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Mamede L, Fall F, Schoumacher M, Ledoux A, Bugli C, De Tullio P, Quetin-Leclercq J, Govaerts B, Frédérich M. Comparison of extraction methods in vitro Plasmodium falciparum: A 1H NMR and LC-MS joined approach. Biochem Biophys Res Commun 2024; 703:149684. [PMID: 38367514 DOI: 10.1016/j.bbrc.2024.149684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 02/12/2024] [Indexed: 02/19/2024]
Abstract
Malaria is a parasitic disease that remains a global concern and the subject of many studies. Metabolomics has emerged as an approach to better comprehend complex pathogens and discover possible drug targets, thus giving new insights that can aid in the development of antimalarial therapies. However, there is no standardized method to extract metabolites from in vitro Plasmodium falciparum intraerythrocytic parasites, the stage that causes malaria. Additionally, most methods are developed with either LC-MS or NMR analysis in mind, and have rarely been evaluated with both tools. In this work, three extraction methods frequently found in the literature were reproduced and samples were analyzed through both LC-MS and 1H NMR, and evaluated in order to reveal which is the most repeatable and consistent through an array of different tools, including chemometrics, peak detection and annotation. The most reliable method in this study proved to be a double extraction with methanol and methanol/water (80:20, v/v). Metabolomic studies in the field should move towards standardization of methodologies and the use of both LC-MS and 1H NMR in order to make data more comparable between studies and facilitate the achievement of biologically interpretable information.
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Affiliation(s)
- Lúcia Mamede
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Brussels, Belgium
| | - Matthieu Schoumacher
- Laboratory of Pharmaceutical Chemistry, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Allison Ledoux
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Céline Bugli
- Statistical Methodology and Computing Service (SMCS/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Pascal De Tullio
- Laboratory of Pharmaceutical Chemistry, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Brussels, Belgium
| | - Bernadette Govaerts
- Statistical Methodology and Computing Service (SMCS/LIDAM), UCLouvain, Louvain-la-Neuve, Belgium
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research on Medicines (CIRM), University of Liège, Belgium.
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2
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Morgan AE, Salcedo-Sora JE, Mc Auley MT. A new mathematical model of folate homeostasis in E. coli highlights the potential importance of the folinic acid futile cycle in cell growth. Biosystems 2024; 235:105088. [PMID: 38000545 DOI: 10.1016/j.biosystems.2023.105088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 11/26/2023]
Abstract
Folate (vitamin B9) plays a central role in one-carbon metabolism in prokaryotes and eukaryotes. This pathway mediates the transfer of one-carbon units, playing a crucial role in nucleotide synthesis, methylation, and amino acid homeostasis. The folinic acid futile cycle adds a layer of intrigue to this pathway, due to its associations with metabolism, cell growth, and dormancy. It also introduces additional complexity to folate metabolism. A logical way to deal with such complexity is to examine it by using mathematical modelling. This work describes the construction and analysis of a model of folate metabolism, which includes the folinic acid futile cycle. This model was tested under three in silico growth conditions. Model simulations revealed: 1) the folate cycle behaved as a stable biochemical system in three growth states (slow, standard, and rapid); 2) the initial concentration of serine had the greatest impact on metabolite concentrations; 3) 5-formyltetrahydrofolate cyclo-ligase (5-FCL) activity had a significant impact on the levels of the 7 products that carry the one-carbon donated from folates, and the redox couple NADP/NADPH; this was particularly evident in the rapid growth state; 4) 5-FCL may be vital to the survival of the cells by maintaining low levels of homocysteine, as high levels can induce toxicity; and 5) the antifolate therapeutic trimethoprim had a greater impact on folate metabolism with higher nutrient availability. These results highlight the important role of 5-FCL in intracellular folate homeostasis and mass generation under different metabolic scenarios.
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Affiliation(s)
- Amy E Morgan
- School of Health & Sport Sciences, Hope Park, Liverpool Hope University, Liverpool, L16 9JD, UK.
| | - J Enrique Salcedo-Sora
- Liverpool Shared Research Facilities, GeneMill, University of Liverpool, Liverpool, L69 7ZB, UK
| | - Mark T Mc Auley
- School of Science, Engineering and Environment, University of Salford, Manchester, M5 4NT, UK
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Ghosh S, Kundu R, Chandana M, Das R, Anand A, Beura S, Bobde RC, Jain V, Prabhu SR, Behera PK, Mohanty AK, Chakrapani M, Satyamoorthy K, Suryawanshi AR, Dixit A, Padmanaban G, Nagaraj VA. Distinct evolution of type I glutamine synthetase in Plasmodium and its species-specific requirement. Nat Commun 2023; 14:4216. [PMID: 37452051 PMCID: PMC10349072 DOI: 10.1038/s41467-023-39670-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/22/2023] [Indexed: 07/18/2023] Open
Abstract
Malaria parasite lacks canonical pathways for amino acid biosynthesis and depends primarily on hemoglobin degradation and extracellular resources for amino acids. Interestingly, a putative gene for glutamine synthetase (GS) is retained despite glutamine being an abundant amino acid in human and mosquito hosts. Here we show Plasmodium GS has evolved as a unique type I enzyme with distinct structural and regulatory properties to adapt to the asexual niche. Methionine sulfoximine (MSO) and phosphinothricin (PPT) inhibit parasite GS activity. GS is localized to the parasite cytosol and abundantly expressed in all the life cycle stages. Parasite GS displays species-specific requirement in Plasmodium falciparum (Pf) having asparagine-rich proteome. Targeting PfGS affects asparagine levels and inhibits protein synthesis through eIF2α phosphorylation leading to parasite death. Exposure of artemisinin-resistant Pf parasites to MSO and PPT inhibits the emergence of viable parasites upon artemisinin treatment.
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Affiliation(s)
- Sourav Ghosh
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Rajib Kundu
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Manjunatha Chandana
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- School of Biotechnology, Kalinga Institute of Industrial Technology, Bhubaneswar, 751024, Odisha, India
| | - Rahul Das
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Aditya Anand
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Subhashree Beura
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Ruchir Chandrakant Bobde
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Regional Centre for Biotechnology, Faridabad, 121001, Haryana, India
| | - Vishal Jain
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Sowmya Ramakant Prabhu
- Department of Biotechnology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Akshaya Kumar Mohanty
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
- Ispat General Hospital, Sector 19, Rourkela, 769005, Odisha, India
| | - Mahabala Chakrapani
- Department of Medicine, Kasturba Medical College, Mangalore, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | - Kapaettu Satyamoorthy
- Department of Cell and Molecular Biology, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal, 576104, Karnataka, India
| | | | - Anshuman Dixit
- Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, Odisha, India
| | - Govindarajan Padmanaban
- Department of Biochemistry, Indian Institute of Science, Bangalore, 560012, Karnataka, India
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Stockman BJ, Ventura CA, Deykina VS, Khayan Lontscharitsch N, Saljanin E, Gil A, Canestrari M, Mahmood M. Direct Measurement of Nucleoside Ribohydrolase Enzyme Activities in Trichomonas vaginalis Cells Using 19F and 13C-Edited 1H NMR Spectroscopy. Anal Chem 2023; 95:5300-5306. [PMID: 36917470 PMCID: PMC10825731 DOI: 10.1021/acs.analchem.2c05330] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
Trichomoniasis is the most common nonviral sexually transmitted infection, affecting an estimated 275 million people worldwide. The causative agent is the parasitic protozoan Trichomonas vaginalis. Although the disease itself is typically mild, individuals with trichomonal infections have a higher susceptibility to more serious conditions. The emergence of parasite strains resistant to current therapies necessitates the need for novel treatment strategies. Since T. vaginalis is an obligate parasite that requires nucleoside salvage pathways, essential nucleoside ribohydrolase enzymes are promising new drug targets. Fragment screening and X-ray crystallography have enabled structure-guided design of inhibitors for two of these enyzmes. Linkage of enzymatic and antiprotozoal activity would be a transformative step toward designing novel, mechanism-based therapeutic agents. While a correlation with inhibition of purified enzyme would be mechanistically suggestive, a correlation with inhibition of in-cell enzyme activity would definitively establish this linkage. To demonstrate this linkage, we have translated our NMR-based activity assays that measure the activity of purified enzymes for use in T. vaginalis cells. The 19F NMR-based activity assay for the pyrimidine-specific enzyme translated directly to in-cell assays. However, the 1H NMR-based activity assay for the purine-specific enzyme required a switch from adenosine to guanosine substrate and the use of 13C-editing to resolve the substrate 1H signals from cell and growth media background signals. The in-cell NMR assays are robust and have been demonstrated to provide inhibition data on test compounds. The results described here represent the first direct measurement of enzyme activity in protozoan parasite cells.
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Affiliation(s)
- Brian J Stockman
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | - Carlos A Ventura
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | - Valerie S Deykina
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | | | - Edina Saljanin
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | - Ari Gil
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | - Madison Canestrari
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
| | - Maham Mahmood
- Department of Chemistry, Adelphi University, 1 South Avenue, Garden City, New York 11530, United States
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5
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van der Watt ME, Reader J, Birkholtz LM. Adapt or Die: Targeting Unique Transmission-Stage Biology for Malaria Elimination. Front Cell Infect Microbiol 2022; 12:901971. [PMID: 35755845 PMCID: PMC9218253 DOI: 10.3389/fcimb.2022.901971] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Accepted: 05/06/2022] [Indexed: 12/25/2022] Open
Abstract
Plasmodium parasites have a complex life cycle that includes development in the human host as well as the Anopheles vector. Successful transmission of the parasite between its host and vector therefore requires the parasite to balance its investments in asexual replication and sexual reproduction, varying the frequency of sexual commitment to persist within the human host and generate future opportunities for transmission. The transmission window is extended further by the ability of stage V gametocytes to circulate in peripheral blood for weeks, whereas immature stage I to IV gametocytes sequester in the bone marrow and spleen until final maturation. Due to the low gametocyte numbers in blood circulation and with the ease of targeting such life cycle bottlenecks, transmission represents an efficient target for therapeutic intervention. The biological process of Plasmodium transmission is a multistage, multifaceted process and the past decade has seen a much deeper understanding of the molecular mechanisms and regulators involved. Clearly, specific and divergent processes are used during transmission compared to asexual proliferation, which both poses challenges but also opportunities for discovery of transmission-blocking antimalarials. This review therefore presents an update of our molecular understanding of gametocyte and gamete biology as well as the status of transmission-blocking activities of current antimalarials and lead development compounds. By defining the biological components associated with transmission, considerations for the development of new transmission-blocking drugs to target such untapped but unique biology is suggested as an important, main driver for transmission-blocking drug discovery.
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Affiliation(s)
- Mariëtte E van der Watt
- Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa
| | - Janette Reader
- Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Lyn-Marié Birkholtz
- Institute for Sustainable Malaria Control, School of Health Systems and Public Health, University of Pretoria, Pretoria, South Africa.,Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
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6
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Lopez JM, Leyva VE, Bustos JA, Perez E, Sanchez SS, Saavedra H, Gonzales I, Maruenda H, Garcia HH. Urine 1H-NMR Metabolomics to Discriminate Neurocysticercosis Patients from Healthy Controls: An Exploratory Study. Am J Trop Med Hyg 2022; 107:tpmd220045. [PMID: 35605633 PMCID: PMC9294696 DOI: 10.4269/ajtmh.22-0045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 02/20/2022] [Indexed: 11/07/2022] Open
Abstract
The diagnosis of neurocysticercosis (NCC) is principally based on neuroimaging (magnetic resonance imaging or computed tomography), instrumentation that is scarcely available in the rural regions where Taenia solium transmission, primarily occurs due to poor sanitation conditions. Immunological assays for antigen or antibody detection complement the neuroimaging approach. However, no field-applicable assays to diagnose viable NCC or to guide the referral of cases for neuroimaging or for appropriate management are available. We performed an exploratory study on urine and serum samples using 1H-nuclear magnetic resonance (NMR)-based metabolomics to discriminate NCC patients (n = 14) from healthy control subjects (n = 22). Metabolic profiles demonstrated a discrimination between the urines of NCC patients and noninfected control subjects with a moderate predictive accuracy (R2 = 0.999, Q2 = 0.434). NMR metabolomics analysis has been proven useful in depicting biomarkers linked to other infectious diseases, various types of cancer, and other disorders. Our results, albeit preliminary, open a door to the development of better methods for detecting NCC through the identification of biomarkers participating in disturbed metabolic pathways.
