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Opperdoes FR, Záhonová K, Škodová-Sveráková I, Bučková B, Chmelová Ľ, Lukeš J, Yurchenko V. In silico prediction of the metabolism of Blastocrithidia nonstop, a trypanosomatid with non-canonical genetic code. BMC Genomics 2024; 25:184. [PMID: 38365628 PMCID: PMC10874023 DOI: 10.1186/s12864-024-10094-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Accepted: 02/06/2024] [Indexed: 02/18/2024] Open
Abstract
BACKGROUND Almost all extant organisms use the same, so-called canonical, genetic code with departures from it being very rare. Even more exceptional are the instances when a eukaryote with non-canonical code can be easily cultivated and has its whole genome and transcriptome sequenced. This is the case of Blastocrithidia nonstop, a trypanosomatid flagellate that reassigned all three stop codons to encode amino acids. RESULTS We in silico predicted the metabolism of B. nonstop and compared it with that of the well-studied human parasites Trypanosoma brucei and Leishmania major. The mapped mitochondrial, glycosomal and cytosolic metabolism contains all typical features of these diverse and important parasites. We also provided experimental validation for some of the predicted observations, concerning, specifically presence of glycosomes, cellular respiration, and assembly of the respiratory complexes. CONCLUSIONS In an unusual comparison of metabolism between a parasitic protist with a massively altered genetic code and its close relatives that rely on a canonical code we showed that the dramatic differences on the level of nucleic acids do not seem to be reflected in the metabolisms. Moreover, although the genome of B. nonstop is extremely AT-rich, we could not find any alterations of its pyrimidine synthesis pathway when compared to other trypanosomatids. Hence, we conclude that the dramatic alteration of the genetic code of B. nonstop has no significant repercussions on the metabolism of this flagellate.
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Affiliation(s)
- Fred R Opperdoes
- de Duve Institute, Université catholique de Louvain, Brussels, Belgium
| | - Kristína Záhonová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Ingrid Škodová-Sveráková
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Barbora Bučková
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Ľubomíra Chmelová
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, Ostrava, Czechia.
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Bertsova YV, Serebryakova MV, Anashkin VA, Baykov AA, Bogachev AV. A Redox-Regulated, Heterodimeric NADH:cinnamate Reductase in Vibrio ruber. Biochemistry (Mosc) 2024; 89:241-256. [PMID: 38622093 DOI: 10.1134/s0006297924020056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 10/09/2023] [Accepted: 10/10/2023] [Indexed: 04/17/2024]
Abstract
Genes of putative reductases of α,β-unsaturated carboxylic acids are abundant among anaerobic and facultatively anaerobic microorganisms, yet substrate specificity has been experimentally verified for few encoded proteins. Here, we co-produced in Escherichia coli a heterodimeric protein of the facultatively anaerobic marine bacterium Vibrio ruber (GenBank SJN56019 and SJN56021; annotated as NADPH azoreductase and urocanate reductase, respectively) with Vibrio cholerae flavin transferase. The isolated protein (named Crd) consists of the sjn56021-encoded subunit CrdB (NADH:flavin, FAD binding 2, and FMN bind domains) and an additional subunit CrdA (SJN56019, a single NADH:flavin domain) that interact via their NADH:flavin domains (Alphafold2 prediction). Each domain contains a flavin group (three FMNs and one FAD in total), one of the FMN groups being linked covalently by the flavin transferase. Crd readily reduces cinnamate, p-coumarate, caffeate, and ferulate under anaerobic conditions with NADH or methyl viologen as the electron donor, is moderately active against acrylate and practically inactive against urocanate and fumarate. Cinnamates induced Crd synthesis in V. ruber cells grown aerobically or anaerobically. The Crd-catalyzed reduction started by NADH demonstrated a time lag of several minutes, suggesting a redox regulation of the enzyme activity. The oxidized enzyme is inactive, which apparently prevents production of reactive oxygen species under aerobic conditions. Our findings identify Crd as a regulated NADH-dependent cinnamate reductase, apparently protecting V. ruber from (hydroxy)cinnamate poisoning.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Marina V Serebryakova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Victor A Anashkin
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Alexander A Baykov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow, 119234, Russia.
