Kinetic modelling of phospholipid synthesis in Plasmodium knowlesi unravels crucial steps and relative importance of multiple pathways

BMC Systems Biology

Ovidiu Radulescu¹  Henri J Vial¹  Partho Sen¹ 

[1] Dynamique des Interactions Membranaires Normales et Pathologiques, UMR 5235 CNRS, UM1, UM2, CP 107, Place Eugène Bataillon, 34095 Montpellier Cedex 5, France

关键词: Hybrid optimization;    Fluxomics;    Mathematical model;    Plasmodium knowlesi;    Phospholipid metabolism;    Malaria;   

Others  :  1141816
DOI  :  10.1186/1752-0509-7-123

 received in 2013-06-26, accepted in 2013-11-01,  发布年份 2013

【 摘 要 】

Background

Plasmodium is the causal parasite of malaria, infectious disease responsible for the death of up to one million people each year. Glycerophospholipid and consequently membrane biosynthesis are essential for the survival of the parasite and are targeted by a new class of antimalarial drugs developed in our lab. In order to understand the highly redundant phospholipid synthethic pathways and eventual mechanism of resistance to various drugs, an organism specific kinetic model of these metabolic pathways need to be developed in Plasmodium species.

Results

Fluxomic data were used to build a quantitative kinetic model of glycerophospholipid pathways in Plasmodium knowlesi. In vitro incorporation dynamics of phospholipids unravels multiple synthetic pathways. A detailed metabolic network with values of the kinetic parameters (maximum rates and Michaelis constants) has been built. In order to obtain a global search in the parameter space, we have designed a hybrid, discrete and continuous, optimization method. Discrete parameters were used to sample the cone of admissible fluxes, whereas the continuous Michaelis and maximum rates constants were obtained by local minimization of an objective function.The model was used to predict the distribution of fluxes within the network of various metabolic precursors.

The quantitative analysis was used to understand eventual links between different pathways. The major source of phosphatidylcholine (PC) is the CDP-choline Kennedy pathway.

In silico knock-out experiments showed comparable importance of phosphoethanolamine-N-methyltransferase (PMT) and phosphatidylethanolamine-N-methyltransferase (PEMT) for PC synthesis.

The flux values indicate that, major part of serine derived phosphatidylethanolamine (PE) is formed via serine decarboxylation, whereas major part of phosphatidylserine (PS) is formed by base-exchange reactions.

Sensitivity analysis of CDP-choline pathway shows that the carrier-mediated choline entry into the parasite and the phosphocholine cytidylyltransferase reaction have the largest sensitivity coefficients in this pathway, but does not distinguish a reaction as an unique rate-limiting step.

Conclusion

We provide a fully parametrized kinetic model for the multiple phospholipid synthetic pathways in P. knowlesi. This model has been used to clarify the relative importance of the various reactions in these metabolic pathways. Future work extensions of this modelling strategy will serve to elucidate the regulatory mechanisms governing the development of Plasmodium during its blood stages, as well as the mechanisms of action of drugs on membrane biosynthetic pathways and eventual mechanisms of resistance.

