Comparative genome-wide analysis and evolutionary history of haemoglobin-processing and haem detoxification enzymes in malarial parasites
- Patrath Ponsuwanna†1,
- Theerarat Kochakarn†1, 2,
- Duangkamon Bunditvorapoom1, 3, 4,
- Krittikorn Kümpornsin1,
- Thomas D. Otto5,
- Chase Ridenour1,
- Kesinee Chotivanich6, 7,
- Prapon Wilairat2,
- Nicholas J. White6, 8,
- Olivo Miotto6, 9, 10 and
- Thanat Chookajorn1Email author
© Ponsuwanna et al. 2016
Received: 15 October 2015
Accepted: 12 January 2016
Published: 29 January 2016
Malaria parasites have evolved a series of intricate mechanisms to survive and propagate within host red blood cells. Intra-erythrocytic parasitism requires these organisms to digest haemoglobin and detoxify iron-bound haem. These tasks are executed by haemoglobin-specific proteases and haem biocrystallization factors that are components of a large multi-subunit complex. Since haemoglobin processing machineries are functionally and genetically linked to the modes of action and resistance mechanisms of several anti-malarial drugs, an understanding of their evolutionary history is important for drug development and drug resistance prevention.
Maximum likelihood trees of genetic repertoires encoding haemoglobin processing machineries within Plasmodium species, and with the representatives of Apicomplexan species with various host tropisms, were created. Genetic variants were mapped onto existing three-dimensional structures. Genome-wide single nucleotide polymorphism data were used to analyse the selective pressure and the effect of these mutations at the structural level.
Recent expansions in the falcipain and plasmepsin repertoires are unique to human malaria parasites especially in the Plasmodium falciparum and P. reichenowi lineage. Expansion of haemoglobin-specific plasmepsins occurred after the separation event of Plasmodium species, but the other members of the plasmepsin family were evolutionarily conserved with one copy for each sub-group in every Apicomplexan species. Haemoglobin-specific falcipains are separated from invasion-related falcipain, and their expansions within one specific locus arose independently in both P. falciparum and P. vivax lineages. Gene conversion between P. falciparum falcipain 2A and 2B was observed in artemisinin-resistant strains. Comparison between the numbers of non-synonymous and synonymous mutations suggests a strong selective pressure at falcipain and plasmepsin genes. The locations of amino acid changes from non-synonymous mutations mapped onto protein structures revealed clusters of amino acid residues in close proximity or near the active sites of proteases.
A high degree of polymorphism at the haemoglobin processing genes implicates an imposition of selective pressure. The identification in recent years of functional redundancy of haemoglobin-specific proteases makes them less appealing as potential drug targets, but their expansions, especially in the human malaria parasite lineages, unequivocally point toward their functional significance during the independent and repetitive adaptation events in malaria parasite evolutionary history.
In order for Plasmodium to evolutionarily become a parasite of red blood cells, it has to gain two functions, namely, Hb degradation and haem detoxification. The cellular machinery required for executing these two tasks has been biochemically and functionally characterized in P. falciparum to occur within a single protein complex (Fig. 1) . The major component of the complex is haem detoxification protein (HDP), which catalyzes haem biocrystallization by tethering haem molecules together . Three families of proteases, namely, cysteine protease (falcipain 2A and falcipain 2B), aspartic protease (plasmepsin II, III and IV) and metalloprotease (falcilysin) are associated with the complex . These proteases have been functionally shown to target Hb . The diversity and redundancy in Hb-targeted proteases indicate that the process of Hb degradation is vital for malaria survival as the evolutionary process has generated an array of proteases to accomplish the task. These proteases target different Hb parts and act sequentially to degrade globin chains .
