets were obtained by saponin lysis: erythrocytes were centrifuged at 1300 g for 2 min. at room temperature, washed in an equal volume of Phosphate Buffered Saline (PBS), pH 7.5, and centrifuged at 1300 g for 2 min. at 4°C. Erythrocytes were lysed on ice by resuspension and repeated pipetting in 0.15% saponin in PBS. The PBS volume was then increased and parasites recovered by centrifugation at 5500 g for 5 min., at 4°C. After two washes in PBS, the parasite pellets were stored at -80°C.
Plasmodium falciparum amino acid starvation assay
Plasmodium falciparum 3D7 parasites and clonal lines of pfeik1- and pfeik2- parasites were synchronized to the late ring stage, cultured in complete RPMI at 2% haematocrit, and grown to approximately 8 – 10% parasitaemia. The parasites were washed two times in 1× PBS, equally partitioned and washed with either complete RPMI or RPMI medium lacking amino acids, after which, the parasites were re-plated in their respective medium. The plates were incubated at 37°C with 5% CO2 for 5 hours. After 5 hours, one culture maintained in amino acid free medium was supplemented with complete RPMI, and re-incubated at 37°C for an additional 45 minutes. Post-incubation, the parasites were isolated by tetanolysin (List Biological) treatment, washed with 1× PBS buffer containing Complete™ protease inhibitor cocktail (Roche), 2 mM NaF, and 2 mM Na3VO4. Samples were resuspended in 2× SDS-Laemmli buffer. Parasite proteins were resolved by SDS-PAGE and transferred to nitrocellulose for immunoblotting.
Antibodies and immunoblotting
Rabbit anti-phosphorylated eIF2α (Ser 51) was purchased from Cell Signaling Technology (Danvers, MA). Rat anti-BiP was acquired from the Malaria Research and Reference Reagent Resource Center (ATCC, Manassas, VA). Secondary antibodies used were conjugated with horseradish peroxidase (HRP). For immunoblotting, nitrocellulose membranes were blocked with 5% BSA in TBS-0.1% Tween 20 (TBST) for 1 hour at room temperature. Rabbit anti-phosphorylated eIF2α (Ser 51) was diluted 1:1000 in TBST. Rat anti-BiP was diluted 1:10,000 in TBST. Respective secondary antibodies were diluted 1:20,000. Bound antibodies were detected with Western Lightning™ Chemiluminescence reagent (Perkin Elmer).
To obtain genomic DNA, parasite pellets were resuspended in PBS and treated with 150 μg/ml proteinase K and 2% SDS at 55°C for 4 hours. The DNA was extracted using phenol/chloroform/isoamyl alcohol (25:24:1), and precipitated in ethanol with 0.3 M sodium acetate at -20°C. Restriction digests were carried out with Hind III. Probes were labelled with alkaline phosphatase using the Gene Images AlkPhos Direct Labelling kit (Amersham).
Results and Discussion
Stress-dependent phosphorylation of the P. falciparum eIF2α orthologue
The presence of the target serine residues, and of residues which in other species are involved in interaction with eIF2α kinases, suggests that PfeIF2α may be regulated by phosphorylation under stress conditions. To test this hypothesis, cultured intraerythrocytic parasites were starved of amino acids, and the phosphorylation status of PfeIF2α was monitored by western blot using an antibody that specifically recognizes the phosphorylated form (Ser51) of human eIF2α, reasoning that the high level of sequence conservation between the human and plasmodial sequences would allow cross-reaction of the antibody (Figure 1B). Indeed, the antibody recognized the expected 37-kDa band in parasite extract, and the intensity of the signal was considerably stronger in the lane containing extracts from parasites that had been stressed by amino-acid starvation than in extracts from unstressed parasites, despite equal quantities of the eIF2α factor (as quantitated with a non-phosphodependent antibody). Furthermore, this effect was removed by restoring the amino acids in the culture medium. This demonstrates that the P. falciparum equivalent residue of human eIF2α Ser51 is phosphorylated in response to starvation.
Identification of eIF2α kinases in P. falciparum
The PF14_0423 gene model proposed in PlasmoDB  predicts a single intron that falls close to the 5' end of the sequence so that the kinase domain is encoded entirely within the second exon. All the residues that are required for catalytic activity  are present in the kinase domain, suggesting the gene encodes an active enzyme. The sequence shares the feature of insertions within the catalytic domain with other eIF2α kinases  (Figures 2B and 2C). Three of the human eIF2α kinases have N-terminal extensions containing regulatory domains; the fourth, GCN2, has extensions on either side of the kinase domain (reviewed in ). As PfeIK1 has extensions on both sides of the catalytic domain, it is most similar to GCN2 not only in the sequence of its catalytic domain, as the phylogenetic tree (Figure 2A) demonstrates, but also in overall structure (Figure 1C). Furthermore, the C-terminal extension of PfeIK1 contains an "anti-codon binding" domain (Superfamily entry SSF52954) that may mediate binding to uncharged tRNAs, a function that is performed in GCN2 by the HisRS domain present in the C-terminal extension (Figure 1C) . This adds weight to the possibility that PfeIK1 is involved in the response to amino acid starvation, like GCN2. The other functional domains present in the GCN2 extensions were not recognisable in PfeIK1.