【 授权许可】

   
2013 Sen et al.; licensee BioMed Central Ltd.

【 图 表 】

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【 参考文献 】

• [1]World malaria report, World Health Organization, Geneva, Switzerland, 2012 2012. http://www.who.int/malaria/publications/world_malaria_report_2012/report/en/index.html webcite
• [2]Cox-Singh J, Davis T, Lee K, Shamsul S, Matusop A, Ratnam S, Rahman H, Conway D, Singh B: Plasmodium knowlesi malaria in humans is widely distributed and potentially life threatening. Clin Infect Dis 2008, 46(2):165-171.
• [3]Kantele A, Jokiranta T: Review of cases with the emerging fifth human malaria parasite, plasmodium knowlesi. Clin Infect Dis 2011, 52(11):1356.
• [4]Tilley L, Dixon MW, Kirk K: The Plasmodium falciparum-infected red blood cell. Int J Biochem Cell Biol 2011, 43(6):839-842.
• [5]Le Roch KG, Zhou Y, Blair PL, Grainger M, Moch JK, Haynes JD, De la Vega P, Holder AA, Batalov S, Carucci DJ, et al.: Discovery of gene function by expression profiling of the malaria parasite life cycle. Science 2003, 301(5639):1503-1508.
• [6]Mamoun C, Gluzman I, Hott C, MacMillan S, Amarakone A, Anderson D, Carlton J, Dame J, Chakrabarti D, Martin R, et al.: Co-ordinated programme of gene expression during asexual intraerythrocytic development of the human malaria parasite Plasmodium falciparum revealed by microarray analysis. Mol Microbiol 2001, 39:26-36.
• [7]Holz GJr: Lipids and the malarial parasite. Bulletin World Health Organ 1977, 55(2–3):237.
• [8]Vial H, Ancelin M: Malarial lipids. In Malaria: Parasite Biology, Pathogenesis, and Protection. Washington: ASM Press; 1998:159-175.
• [9]Vial H, Mamoun C: Plasmodium lipids: metabolism and function. Mol Approach Malar 2005, 327-352.
• [10]Vial HJ, Thuet MJ, Philippot JR: Phospholipid biosynthesis in synchronous plasmodium falciparum cultures. J Eukaryotic Microbiol 1982, 29(2):258-263.
• [11]Beaumelle BD, Vial HJ: Modification of the fatty acid composition of individual phospholipids and neutral lipids after infection of the simian erythrocyte by Plasmodium knowlesi. Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism 1986, 877(2):262-270.
• [12]Vial H, Ancelin M, Avila J, Harris J, et al.: Malarial lipids: an overview. In Subcellular Biochemistry, volume 18: Intracellular Parasites. Plenum Press; 1992:259-306. http://www.cabdirect.org/abstracts/19930803670.html webcite
• [13]Coppens I, Vielemeyer O: Insights into unique physiological features of neutral lipids in Apicomplexa: from storage to potential mediation in parasite metabolic activities. Int J Parasitol 2005, 35(6):597-615.
• [14]Vial HJ, Philippot JR, Wallach DF: A reevaluation of the status of cholesterol in erythrocytes infected by Plasmodium knowlesi and P.falciparum. Mol Biocheml Parasitol 1984, 13:53-65.
• [15]Raabe A, Wengelnik K, Billker O, Vial H: Multiple roles for Plasmodium berghei phosphoinositide-specific phospholipase C in regulating gametocyte activation and differentiation. Cell Microbiol 2011, 13:955-966.
• [16]Tawk L, Chicanne G, Dubremetz J, Richard V, Payrastre B, Vial H, Roy C, Wengelnik K: Phosphatidylinositol 3-phosphate, an essential lipid in Plasmodium, localizes to the food vacuole membrane and the apicoplast. Eukaryot Cell 2010, 9(10):1519-1530.
• [17]Vaid A, Ranjan R, Smythe WA, Hoppe HC, Sharma P: PfPI3K, a phosphatidylinositol-3 kinase from Plasmodium falciparum, is exported to the host erythrocyte and is involved in hemoglobin trafficking. Blood 2010, 115(12):2500-2507.
• [18]Bhattacharjee S, Stahelin R, Speicher K, Speicher D, Haldar K: Endoplasmic reticulum PI (3) P lipid binding targets malaria proteins to the host cell. Cell 2012, 148:201-212.
• [19]Vial H, Wein S, Farenc C, Kocken C, Nicolas O, Ancelin M, Bressolle F, Thomas A, Calas M: Prodrugs of bisthiazolium salts are orally potent antimalarials. Proc Natl Acad Sci USA 2004, 101(43):15458-15463.
• [20]Wein S, Maynadier M, Bordat Y, Perez J, Maheshwari S, Bette-Bobillo P, Tran Van Ba C, Penarete-Vargas D, Fraisse L, Cerdan R, et al.: Transport and pharmacodynamics of albitazolium, a candidate antimalarial drug. Br J Pharmacol 2012, 166:2263-2276.
• [21]Déchamps S, Shastri S, Wengelnik K, Vial HJ: Glycerophospholipid acquisition in Plasmodium – A puzzling assembly of biosynthetic pathways. Int J Parasitol 2010, 40(12):1347-1365.