Genetic alterations of Hb processing genes are linked to loss in anti-malarial drug sensitivity. For instance, knock-out of falcipain 2A reduces artemisinin sensitivity . Interestingly, a mutation in falcipain 2A also arose during long-term selection of artemisinin resistance . Both artemisinin and chloroquine inhibit HDP complex function, but with different modes of action [10, 11]. In addition, quinolone anti-malarials also affect Hb degradation and haem detoxification . The selective pressure from such drugs is likely to alter the course of parasite evolution through changes in genes encoding members of the HDP complex, especially in ‘hotspot’ areas of drug resistance in Southeast Asia, where there is well-established evidence for loss in artemisinin sensitivity .
Here, the evolution history of Plasmodium protease families known to target Hb, including members of the HDP complex, was traced. Variations of P. falciparum HDP complex genes obtained from subjects in hotspot areas, including those from emerging artemisinin-resistant isolates, were analysed and mapped onto protein structures. Genes under selective pressure and mutations at key positions are described.
Amino acid sequences of falcipains, plasmepsins, falcilysin, and HDP from P. falciparum strain 3D7 were retrieved from NCBI Protein database (Additional file 1) and SNP data of P. falciparum candidate genes were obtained from MalariaGEN . Sequences from P. falciparum were used as a BLAST query against non-redundant protein sequence database (nr). BLASTp parameters were set as follows: scoring matrix, BLOSUM62; gap penalty, 11; and, gap extension penalty, 1. BLASTp hits that fulfilled the following criteria were selected as candidates for further analysis: (1) E-value <10−6; (2) alignment score >80; and, (3) BLAST alignment covering the functional domain. Homologue candidates in other Plasmodium spp. (P. reichenowi, P. vivax, P. knowlesi, P. berghei, and P. yoelii) and other protozoa (Babesia bovis, Babesia microti, Eimeria tenella, Toxoplasma gondii, Theileria parva, and Theileria annulata) were retrieved from NCBI database. The DNA sequences encoding falcipain 2A and falcipain 2B from P. reichenowi PrCDC were obtained by de novo assembly . Sequences of interest were aligned using MUSCLE [18, 19]. Neighbour-joining (NJ) tree and 1000 bootstrap replicates were constructed using ClustalX version 2.0 . The best-fit protein evolutionary model was determined using ProtTest . Unrooted maximum likelihood (ML) tree was estimated using RAxML software [22, 23] and constructed using Dendroscope version 3.2.10 .
Nested-PCR and sequence analysis of falcipain genes
In nested-PCR amplification of falcipain 2A and falcipain 2B genes, first round PCR was performed in a 25-µl reaction containing 1X HF buffer (Thermo Scientific), 1.5 mM MgCl2 for falcipain 2A or 5 mM MgCl2 for falcipain 2B, 0.5 pmol of dNTPs, 10 pmol of each primer (Additional file 2), 25 ng of parasite DNA, and 0.2 U Phusion DNA polymerase (Thermo Scientific). PCR was performed in an Eppendorf Mastercycler Pro under the following conditions: 98 °C for 30 s; 35 cycles of 98 °C for 10 s, 55 °C for 30 s, and 72 °C (for falcipain 2A) or 68 °C (for falcipain 2B) for 135 s; and, 72 °C for 5 min. Second-round PCR was carried out as described above except that 1 µl of 10−4 dilution of first-round PCR solution, second-round PCR primers (Additional file 2) and the extension step of 72 °C for 45 s were used. The nested-PCR amplicons were sequenced in both directions in ABI3130XL DNA sequencer (Applied Biosystems).
Homology modelling and structural analysis
Structural data of plasmepsin I (accession no 3QS1), plasmepsin II (accession no 1XDH), HAP (accession no 3FNT), falcipain 2A (accession no 1YVB), falcipain 3 (accession no 3BPM), and falcilysin (accession no 3S5M) were retrieved from RCSB Protein Data Bank. Homology model of falcipain 2B was constructed using SWISS-MODEL with falcipain 2A (accession no 1YVB) as a template, and the model was subsequently refined using AMBER03 force field in GROMACS and checked for Ramachandran outlier by RAMPAGE [25, 26]. Structural models were visualized by PyMOL.