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Affiliation(s)
- Juan M. Lopez
- Departamento de Ciencias—Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Vanessa E. Leyva
- Departamento de Ciencias—Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Javier A. Bustos
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Perú
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Erika Perez
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Perú
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Sofía S. Sanchez
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Herbert Saavedra
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Isidro Gonzales
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
| | - Helena Maruenda
- Departamento de Ciencias—Química, CERMN, Pontificia Universidad Católica del Perú, Lima, Perú
| | - Hector H. Garcia
- Cysticercosis Unit, Instituto Nacional de Ciencias Neurologicas, Lima, Perú
- Center for Global Health, Universidad Peruana Cayetano Heredia, Lima, Perú
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7
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Grube CD, Gill CP, Roy H. Development of a continuous assay for high throughput screening to identify inhibitors of the purine salvage pathway in Plasmodium falciparum. SLAS DISCOVERY : ADVANCING LIFE SCIENCES R & D 2022; 27:114-120. [PMID: 35058189 DOI: 10.1016/j.slasd.2021.12.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Malaria, an infectious disease caused by protozoan parasites from the genus Plasmodium, represents a serious global health threat. The continued emergence of drug resistant strains has severely decreased current antimalarial drug efficacy and led to a perpetual race for drug discovery. Most protozoan parasites, including Plasmodium spp., are unable to synthesize purines de novo and instead rely on an essential purine salvage pathway for acquisition of purines from the infected host. Because purines are essential for Plasmodium growth and survival, the enzymes of the purine salvage pathway represent promising targets for drug discovery. Target-based high-throughput screening (HTS) assays traditionally focus on a single target, which severely limits the screening power of this type of approach. To circumvent this limitation, we have reconstituted the purine salvage pathway from Plasmodium falciparum in an assay combining four drug targets. This assay was developed for HTS and optimized to detect partial inhibition of any of the four enzymes in the pathway. Inhibitors of several enzymes in the pathway were identified in a pilot screen, with several compounds exhibiting effective inhibition when provided in micromolar amounts.
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Affiliation(s)
- Christopher D Grube
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Cameron P Gill
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA
| | - Hervé Roy
- Burnett School of Biomedical Sciences, College of Medicine, University of Central Florida, Orlando, Florida, USA.
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8
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Alapid AAI, Abd. Majid R, Ibraheem ZO, Mediani A, Ismail IS, Unyah NZ, Alhassan Abdullahi S, Nordin N, Nasiru Wana M, Basir R. Investigation of Andrographolide Effect on Non-Infected Red Blood Cells Using the 1H-NMR-Based Metabolomics Approach. Metabolites 2021; 11:metabo11080486. [PMID: 34436427 PMCID: PMC8400355 DOI: 10.3390/metabo11080486] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Revised: 07/08/2021] [Accepted: 07/15/2021] [Indexed: 01/02/2023] Open
Abstract
Andrographolide (AG) has been shown to have several medicinal and pharmaceutical effects, such as antimicrobial, anti-inflammatory, antioxidant, anti-diabetic, and anti-malarial activities. Moreover, studies to assess the pharmacological effect of AG on the metabolic changes of uninfected red blood cells (uRBCs) have not yet been investigated. This study aims to evaluate the pharmacological effects of AG compared to chloroquine (CQ) on the metabolic variations of uRBCs in vitro using a proton nuclear magnetic resonance (1H-NMR)-based metabolomics approach coupled with multivariate data analysis (MVDA). Forty-one metabolites were successfully identified by 1H-NMR. The results of the unsupervised data analysis principal component analysis (PCA) showed ideal differentiation between AG and CQ. PC1 and PC2 accounted for 71.4% and 17.7% of the explained variation, respectively, with a total variance of 89.10%. Based on S-plot and VIP values, a total of 28 and 32 metabolites were identified as biomarkers in uRBCs-AG and uRBCs-CQ, respectively. In uRBCs treated with AG, ten metabolic pathways were determined to be disturbed, including riboflavin metabolism, d-glutamate and d-glutamine metabolism, phenylalanine metabolism, glutathione metabolism, proline and arginine metabolism, arginine biosynthesis, citrate cycle, glycolysis/gluconeogenesis, and pyruvate metabolism as well as alanine, aspartate, and glutamate metabolism. In contrast, in CQ-treated uRBCs, nine affected metabolic pathways were determined, which involved the same metabolic pathways for uRBCs-AG, except for glutathione metabolism. These findings suggest an evident relationship between AG and CQ associated with metabolic changes in intact RBCs after being exposed to the treatment. The metabolomics results could allow useful comprehensive insights into the underlying mechanism of the action of AG and CQ on red blood cells. Consequently, the 1H-NMR-based metabolomics approach was successfully utilized to identify the pharmacological effects of AG and CQ on the metabolic variations of uRBCs.
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Affiliation(s)
- Ashraf Ahmad Issa Alapid
- Medical Parasitology Unit, Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.I.A.); (N.Z.U.)
- Department of Zoology, Faculty of Science-Alasaba, University of Gharyan, Gharyan 010101, Libya
| | - Roslaini Abd. Majid
- Faculty of Medicine and Defence Health, National Defence University of Malaysia, Kuala Lumpur 57000, Malaysia;
| | - Zaid O. Ibraheem
- Department of Pharmacy, Al Rafidain University College, Al Mustansyria, Baghdad 10052, Iraq;
| | - Ahmed Mediani
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia;
| | - Intan Safinar Ismail
- Natural Medicine and Products Research Laboratory, Institute of Bioscience, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Ngah Zasmy Unyah
- Medical Parasitology Unit, Department of Medical Microbiology and Parasitology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia; (A.A.I.A.); (N.Z.U.)
| | - Sharif Alhassan Abdullahi
- Department of Medical Microbiology and Parasitology, Faculty of Clinical Sciences, Bayero University Kano, Kano 700241, Nigeria;
| | - Norshariza Nordin
- Department of Biomedical Sciences, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia;
| | - Mohammed Nasiru Wana
- Department of Biological Sciences, Faculty of Science, Abubakar Tafawa Balewa University Bauchi, Bauchi 740272, Nigeria;
| | - Rusliza Basir
- Pharmacology Unit, Department of Human Anatomy, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia, Serdang 43400, Selangor, Malaysia
- Correspondence: ; Tel.: +60-124-747-459
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9
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Proteome of Stored RBC Membrane and Vesicles from Heterozygous Beta Thalassemia Donors. Int J Mol Sci 2021; 22:ijms22073369. [PMID: 33806028 PMCID: PMC8037027 DOI: 10.3390/ijms22073369] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/19/2021] [Accepted: 03/22/2021] [Indexed: 01/19/2023] Open
Abstract
Genetic characteristics of blood donors may impact the storability of blood products. Despite higher basal stress, red blood cells (RBCs) from eligible donors that are heterozygous for beta-thalassemia traits (βThal+) possess a differential nitrogen-related metabolism, and cope better with storage stress compared to the control. Nevertheless, not much is known about how storage impacts the proteome of membrane and extracellular vesicles (EVs) in βThal+. For this purpose, RBC units from twelve βThal+ donors were studied through proteomics, immunoblotting, electron microscopy, and functional ELISA assays, versus units from sex- and aged-matched controls. βThal+ RBCs exhibited less irreversible shape modifications. Their membrane proteome was characterized by different levels of structural, lipid raft, transport, chaperoning, redox, and enzyme components. The most prominent findings include the upregulation of myosin proteoforms, arginase-1, heat shock proteins, and protein kinases, but the downregulation of nitrogen-related transporters. The unique membrane proteome was also mirrored, in part, to that of βThal+ EVs. Network analysis revealed interesting connections of membrane vesiculation with storage and stress hemolysis, along with proteome control modulators of the RBC membrane. Our findings, which are in line with the mild but consistent oxidative stress these cells experience in vivo, provide insight into the physiology and aging of stored βThal+ RBCs.
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10
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Chiappino-Pepe A, Hatzimanikatis V. PhenoMapping: a protocol to map cellular phenotypes to metabolic bottlenecks, identify conditional essentiality, and curate metabolic models. STAR Protoc 2021; 2:100280. [PMID: 33532729 PMCID: PMC7829271 DOI: 10.1016/j.xpro.2020.100280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Targeted identification of cellular processes responsible for a phenotype is of major importance in guiding efforts in bioengineering and medicine. Genome-scale metabolic models (GEMs) are widely used to integrate various types of omics data and study the cellular physiology under different conditions. Here, we present PhenoMapping, a protocol that uses GEMs, omics, and phenotypic data to map cellular processes and observed phenotypes. PhenoMapping also classifies genes as conditionally and unconditionally essential and guides a comprehensive curation of GEMs. For complete details on the use and execution of this protocol, please refer to Stanway et al. (2019) and Krishnan et al. (2020).
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Affiliation(s)
- Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
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11
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Krishnan A, Soldati-Favre D. Amino Acid Metabolism in Apicomplexan Parasites. Metabolites 2021; 11:61. [PMID: 33498308 PMCID: PMC7909243 DOI: 10.3390/metabo11020061] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 12/22/2022] Open
Abstract
Obligate intracellular pathogens have coevolved with their host, leading to clever strategies to access nutrients, to combat the host's immune response, and to establish a safe niche for intracellular replication. The host, on the other hand, has also developed ways to restrict the replication of invaders by limiting access to nutrients required for pathogen survival. In this review, we describe the recent advancements in both computational methods and high-throughput -omics techniques that have been used to study and interrogate metabolic functions in the context of intracellular parasitism. Specifically, we cover the current knowledge on the presence of amino acid biosynthesis and uptake within the Apicomplexa phylum, focusing on human-infecting pathogens: Toxoplasma gondii and Plasmodium falciparum. Given the complex multi-host lifecycle of these pathogens, we hypothesize that amino acids are made, rather than acquired, depending on the host niche. We summarize the stage specificities of enzymes revealed through transcriptomics data, the relevance of amino acids for parasite pathogenesis in vivo, and the role of their transporters. Targeting one or more of these pathways may lead to a deeper understanding of the specific contributions of biosynthesis versus acquisition of amino acids and to design better intervention strategies against the apicomplexan parasites.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland;
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12
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Swift RP, Rajaram K, Keutcha C, Liu HB, Kwan B, Dziedzic A, Jedlicka AE, Prigge ST. The NTP generating activity of pyruvate kinase II is critical for apicoplast maintenance in Plasmodium falciparum. eLife 2020; 9:e50807. [PMID: 32815516 PMCID: PMC7556864 DOI: 10.7554/elife.50807] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 08/20/2020] [Indexed: 12/20/2022] Open
Abstract
The apicoplast of Plasmodium falciparum parasites is believed to rely on the import of three-carbon phosphate compounds for use in organelle anabolic pathways, in addition to the generation of energy and reducing power within the organelle. We generated a series of genetic deletions in an apicoplast metabolic bypass line to determine which genes involved in apicoplast carbon metabolism are required for blood-stage parasite survival and organelle maintenance. We found that pyruvate kinase II (PyrKII) is essential for organelle maintenance, but that production of pyruvate by PyrKII is not responsible for this phenomenon. Enzymatic characterization of PyrKII revealed activity against all NDPs and dNDPs tested, suggesting that it may be capable of generating a broad range of nucleotide triphosphates. Conditional mislocalization of PyrKII resulted in decreased transcript levels within the apicoplast that preceded organelle disruption, suggesting that PyrKII is required for organelle maintenance due to its role in nucleotide triphosphate generation.
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Affiliation(s)
- Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Krithika Rajaram
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Cyrianne Keutcha
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Hans B Liu
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Bobby Kwan
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Amanda Dziedzic
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Anne E Jedlicka
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins Bloomberg School of Public HealthBaltimoreUnited States
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Lozano-Amado D, Ávila-López PA, Hernández-Montes G, Briseño-Díaz P, Vargas M, Lopez-Rubio JJ, Carrero JC, Hernández-Rivas R. A class I histone deacetylase is implicated in the encystation of Entamoeba invadens. Int J Parasitol 2020; 50:1011-1022. [PMID: 32822677 DOI: 10.1016/j.ijpara.2020.05.014] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 05/26/2020] [Accepted: 05/28/2020] [Indexed: 12/29/2022]
Abstract
Epigenetic mechanisms such as histone acetylation and deacetylation participate in regulation of the genes involved in encystation of Entamoeba invadens. However, the histones and target residues involved, and whether the acetylation and deacetylation of the histones leads to the regulation of gene expression associated with the encystation of this parasite, remain unknown. In this study, we found that E. invadens histone H4 is acetylated in both stages of the parasite and is more highly acetylated during the trophozoite stage than in the cyst. Histone hyperacetylation induced by Trichostatin A negatively affects the encystation of E. invadens, and this inhibition is associated with the downregulation of the expression of genes implicated in the synthesis of chitin, polyamines, gamma-aminobutyric acid pathways and cyst wall proteins, all of which are important in the formation of cysts. Finally, in silico analysis and activity assays suggest that a class I histone deacetylase (EiHDAC3) could be involved in control of the expression of a subset of genes that are important in several pathways during encystation. Therefore, the identification of enzymes that acetylate and/or deacetylate histones that control encystation in E. invadens could be a promising therapeutic target for preventing transmission of other amoebic parasites such as E. histolytica, the causative agent of amoebiasis in humans.