• [22]Vial H, Penarete D, Wein S, Caldarelli S, Fraisse L, Peyrottes S: Lipids as drug targets for malaria therapy. Apicomplexan Parasites 2011, 137-162.
• [23]Déchamps S, Wengelnik K, Berry-Sterkers L, Cerdan R, Vial HJ, Gannoun-Zaki L: The Kennedy phospholipid biosynthesis pathways are refractory to genetic disruption in Plasmodium berghei and therefore appear essential in blood stages. Mol Biochem Parasitol 2010, 173(2):69-80.
• [24]Chance E, Seeholzer S, Kobayashi K, Williamson J: Mathematical analysis of isotope labeling in the citric acid cycle with applications to 13C NMR studies in perfused rat hearts. J Biol Chem 1983, 258(22):13785-13794.
• [25]de Mas I, Selivanov V, Marin S, Roca J, Oreṡiċ M, Agius L, Cascante M: Compartmentation of glycogen metabolism revealed from 13C isotopologue distributions. BMC Syst Biol 2011, 5:175. BioMed Central Full Text
• [26]Henri V: Théorie générale de laction de quelques diastases. CR Acad Sci Paris 1902, 135:916-919.
• [27]Michaelis L, Menten ML: Die kinetik der invertinwirkung. Biochem z 1913, 49(333–369):352.
• [28]Elabbadi N, Ancelin M, Vial H: Phospholipid metabolism of serine in Plasmodium-infected erythrocytes involves phosphatidylserine and direct serine decarboxylation. Biochem J 1997, 324(Pt 2):435.
• [29]Alberge B, Gannoun-Zaki L, Bascunana C, Tran van Ba C, Vial H, Cerdan R: Comparison of the cellular and biochemical properties of plasmodium falciparum choline and ethanolamine kinases. Biochem J 2010, 425:149-158.
• [30]Pessi G, Choi J, Reynolds J, Voelker D, Mamoun C: In vivo evidence for the specificity of Plasmodium falciparum phosphoethanolamine methyltransferase and its coupling to the Kennedy pathway. J Biol Chem 2005, 280(13):12461.
• [31]Pessi G, Kociubinski G, Mamoun CB: A pathway for phosphatidylcholine biosynthesis in Plasmodium falciparum involving phosphoethanolamine methylation. Proc Natl Acad Sci USA 2004, 101(16):6206-6211.
• [32]Baunaure F, Eldin P, Cathiard A, Vial H: Characterization of a non-mitochondrial type I phosphatidylserine decarboxylase in Plasmodium falciparum. Mol Microbiol 2004, 51:33-46.
• [33]Vial HJ, Thuet MJ, Philippot JR: Cholinephosphotransferase and ethanolaminephosphotransferase activities in Plasmodium knowlesi-infected erythrocytes: Their use as parasite-specific markers. Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism 1984, 795(2):372-383.
• [34]Yeo HJ, Widada JS, Mercereau-Puijalon O, Vial HJ: Molecular cloning of CTP: phosphocholine cytidylyltransferase from Plasmodium falciparum. Eur J Biochem 1995, 233:62-72.
• [35]Yeo HJ, Larvor MP, Ancelin ML, Vial HJ, Plasmodium falciparum CTP:: phosphocholine cytidylyltransferase expressed in Escherichia coli: purification, characterization and lipid regulation. Biochem J 1997, 324(Pt 3):903.
• [36]Aurrecoechea C, Brestelli J, Brunk BP, Dommer J, Fischer S, Gajria B, Gao X, Gingle A, Grant G, Harb OS, et al.: PlasmoDB: a functional genomic database for malaria parasites. Nucleic Acids Res 2009, 37(suppl 1):D539-D543.
• [37]Moll G, Vial H, Ancelin M, Op den KampJ, Roelofsen B, Van Deenen L: Phospholipid uptake by plasmodium knowlesi infected erythrocytes. FEBS Lett 1988, 232(2):341-346.
• [38]Biagini G, Pasini E, Hughes R, De Koning H, Vial H, O’Neill P, Ward S, Bray P: Characterization of the choline carrier of plasmodium falciparum: a route for the selective delivery of novel antimalarial drugs. Blood 2004, 104(10):3372-3377.
• [39]Kirk K, Wong H, Elford B, Newbold C, Ellory J: Enhanced choline and Rb+ transport in human erythrocytes infected with the malaria parasite Plasmodium falciparum. Biochem J 1991, 278(Pt 2):521.
• [40]Goldberg D, Slater A, Cerami A, Henderson G: Hemoglobin degradation in the malaria parasite Plasmodium falciparum: an ordered process in a unique organelle. Proc Natl Acad Sci 1990, 87(8):2931.
• [41]Choubey V, Guha M, Maity P, Kumar S, Raghunandan R, Maulik PR, Mitra K, Halder UC, Bandyopadhyay U: Molecular characterization and localization of Plasmodium falciparum choline kinase. Biochimica et Biophysica Acta (BBA)-General Subjects 2006, 1760(7):1027-1038.
• [42]Li C, Donizelli M, Rodriguez N, Dharuri H, Endler L, Chelliah V, Li L, He E, Henry A, Stefan MI, et al.: BioModels database: an enhanced, curated and annotated resource for published quantitative kinetic models. BMC Syst Biol 2010, 4:92. BioMed Central Full Text
