A three-dimensional structure of Plasmodium falciparum serine hydroxymethyltransferase in complex with glycine and 5-formyl-tetrahydrofolate. Homology modeling and molecular dynamics

França, Tanos C. C.; Pascutti, Pedro Geraldo; Ramalho, Teodorico C.; Figueroa‐Villar, José Daniel

doi:10.1016/j.bpc.2004.12.002

Cited by 36 publications

(21 citation statements)

References 45 publications

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“…Therefore, in our sensitive models, neither SHMT nor the glycine cleavage system is essential when knocked out individually. This observation conflicts with the literature, as SHMT is essential in cultured parasites [118, 120, 121]. Thus, iPfal17 is unable to predict this intricacy of parasite metabolism, revealing interesting regulatory effects, an uncharacterized location dependency for metabolite generation, or in vivo/in vitro differences in enzyme reversibility (Additional file 6).…”

Section: Discussionmentioning

confidence: 89%

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

2017

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BackgroundMalaria remains a major public health burden and resistance has emerged to every antimalarial on the market, including the frontline drug, artemisinin. Our limited understanding of Plasmodium biology hinders the elucidation of resistance mechanisms. In this regard, systems biology approaches can facilitate the integration of existing experimental knowledge and further understanding of these mechanisms.ResultsHere, we developed a novel genome-scale metabolic network reconstruction, iPfal17, of the asexual blood-stage P. falciparum parasite to expand our understanding of metabolic changes that support resistance. We identified 11 metabolic tasks to evaluate iPfal17 performance. Flux balance analysis and simulation of gene knockouts and enzyme inhibition predict candidate drug targets unique to resistant parasites. Moreover, integration of clinical parasite transcriptomes into the iPfal17 reconstruction reveals patterns associated with antimalarial resistance. These results predict that artemisinin sensitive and resistant parasites differentially utilize scavenging and biosynthetic pathways for multiple essential metabolites, including folate and polyamines. Our findings are consistent with experimental literature, while generating novel hypotheses about artemisinin resistance and parasite biology. We detect evidence that resistant parasites maintain greater metabolic flexibility, perhaps representing an incomplete transition to the metabolic state most appropriate for nutrient-rich blood.ConclusionUsing this systems biology approach, we identify metabolic shifts that arise with or in support of the resistant phenotype. This perspective allows us to more productively analyze and interpret clinical expression data for the identification of candidate drug targets for the treatment of resistant parasites.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3905-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 89%

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

2017

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“…However, a predicted SHMT-like gene product (PfSHMTm, encoded on PF14_ 0534) was also identified that carries a putative mitochondrial signal sequence [24] with 18% amino acid identity and 44% similarity to PfSHMTc, but lacks almost all (16 of 21) of the known, very highly conserved residues [42] contributing to the active site in SHMT orthologues from other organisms, whether cytoplasmic or organellar (See Additional file 2 Sequence alignments of the PfSHMT isoforms). Despite the relatively low level of identity, it was essential to establish the specificity of the anti-PfSHMTc and anti-PfSHMTm antibodies that had been raised to be certain of the identity of the protein yielding positive signals.…”

Section: Resultsmentioning

confidence: 99%

“…Of the two SHMT isoforms expressed by P. falciparum , PfSHMTc is an enzymatically active member of the thymidylate cycle [21-23], whereas PfSHMTm is more enigmatic, as it lacks most of the conserved active site residues found in other SHMTs, whether cytoplasmic or organellar [24,42] and has been found to be inactive in studies of the recombinant protein [23]. With a combination of antibody probes and endogenous expression of tagged molecules, the cellular distribution of these two species across the parasite erythrocytic cycle has been investigated to gain possible insight into their biological function.…”

Section: Discussionmentioning

confidence: 99%

Dynamic subcellular localization of isoforms of the folate pathway enzyme serine hydroxymethyltransferase (SHMT) through the erythrocytic cycle of Plasmodium falciparum