Kinase activity of recombinant PfeIK1
In order to establish whether PfeIK1 is an eIF2α kinase as predicted, its activity was tested towards recombinant P. falciparum eIF2α expressed as a 64 kDa GST fusion. Figure 3B (left lane) shows that GST-PfeIK1 can phosphorylate wild-type GST-PfeIF2α. The signal appears very weak, which may be explained by the fact that the recombinant kinase contains only the catalytic domain and may not mimic the enzyme in a fully activated, physiological status. Indeed, an activation mechanism for GCN2 has been proposed , in which a conformational alteration of the so-called "hinge region" of the catalytic domain is induced by uncharged tRNA binding to the HisRS domain, which would favour productive binding of ATP to the active site. Such a positive effect of the regulatory domain would not be possible with GST-PfeIK1, since it contains only the catalytic domain.
Consistent with the hypothesis that PfeIK1 may regulate translation through PfeIF2α phosphorylation, mutation of the predicted target for phosphorylation in the substrate (Ser59→Ala) prevents labelling with the recombinant enzyme (Figure 3B).
Generation of pfeik1- clones
eIF2α is not phosphorylated in pfeik1- clones during amino acid starvation
pfeik1- clones are competent for sexual development and mosquito infection
Oocyst and sporozoite formation by pfeik1- parasite clones.
% Infection (no. infected/no. dissected)
Median oocyst no. per infected mosquito (range)
% Sporozoite-positive (no. infected/no. dissected)
On the basis of the similarities between PfeIK1 and GCN2, we hypothesized that PfeIK1 is involved in modulating the response to amino acid starvation depicted in Figure 1B. That this is indeed the case was demonstrated through a reverse genetics approach: parasites lacking PfeIK1 do not phosphorylate eIF2α in response to amino-acid depletion (Figure 6). Future work will determine the impact of PfeIK1 activation on both the rate of translation and the possible selection of specific messages that are translated under stress conditions. Overall, the data presented here suggest that eIF2α phosphorylation in response to amino-acid starvation is not essential to parasite survival during the erythrocytic asexual cycle (at least in an in vitro cultivation context), or for completion of sporogony.
Commitment to gametocytogenesis has been proposed to be linked to stress response, and eIF2α might possibly be involved in this process. At first sight, the data presented here suggest that PfeIK1 does not regulate gametocytogenesis, since pfeik1- parasite are able to undergo sexual development. However, caution must be exercised, as compensatory mechanisms can be at play in knock-out parasites. Indeed, in a similar situation concerning another protein kinase family, it was observed that disruption of the gene encoding one of the two P. falciparum mitogen-activated protein kinases (MAPKs), pfmap-1, does not cause any detectable phenotype, but that pfmap-1- parasites overexpress the second parasite MAPK, Pfmap-2 . A similar compensation mechanism may operate between the three PfeIKs represented in the parasite kinome (Figure 2A). Even though compensatory mechanisms to permit sexual differentiation are presumably less likely to occur than those allowing the survival of asexual parasites (because of the absence of a true selection pressure), it cannot be formally excluded that PfeIK1 plays a role in gametocytogenesis in a wild-type parasite background. Investigating this possibility will require inducible and/or multiple knock-outs and the availability of mono-specific antibodies to monitor the levels of each PfeIK in parasites lacking one of them.
Phylogenetic analysis indicates that the P. falciparum kinome includes three putative eIF2α kinases. One of these, PfPK4, was previously shown to phosphorylate a peptide corresponding to the target region of human eIF2α . It is demonstrated here that PfeIK1 is able to phosphorylate the conserved regulatory site on the Plasmodium orthologue of the translation factor in vitro, and that eIF2α phopshorylation in response to amino-acid starvation does not occur in pfeik1- parasites. The present study thus establishes that malaria parasites possess the molecular machinery that pertains to stress-dependent regulation of translation, and that this machinery is actually used in stress response.
This work is based on gene identification made possible by the availability of the genome sequences of P. falciparum and P. berghei, and of the PlasmoDB database. Financial support for the Plasmodium Genome Consortium was provided by the Burroughs Wellcome Fund, the Wellcome Trust, the National Institutes of Health (NIAID) and the U.S. Department of Defense, Military Infectious Diseases Research Program. Financial Support for PlasmoDB was provided by the Burroughs Wellcome Fund. We thank Luc Reininger for his input at the onset of this project and for frequent discussions about this and other topics, and Jacques Chevalier (Service Scientifique de l'Ambassade de France in London) for continuing support. Work in the C.D. laboratory is funded by Inserm, the FP6 (SIGMAL and ANTIMAL projects, and BioMalPar Network of Excellence) and FP7 (MALSIG project) programmes of the European Commission and a grant from the Novartis Institute for Tropical Diseases. C.F is the recipient of a PhD studentship awarded by the Wellcome Trust.
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