• [43]Cornish-Bowden A, Cornish-Bowden A: Fundamentals of Enzyme Kinetics, Volume 3. London: Portland Press; 1995.
• [44]Klamt S, Stelling J, Ginkel M, Gilles E: FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps. Bioinformatics 2003, 19(2):261-269.
• [45]Gorban A, Radulescu O: Dynamic and static limitation in reaction networks, revisited. In Advances in Chemical Engineering - Mathematics in Chemical Kinetics and Engineering, Volume 34 of Advances in Chemical Engineering. Edited by Guy B, Marin DW, Yablonsky GS. Elsevier; 2008:103-173.
• [46]Reder C: Metabolic control theory: a structural approach. J Theor Biol 1988, 135(2):175-201.
• [47]Ray Jr WJ: Rate-limiting step: a quantitative definition. Application to steady-state enzymic systems. Biochemistry 1983, 22(20):4625-4637.
• [48]Fell D, et al.: Understanding the Control of Metabolism. Portland Press Ltd.; 1997.
• [49]Vial H, Ancelin M, Thuet M, Philippot J, et al.: Phospholipid metabolism in Plasmodium-infected erythrocytes: guidelines for further studies using radioactive precursor incorporation. Parasitology 1989, 98(03):351-357.
• [50]Ancelin M, Vial H: Regulation of phosphatidylcholine biosynthesis in Plasmodium-infected erythrocytes. Biochimica et Biophysica Acta (BBA)-Lipids and Lipid Metabolism 1989, 1001:82-89.
• [51]Ancelin M, Parant M, Thuet M, Philippot J, Vial H: Increased permeability to choline in simian erythrocytes after Plasmodium knowlesi infection. Biochem J 1991, 273(Pt 3):701.
• [52]Rontein D, Nishida I, Tashiro G, Yoshioka K, Wu W, Voelker D, Basset G, Hanson A: Plants synthesize ethanolamine by direct decarboxylation of serine using a pyridoxal phosphate enzyme. J Biol Chem 2001, 276(38):35523.
• [53]Déchamps S, Maynadier M, Wein S, Gannoun-Zaki L, Maréchal E, Vial HJ: Rodent and nonrodent malaria parasites differ in their phospholipid metabolic pathways. Sci Signal 2010, 51:81.
• [54]Vincent P, Maneta-Peyret L, Cassagne C, Moreau P: Phosphatidylserine delivery to endoplasmic reticulum-derived vesicles of plant cells depends on two biosynthetic pathways. FEBS Lett 2001, 498:32-36.
• [55]Lew V: A choline “vacuum cleaner”. Blood 2004, 104(10):3006-3007.
• [56]Vial H, Thuet M, Broussal J, Philippot J: Phospholipid biosynthesis by Plasmodium knowlesi-infected erythrocytes: the incorporation of phospholipid precursors and the identification of previously undetected metabolic pathways. J Parasitol 1982, 68:379-391.
• [57]Divo A, Geary T, Davis N, Jensen J: Nutritional requirements of Plasmodium falciparum in culture. I. Exogenously supplied dialyzable components necessary for continuous growth. J Eukaryot Microbiol 1985, 32:59-64.
• [58]Mitamura T, Hanada K, Ko-Mitamura E, Nishijima M, Horii T: Serum factors governing intraerythrocytic development and cell cycle progression of Plasmodium falciparum. Parasitol Int 2000, 49(3):219-229.
• [59]Gardner MJ, Shallom SJ, Carlton JM, Salzberg SL, Nene V, Shoaibi A, Ciecko A, Lynn J, Rizzo M, Weaver B, et al.: Sequence of plasmodium falciparum chromosomes 2, 10, 11 and 14. Nature 2002, 419(6906):531-534.
• [60]Witola WH, El Bissati K, Pessi G, Xie C, Roepe PD, Mamoun CB: Disruption of the Plasmodium falciparum PfPMT gene results in a complete loss of phosphatidylcholine biosynthesis via the serine-decarboxylase-phosphoethanolamine-methyltransferase pathway and severe growth and survival defects. J Biol Chem 2008, 283(41):27636-27643.
• [61]Kanehisa M, Goto S: KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 2000, 28:27-30.
• [62]Ben Mamoun C, Prigge ST, Vial H: Targeting the lipid metabolic pathways for the treatment of malaria. Drug Dev Res 2010, 71:44-55.
• [63]Wengelnik K, Vidal V, Ancelin M, Cathiard A, Morgat J, Kocken C, Calas M, Herrera S, Thomas A, Vial H: A class of potent antimalarials and their specific accumulation in infected erythrocytes. Science 2002, 295(5558):1311-1314.
• [64]Vial H, Penarete D, Wein S, Caldarelli S, Fraisse L, Peyrottes S: Lipids as drug targets for malaria therapy. In Apicomplexan Parasites: Molecular Approaches Toward Targeted Drug Development. Edited by Selzer P, Becker K. Weinheim: Wiley-VCH Verlag GmbH & Co. KGaA; 2011:23-23.