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Affiliation(s)
- Daniela Lozano-Amado
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Pedro Antonio Ávila-López
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Georgina Hernández-Montes
- Coordinación de la Investigación Científica, Red de Apoyo a la Investigación, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Paola Briseño-Díaz
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Miguel Vargas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico
| | - Jose-Juan Lopez-Rubio
- LPHI - Laboratory of Pathogen Host Interactions - UMR5235, CNRS, INSERM, Université de Montpellier, Montpellier, France
| | - Julio César Carrero
- Departamento de Inmunología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, Ciudad Universitaria, Ciudad de México, Mexico
| | - Rosaura Hernández-Rivas
- Departamento de Biomedicina Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Ciudad de México, Mexico.
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Stanway RR, Bushell E, Chiappino-Pepe A, Roques M, Sanderson T, Franke-Fayard B, Caldelari R, Golomingi M, Nyonda M, Pandey V, Schwach F, Chevalley S, Ramesar J, Metcalf T, Herd C, Burda PC, Rayner JC, Soldati-Favre D, Janse CJ, Hatzimanikatis V, Billker O, Heussler VT. Genome-Scale Identification of Essential Metabolic Processes for Targeting the Plasmodium Liver Stage. Cell 2020; 179:1112-1128.e26. [PMID: 31730853 PMCID: PMC6904910 DOI: 10.1016/j.cell.2019.10.030] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 07/23/2019] [Accepted: 10/23/2019] [Indexed: 12/11/2022]
Abstract
Plasmodium gene functions in mosquito and liver stages remain poorly characterized due to limitations in the throughput of phenotyping at these stages. To fill this gap, we followed more than 1,300 barcoded P. berghei mutants through the life cycle. We discover 461 genes required for efficient parasite transmission to mosquitoes through the liver stage and back into the bloodstream of mice. We analyze the screen in the context of genomic, transcriptomic, and metabolomic data by building a thermodynamic model of P. berghei liver-stage metabolism, which shows a major reprogramming of parasite metabolism to achieve rapid growth in the liver. We identify seven metabolic subsystems that become essential at the liver stages compared with asexual blood stages: type II fatty acid synthesis and elongation (FAE), tricarboxylic acid, amino sugar, heme, lipoate, and shikimate metabolism. Selected predictions from the model are individually validated in single mutants to provide future targets for drug development. 1,342 barcoded P. berghei knockout (KO) mutants analyzed for stage-specific phenotypes Life-stage-specific metabolic models reveal reprogramming of cellular function High agreement between blood/liver stage metabolic models and genetic screening data Essential metabolic pathways for parasite development and mechanistic origin revealed
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Affiliation(s)
- Rebecca R Stanway
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - Ellen Bushell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Magali Roques
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | - Theo Sanderson
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Blandine Franke-Fayard
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Reto Caldelari
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland
| | | | - Mary Nyonda
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Vikash Pandey
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden
| | - Frank Schwach
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Séverine Chevalley
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Jai Ramesar
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Tom Metcalf
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Colin Herd
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK
| | - Paul-Christian Burda
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland; Bernhard Nocht Institute for Tropical Medicine, Hamburg 20359, Germany
| | - Julian C Rayner
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Cambridge Institute for Medical Research, University of Cambridge, Hills Road, Cambridge CB2, 0XY, UK
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Chris J Janse
- Leiden Malaria Research Group, Parasitology, Center of Infectious Diseases, Leiden University Medical Center (LUMC), Leiden 2333ZA, the Netherlands
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne 1015, Switzerland
| | - Oliver Billker
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SA, UK; Molecular Infection Medicine Sweden (MIMS), Department of Molecular Biology, Umeå University, Umeå 901 87, Sweden.
| | - Volker T Heussler
- Institute of Cell Biology, University of Bern, Bern 3012, Switzerland.
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15
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Tewari SG, Swift RP, Reifman J, Prigge ST, Wallqvist A. Metabolic alterations in the erythrocyte during blood-stage development of the malaria parasite. Malar J 2020; 19:94. [PMID: 32103749 PMCID: PMC7045481 DOI: 10.1186/s12936-020-03174-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 02/20/2020] [Indexed: 02/08/2023] Open
Abstract
Background Human blood cells (erythrocytes) serve as hosts for the malaria parasite Plasmodium falciparum during its 48-h intraerythrocytic developmental cycle (IDC). Established in vitro protocols allow for the study of host–parasite interactions during this phase and, in particular, high-resolution metabolomics can provide a window into host–parasite interactions that support parasite development. Methods Uninfected and parasite-infected erythrocyte cultures were maintained at 2% haematocrit for the duration of the IDC, while parasitaemia was maintained at 7% in the infected cultures. The parasite-infected cultures were synchronized to obtain stage-dependent information of parasite development during the IDC. Samples were collected in quadruplicate at six time points from the uninfected and parasite-infected cultures and global metabolomics was used to analyse cell fractions of these cultures. Results In uninfected and parasite-infected cultures during the IDC, 501 intracellular metabolites, including 223 lipid metabolites, were successfully quantified. Of these, 19 distinct metabolites were present only in the parasite-infected culture, 10 of which increased to twofold in abundance during the IDC. This work quantified approximately five times the metabolites measured in previous studies of similar research scope, which allowed for more detailed analyses. Enrichment in lipid metabolism pathways exhibited a time-dependent association with different classes of lipids during the IDC. Specifically, enrichment occurred in sphingolipids at the earlier stages, and subsequently in lysophospholipid and phospholipid metabolites at the intermediate and end stages of the IDC, respectively. In addition, there was an accumulation of 18-, 20-, and 22-carbon polyunsaturated fatty acids, which produce eicosanoids and promote gametocytogenesis in infected erythrocyte cultures. Conclusions The current study revealed a number of heretofore unidentified metabolic components of the host–parasite system, which the parasite may exploit in a time-dependent manner to grow over the course of its development in the blood stage. Notably, the analyses identified components, such as precursors of immunomodulatory molecules, stage-dependent lipid dynamics, and metabolites, unique to parasite-infected cultures. These conclusions are reinforced by the metabolic alterations that were characterized during the IDC, which were in close agreement with those known from previous studies of blood-stage infection.
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Affiliation(s)
- Shivendra G Tewari
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA. .,The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc. (HJF), Bethesda, MD, USA.
| | - Russell P Swift
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Jaques Reifman
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA
| | - Anders Wallqvist
- Department of Defense Biotechnology High Performance Computing Software Applications Institute, Telemedicine and Advanced Technology Research Center, U.S. Army Medical Research and Development Command, Ft. Detrick, MD, USA.
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Krishnan A, Kloehn J, Lunghi M, Chiappino-Pepe A, Waldman BS, Nicolas D, Varesio E, Hehl A, Lourido S, Hatzimanikatis V, Soldati-Favre D. Functional and Computational Genomics Reveal Unprecedented Flexibility in Stage-Specific Toxoplasma Metabolism. Cell Host Microbe 2020; 27:290-306.e11. [PMID: 31991093 DOI: 10.1016/j.chom.2020.01.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Revised: 11/02/2019] [Accepted: 01/03/2020] [Indexed: 12/31/2022]
Abstract
To survive and proliferate in diverse host environments with varying nutrient availability, the obligate intracellular parasite Toxoplasma gondii reprograms its metabolism. We have generated and curated a genome-scale metabolic model (iTgo) for the fast-replicating tachyzoite stage, harmonized with experimentally observed phenotypes. To validate the importance of four metabolic pathways predicted by the model, we have performed in-depth in vitro and in vivo phenotyping of mutant parasites including targeted metabolomics and CRISPR-Cas9 fitness screening of all known metabolic genes. This led to unexpected insights into the remarkable flexibility of the parasite, addressing the dependency on biosynthesis or salvage of fatty acids (FAs), purine nucleotides (AMP and GMP), a vitamin (pyridoxal-5P), and a cofactor (heme) in both the acute and latent stages of infection. Taken together, our experimentally validated metabolic network leads to a deeper understanding of the parasite's biology, opening avenues for the development of therapeutic intervention against apicomplexans.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Joachim Kloehn
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Matteo Lunghi
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | | | - Damien Nicolas
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland
| | - Emmanuel Varesio
- School of Pharmaceutical Sciences Geneva-Lausanne (EPGL), Geneva 1211, Switzerland; Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, Geneva 1211, Switzerland
| | - Adrian Hehl
- Institute of Parasitology, University of Zürich, Zürich 8057, Switzerland
| | - Sebastian Lourido
- Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA; Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, Ecole Polytechnique Fédérale de Lausanne (EPFL), Lausanne 1015, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology & Molecular Medicine, Faculty of Medicine, University of Geneva, Geneva 1211, Switzerland.
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Comparative serum metabolomics between SCID mice and BALB/c mice with or without Schistosoma japonicum infection: Clues to the abnormal growth and development of schistosome in SCID mice. Acta Trop 2019; 200:105186. [PMID: 31542371 DOI: 10.1016/j.actatropica.2019.105186] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Revised: 09/12/2019] [Accepted: 09/18/2019] [Indexed: 12/16/2022]
Abstract
The small blood flukes of genus Schistosoma, which cause one of the most prevalent and serious parasitic zoonosis schistosomiasis, are dependent on immune-related factors of their mammalian host to facilitate their growth and development, and the formation of granulomatous pathology caused by eggs deposited in host's liver and intestinal wall. Schistosome development is hampered in the mice lacking just T cells, and is even more heavily retarded in the severe combined immunodeficient (SCID) mice lacking both T and B lymphocytes. Nevertheless, it's still not clear about the underlying regulatory molecular mechanisms of schistosome growth and development by host's immune system. This study, therefore, detected and compared the serum metabolic profiles between the immunodeficient mice and immunocompetent mice (SCID mice vs. BALB/c mice) before and after S. japonicum infection (on the thirty-fifth day post infection using liquid chromatography-mass spectrometry (LC-MS). Totally, 705 ion features in electrospray ionization in positive-ion mode (ESI+) and 242 ion features in ESI- mode were identified, respectively. First, distinct serum metabolic profiles were identified between SCID mice and BALB/c mice without S. japonicum worms infection. Second, uniquely perturbed serum metabolites and their enriched pathways were also obtained between SCID mice and BALB/c mice after S. japonicum infection, which included differential metabolites due to both species differences and differential responses to S. japonicum infection. The metabolic pathways analysis revealed that arachidonic acid metabolism, biosynthesis of unsaturated fatty acids, linoleic acid metabolism, glycosylphosphatidylinositol (GPI)-anchor biosynthesis, alpha-linolenic acid metabolism, glycerophospholipid metabolism, sphingolipid metabolism and purine metabolism were enriched based on the differential serum metabolites between SCID mice and BALB/c mice after S. japonicum infection, which was addressed to be related to the retarded growth and development of S. japonicum in SCID mice. These findings provide new clues to the underlying molecular events of host's systemic metabolic changes on the growth and development of S. japonicum worms, and also provide quite promising candidates for exploitation of drugs or vaccines against schistosome and schistosomiasis.
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Sexton AE, Doerig C, Creek DJ, Carvalho TG. Post-Genomic Approaches to Understanding Malaria Parasite Biology: Linking Genes to Biological Functions. ACS Infect Dis 2019; 5:1269-1278. [PMID: 31243988 DOI: 10.1021/acsinfecdis.9b00093] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Plasmodium species are evolutionarily distant from model eukaryotes, and as a consequence they exhibit many non-canonical cellular processes. In the post-genomic era, functional "omics" disciplines (transcriptomics, proteomics, and metabolomics) have accelerated our understanding of unique aspects of the biology of malaria parasites. Functional "omics" tools, in combination with genetic manipulations, have offered new opportunities to investigate the function of previously uncharacterized genes. Knowledge of basic parasite biology is fundamental to understanding drug modes of action, mechanisms of drug resistance, and relevance of vaccine candidates. This Perspective highlights recent "omics"-based discoveries in basic biology and gene function of the most virulent human malaria parasite, Plasmodium falciparum.