Evolution of Plasmodium Hb processing genes
Members of two Plasmodium protease families, falcipain and plasmepsin, have been functionally characterized as being Hb-specific . Falcipain 2A, falcipain 2B, plasmepsin II, plasmepsin III, plasmepsin IV, and falcilysin are associated with the HDP complex (Fig. 1) , but both protease families also have members that function in pathways not related to Hb processing, and some are not expressed during the intra-erythrocytic stages .
Plasmodium falciparum has two copies of falcipain 2, falcipain 2A and falcipain 2B that are almost identical (93.4 % identity at the amino acid sequence level) (Fig. 4). The presence of highly similar falcipain 2A and falcipain 2B genes at the same locus can result in gene conversion and promotion of genetic exchanges between the two repertoires, which might be a strong evolutionary driver for improving gene diversity  (Additional file 3: Figure S8). Plasmodium vivax and P. knowlesi also have three falcipain genes at their respective fvf locus, but the degree of similarity between the two species is approximately 70 %. There is only one falcipain gene at the fvf locus of P. berghei and P. yoelii, but the gene is still flanked by the conserved histone methyltransferase Set 7 and one of the AP2 transcription factor genes.
Phylogenetic analysis established that members of the falcipain family exist as a common ancestor of Plasmodium and independently undergo expansion. There was a diversification between falcipains specific to Hb digestion (falcipains 2 and 3 at the fvf locus) and falcipain 1 prior to malarial speciation (Fig. 3). Every Plasmodium sp. has a single falcipain 1 gene, and in the primate malaria parasite branch (P. falciparum, P. reichenowi, P. vivax, P. knowlesi), Hb-specific falcipain genes have expanded into three copies. Plasmodium vivax/P. knowlesi branch is clustered together with three matching pairs between the two species, suggesting that the expansion into three genes occurred prior to their speciation. Diversification into falcipain 2 and falcipain 3 in the P. falciparum/P. reichenowi branch is likely to be an independent event from that of P. vivax/P. knowlesi branch based on the phylogenetic tree structure (Fig. 3) .
It is worth noting that Theileria parva and Theileria annulata, members of the Apicomplexan species, have a large expansion of their falcipain family with ten putative members in their respective family prior to speciation (Additional file 3: Figure S1). The expansion might have facilitated their growth in both white and red blood cells. Nevertheless, the expansion into ten genes is not a necessity for parasitism in red blood cells since Plasmodium and Babesia spp. have only three to four falcipain genes.
Falcilysin is a member of metalloprotease family and is localized at the apicoplast and food vacuole [31, 32]. Peptides corresponded to P. falciparum falcilysin were identified by mass spectrometry during HDP complex purification . A homologue of falcilysin is found in every Plasmodium sp., and the phylogenetic tree demonstrates conventional species evolution in malaria parasites (Additional file 3: Figure S2) . Plasmodium falcilysins are highly conserved with more than 70 % amino acid sequence similarity among Plasmodium species. Both Theileria parva and Theileria annulata have two copies of falcilysin, and phylogenetic tree structure indicates that falcilysin duplication occurred before Theileria speciation (Additional file 3: Figure S2).
HDP is localized in malaria parasite food vacuole where it detoxifies haem released from digested Hb by facilitating the crystallization of haem into haemozoin . HDP phylogenetic tree structure is similar to that of falcilysin (Additional file 3: Figure S3). Plasmodium HDPs are highly conserved and are essential for P. falciparum and P. berghei intra-erythrocytic development . Blood parasites that do not produce haemozoin, such as Babesia and Theileria, have only one copy of P. falciparum HDP homologue, suggesting that HDP in these two species may have another function or that a different form of haemozoin exists.
Selective pressure on Hb processing genes
In order to understand the effects of selective pressure of drugs, such as artemisinin and chloroquine, the ratio between single nucleotide polymorphism (SNPs) causing non-synonymous mutations and synonymous mutations (N/S ratio) and the positions of mutated residues in the three-dimensional structures were determined [34, 35]. Bias towards non-synonymous mutations means that the gene of interest is under pressure to diversify, probably due to drug selective pressure. In addition, functional significance of these mutations could be reflected in their locations either at functional motif or as a cluster.