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Cui Z, Zhong Y, Sun Z, Jiang Z, Deng J, Wang Q, Nielsen J, Hou J, Qi Q. Reconfiguration of the reductive TCA cycle enables high-level succinic acid production by Yarrowia lipolytica. Nat Commun 2023; 14:8480. [PMID: 38123538 PMCID: PMC10733433 DOI: 10.1038/s41467-023-44245-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 12/05/2023] [Indexed: 12/23/2023] Open
Abstract
Succinic acid (SA) is an important C4-dicarboxylic acid. Microbial production of SA at low pH results in low purification costs and hence good overall process economics. However, redox imbalances limited SA biosynthesis from glucose via the reductive tricarboxylic acid (TCA) cycle in yeast. Here, we engineer the strictly aerobic yeast Yarrowia lipolytica for efficient SA production without pH control. Introduction of the reductive TCA cycle into the cytosol of a succinate dehydrogenase-disrupted yeast strain causes arrested cell growth. Although adaptive laboratory evolution restores cell growth, limited NADH supply restricts SA production. Reconfiguration of the reductive SA biosynthesis pathway in the mitochondria through coupling the oxidative and reductive TCA cycle for NADH regeneration results in improved SA production. In pilot-scale fermentation, the engineered strain produces 111.9 g/L SA with a yield of 0.79 g/g glucose within 62 h. This study paves the way for industrial production of biobased SA.
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Affiliation(s)
- Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China
| | - Yutao Zhong
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China
| | - Zhijie Sun
- Marine Biology Institute, Shantou University, 515063, Shantou, P. R. China
| | - Zhennan Jiang
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China
| | - Jingyu Deng
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China
| | - Qian Wang
- National Glycoengineering Research Center, Shandong University, 266237, Qingdao, P. R. China
| | - Jens Nielsen
- Department of Life Sciences, Chalmers University of Technology, Gothenburg, SE41296, Sweden
- BioInnovation Institute, Copenhagen N, DK2200, Denmark
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China.
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, 266237, Qingdao, P. R. China.
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McLean R, Schwander T, Diehl C, Cortina NS, Paczia N, Zarzycki J, Erb TJ. Exploring alternative pathways for the in vitro establishment of the HOPAC cycle for synthetic CO 2 fixation. Sci Adv 2023; 9:eadh4299. [PMID: 37315145 DOI: 10.1126/sciadv.adh4299] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Accepted: 05/08/2023] [Indexed: 06/16/2023]
Abstract
Nature has evolved eight different pathways for the capture and conversion of CO2, including the Calvin-Benson-Bassham cycle of photosynthesis. Yet, these pathways underlie constrains and only represent a fraction of the thousands of theoretically possible solutions. To overcome the limitations of natural evolution, we introduce the HydrOxyPropionyl-CoA/Acrylyl-CoA (HOPAC) cycle, a new-to-nature CO2-fixation pathway that was designed through metabolic retrosynthesis around the reductive carboxylation of acrylyl-CoA, a highly efficient principle of CO2 fixation. We realized the HOPAC cycle in a step-wise fashion and used rational engineering approaches and machine learning-guided workflows to further optimize its output by more than one order of magnitude. Version 4.0 of the HOPAC cycle encompasses 11 enzymes from six different organisms, converting ~3.0 mM CO2 into glycolate within 2 hours. Our work moves the hypothetical HOPAC cycle from a theoretical design into an established in vitro system that forms the basis for different potential applications.