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Affiliation(s)
- Anna E. Sexton
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Christian Doerig
- Centre for Chronic, Inflammatory and Infectious Diseases, Biomedical Sciences Cluster, School of Health and Biomedical Sciences, RMIT University, 264 Plenty Road, Bundoora, VIC 3083, Australia
| | - Darren J. Creek
- Drug Delivery Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, 381 Royal Parade, Parkville, VIC 3052, Australia
| | - Teresa G. Carvalho
- Molecular Parasitology Laboratory, Department of Physiology, Anatomy and Microbiology, La Trobe University, Kingsbury Drive, Bundoora, VIC 3086, Australia
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Aroonsri A, Posayapisit N, Kongsee J, Siripan O, Vitsupakorn D, Utaida S, Uthaipibull C, Kamchonwongpaisan S, Shaw PJ. Validation of Plasmodium falciparum deoxyhypusine synthase as an antimalarial target. PeerJ 2019; 7:e6713. [PMID: 31024761 PMCID: PMC6475138 DOI: 10.7717/peerj.6713] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 03/05/2019] [Indexed: 11/20/2022] Open
Abstract
Background Hypusination is an essential post-translational modification in eukaryotes. The two enzymes required for this modification, namely deoxyhypusine synthase (DHS) and deoxyhypusine hydrolase are also conserved. Plasmodium falciparum human malaria parasites possess genes for both hypusination enzymes, which are hypothesized to be targets of antimalarial drugs. Methods Transgenic P. falciparum parasites with modification of the PF3D7_1412600 gene encoding PfDHS enzyme were created by insertion of the glmS riboswitch or the M9 inactive variant. The PfDHS protein was studied in transgenic parasites by confocal microscopy and Western immunoblotting. The biochemical function of PfDHS enzyme in parasites was assessed by hypusination and nascent protein synthesis assays. Gene essentiality was assessed by competitive growth assays and chemogenomic profiling. Results Clonal transgenic parasites with integration of glmS riboswitch downstream of the PfDHS gene were established. PfDHS protein was present in the cytoplasm of transgenic parasites in asexual stages. The PfDHS protein could be attenuated fivefold in transgenic parasites with an active riboswitch, whereas PfDHS protein expression was unaffected in control transgenic parasites with insertion of the riboswitch-inactive sequence. Attenuation of PfDHS expression for 72 h led to a significant reduction of hypusinated protein; however, global protein synthesis was unaffected. Parasites with attenuated PfDHS expression showed a significant growth defect, although their decline was not as rapid as parasites with attenuated dihydrofolate reductase-thymidylate synthase (PfDHFR-TS) expression. PfDHS-attenuated parasites showed increased sensitivity to N 1-guanyl-1,7-diaminoheptane, a structural analog of spermidine, and a known inhibitor of DHS enzymes. Discussion Loss of PfDHS function leads to reduced hypusination, which may be important for synthesis of some essential proteins. The growth defect in parasites with attenuated Pf DHS expression suggests that this gene is essential. However, the slower decline of PfDHS mutants compared with PfDHFR-TS mutants in competitive growth assays suggests that PfDHS is less vulnerable as an antimalarial target. Nevertheless, the data validate PfDHS as an antimalarial target which can be inhibited by spermidine-like compounds.
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Affiliation(s)
- Aiyada Aroonsri
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Navaporn Posayapisit
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Jindaporn Kongsee
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand
| | - Onsiri Siripan
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Danoo Vitsupakorn
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sugunya Utaida
- Department of Biotechnology, Faculty of Science and Technology, Thammasat University, Pathum Thani, Thailand
| | - Chairat Uthaipibull
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Sumalee Kamchonwongpaisan
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
| | - Philip J Shaw
- Protein-Ligand Engineering and Molecular Biology Laboratory, Medical Molecular Biology Research Unit, National Center for Genetic Engineering and Biotechnology (BIOTEC), National Science and Technology Development Agency (NSTDA), Pathum Thani, Thailand
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20
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Liu R, Cheng WJ, Tang HB, Zhong QP, Ming ZP, Dong HF. Comparative Metabonomic Investigations of Schistosoma japonicum From SCID Mice and BALB/c Mice: Clues to Developmental Abnormality of Schistosome in the Immunodeficient Host. Front Microbiol 2019; 10:440. [PMID: 30915055 PMCID: PMC6423161 DOI: 10.3389/fmicb.2019.00440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 02/20/2019] [Indexed: 12/04/2022] Open
Abstract
The growth and development of schistosome has been affected in the immunodeficient hosts. But it remains unresolved about the molecular mechanisms involved in the development and reproduction regulation of schistosomes. This study tested and compared the metabolic profiles of the male and female Schistosoma japonicum worms collected from SCID mice and BALB/c mice at 5 weeks post infection using liquid chromatography tandem mass spectrometry (LC-MS/MS) platform, in which the worms from SCID mice were the investigated organisms and the worms from BALB/c mice were used as the controls. There were 1015 ion features in ESI+ mode and 342 ion features in ESI- mode were identified after filtration by false discovery rate. Distinct metabolic profiles were found to clearly differentiate both male and female worms in SCID mice from those in BALB/c mice using multivariate modeling methods including the Principal Component Analysis (PCA), Partial Least Squares Discriminant Analysis (PLS-DA), and Orthogonal Partial Least Squares Discriminant Analysis (OPLS-DA). There were more differential metabolites in female worms than in male worms between SCID mice and BALB/c mice. And common and uniquely perturbed metabolites and pathways were identified among male and female worms from SCID mice when compared with BALB/c mice. The enriched metabolite sets of the differential metabolites in male worms between SCID mice and BALB/c mice included bile acid biosynthesis, taurine and hypotaurine metabolism, sphingolipid metabolism, retinol metabolism, purine metabolism, etc. And the enriched metabolite sets of differential metabolites in female worms included retinol metabolism, alpha linolenic acid and linoleic acid metabolism, purine metabolism, sphingolipid metabolism, glutamate metabolism, etc. Further detection and comparison in transcript abundance of genes of the perturbed retinol metabolism and its associated meiosis process in worms identified clues suggesting accumulated retinyl ester and perturbed meiotic process. These findings suggested an association between the schistosome with retarded growth and development in SCID mice and their perturbed metabolites and metabolic pathways, and provided a new insight into the growth and development regulation of S. japonicum worms from the metabolic level, which indicated great clues for discovery of drugs or vaccines against the parasites and disease with more researches.
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Affiliation(s)
- Rong Liu
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Wen-Jun Cheng
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Hong-Bin Tang
- Laboratory Animal Center, School of Medicine, Wuhan University, Wuhan, China
| | - Qin-Ping Zhong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zhen-Ping Ming
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Hui-Fen Dong
- School of Basic Medical Sciences, Wuhan University, Wuhan, China
- Hubei Province Key Laboratory of Allergy and Immunology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
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21
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Inducing controlled cell cycle arrest and re-entry during asexual proliferation of Plasmodium falciparum malaria parasites. Sci Rep 2018; 8:16581. [PMID: 30409996 PMCID: PMC6224408 DOI: 10.1038/s41598-018-34964-w] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2018] [Accepted: 10/26/2018] [Indexed: 02/08/2023] Open
Abstract
The life cycle of the malaria parasite Plasmodium falciparum is tightly regulated, oscillating between stages of intense proliferation and quiescence. Cyclic 48-hour asexual replication of Plasmodium is markedly different from cell division in higher eukaryotes, and mechanistically poorly understood. Here, we report tight synchronisation of malaria parasites during the early phases of the cell cycle by exposure to DL-α-difluoromethylornithine (DFMO), which results in the depletion of polyamines. This induces an inescapable cell cycle arrest in G1 (~15 hours post-invasion) by blocking G1/S transition. Cell cycle-arrested parasites enter a quiescent G0-like state but, upon addition of exogenous polyamines, re-initiate their cell cycle. This ability to halt malaria parasites at a specific point in their cell cycle, and to subsequently trigger re-entry into the cell cycle, provides a valuable framework to investigate cell cycle regulation in these parasites. We subsequently used gene expression analyses to show that re-entry into the cell cycle involves expression of Ca2+-sensitive (cdpk4 and pk2) and mitotic kinases (nima and ark2), with deregulation of the pre-replicative complex associated with expression of pk2. Changes in gene expression could be driven through transcription factors MYB1 and two ApiAP2 family members. This new approach to parasite synchronisation therefore expands our currently limited toolkit to investigate cell cycle regulation in malaria parasites.
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22
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Cell Swelling Induced by the Antimalarial KAE609 (Cipargamin) and Other PfATP4-Associated Antimalarials. Antimicrob Agents Chemother 2018; 62:AAC.00087-18. [PMID: 29555632 DOI: 10.1128/aac.00087-18] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2018] [Accepted: 02/18/2018] [Indexed: 12/15/2022] Open
Abstract
For an increasing number of antimalarial agents identified in high-throughput phenotypic screens, there is evidence that they target PfATP4, a putative Na+ efflux transporter on the plasma membrane of the human malaria parasite Plasmodium falciparum For several such "PfATP4-associated" compounds, it has been noted that their addition to parasitized erythrocytes results in cell swelling. Here we show that six structurally diverse PfATP4-associated compounds, including the clinical candidate KAE609 (cipargamin), induce swelling of both isolated blood-stage parasites and intact parasitized erythrocytes. The swelling of isolated parasites is dependent on the presence of Na+ in the external environment and may be attributed to the osmotic consequences of Na+ uptake. The swelling of the parasitized erythrocyte results in an increase in its osmotic fragility. Countering cell swelling by increasing the osmolarity of the extracellular medium reduces the antiplasmodial efficacy of PfATP4-associated compounds, consistent with cell swelling playing a role in the antimalarial activity of this class of compounds.
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23
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Smith ML, Styczynski MP. Systems Biology-Based Investigation of Host-Plasmodium Interactions. Trends Parasitol 2018; 34:617-632. [PMID: 29779985 DOI: 10.1016/j.pt.2018.04.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2017] [Revised: 04/10/2018] [Accepted: 04/16/2018] [Indexed: 12/20/2022]
Abstract
Malaria is a serious, complex disease caused by parasites of the genus Plasmodium. Plasmodium parasites affect multiple tissues as they evade immune responses, replicate, sexually reproduce, and transmit between vertebrate and invertebrate hosts. The explosion of omics technologies has enabled large-scale collection of Plasmodium infection data, revealing systems-scale patterns, mechanisms of pathogenesis, and the ways that host and pathogen affect each other. Here, we provide an overview of recent efforts using systems biology approaches to study host-Plasmodium interactions and the biological themes that have emerged from these efforts. We discuss some of the challenges in using systems biology for this goal, key research efforts needed to address those issues, and promising future malaria applications of systems biology.
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Affiliation(s)
- Maren L Smith
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA
| | - Mark P Styczynski
- School of Chemical & Biomolecular Engineering, Georgia Institute of Technology, Atlanta, GA 30332, USA; Malaria Host-Pathogen Interaction Center, Emory University, Atlanta, GA 30322, USA.
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24
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Lunev S, Butzloff S, Romero AR, Linzke M, Batista FA, Meissner KA, Müller IB, Adawy A, Wrenger C, Groves MR. Oligomeric interfaces as a tool in drug discovery: Specific interference with activity of malate dehydrogenase of Plasmodium falciparum in vitro. PLoS One 2018; 13:e0195011. [PMID: 29694407 PMCID: PMC5919072 DOI: 10.1371/journal.pone.0195011] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Accepted: 02/28/2018] [Indexed: 01/29/2023] Open
Abstract
Malaria remains a major threat to human health, as strains resistant to current therapeutics are discovered. Efforts in finding new drug targets are hampered by the lack of sufficiently specific tools to provide target validation prior to initiating expensive drug discovery projects. Thus, new approaches that can rapidly enable drug target validation are of significant interest. In this manuscript we present the crystal structure of malate dehydrogenase from Plasmodium falciparum (PfMDH) at 2.4 Å resolution and structure-based mutagenic experiments interfering with the inter-oligomeric interactions of the enzyme. We report decreased thermal stability, significantly decreased specific activity and kinetic parameters of PfMDH mutants upon mutagenic disruption of either oligomeric interface. In contrast, stabilization of one of the interfaces resulted in increased thermal stability, increased substrate/cofactor affinity and hyperactivity of the enzyme towards malate production at sub-millimolar substrate concentrations. Furthermore, the presented data show that our designed PfMDH mutant could be used as specific inhibitor of the wild type PfMDH activity, as mutated PfMDH copies were shown to be able to self-incorporate into the native assembly upon introduction in vitro, yielding deactivated mutant:wild-type species. These data provide an insight into the role of oligomeric assembly in regulation of PfMDH activity and reveal that recombinant mutants could be used as probe tool for specific modification of the wild type PfMDH activity, thus offering the potential to validate its druggability in vivo without recourse to complex genetics or initial tool compounds. Such tool compounds often lack specificity between host or pathogen proteins (or are toxic in in vivo trials) and result in difficulties in assessing cause and effect-particularly in cases when the enzymes of interest possess close homologs within the human host. Furthermore, our oligomeric interference approach could be used in the future in order to assess druggability of other challenging human pathogen drug targets.