N/S ratios were analysed in samples collected from different parts of the world and those specific to Southeast Asia, a hot spot of anti-malarial resistance. As high-throughput sequencing data for falcipain 2A and 2B are limited by their sequence similarity, nested-PCR falcipain 2A and 2B amplicons were sequenced from artemisinin-resistant ANL2 and ANL4 and artemisinin-sensitive ANL1 and ANL3 strains obtained from the same area . Mutations data are listed in Additional file 4 and Additional file 5.
The three mutations of plasmepsin I found in Southeast Asia are located in close proximity on the enzyme surface (Additional file 3: Figure S4). N148I and L180H are exclusive to Southeast Asia and I213V is found in Southeast Asia and South Asia. Mutation F112L is also specific to Southeast Asia (allele frequency = 0.2 %) and South Asia (allele frequency = 3.9 %). Its location is in the pro-domain region, which was not included in the structure.
Plasmepsin II mutations (V133A, Y141C, E145D, T154I, D286N, T289I), found in Asia and Africa except for Southeast Asia-specific C141 variant, also form a cluster on the negatively charged surface (Fig. 6a). N286 variant is found more often in Southeast Asia (allele frequency = 1.4 %) than in Africa (allele frequency < 0.1 %). Mutations L321F and A323T/V, found in Asia and Africa, are located on the same side of a β-strand in the interior hydrophobic milieu of the enzyme (Additional file 3: Figure S5). The Southeast Asia-specific L411V mutation is located also within the enzyme interior and close to the substrate-binding cleft (Additional file 3: Figure S5). Mutations N271S and Y302H, located on the surface, are exclusive to Southeast Asia (Additional file 3: Figure S5).
Plasmepsin III mutations N411K and G233R are located near the substrate-binding cleft (Fig. 6b), with K411 variant found only in Southeast Asia (allele frequency = 0.1 %) and R233 variant throughout Asia (allele frequency >20 %). Plasmepsin III has a surface negative-charge patch similar to that of plasmepsin II but at a different location and contains mutation E173V that is not specific to Southeast Asia (Fig. 6b).
Plasmepsin IV mutation P397S, located near the substrate-binding pocket, is specific to Southeast Asia (allele frequency = 0.5 %) and is in the same binding pocket as plasmepsin III K411 variant (Additional file 3: Figure S6). Mutation N268K is equivalent to plasmepsin II N271S, but is not unique to Southeast Asia (Additional file 3: Figure S6). Of the three mutations, N272I, R353T and N268K, N272I variant is specific to Southeast Asia (allele frequency = 0.1 %) and R353T variant is global (allele frequency = 30.8 %).
Falcipain 2A mutation A400P is located in α5 helix (thereby causing a kink) that is close to the substrate-binding cleft and is likely to come from falcipain 2B (Fig. 7). This mutation is found in Asia and Africa (global allele frequency = 0.3 %). Falcipain 2B also has the matching mutation of P398A, again as the result of gene conversion. Falcipain 2B A398 variant is found worldwide (allele frequency = 11 %) but with a lower prevalence (6.4 %) in Southeast Asia.
Falcipain 2A mutation M245I, equivalent to mutation I243M in falcipain 2B, is more prevalent in Africa (allele frequency = 2.1 %) than in Southeast Asia (allele frequency = 0.1 %), but conversely, falcipain 2B M243 variant is more prevalent in Southeast Asia (allele frequency = 2.9 %) than in Africa (allele frequency = 0.6 %). These mutations are located in α1 helix of the ‘nose’ domain (Fig. 7).