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Affiliation(s)
- Richard McLean
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Thomas Schwander
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Christoph Diehl
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Niña Socorro Cortina
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Nicole Paczia
- Core Facility for Metabolomics and Small Molecule Mass Spectrometry, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Zarzycki
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Tobias J Erb
- Department of Biochemistry and Synthetic Metabolism, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
- SYNMIKRO Center of Synthetic Microbiology, Marburg, Germany
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Chaudhry S, Zurbriggen R, Preza M, Kämpfer T, Kaethner M, Memedovski R, Scorrano N, Hemphill A, Doggett JS, Lundström-Stadelmann B. Dual inhibition of the Echinococcus multilocularis energy metabolism. Front Vet Sci 2022; 9:981664. [PMID: 35990276 PMCID: PMC9388906 DOI: 10.3389/fvets.2022.981664] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 07/18/2022] [Indexed: 11/13/2022] Open
Abstract
Alveolar echinococcosis is caused by the metacestode stage of the zoonotic parasite Echinococcus multilocularis. Current chemotherapeutic treatment options rely on benzimidazoles, which have limited curative capabilities and can cause severe side effects. Thus, novel treatment options are urgently needed. In search for novel targetable pathways we focused on the mitochondrial energy metabolism of E. multilocularis. The parasite relies hereby on two pathways: The classical oxidative phosphorylation including the electron transfer chain (ETC), and the anaerobic malate dismutation (MD). We screened 13 endochin-like quinolones (ELQs) in vitro for their activities against two isolates of E. multilocularis metacestodes and isolated germinal layer cells by the phosphoglucose isomerase (PGI) assay and the CellTiter Glo assay. For the five most active ELQs (ELQ-121, ELQ-136, ELQ-271, ELQ-400, and ELQ-437), EC50 values against metacestodes were assessed by PGI assay, and IC50 values against mammalian cells were measured by Alamar Blue assay. Further, the gene sequence of the proposed target, the mitochondrial cytochrome b, was analyzed. This allowed for a limited structure activity relationship study of ELQs against E. multilocularis, including analyses of the inhibition of the two functional sites of the cytochrome b. By applying the Seahorse XFp Extracellular Flux Analyzer, oxygen consumption assays showed that ELQ-400 inhibits the E. multilocularis cytochrome bc1 complex under normoxic conditions. When tested under anaerobic conditions, ELQ-400 was hardly active against E. multilocularis metacestodes. These results were confirmed by transmission electron microscopy. ELQ-400 treatment increased levels of parasite-released succinate, the final electron acceptor of the MD. This suggests that the parasite switched to MD for energy generation. Therefore, MD was inhibited with quinazoline, which did not induce damage to metacestodes under anaerobic conditions. However, it reduced the production of succinate compared to control treated parasites (i.e., inhibited the MD). The combination treatment with quinazoline strongly improved the activity of the bc1 inhibitor ELQ-400 against E. multilocularis metacestodes under anaerobic conditions. We conclude that simultaneous targeting of the ETC and the MD of E. multilocularis is a possible novel treatment approach for alveolar echinococcosis, and possibly also other foodborne diseases inflicted by platyhelminths, which cause substantial economic losses in livestock industry.
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Affiliation(s)
- Sheena Chaudhry
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Raphael Zurbriggen
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Matías Preza
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Tobias Kämpfer
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Marc Kaethner
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- Graduate School for Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Roman Memedovski
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Nathalie Scorrano
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Andrew Hemphill
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Joseph Stone Doggett
- Department of Infectious Diseases and Pathobiology, Oregon Health and Science University, Portland, OR, United States
- Department of Infectious Diseases and Pathobiology, Veterans Affairs Portland Health Care System, Portland, OR, United States
| | - Britta Lundström-Stadelmann
- Institute of Parasitology, Vetsuisse Faculty, University of Bern, Bern, Switzerland
- *Correspondence: Britta Lundström-Stadelmann
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Davoodi A, Eslami S, Fakhar M, Aazadbakht M, Montazeri M, Khoshvishkaie E, Keighobadi M. Aurothiomalate-Based Drugs as Potentially Novel Agents Against Leishmania major: A Mini Review. Acta Parasitol 2022; 67:640-647. [PMID: 35380401 DOI: 10.1007/s11686-022-00536-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 03/10/2022] [Indexed: 12/01/2022]
Abstract
PURPOSE Leishmaniasis is a major public health problem worldwide in many parts of the world. Current anti-leishmanial drugs have only limited clinical efficacy. Aurothiomalate derivatives are useful for treating rheumatoid arthritis, but have emerged as a promising therapeutic candidate for leishmaniasis. This paper gives a review of the literature about the usefulness of aurothiomalate derivatives against leishmaniasis. METHODS In this study, we reviewed the proposed mechanisms of action of aurothiomalate and related compounds on the metabolism of L. major and collected data by searching relevant articles. RESULTS Aurothiomalate-based drugs could be effective against leishmaniasis through two direct and indirect mechanisms: first, cytotoxic effects on parasites via thiomalate's false substrate role in the citric acid cycle against malate; and second, immunosuppressive and anti-inflammatory effects of aurothiomalate derivatives with prostaglandin production inhibitory effects. CONCLUSIONS The current study documented that aurothiomalate-based drugs could be effective against leishmaniasis through two direct and indirect mechanisms of action. Gold thiomalate as a promising hit should be evaluated against L. major in vitro and in vivo conditions in the future.