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Affiliation(s)
- Sergey Lunev
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Sabine Butzloff
- LG Müller, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Atilio R. Romero
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Marleen Linzke
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Saõ Paulo, Brazil
| | - Fernando A. Batista
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Kamila A. Meissner
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Saõ Paulo, Brazil
| | - Ingrid B. Müller
- LG Müller, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
| | - Alaa Adawy
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
| | - Carsten Wrenger
- Unit for Drug Discovery, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, Saõ Paulo, Brazil
- * E-mail: (MRG); (CW)
| | - Matthew R. Groves
- Structural Biology Unit, XB20 Drug Design, Department of Pharmacy, University of Groningen, Groningen, The Netherlands
- * E-mail: (MRG); (CW)
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25
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Low CF, Rozaini MZH, Musa N, Syarul Nataqain B. Current knowledge of metabolomic approach in infectious fish disease studies. JOURNAL OF FISH DISEASES 2017; 40:1267-1277. [PMID: 28252175 DOI: 10.1111/jfd.12610] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2016] [Revised: 12/17/2016] [Accepted: 12/19/2016] [Indexed: 05/20/2023]
Abstract
The approaches of transcriptomic and proteomic have been widely used to study host-pathogen interactions in fish diseases, and this is comparable to the recently emerging application of metabolomic in elucidating disease-resistant mechanisms in fish that gives new insight into potential therapeutic strategies to improve fish health. Metabolomic is defined as the large-scale study of all metabolites within an organism and represents the frontline in the 'omics' approaches, providing direct information on the metabolic responses and perturbations in metabolic pathways. In this review, the current research in infectious fish diseases using metabolomic approach will be summarized. The metabolomic approach in economically important fish infected with viruses, bacteria and nematodes will also be discussed. The potential of the metabolomic approach for management of these infectious diseases as well as the challenges and the limitations of metabolomic in fish disease studies will be explored. Current review highlights the impacts of metabolomic studies in infectious fish diseases, which proposed the potential of new therapeutic strategies to enhance disease resistance in fish.
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Affiliation(s)
- C-F Low
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
| | - M Z H Rozaini
- Institute of Marine Biotechnology, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - N Musa
- School of Fisheries and Aquaculture Sciences, Universiti Malaysia Terengganu, Terengganu, Malaysia
| | - B Syarul Nataqain
- Institute of Systems Biology, Universiti Kebangsaan Malaysia, Selangor, Malaysia
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26
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Abstract
Prior to infecting erythrocytes and causing malaria symptoms, Plasmodium parasites undergo an obligatory phase of invasion and extensive replication inside their mammalian host's liver cells that depends on the parasite's ability to obtain the nutrients it requires for its intra-hepatic growth and multiplication. Here, we show that L-arginine (Arg) uptake through the host cell's SLC7A2-encoded transporters is essential for the parasite's development and maturation in the liver. Our data suggest that the Arg that is taken up is primarily metabolized by the arginase pathway to produce the polyamines required for Plasmodium growth. Although the parasite may hijack the host's biosynthesis pathway, it relies mainly upon its own arginase-AdoMetDC/ODC pathway to acquire the polyamines it needs to develop. These results identify for the first time a pivotal role for Arg-dependent polyamine production during Plasmodium's hepatic development and pave the way to the exploitation of strategies to impact liver infection by the malaria parasite through the modulation of Arg uptake and polyamine synthesis.
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27
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Abdelrazig S, Ortori CA, Davey G, Deressa W, Mulleta D, Barrett DA, Amberbir A, Fogarty AW. A metabolomic analytical approach permits identification of urinary biomarkers for Plasmodium falciparum infection: a case-control study. Malar J 2017; 16:229. [PMID: 28558710 PMCID: PMC5450092 DOI: 10.1186/s12936-017-1875-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2016] [Accepted: 05/25/2017] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Currently available diagnostic techniques of Plasmodium falciparum infection are not optimal for non-invasive, population-based screening for malaria. It was hypothesized that a mass spectrometry-based metabolomics approach could identify urinary biomarkers of falciparum malaria. METHODS The study used a case-control design, with cases consisting of 21 adults in central Ethiopia with a diagnosis of P. falciparum infection confirmed with microscopy, and 25 controls of adults with negative blood smears for malaria matched on age and sex. Urinary samples were collected from these individuals during presentation at the clinic, and a second sample was collected from both cases and controls 4 weeks later, after the cases had received anti-malarial medication. The urine samples were screened for small molecule urinary biomarkers, using mass spectrometry-based metabolomics analyses followed by multivariate analysis using principal component analysis and orthogonal partial least square-discriminant analysis. The chemical identity of statistically significant malaria biomarkers was confirmed using tandem mass spectrometry. RESULTS The urinary metabolic profiles of cases with P. falciparum infection were distinct from healthy controls. After treatment with anti-malarial medication, the metabolomic profile of cases resembled that of healthy controls. Significantly altered levels of 29 urinary metabolites were found. Elevated levels of urinary pipecolic acid, taurine, N-acetylspermidine, N-acetylputrescine and 1,3-diacetylpropane were identified as potential biomarkers of falciparum malaria. CONCLUSION The urinary biomarkers of malaria identified have potential for the development of non-invasive and rapid diagnostic test of P. falciparum infection.
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Affiliation(s)
- Salah Abdelrazig
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Catharine A Ortori
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
| | - Gail Davey
- Wellcome Trust Centre for Global Health Research, Brighton and Sussex Medical School, Brighton, UK
| | - Wakgari Deressa
- Department of Preventive Medicine, School of Public Health, College of Health Sciences, Addis Ababa University, Addis Ababa, Ethiopia.
| | - Dhaba Mulleta
- East Shewa Zone Health Department, Oromia Regional State, Adama, Ethiopia
| | - David A Barrett
- Centre for Analytical Bioscience, School of Pharmacy, University of Nottingham, Nottingham, NG7 2RD, UK
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Gowda GAN, Raftery D. Whole Blood Metabolomics by 1H NMR Spectroscopy Provides a New Opportunity To Evaluate Coenzymes and Antioxidants. Anal Chem 2017; 89:4620-4627. [PMID: 28318242 PMCID: PMC6245939 DOI: 10.1021/acs.analchem.7b00171] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
Conventional human blood metabolomics employs serum or plasma and provides a wealth of metabolic information therein. However, this approach lacks the ability to measure and evaluate important metabolites such as coenzymes and antioxidants that are present at high concentrations in red blood cells. As an important alternative to serum/plasma metabolomics, we show here that a simple 1H NMR experiment can simultaneously measure coenzymes and antioxidants in extracts of whole human blood, in addition to the nearly 70 metabolites that were shown to be quantitated in serum/plasma recently [ Anal. Chem. 2015 , 87 , 706 - 715 ]. Coenzymes of redox reactions: oxidized/reduced nicotinamide adenine dinucleotide (NAD+ and NADH) and nicotinamide adenine dinucleotide phosphate (NADP+ and NADPH); coenzymes of energy including adenosine triphosphate (ATP), adenosine diphosphate (ADP), and adenosine monophosphate (AMP); and antioxidants, the sum of oxidized and reduced glutathione (GSSG and GSH) can be measured with essentially no additional effort. A new method was developed for detecting many of these unstable species without affecting other blood/blood plasma metabolites. The identities of coenzymes and antioxidants in blood NMR spectra were established combining 1D/2D NMR techniques, chemical shift databases, pH measurements and, finally, spiking with authentic compounds. This is the first study to report identification of major coenzymes and antioxidants and quantify them, simultaneously, with the large pool of other metabolites in human blood using NMR spectroscopy. Considering that the levels of coenzymes and antioxidants represent a sensitive measure of cellular functions in health and numerous diseases, the NMR method presented here potentially opens a new chapter in the metabolomics of blood.
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Affiliation(s)
- G. A. Nagana Gowda
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
| | - Daniel Raftery
- Northwest Metabolomics Research Center, University of Washington, Seattle, Washington 98109, United States
- Mitochondria and Metabolism Center, Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Washington 98109, United States
- Department of Chemistry, University of Washington, Seattle, Washington 98109, United States
- Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, United States
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29
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Chiappino-Pepe A, Tymoshenko S, Ataman M, Soldati-Favre D, Hatzimanikatis V. Bioenergetics-based modeling of Plasmodium falciparum metabolism reveals its essential genes, nutritional requirements, and thermodynamic bottlenecks. PLoS Comput Biol 2017; 13:e1005397. [PMID: 28333921 PMCID: PMC5363809 DOI: 10.1371/journal.pcbi.1005397] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Accepted: 02/04/2017] [Indexed: 11/30/2022] Open
Abstract
Novel antimalarial therapies are urgently needed for the fight against drug-resistant parasites. The metabolism of malaria parasites in infected cells is an attractive source of drug targets but is rather complex. Computational methods can handle this complexity and allow integrative analyses of cell metabolism. In this study, we present a genome-scale metabolic model (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Using previous absolute concentration data of the intraerythrocytic parasite, we applied TFA to iPfa and predicted up to 63 essential genes and 26 essential pairs of genes. Of the 63 genes, 35 have been experimentally validated and reported in the literature, and 28 have not been experimentally tested and include previously hypothesized or novel predictions of essential metabolic capabilities. Without metabolomics data, four of the genes would have been incorrectly predicted to be non-essential. TFA also indicated that substrate channeling should exist in two metabolic pathways to ensure the thermodynamic feasibility of the flux. Finally, analysis of the metabolic capabilities of P. falciparum led to the identification of both the minimal nutritional requirements and the genes that can become indispensable upon substrate inaccessibility. This model provides novel insight into the metabolic needs and capabilities of the malaria parasite and highlights metabolites and pathways that should be measured and characterized to identify potential thermodynamic bottlenecks and substrate channeling. The hypotheses presented seek to guide experimental studies to facilitate a better understanding of the parasite metabolism and the identification of targets for more efficient intervention. Almost half of the world population is at risk of infection by malaria parasites. The rise in drug-resistant parasites requires better understanding and targeting of their metabolism. In this study, we present a genome-scale metabolic reconstruction (iPfa) of the deadliest malaria parasite, Plasmodium falciparum, and its thermodynamics-based flux analysis (TFA). Our results support and extend the available experimental evidence on the essential genes and nutritional requirements of this organism. Besides, we identify metabolites that give rise to thermodynamic bottlenecks and suggest substrate channeling. Overall, these results provide novel insight into the metabolism of P. falciparum and may guide experimental studies to develop a better characterization of the parasite metabolism and the identification of antimalarial drug targets.
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Affiliation(s)
- Anush Chiappino-Pepe
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Stepan Tymoshenko
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
| | - Meriç Ataman
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU, Geneva, Switzerland
| | - Vassily Hatzimanikatis
- Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, EPFL, Lausanne, Switzerland
- * E-mail:
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30
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Rajendran E, Hapuarachchi SV, Miller CM, Fairweather SJ, Cai Y, Smith NC, Cockburn IA, Bröer S, Kirk K, van Dooren GG. Cationic amino acid transporters play key roles in the survival and transmission of apicomplexan parasites. Nat Commun 2017; 8:14455. [PMID: 28205520 PMCID: PMC5316894 DOI: 10.1038/ncomms14455] [Citation(s) in RCA: 43] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2016] [Accepted: 12/30/2016] [Indexed: 11/09/2022] Open
Abstract
Apicomplexans are obligate intracellular parasites that scavenge essential nutrients from their hosts via transporter proteins on their plasma membrane. The identities of the transporters that mediate amino acid uptake into apicomplexans are unknown. Here we demonstrate that members of an apicomplexan-specific protein family-the Novel Putative Transporters (NPTs)-play key roles in the uptake of cationic amino acids. We show that an NPT from Toxoplasma gondii (TgNPT1) is a selective arginine transporter that is essential for parasite survival and virulence. We also demonstrate that a homologue of TgNPT1 from the malaria parasite Plasmodium berghei (PbNPT1), shown previously to be essential for the sexual gametocyte stage of the parasite, is a cationic amino acid transporter. This reveals a role for cationic amino acid scavenging in gametocyte biology. Our study demonstrates a critical role for amino acid transporters in the survival, virulence and life cycle progression of these parasites.