Falcipain 2A mutation Q414E, found in P. falciparum ANL1 and ANL2 strains, is located in the negative-charge patch that extends from the Hb-binding ‘arm’ domain to the surface area near the active site cleft (Fig. 7). In comparison to 3D7, falcipain 2A mutations K255R, N257E, T343P and D345G were found in ANL strains (Additional file 4), and are identical to those in the W2 strain that has a shared origin from Southeast Asia. R255 and E257 substitutions are located close to each other at the ‘nose’ domain, while P343 and G345 substitutions are located in close proximity in a loop connecting α4 helix and β1 sheet at the opposite side of the ‘arm’ domain (Fig. 7).
Falcipain 2B mutations I243M and D246E are present in the ‘nose’ domain, with the former located in α1 helix. Mutation A297V, found in ANL4 strain, is located in α2 helix. I391V mutation, found in ANL1, is located in the interior hydrophobic milieu of the enzyme and has a global allele frequency of 10.5 %.
Falcipain 3 mutations A264V, N371K, R411K, and N468Y were found in Southeast Asia but they are also present in Africa. K371 substitution is located at the negative-charge surface of L domain; K411 and Y468 lie close to the ‘arm’ domain; and V264 is located in the ‘nose’ domain (Additional file 3: Figure S7).
Ten mutations (T752S, Q812H, D841Y, I888N, E893D, K910M, R918C, V972L, T976A/I, S986N/R) found in P. falciparum worldwide are clustered on the same outer surface of the C-terminal domain (Fig. 8a). M910 (allele frequency = 1 %) and N986 (allele frequency = 0.1 %) variants are Southeast Asia-specific. In addition, mutation L453M, located on the inner surface of the enzyme substrate cavity, is specific to Southeast Asia (allele frequency = 0.1 %) (Fig. 8b).
At present, the structural information on HDP is not available. A biochemical study showed the importance of key conserved histidine residues (Histidine 122, 172, 175, and 197 in P. falciparum) in haemozoin formation . Four SNPs are found in Southeast Asia at the gene encoding HDP, but only charge-reversion E112K is specific to Southeast Asia (allele frequency = 0.1 %). The data from MalariaGEN suggested that C41F (allele frequency = 0.2 %) was found only in Southeast Asia, but this mutation was previously reported in the HB3 strain originated from South America . The other two mutations, V164I and I185T, can be found in Southeast Asia and Africa.
Changes in gene dosage by gene duplication play an important role in the survival of malaria parasites under drug-induced stress. One of the original observations was the amplification of P. falciparum mdr 1, linked to resistance to mefloquine . Amplification of GTP cyclohydrolase I gene, encoding the upstream rate-limiting enzyme in the malaria parasite folate pathway, not only results in antifolate resistance, but also drives the evolution of drug resistance of other genes in the folate pathway [46, 47]. Nevertheless, too many copies of a particular gene could be deleterious to an organism. Mutually exclusive expression of multigene families is often adopted in P. falciparum to select a sub-set of genes to be expressed at a particular time or stage of development in order to gain a selective advantage .
Analysis of Hb processing genes in Plasmodium and Apicomplexan spp. has revealed expansion of protease genes (encoding plasmepsin, falcipain and falcilysin) specific to malaria parasites. Hb-specific plasmepsin is encoded by a single gene in every Plasmodium sp. except for P. falciparum/P. rechenowi clade where there are four plasmepsin genes, whereas the remaining members of the family (plasmepsin V-X) that do not degrade Hb are conserved in other Plasmodium and Apicomplexan spp. The expansion of Hb-specific plasmepsin genes indicates a strong selective advantage in maintaining large amounts of such plasmepsin. However, loss of plasmepsin I–IV by genetic ablation does not create a lethal phenotype . In addition to the effect of gene dosage on protein expression level, gene expansion promotes genetic diversity by allowing tolerance to deleterious mutations present in one or more of the genes. Plasmepsin gene expansion probably is not due to direct selective pressure of anti-malarial interventions as the phenomenon also is found in P. reichenowi. Plasmepsin gene expansion itself is not needed for survival in the human host as P. vivax only has one Hb-specific plasmepsin gene copy. It is possible that increased plasmepsin gene expansion promotes Hb consumption in red blood cells allowing effective propagation in Hb-rich mature red blood cells. This notion needs to be tested in other Plasmodium spp.