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Affiliation(s)
- Ali Davoodi
- Department of Pharmacognosy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Shahram Eslami
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, School of Medicine, Mazandaran University of Medical Sciences, Farah Abad, 48471-91971, Sari, Iran
| | - Mahdi Fakhar
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, School of Medicine, Mazandaran University of Medical Sciences, Farah Abad, 48471-91971, Sari, Iran.
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Hydatid Cyst, Mazandaran Branch, Mazandaran University of Medical Sciences, Sari, Iran.
| | - Mohammad Aazadbakht
- Department of Pharmacognosy, Faculty of Pharmacy, Mazandaran University of Medical Sciences, Sari, Iran
| | - Mahbobeh Montazeri
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, School of Medicine, Mazandaran University of Medical Sciences, Farah Abad, 48471-91971, Sari, Iran
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Hydatid Cyst, Mazandaran Branch, Mazandaran University of Medical Sciences, Sari, Iran
| | - Elnaz Khoshvishkaie
- Pharmaceutical Cares Department, Ayatollah Khamenei Hospital, Mazandaran University of Medical Sciences, Abbas Abad, Iran
| | - Masoud Keighobadi
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Lophomoniasis and Toxoplasmosis, School of Medicine, Mazandaran University of Medical Sciences, Farah Abad, 48471-91971, Sari, Iran.
- Toxoplasmosis Research Center, Communicable Diseases Institute, Iranian National Registry Center for Hydatid Cyst, Mazandaran Branch, Mazandaran University of Medical Sciences, Sari, Iran.
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Malubhoy Z, Bahia FM, de Valk SC, de Hulster E, Rendulić T, Ortiz JPR, Xiberras J, Klein M, Mans R, Nevoigt E. Carbon dioxide fixation via production of succinic acid from glycerol in engineered Saccharomyces cerevisiae. Microb Cell Fact 2022; 21:102. [PMID: 35643577 PMCID: PMC9148483 DOI: 10.1186/s12934-022-01817-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/06/2022] [Indexed: 12/21/2022] Open
Abstract
Background The microbial production of succinic acid (SA) from renewable carbon sources via the reverse TCA (rTCA) pathway is a process potentially accompanied by net-fixation of carbon dioxide (CO2). Among reduced carbon sources, glycerol is particularly attractive since it allows a nearly twofold higher CO2-fixation yield compared to sugars. Recently, we described an engineered Saccharomyces cerevisiae strain which allowed SA production in synthetic glycerol medium with a maximum yield of 0.23 Cmol Cmol−1. The results of that previous study suggested that the glyoxylate cycle considerably contributed to SA accumulation in the respective strain. The current study aimed at improving the flux into the rTCA pathway accompanied by a higher CO2-fixation and SA yield. Results By changing the design of the expression cassettes for the rTCA pathway, overexpressing PYC2, and adding CaCO3 to the batch fermentations, an SA yield on glycerol of 0.63 Cmol Cmol−1 was achieved (i.e. 47.1% of the theoretical maximum). The modifications in this 2nd-generation SA producer improved the maximum biomass-specific glycerol consumption rate by a factor of nearly four compared to the isogenic baseline strain solely equipped with the dihydroxyacetone (DHA) pathway for glycerol catabolism. The data also suggest that the glyoxylate cycle did not contribute to the SA production in the new strain. Cultivation conditions which directly or indirectly increased the concentration of bicarbonate, led to an accumulation of malate in addition to the predominant product SA (ca. 0.1 Cmol Cmol−1 at the time point when SA yield was highest). Off-gas analysis in controlled bioreactors with CO2-enriched gas-phase indicated that CO2 was fixed during the SA production phase. Conclusions The data strongly suggest that a major part of dicarboxylic acids in our 2nd-generation SA-producer was formed via the rTCA pathway enabling a net fixation of CO2. The greatly increased capacity of the rTCA pathway obviously allowed successful competition with other pathways for the common precursor pyruvate. The overexpression of PYC2 and the increased availability of bicarbonate, the co-substrate for the PYC reaction, further strengthened this capacity. The achievements are encouraging to invest in future efforts establishing a process for SA production from (crude) glycerol and CO2. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01817-1.