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Affiliation(s)
- Esther Rajendran
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Sanduni V Hapuarachchi
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Catherine M Miller
- College of Public Health, Medical and Veterinary Sciences, James Cook University, Smithfield, Queensland 4878, Australia
| | - Stephen J Fairweather
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Yeping Cai
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Nicholas C Smith
- Queensland Tropical Health Alliance Research Laboratory, Australian Institute of Tropical Health and Medicine, James Cook University, Smithfield, Queensland 4878, Australia
| | - Ian A Cockburn
- John Curtin School of Medical Research, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Stefan Bröer
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Kiaran Kirk
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
| | - Giel G van Dooren
- Research School of Biology, Australian National University, Canberra, Australian Capital Territory 2601, Australia
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Pretzel J, Gehr M, Eisenkolb M, Wang L, Fritz-Wolf K, Rahlfs S, Becker K, Jortzik E. Characterization and redox regulation of Plasmodium falciparum methionine adenosyltransferase. J Biochem 2016; 160:355-367. [PMID: 27466371 DOI: 10.1093/jb/mvw045] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 06/14/2016] [Indexed: 11/12/2022] Open
Abstract
As a methyl group donor for biochemical reactions, S-adenosylmethionine plays a central metabolic role in most organisms. Depletion of S-adenosylmethionine has downstream effects on polyamine metabolism and methylation reactions, and is an effective way to combat pathogenic microorganisms such as malaria parasites. Inhibition of both the methylation cycle and polyamine synthesis strongly affects Plasmodium falciparum growth. Despite its central position in the methylation cycle, not much is currently known about P. falciparum methionine adenosyltransferase (PfalMAT). Notably, however, PfalMAT has been discussed as a target of different redox regulatory modifications. Modulating the redox state of critical cysteine residues is a way to regulate enzyme activity in different pathways in response to changes in the cellular redox state. In the present study, we optimized an assay for detailed characterization of enzymatic activity and redox regulation of PfalMAT. While the presence of reduced thioredoxin increases the activity of the enzyme, it was found to be inhibited upon S-glutathionylation and S-nitrosylation. A homology model and site-directed mutagenesis studies revealed a contribution of the residues Cys52, Cys113 and Cys187 to redox regulation of PfalMAT by influencing its structure and activity. This phenomenon connects cellular S-adenosylmethionine synthesis to the redox state of PfalMAT and therefore to the cellular redox homeostasis.
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Affiliation(s)
- Jette Pretzel
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Marina Gehr
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Maike Eisenkolb
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Lihui Wang
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Karin Fritz-Wolf
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Stefan Rahlfs
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Katja Becker
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
| | - Esther Jortzik
- Biochemistry and Molecular Biology, Justus Liebig University Giessen, Germany
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32
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Lamour SD, Gomez-Romero M, Vorkas PA, Alibu VP, Saric J, Holmes E, Sternberg JM. Discovery of Infection Associated Metabolic Markers in Human African Trypanosomiasis. PLoS Negl Trop Dis 2015; 9:e0004200. [PMID: 26505639 PMCID: PMC4624234 DOI: 10.1371/journal.pntd.0004200] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2015] [Accepted: 10/07/2015] [Indexed: 01/08/2023] Open
Abstract
Human African trypanosomiasis (HAT) remains a major neglected tropical disease in Sub-Saharan Africa. As clinical symptoms are usually non-specific, new diagnostic and prognostic markers are urgently needed to enhance the number of identified cases and optimise treatment. This is particularly important for disease caused by Trypanosoma brucei rhodesiense, where indirect immunodiagnostic approaches have to date been unsuccessful. We have conducted global metabolic profiling of plasma from T.b.rhodesiense HAT patients and endemic controls, using 1H nuclear magnetic resonance (NMR) spectroscopy and ultra-performance liquid chromatography, coupled with mass spectrometry (UPLC-MS) and identified differences in the lipid, amino acid and metabolite profiles. Altogether 16 significantly disease discriminatory metabolite markers were found using NMR, and a further 37 lipid markers via UPLC-MS. These included significantly higher levels of phenylalanine, formate, creatinine, N-acetylated glycoprotein and triglycerides in patients relative to controls. HAT patients also displayed lower concentrations of histidine, sphingomyelins, lysophosphatidylcholines, and several polyunsaturated phosphatidylcholines. While the disease metabolite profile was partially consistent with previous data published in experimental rodent infection, we also found unique lipid and amino acid profile markers highlighting subtle but important differences between the host response to trypanosome infections between animal models and natural human infections. Our results demonstrate the potential of metabolic profiling in the identification of novel diagnostic biomarkers and the elucidation of pathogenetic mechanisms in this disease.
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Affiliation(s)
- Sabrina D. Lamour
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Maria Gomez-Romero
- Section of Hepatology and Gastroenterology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Panagiotis A. Vorkas
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Vincent P. Alibu
- Section of Hepatology and Gastroenterology, Department of Medicine, Imperial College London, London, United Kingdom
| | - Jasmina Saric
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Elaine Holmes
- Section of Biomolecular Medicine, Division of Computational and Systems Medicine, Department of Surgery and Cancer, Imperial College London, London, United Kingdom
| | - Jeremy M. Sternberg
- Institute of Biological and Environmental Sciences, University Of Aberdeen, Aberdeen, United Kingdom
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Zhou CX, Zhou DH, Elsheikha HM, Liu GX, Suo X, Zhu XQ. Global Metabolomic Profiling of Mice Brains following Experimental Infection with the Cyst-Forming Toxoplasma gondii. PLoS One 2015; 10:e0139635. [PMID: 26431205 PMCID: PMC4592003 DOI: 10.1371/journal.pone.0139635] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 09/14/2015] [Indexed: 11/18/2022] Open
Abstract
The interplay between the Apicomplexan parasite Toxoplasma gondii and its host has been largely studied. However, molecular changes at the metabolic level in the host central nervous system and pathogenesis-associated metabolites during brain infection are largely unexplored. We used a global metabolomics strategy to identify differentially regulated metabolites and affected metabolic pathways in BALB/c mice during infection with T. gondii Pru strain at 7, 14 and 21 days post-infection (DPI). The non-targeted Liquid Chromatography-Mass Spectrometry (LC-MS) metabolomics analysis detected approximately 2,755 retention time-exact mass pairs, of which more than 60 had significantly differential profiles at different stages of infection. These include amino acids, organic acids, carbohydrates, fatty acids, and vitamins. The biological significance of these metabolites is discussed. Principal Component Analysis and Orthogonal Partial Least Square-Discriminant Analysis showed the metabolites' profile to change over time with the most significant changes occurring at 14 DPI. Correlated metabolic pathway imbalances were observed in carbohydrate metabolism, lipid metabolism, energetic metabolism and fatty acid oxidation. Eight metabolites correlated with the physical recovery from infection-caused illness were identified. These findings indicate that global metabolomics adopted in this study is a sensitive approach for detecting metabolic alterations in T. gondii-infected mice and generated a comparative metabolic profile of brain tissue distinguishing infected from non-infected host.
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Affiliation(s)
- Chun-Xue Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
| | - Dong-Hui Zhou
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Hany M. Elsheikha
- Faculty of Medicine and Health Sciences, School of Veterinary Medicine and Science, University of Nottingham, Sutton Bonington Campus, Loughborough, LE12 5RD, United Kingdom
| | - Guang-Xue Liu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
| | - Xun Suo
- National Animal Protozoa Laboratory and College of Veterinary Medicine, China Agricultural University, Beijing 100193, PR China
- * E-mail: (XS); (XQZ)
| | - Xing-Quan Zhu
- State Key Laboratory of Veterinary Etiological Biology, Key Laboratory of Veterinary Parasitology of Gansu Province, Lanzhou Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu Province 730046, PR China
- * E-mail: (XS); (XQZ)
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Salinas JL, Kissinger JC, Jones DP, Galinski MR. Metabolomics in the fight against malaria. Mem Inst Oswaldo Cruz 2015; 109:589-97. [PMID: 25185001 PMCID: PMC4156452 DOI: 10.1590/0074-0276140043] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2014] [Accepted: 03/11/2014] [Indexed: 02/06/2023] Open
Abstract
Metabolomics uses high-resolution mass spectrometry to provide a chemical fingerprint of thousands of metabolites present in cells, tissues or body fluids. Such metabolic phenotyping has been successfully used to study various biologic processes and disease states. High-resolution metabolomics can shed new light on the intricacies of host-parasite interactions in each stage of the Plasmodium life cycle and the downstream ramifications on the host's metabolism, pathogenesis and disease. Such data can become integrated with other large datasets generated using top-down systems biology approaches and be utilised by computational biologists to develop and enhance models of malaria pathogenesis relevant for identifying new drug targets or intervention strategies. Here, we focus on the promise of metabolomics to complement systems biology approaches in the quest for novel interventions in the fight against malaria. We introduce the Malaria Host-Pathogen Interaction Center (MaHPIC), a new systems biology research coalition. A primary goal of the MaHPIC is to generate systems biology datasets relating to human and non-human primate (NHP) malaria parasites and their hosts making these openly available from an online relational database. Metabolomic data from NHP infections and clinical malaria infections from around the world will comprise a unique global resource.
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Affiliation(s)
- Jorge L Salinas
- Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Jessica C Kissinger
- Department of Genetics, Institute of Bioinformatics, Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Dean P Jones
- Division of Pulmonary Medicine, Department of Medicine, Emory University School of Medicine, Emory University, Atlanta, GA, USA
| | - Mary R Galinski
- Division of Infectious Diseases, Emory University School of Medicine, Emory University, Atlanta, GA, USA
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Canuto GAB, da Cruz PLR, Faccio AT, Klassen A, Tavares MFM. Neglected diseases prioritized in Brazil under the perspective of metabolomics: A review. Electrophoresis 2015; 36:2336-2347. [PMID: 26095472 DOI: 10.1002/elps.201500102] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2015] [Revised: 05/15/2015] [Accepted: 05/18/2015] [Indexed: 12/21/2022]
Abstract
This review article compiles in a critical manner literature publications regarding seven neglected diseases (ND) prioritized in Brazil (Chagas disease, dengue, leishmaniasis, leprosy, malaria, schistosomiasis, and tuberculosis) under the perspective of metabolomics. Both strategies, targeted and untargeted metabolomics, were considered in the compilation. The majority of studies focused on biomarker discovery for diagnostic purposes, and on the search of novel or alternative therapies against the ND under consideration, although temporal progression of the infection at metabolic level was also addressed. Tuberculosis, followed by schistosomiasis, malaria and leishmaniasis are the diseases that received larger attention in terms of number of publications. Dengue and leprosy were the least studied and Chagas disease received intermediate attention. NMR and HPLC-MS technologies continue to predominate among the analytical platforms of choice in the metabolomic studies of ND. A plethora of metabolites were identified in the compiled studies, with expressive predominancy of amino acids, organic acids, carbohydrates, nucleosides, lipids, fatty acids, and derivatives.
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Affiliation(s)
- Gisele A B Canuto
- Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Pedro L R da Cruz
- Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Andrea T Faccio
- Institute of Chemistry, University of Sao Paulo, Sao Paulo, SP, Brazil
| | - Aline Klassen
- Federal University of Sao Paulo, Diadema, SP, Brazil
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Galvez Rojas RL, Ahn IY, Suárez Mantilla B, Sant'Anna C, Pral EMF, Silber AM. The Uptake of GABA in Trypanosoma cruzi. J Eukaryot Microbiol 2015; 62:629-36. [PMID: 25851259 DOI: 10.1111/jeu.12219] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2014] [Revised: 01/12/2015] [Accepted: 02/02/2015] [Indexed: 12/27/2022]
Abstract
Gamma aminobutyric acid (GABA) is widely known as a neurotransmitter and signal transduction molecule found in vertebrates, plants, and some protozoan organisms. However, the presence of GABA and its role in trypanosomatids is unknown. Here, we report the presence of intracellular GABA and the biochemical characterization of its uptake in Trypanosoma cruzi, the etiological agent of Chagas' disease. Kinetic parameters indicated that GABA is taken up by a single transport system in pathogenic and nonpathogenic forms. Temperature dependence assays showed a profile similar to glutamate transport, but the effect of extracellular cations Na(+) , K(+) , and H(+) on GABA uptake differed, suggesting a different uptake mechanism. In contrast to reports for other amino acid transporters in T. cruzi, GABA uptake was Na(+) dependent and increased with pH, with a maximum activity at pH 8.5. The sensitivity to oligomycin showed that GABA uptake is dependent on ATP synthesis. These data point to a secondary active Na(+) /GABA symporter energized by Na(+) -exporting ATPase. Finally, we show that GABA occurs in the parasite's cytoplasm under normal culture conditions, indicating that it is regularly taken up from the culture medium or synthesized through an still undescribed metabolic pathway.
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Affiliation(s)
- Robert L Galvez Rojas
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Il-Young Ahn
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Brian Suárez Mantilla
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
| | - Celso Sant'Anna
- Instituto Nacional de Metrologia (INMetro), Rio de Janeiro, Brazil
| | | | - Ariel Mariano Silber
- Departamento de Parasitologia, Instituto de Ciências Biomédicas, Universidade de São Paulo, São Paulo, Brazil
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A lactate and formate transporter in the intraerythrocytic malaria parasite, Plasmodium falciparum. Nat Commun 2015; 6:6721. [PMID: 25823844 DOI: 10.1038/ncomms7721] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 02/23/2015] [Indexed: 12/24/2022] Open
Abstract
The intraerythrocytic malaria parasite relies primarily on glycolysis to fuel its rapid growth and reproduction. The major byproduct of this metabolism, lactic acid, is extruded into the external medium. In this study, we show that the human malaria parasite Plasmodium falciparum expresses at its surface a member of the microbial formate-nitrite transporter family (PfFNT), which, when expressed in Xenopus laevis oocytes, transports both formate and lactate. The transport characteristics of PfFNT in oocytes (pH-dependence, inhibitor-sensitivity and kinetics) are similar to those of the transport of lactate and formate across the plasma membrane of mature asexual-stage P. falciparum trophozoites, consistent with PfFNT playing a major role in the efflux of lactate and hence in the energy metabolism of the intraerythrocytic parasite.