Furthermore, the presence of closely similar genes, e.g., falcipain 2A and 2B, allows genetic variation by means of gene conversion. Falcipain gene duplications at the fvf locus are found in both P. falciparum/P. reichenowi and P. vivax/P. knowlesi clades and have occurred independently based on the constructed phylogenetic tree and close homology between falcipain 2A and 2B.
Two components of the haem processing genes, HDP and falcilysin, have only one copy per genome. It is not unexpected that their deletions are lethal to malaria parasites . The degree of diversification for HDP is low with an N/S ratio of 1 (Fig. 5). Falcilysin does not have a high N/S ratio at the global scale, but this ratio is higher among P. falciparum isolates in Southeast Asia (Fig. 5).
The majority of non-synonymous mutations in P. falciparum falcipain 2A, falcipain 2B and falcipain 3 are located more in the prodomain than in core enzyme, contrary to those observed for plasmepsins (Additional file 5). This preference may indicate a strong requirement for intact enzymes over protein regulation mediated by the prodomain sequence. Even though no direct protease inhibitor has been adopted for malaria treatment, compounds in both 4-aminoquinoline and artemisinin families are known to perturb haemoglobin degradation and haemozoin formation . Their activities could impose selective pressure on haemoglobin-specific proteases since genetic alterations at the Hb processing genes were experimentally linked to reduced drug sensitivity [10, 13].
Selective pressure on Hb processing genes can be observed by analysing the N/S ratio of existing SNPs. N/S ratio analysis revealed that HDP and most non Hb-targeting plasmepsin genes are not under positive selection. On a global scale, falcipain 2A and falcipain 2B significantly have more SNPs with non-synonymous mutations than those with synonymous mutations. When the analysis is limited to parasites from Southeast Asia, N/S ratio for falcilysin, plasmepsin I and plasmepsin III are elevated significantly. Another important factor is gene conversion between falcipain 2A and falcipain 2B. Sequence analysis of a few strains showed extensive exchanges between the two genes. This issue has been largely overlooked because these two genes are considered a ‘blind spot’ in whole genome sequencing. Analysis of these genes by an alternative approach, such as PCR-based sequencing as conducted in this study, may reveal correlations between falcipain mutations and drug resistance, especially given the fact that gene conversion increases genetic diversity .
This study demonstrates that Plasmodium Hb processing genes are currently under-appreciated despite the degree of evolutionary pressure to expand and diversify. This is due largely in part to the lack of lethal intra-erythrocytic-stage phenotypes as ex vivo gene knock-out experiments were performed in rich media culture, which may have prevented the generation of such phenotypes. Adaptation of more stringent growth conditions could reveal hidden phenotypes of intra-erythrocytic-stage parasites (Bunditvorapoom et al., unpublished data). Systemic analysis of malaria parasite Hb processing genes will be important in dissecting their roles in developing drug resistance and in pathogenesis.
PP, TK, DK, TDO, and CR carried out sequence analysis and molecular genetic studies. KK and KC carried out parasite culture and isolate collection. PW, NJW, OM, and TC conceived of the study and participated in data analysis. PP, TK, DK, PW, and TC drafted the manuscript. All authors read and approved the final manuscript.
We thank Professor DE Goldberg for his comments and suggestions. The work in the Chookajorn laboratory is supported by Grand Challenges Canada and Thailand Research Fund-Mahidol University (RSA5880062). TC is supported by the Office of the Higher Education Commission and Mahidol University under the National Research Universities Initiative. TK is supported by the Royal Golden Jubilee Ph.D. Program (Grant No PHD/0204/2552). This work is partially supported by a Fogarty training grant (D43TW006571) from the National Institutes of Health, USA.
The authors declare that they have no competing interests.
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