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Bertsova YV, Serebryakova MV, Baykov AA, Bogachev AV. A Novel, NADH-Dependent Acrylate Reductase in Vibrio harveyi. Appl Environ Microbiol 2022;:e0051922. [PMID: 35612301 DOI: 10.1128/aem.00519-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Bacteria coping with oxygen deficiency use alternative terminal electron acceptors for NADH regeneration, particularly fumarate. Fumarate is reduced by the FAD_binding_2 domain of cytoplasmic fumarate reductase in many bacteria. The variability of the primary structure of this domain in homologous proteins suggests the existence of reducing activities with different specificities. Here, we produced and characterized one such protein encoded in the Vibrio harveyi genome (GenBank ID: AIV07243) and found it to be a specific NADH:acrylate oxidoreductase (ARD). This previously unknown enzyme is formed by the OYE-like, FMN_bind, and FAD_binding_2 domains and contains covalently bound flavin mononucleotide (FMN) and noncovalently bound flavin adenine dinucleotide (FAD) and FMN in a ratio of 1:1:1. The covalently bound FMN is absolutely required for activity and is attached by the specific flavin transferase, ApbE, to the FMN_bind domain. Quantitative reverse transcription PCR (RT-qPCR) and activity measurements indicated dramatic stimulation of ARD biosynthesis by acrylate in the V. harveyi cells grown aerobically. In contrast, the ard gene expression in the cells grown anaerobically without acrylate was higher than that in aerobic cultures and increased only 2-fold in the presence of acrylate. These findings suggest that the principal role of ARD in Vibrio is energy-saving detoxification of acrylate coming from the environment. IMPORTANCE The benefits of the massive genomic information accumulated in recent years for biological sciences have been limited by the lack of data on the function of most gene products. Approximately half of the known prokaryotic genes are annotated as "proteins with unknown functions," and many other genes are annotated incorrectly. Thus, the functional and structural characterization of the products of such genes, including identification of all existing enzymatic activities, is a pressing issue in modern biochemistry. In this work, we have shown that the product of the V. harveyi ard gene exhibits a yet-undescribed NADH:acrylate oxidoreductase activity. This activity may allow acrylate detoxification and its use as a terminal electron acceptor in anaerobic or substrate in aerobic respiration of marine and other bacteria.
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Fall F, Mamede L, Schioppa L, Ledoux A, De Tullio P, Michels P, Frédérich M, Quetin-Leclercq J. Trypanosoma brucei: Metabolomics for analysis of cellular metabolism and drug discovery. Metabolomics 2022; 18:20. [PMID: 35305174 DOI: 10.1007/s11306-022-01880-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 03/12/2022] [Indexed: 11/28/2022]
Abstract
BACKGROUND Trypanosoma brucei is the causative agent of Human African Trypanosomiasis (also known as sleeping sickness), a disease causing serious neurological disorders and fatal if left untreated. Due to its lethal pathogenicity, a variety of treatments have been developed over the years, but which have some important limitations such as acute toxicity and parasite resistance. Metabolomics is an innovative tool used to better understand the parasite's cellular metabolism, and identify new potential targets, modes of action and resistance mechanisms. The metabolomic approach is mainly associated with robust analytical techniques, such as NMR and Mass Spectrometry. Applying these tools to the trypanosome parasite is, thus, useful for providing new insights into the sleeping sickness pathology and guidance towards innovative treatments. AIM OF REVIEW The present review aims to comprehensively describe the T. brucei biology and identify targets for new or commercialized antitrypanosomal drugs. Recent metabolomic applications to provide a deeper knowledge about the mechanisms of action of drugs or potential drugs against T. brucei are highlighted. Additionally, the advantages of metabolomics, alone or combined with other methods, are discussed. KEY SCIENTIFIC CONCEPTS OF REVIEW Compared to other parasites, only few studies employing metabolomics have to date been reported on Trypanosoma brucei. Published metabolic studies, treatments and modes of action are discussed. The main interest is to evaluate the metabolomics contribution to the understanding of T. brucei's metabolism.