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Penkler G, du Toit F, Adams W, Rautenbach M, Palm DC, van Niekerk DD, Snoep JL. Construction and validation of a detailed kinetic model of glycolysis in Plasmodium falciparum. FEBS J 2015; 282:1481-511. [PMID: 25693925 DOI: 10.1111/febs.13237] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2014] [Revised: 02/07/2015] [Accepted: 02/13/2015] [Indexed: 11/26/2022]
Abstract
UNLABELLED The enzymes in the Embden-Meyerhof-Parnas pathway of Plasmodium falciparum trophozoites were kinetically characterized and their integrated activities analyzed in a mathematical model. For validation of the model, we compared model predictions for steady-state fluxes and metabolite concentrations of the hexose phosphates with experimental values for intact parasites. The model, which is completely based on kinetic parameters that were measured for the individual enzymes, gives an accurate prediction of the steady-state fluxes and intermediate concentrations. This is the first detailed kinetic model for glucose metabolism in P. falciparum, one of the most prolific malaria-causing protozoa, and the high predictive power of the model makes it a strong tool for future drug target identification studies. The modelling workflow is transparent and reproducible, and completely documented in the SEEK platform, where all experimental data and model files are available for download. DATABASE The mathematical models described in the present study have been submitted to the JWS Online Cellular Systems Modelling Database (http://jjj.bio.vu.nl/database/penkler). The investigation and complete experimental data set is available on SEEK (10.15490/seek.1. INVESTIGATION 56).
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Affiliation(s)
- Gerald Penkler
- Department of Biochemistry, Stellenbosch University, Matieland, South Africa; Molecular Cell Physiology, Vrije Universiteit Amsterdam, The Netherlands
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von Koschitzky I, Gerhardt H, Lämmerhofer M, Kohout M, Gehringer M, Laufer S, Pink M, Schmitz-Spanke S, Strube C, Kaiser A. New insights into novel inhibitors against deoxyhypusine hydroxylase from plasmodium falciparum: compounds with an iron chelating potential. Amino Acids 2015; 47:1155-66. [PMID: 25715757 DOI: 10.1007/s00726-015-1943-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 02/14/2015] [Indexed: 01/30/2023]
Abstract
Deoxyhypusine hydroxylase (DOHH) is a dinuclear iron enzyme required for hydroxylation of the aminobutyl side chain of deoxyhypusine in eukaryotic translation initiation factor 5A (eIF-5A), the second step in hypusine biosynthesis. DOHH has been recently identified in P. falciparum and P. vivax. Both enzymes have very peculiar features including E-Z type HEAT-like repeats and a diiron centre in their active site. Both proteins share only 26 % amino acid identity to the human paralogue. Hitherto, no X-ray structure exists from either enzyme. However, structural predictions based on the amino acid sequence of the active site in comparison to the human enzyme show that four conserved histidine and glutamate residues provide the coordination sites for chelating the ferrous iron ions. Recently, we showed that P. vivax DOHH is inhibited by zileuton (N-[1-(1-benzothien-2-yl)ethyl]-N-hydroxyurea), a drug that is known for inhibiting human 5-lipoygenase (5-LOX) by the complexation of ferrous iron. A novel discovery program was launched to identify inhibitors of the P. falciparum DOHH from the Malaria Box, consisting of 400 chemical compounds, which are highly active in the erythrocytic stages of Malaria infections. In a first visual selection for potential ligands of ferrous iron, three compounds from different scaffold classes namely the diazonapthyl benzimidazole MMV666023 (Malaria Box plate A, position A03), the bis-benzimidazole MMV007384 (plate A, position B08), and a 1,2,5,-oxadiazole MMV665805 (plate A, position C03) were selected and subsequently evaluated in silico for their potential to complex iron ions. As a proof of principle, a bioanalytical assay was performed and the inhibition of hypusine biosynthesis was determined by GC-MS. All tested compounds proved to be active in this assay and MMV665805 exhibited the strongest inhibitory effect. Notably, the results were in accordance with the preliminary quantum-mechanical calculations suggesting the strongest iron complexation capacity for MMV665805. This compound might be a useful tool as well as a novel lead structure for inhibitors of P. falciparum DOHH.
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Affiliation(s)
- Imke von Koschitzky
- Institute for Pharmacogenetics, Medical Research Centre, University Duisburg-Essen, Hufelandstrasse 55, 45147, Essen, Germany
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A novel inhibitor of Plasmodium falciparum spermidine synthase: a twist in the tail. Malar J 2015; 14:54. [PMID: 25651815 PMCID: PMC4342090 DOI: 10.1186/s12936-015-0572-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2014] [Accepted: 01/18/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Plasmodium falciparum is the most pathogenic of the human malaria parasite species and a major cause of death in Africa. It's resistance to most of the current drugs accentuates the pressing need for new chemotherapies. Polyamine metabolism of the parasite is distinct from the human pathway making it an attractive target for chemotherapeutic development. Plasmodium falciparum spermidine synthase (PfSpdS) catalyzes the synthesis of spermidine and spermine. It is a major polyamine flux-determining enzyme and spermidine is a prerequisite for the post-translational activation of P. falciparum eukaryotic translation initiation factor 5A (elF5A). The most potent inhibitors of eukaryotic SpdS's are not specific for PfSpdS. METHODS 'Dynamic' receptor-based pharmacophore models were generated from published crystal structures of SpdS with different ligands. This approach takes into account the inherent flexibility of the active site, which reduces the entropic penalties associated with ligand binding. Four dynamic pharmacophore models were developed and two inhibitors, (1R,4R)-(N1-(3-aminopropyl)-trans-cyclohexane-1,4-diamine (compound 8) and an analogue, N-(3-aminopropyl)-cyclohexylamine (compound 9), were identified. RESULTS A crystal structure containing compound 8 was solved and confirmed the in silico prediction that its aminopropyl chain traverses the catalytic centre in the presence of the byproduct of catalysis, 5'-methylthioadenosine. The IC50 value of compound 9 is in the same range as that of the most potent inhibitors of PfSpdS, S-adenosyl-1,8-diamino-3-thio-octane (AdoDATO) and 4MCHA and 100-fold lower than that of compound 8. Compound 9 was originally identified as a mammalian spermine synthase inhibitor and does not inhibit mammalian SpdS. This implied that these two compounds bind in an orientation where their aminopropyl chains face the putrescine binding site in the presence of the substrate, decarboxylated S-adenosylmethionine. The higher binding affinity and lower receptor strain energy of compound 9 compared to compound 8 in the reversed orientation explained their different IC50 values. CONCLUSION The specific inhibition of PfSpdS by compound 9 is enabled by its binding in the additional cavity normally occupied by spermidine when spermine is synthesized. This is the first time that a spermine synthase inhibitor is shown to inhibit PfSpdS, which provides new avenues to explore for the development of novel inhibitors of PfSpdS.
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Lamour SD, Straschil U, Saric J, Delves MJ. Changes in metabolic phenotypes of Plasmodium falciparum in vitro cultures during gametocyte development. Malar J 2014; 13:468. [PMID: 25439984 PMCID: PMC4289216 DOI: 10.1186/1475-2875-13-468] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 11/24/2014] [Indexed: 12/18/2022] Open
Abstract
Background Gametocytes are the Plasmodium life stage that is solely responsible for malaria transmission. Despite their important role in perpetuating malaria, gametocyte differentiation and development is poorly understood. Methods To shed light on the biochemical changes that occur during asexual and gametocyte development, metabolic characterization of media from in vitro intra-erythrocytic Plasmodium falciparum cultures was performed throughout gametocyte development by applying 1H nuclear magnetic spectroscopy, and using sham erythrocyte cultures as controls. Spectral differences between parasite and sham cultures were assessed via principal component analyses and partial-least squares analyses, and univariate statistical methods. Results Clear parasite-associated changes in metabolism were observed throughout the culture period, revealing differences between asexual parasites and gametocyte stages. With culture progression and development of gametocytes, parasitic release of the glycolytic end products lactate, pyruvate, alanine, and glycerol, were found to be dramatically reduced whilst acetate release was greatly increased. Also, uptake of lipid moieties CH2, CH3, and CH = CH-CH2-CH2 increased throughout gametocyte development, peaking with maturity. Conclusions This study uniquely presents an initial characterization of the metabolic exchange between parasite and culture medium during in vitro P. falciparum gametocyte culture. Results suggest that energy metabolism and lipid utilization between the asexual stages and gametocytes is different. This study provides new insights for gametocyte-specific nutritional requirements to aid future optimization and standardization of in vitro gametocyte cultivation, and highlights areas of novel gametocyte cell biology that deserve to be studied in greater detail and may yield new targets for transmission-blocking drugs. Electronic supplementary material The online version of this article (doi:10.1186/1475-2875-13-468) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | - Michael J Delves
- Department of Life Sciences, Imperial College London, London SW7 2AZ, UK.
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Abstract
Although efforts to understand the basis for inter-strain phenotypic variation in the most virulent malaria species, Plasmodium falciparum, have benefited from advances in genomic technologies, there have to date been few metabolomic studies of this parasite. Using 1H-NMR spectroscopy, we have compared the metabolite profiles of red blood cells infected with different P. falciparum strains. These included both chloroquine-sensitive and chloroquine-resistant strains, as well as transfectant lines engineered to express different isoforms of the chloroquine-resistance-conferring pfcrt (P. falciparum chloroquine resistance transporter). Our analyses revealed strain-specific differences in a range of metabolites. There was marked variation in the levels of the membrane precursors choline and phosphocholine, with some strains having >30-fold higher choline levels and >5-fold higher phosphocholine levels than others. Chloroquine-resistant strains showed elevated levels of a number of amino acids relative to chloroquine-sensitive strains, including an approximately 2-fold increase in aspartate levels. The elevation in amino acid levels was attributable to mutations in pfcrt. Pfcrt-linked differences in amino acid abundance were confirmed using alternate extraction and detection (HPLC) methods. Mutations acquired to withstand chloroquine exposure therefore give rise to significant biochemical alterations in the parasite. The metabolite profiles of red blood cells infected with different malaria parasite strains were compared. Amino acid profiles varied with the chloroquine resistance status of the strain, and this was linked specifically to mutations in the parasite's chloroquine resistance transporter.
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Targeting NAD+ metabolism in the human malaria parasite Plasmodium falciparum. PLoS One 2014; 9:e94061. [PMID: 24747974 PMCID: PMC3991606 DOI: 10.1371/journal.pone.0094061] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2013] [Accepted: 03/11/2014] [Indexed: 11/19/2022] Open
Abstract
Nicotinamide adenine dinucleotide (NAD+) is an essential metabolite utilized as a redox cofactor and enzyme substrate in numerous cellular processes. Elevated NAD+ levels have been observed in red blood cells infected with the malaria parasite Plasmodium falciparum, but little is known regarding how the parasite generates NAD+. Here, we employed a mass spectrometry-based metabolomic approach to confirm that P. falciparum lacks the ability to synthesize NAD+ de novo and is reliant on the uptake of exogenous niacin. We characterized several enzymes in the NAD+ pathway and demonstrate cytoplasmic localization for all except the parasite nicotinamidase, which concentrates in the nucleus. One of these enzymes, the P. falciparum nicotinate mononucleotide adenylyltransferase (PfNMNAT), is essential for NAD+ metabolism and is highly diverged from the human homolog, but genetically similar to bacterial NMNATs. Our results demonstrate the enzymatic activity of PfNMNAT in vitro and demonstrate its ability to genetically complement the closely related Escherichia coli NMNAT. Due to the similarity of PfNMNAT to the bacterial enzyme, we tested a panel of previously identified bacterial NMNAT inhibitors and synthesized and screened twenty new derivatives, which demonstrate a range of potency against live parasite culture. These results highlight the importance of the parasite NAD+ metabolic pathway and provide both novel therapeutic targets and promising lead antimalarial compounds.
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Abstract
As it grows and replicates within the erythrocytes of its host the malaria parasite takes up nutrients from the extracellular medium, exports metabolites and maintains a tight control over its internal ionic composition. These functions are achieved via membrane transport proteins, integral membrane proteins that mediate the passage of solutes across the various membranes that separate the biochemical machinery of the parasite from the extracellular environment. Proteins of this type play a key role in antimalarial drug resistance, as well as being candidate drug targets in their own right. This review provides an overview of recent work on the membrane transport biology of the malaria parasite-infected erythrocyte, encompassing both the parasite-induced changes in the membrane transport properties of the host erythrocyte and the cell physiology of the intracellular parasite itself.