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Müller

Mitchell

et al. 2010

Malar J

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BackgroundThe folate pathway enzyme serine hydroxymethyltransferase (SHMT) converts serine to glycine and 5,10-methylenetetrahydrofolate and is essential for the acquisition of one-carbon units for subsequent transfer reactions. 5,10-methylenetetrahydrofolate is used by thymidylate synthase to convert dUMP to dTMP for DNA synthesis. In Plasmodium falciparum an enzymatically functional SHMT (PfSHMTc) and a related, apparently inactive isoform (PfSHMTm) are found, encoded by different genes. Here, patterns of localization of the two isoforms during the parasite erythrocytic cycle are investigated.MethodsPolyclonal antibodies were raised to PfSHMTc and PfSHMTm, and, together with specific markers for the mitochondrion and apicoplast, were employed in quantitative confocal fluorescence microscopy of blood-stage parasites.ResultsAs well as the expected cytoplasmic occupancy of PfSHMTc during all stages, localization into the mitochondrion and apicoplast occurred in a stage-specific manner. Although early trophozoites lacked visible organellar PfSHMTc, a significant percentage of parasites showed such fluorescence during the mid-to-late trophozoite and schizont stages. In the case of the mitochondrion, the majority of parasites in these stages at any given time showed no marked PfSHMTc fluorescence, suggesting that its occupancy of this organelle is of limited duration. PfSHMTm showed a distinctly more pronounced mitochondrial location through most of the erythrocytic cycle and GFP-tagging of its N-terminal region confirmed the predicted presence of a mitochondrial signal sequence. Within the apicoplast, a majority of mitotic schizonts showed a marked concentration of PfSHMTc, whose localization in this organelle was less restricted than for the mitochondrion and persisted from the late trophozoite to the post-mitotic stages. PfSHMTm showed a broadly similar distribution across the cycle, but with a distinctive punctate accumulation towards the ends of elongating apicoplasts. In very late post-mitotic schizonts, both PfSHMTc and PfSHMTm were concentrated in the central region of the parasite that becomes the residual body on erythrocyte lysis and merozoite release.ConclusionsBoth PfSHMTc and PfSHMTm show dynamic, stage-dependent localization among the different compartments of the parasite and sequence analysis suggests they may also reversibly associate with each other, a factor that may be critical to folate cofactor function, given the apparent lack of enzymic activity of PfSHMTm.

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“…Bulusu and collaborators [71] highlighted that AspAT also acts together with the fumarate hydratase (FH) and the malate-quinone oxidoreductase (MQO) in the conversion of fumarate to aspartate. The enzyme has also been appearance due to the lack of amino acid residues proposed to be involved in tetramerisation (like the His 135 and a poly-K sequence in the N-terminal domain) [88] . Despite all the similarities between the human and the malaria SHMT, the plasmodial enzyme possesses some peculiarities in the regulation of the folate metabolism such as the binding to its own RNA [87], thus inhibiting protein translation [89].…”

Section: Thementioning

confidence: 99%

“…Since the substrates of SHMT and DHFR are structurally similar ( Figure 4), pyrimethamine, a potent inhibitor of the plasmodial DHFR, has also been tested on the recombinant SHMT, however only with a marginal effect (IC 50 -value in the mid micro-molar range) [87]. The comparison between the active site of the human enzyme and the plasmodial one showed a high degree of similarity as illustrated in figure 4 [88], but in contrast to the mammalian SHMT, which reveals an homotetrameric structure, the structural conformation of plasmodial protein pointed towards a homodimeric Replacement and elimination of C β -groups Serine and threonine dehydratases and the tryptophan synthase (prototype) 3…”

Section: Serine Hydroxymethyltransferase (Shmt)mentioning

confidence: 99%

Implicações estruturais de mutantes da piridoxal quinase de Plasmodium falciparum

Kronenberger¹

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A three-dimensional structure of Plasmodium falciparum serine hydroxymethyltransferase in complex with glycine and 5-formyl-tetrahydrofolate. Homology modeling and molecular dynamics

Cited by 36 publications

References 45 publications

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

Novel Plasmodium falciparum metabolic network reconstruction identifies shifts associated with clinical antimalarial resistance

Dynamic subcellular localization of isoforms of the folate pathway enzyme serine hydroxymethyltransferase (SHMT) through the erythrocytic cycle of Plasmodium falciparum

Implicações estruturais de mutantes da piridoxal quinase de Plasmodium falciparum

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