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Macrae JI, Lopaticki S, Maier AG, Rupasinghe T, Nahid A, Cowman AF, McConville MJ. Plasmodium falciparum is dependent on de novo myo-inositol biosynthesis for assembly of GPI glycolipids and infectivity. Mol Microbiol 2014; 91:762-76. [PMID: 24350823 DOI: 10.1111/mmi.12496] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/15/2013] [Indexed: 12/27/2022]
Abstract
Intra-erythrocytic stages of the malaria parasite, Plasmodium falciparum, are thought to be dependent on de novo synthesis of phosphatidylinositol, as red blood cells (RBC) lack the capacity to synthesize this phospholipid. The myo-inositol headgroup of PI can either be synthesized de novo or scavenged from the RBC. An untargeted metabolite profiling of P. falciparum infected RBC showed that trophozoite and schizont stages accumulate high levels of myo-inositol-3-phosphate, indicating increased de novo biosynthesis of myo-inositol from glucose 6-phosphate. Metabolic labelling studies with (13) C-U-glucose in the presence and absence of exogenous inositol confirmed that de novo myo-inositol synthesis occurs in parallel with myo-inositol salvage pathways. Unexpectedly, while both endogenous and scavenged myo-inositol was used to synthesize bulk PI, only de novo-synthesized myo-inositol was incorporated into GPI glycolipids. Moreover, gene disruption studies suggested that the INO1 gene, encoding myo-inositol 3-phosphate synthase, is essential in asexual parasite stages. Together these findings suggest that P. falciparum asexual stages are critically dependent on de novo myo-inositol biosynthesis for assembly of a sub-pool of PI species and GPI biosynthesis. These findings highlight unexpected complexity in phospholipid biosynthesis in P. falciparum and a lack of redundancy in some nutrient salvage versus endogenous biosynthesis pathways.
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Affiliation(s)
- James I Macrae
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, 30 Flemington Road, Melbourne, Vic., 3010, Australia
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le Roux D, Burger PB, Niemand J, Grobler A, Urbán P, Fernàndez-Busquets X, Barker RH, Serrano AE, I Louw A, Birkholtz LM. Novel S-adenosyl-L-methionine decarboxylase inhibitors as potent antiproliferative agents against intraerythrocytic Plasmodium falciparum parasites. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2013; 4:28-36. [PMID: 24596666 PMCID: PMC3940083 DOI: 10.1016/j.ijpddr.2013.11.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Revised: 11/19/2013] [Accepted: 11/20/2013] [Indexed: 12/31/2022]
Abstract
S-adenosyl-l-methionine decarboxylase (AdoMetDC) in the polyamine biosynthesis pathway has been identified as a suitable drug target in Plasmodium falciparum parasites, which causes the most lethal form of malaria. Derivatives of an irreversible inhibitor of this enzyme, 5'-{[(Z)-4-amino-2-butenyl]methylamino}-5'-deoxyadenosine (MDL73811), have been developed with improved pharmacokinetic profiles and activity against related parasites, Trypanosoma brucei. Here, these derivatives were assayed for inhibition of AdoMetDC from P. falciparum parasites and the methylated derivative, 8-methyl-5'-{[(Z)-4-aminobut-2-enyl]methylamino}-5'-deoxyadenosine (Genz-644131) was shown to be the most active. The in vitro efficacy of Genz-644131 was markedly increased by nanoencapsulation in immunoliposomes, which specifically targeted intraerythrocytic P. falciparum parasites.
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Affiliation(s)
- Dina le Roux
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Pieter B Burger
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Jandeli Niemand
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Anne Grobler
- DST/NWU Preclinical Drug Development Platform, North-West University, Potchefstroom 2531, South Africa
| | - Patricia Urbán
- Nanobioengineering Group, Institute for Bioengineering of Catalonia, Baldiri Reixac 10-12, Barcelona E08028, Spain ; Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Rosselló 149-153, Barcelona E08036, Spain ; Biomolecular Interactions Team, Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona E08028, Spain
| | - Xavier Fernàndez-Busquets
- Nanobioengineering Group, Institute for Bioengineering of Catalonia, Baldiri Reixac 10-12, Barcelona E08028, Spain ; Barcelona Centre for International Health Research (CRESIB), Hospital Clínic-Universitat de Barcelona, Rosselló 149-153, Barcelona E08036, Spain ; Biomolecular Interactions Team, Nanoscience and Nanotechnology Institute (IN2UB), University of Barcelona, Martí i Franquès 1, Barcelona E08028, Spain
| | - Robert H Barker
- Genzyme Corporation, 153 Second Avenue, Waltham, MA 02451, USA
| | - Adelfa E Serrano
- University of Puerto Rico-School of Medicine, Department of Microbiology and Medical Zoology, P.O. Box 365067, San Juan PR 00936-5067, Puerto Rico
| | - Abraham I Louw
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
| | - Lyn-Marie Birkholtz
- Department of Biochemistry, Centre for Sustainable Malaria Control, University of Pretoria, Private Bag X20, Hatfield 0028, South Africa
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Cobbold SA, Vaughan AM, Lewis IA, Painter HJ, Camargo N, Perlman DH, Fishbaugher M, Healer J, Cowman AF, Kappe SHI, Llinás M. Kinetic flux profiling elucidates two independent acetyl-CoA biosynthetic pathways in Plasmodium falciparum. J Biol Chem 2013; 288:36338-50. [PMID: 24163372 DOI: 10.1074/jbc.m113.503557] [Citation(s) in RCA: 65] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The malaria parasite Plasmodium falciparum depends on glucose to meet its energy requirements during blood-stage development. Although glycolysis is one of the best understood pathways in the parasite, it is unclear if glucose metabolism appreciably contributes to the acetyl-CoA pools required for tricarboxylic acid metabolism (TCA) cycle and fatty acid biosynthesis. P. falciparum possesses a pyruvate dehydrogenase (PDH) complex that is localized to the apicoplast, a specialized quadruple membrane organelle, suggesting that separate acetyl-CoA pools are likely. Herein, we analyze PDH-deficient parasites using rapid stable-isotope labeling and show that PDH does not appreciably contribute to acetyl-CoA synthesis, tricarboxylic acid metabolism, or fatty acid synthesis in blood stage parasites. Rather, we find that acetyl-CoA demands are supplied through a "PDH-like" enzyme and provide evidence that the branched-chain keto acid dehydrogenase (BCKDH) complex is performing this function. We also show that acetyl-CoA synthetase can be a significant contributor to acetyl-CoA biosynthesis. Interestingly, the PDH-like pathway contributes glucose-derived acetyl-CoA to the TCA cycle in a stage-independent process, whereas anapleurotic carbon enters the TCA cycle via a stage-dependent phosphoenolpyruvate carboxylase/phosphoenolpyruvate carboxykinase process that decreases as the parasite matures. Although PDH-deficient parasites have no blood-stage growth defect, they are unable to progress beyond the oocyst phase of the parasite mosquito stage.
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Affiliation(s)
- Simon A Cobbold
- From the Department of Biochemistry and Molecular Biology and Center for Infectious Disease Dynamics, Pennsylvania State University, State College, Pennsylvania 16802
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Tymoshenko S, Oppenheim RD, Soldati-Favre D, Hatzimanikatis V. Functional genomics of Plasmodium falciparum using metabolic modelling and analysis. Brief Funct Genomics 2013; 12:316-27. [PMID: 23793264 PMCID: PMC3743259 DOI: 10.1093/bfgp/elt017] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Plasmodium falciparum is an obligate intracellular parasite and the leading cause of severe malaria responsible for tremendous morbidity and mortality particularly in sub-Saharan Africa. Successful completion of the P. falciparum genome sequencing project in 2002 provided a comprehensive foundation for functional genomic studies on this pathogen in the following decade. Over this period, a large spectrum of experimental approaches has been deployed to improve and expand the scope of functionally annotated genes. Meanwhile, rapidly evolving methods of systems biology have also begun to contribute to a more global understanding of various aspects of the biology and pathogenesis of malaria. Herein we provide an overview on metabolic modelling, which has the capability to integrate information from functional genomics studies in P. falciparum and guide future malaria research efforts towards the identification of novel candidate drug targets.
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Affiliation(s)
- Stepan Tymoshenko
- Institute of Chemical Engineering, Laboratory of Computational Systems Biotechnology, École Polytechnique Fédérale de Lausanne, CH-1015, Switzerland.
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MacRae JI, Sheiner L, Nahid A, Tonkin C, Striepen B, McConville MJ. Mitochondrial metabolism of glucose and glutamine is required for intracellular growth of Toxoplasma gondii. Cell Host Microbe 2013; 12:682-92. [PMID: 23159057 DOI: 10.1016/j.chom.2012.09.013] [Citation(s) in RCA: 171] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 07/07/2012] [Accepted: 09/20/2012] [Indexed: 12/23/2022]
Abstract
Toxoplasma gondii proliferates within host cell vacuoles where the parasite relies on host carbon and nutrients for replication. To assess how T. gondii utilizes these resources, we mapped the carbon metabolism pathways in intracellular and egressed parasite stages. We determined that intracellular T. gondii stages actively catabolize host glucose via a canonical, oxidative tricarboxylic acid (TCA) cycle, a mitochondrial pathway in which organic molecules are broken down to generate energy. These stages also catabolize glutamine via the TCA cycle and an unanticipated γ-aminobutyric acid (GABA) shunt, which generates GABA and additional molecules that enter the TCA cycle. Chemically inhibiting the TCA cycle completely prevents intracellular parasite replication. Parasites lacking the GABA shunt exhibit attenuated growth and are unable to sustain motility under nutrient-limited conditions, suggesting that GABA functions as a short-term energy reserve. Thus, T. gondii tachyzoites have metabolic flexibility that likely allows the parasite to infect diverse cell types.
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Affiliation(s)
- James I MacRae
- Department of Biochemistry and Molecular Biology, Bio21 Institute of Molecular Science and Biotechnology, University of Melbourne, Parkville, VIC 3010, Australia
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Sana TR, Gordon DB, Fischer SM, Tichy SE, Kitagawa N, Lai C, Gosnell WL, Chang SP. Global mass spectrometry based metabolomics profiling of erythrocytes infected with Plasmodium falciparum. PLoS One 2013; 8:e60840. [PMID: 23593322 PMCID: PMC3621881 DOI: 10.1371/journal.pone.0060840] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2012] [Accepted: 03/05/2013] [Indexed: 12/20/2022] Open
Abstract
Malaria is a global infectious disease that threatens the lives of millions of people. Transcriptomics, proteomics and functional genomics studies, as well as sequencing of the Plasmodium falciparum and Homo sapiens genomes, have shed new light on this host-parasite relationship. Recent advances in accurate mass measurement mass spectrometry, sophisticated data analysis software, and availability of biological pathway databases, have converged to facilitate our global, untargeted biochemical profiling study of in vitro P. falciparum-infected (IRBC) and uninfected (NRBC) erythrocytes. In order to expand the number of detectable metabolites, several key analytical steps in our workflows were optimized. Untargeted and targeted data mining resulted in detection of over one thousand features or chemical entities. Untargeted features were annotated via matching to the METLIN metabolite database. For targeted data mining, we queried the data using a compound database derived from a metabolic reconstruction of the P. falciparum genome. In total, over one hundred and fifty differential annotated metabolites were observed. To corroborate the representation of known biochemical pathways from our data, an inferential pathway analysis strategy was used to map annotated metabolites onto the BioCyc pathway collection. This hypothesis-generating approach resulted in over-representation of many metabolites onto several IRBC pathways, most prominently glycolysis. In addition, components of the “branched” TCA cycle, partial urea cycle, and nucleotide, amino acid, chorismate, sphingolipid and fatty acid metabolism were found to be altered in IRBCs. Interestingly, we detected and confirmed elevated levels for cyclic ADP ribose and phosphoribosyl AMP in IRBCs, a novel observation. These metabolites may play a role in regulating the release of intracellular Ca2+ during P. falciparum infection. Our results support a strategy of global metabolite profiling by untargeted data acquisition. Untargeted and targeted data mining workflows, when used together to perform pathway-inferred metabolomics, have the benefit of obviating MS/MS confirmation for every detected compound.
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Affiliation(s)
- Theodore R. Sana
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - D. Benjamin Gordon
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Steven M. Fischer
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Shane E. Tichy
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Norton Kitagawa
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - Cindy Lai
- Life Sciences Group, Agilent Technologies, Santa Clara, California, United States of America
| | - William L. Gosnell
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
| | - Sandra P. Chang
- Department of Tropical Medicine, Medical Microbiology and Pharmacology, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, Hawaii, United States of America
- * E-mail:
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