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Affiliation(s)
- Fanta Fall
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier B1 72.03, B-1200, Brussels, Belgium.
| | - Lucia Mamede
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research On Medicines (CIRM), University of Liège, Liège, Belgium
| | - Laura Schioppa
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier B1 72.03, B-1200, Brussels, Belgium
| | - Allison Ledoux
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research On Medicines (CIRM), University of Liège, Liège, Belgium
| | - Pascal De Tullio
- Metabolomics Group, Center of Interdisciplinary Research On Medicines (CIRM), University of Liège, Liège, Belgium
| | - Paul Michels
- Centre for Immunity, Infection and Evolution (CIIE) and Centre for Translational and Chemical Biology (CTCB), School of Biological Sciences, The University of Edinburgh, Edinburgh, Scotland
| | - Michel Frédérich
- Laboratory of Pharmacognosy, Center of Interdisciplinary Research On Medicines (CIRM), University of Liège, Liège, Belgium
| | - Joëlle Quetin-Leclercq
- Pharmacognosy Research Group, Louvain Drug Research Institute (LDRI), UCLouvain, Avenue E. Mounier B1 72.03, B-1200, Brussels, Belgium
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Deka RK, Deka A, Liu WZ, Norgard MV, Brautigam CA. Inhibition of bacterial FMN transferase: A potential avenue for countering antimicrobial resistance. Protein Sci 2022; 31:545-551. [PMID: 34796555 PMCID: PMC8819833 DOI: 10.1002/pro.4241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/01/2021] [Accepted: 11/15/2021] [Indexed: 02/03/2023]
Abstract
Antibiotic resistance is a challenge for the control of bacterial infections. In an effort to explore unconventional avenues for antibacterial drug development, we focused on the FMN-transferase activity of the enzyme Ftp from the syphilis spirochete, Treponema pallidum (Ftp_Tp). This enzyme, which is only found in prokaryotes and trypanosomatids, post-translationally modifies proteins in the periplasm, covalently linking FMN (from FAD) to proteins that typically are important for establishing an essential electrochemical gradient across the cytoplasmic membrane. As such, Ftp inhibitors potentially represent a new class of antimicrobials. Previously, we showed that AMP is both a product of the Ftp_tp-catalyzed reaction and an inhibitor of the enzyme. As a preliminary step in exploiting this property to develop a novel Ftp_Tp inhibitor, we have used structural and solution studies to examine the inhibitory and enzyme-binding properties of several adenine-based nucleosides, with particular focus on the 2-position of the purine ring. Implications for future drug design are discussed.
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Affiliation(s)
- Ranjit K. Deka
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA
| | | | - Wei Z. Liu
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA
| | | | - Chad A. Brautigam
- Department of MicrobiologyUT Southwestern Medical CenterDallasTexasUSA,Department of BiophysicsUT Southwestern Medical CenterDallasTexasUSA
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11
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Shaw S, Knüsel S, Abbühl D, Naguleswaran A, Etzensperger R, Benninger M, Roditi I. Cyclic AMP signalling and glucose metabolism mediate pH taxis by African trypanosomes. Nat Commun 2022; 13:603. [PMID: 35105902 PMCID: PMC8807625 DOI: 10.1038/s41467-022-28293-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/18/2022] [Indexed: 01/20/2023] Open
Abstract
The collective movement of African trypanosomes on semi-solid surfaces, known as social motility, is presumed to be due to migration factors and repellents released by the parasites. Here we show that procyclic (insect midgut) forms acidify their environment as a consequence of glucose metabolism, generating pH gradients by diffusion. Early and late procyclic forms exhibit self-organising properties on agarose plates. While early procyclic forms are repelled by acid and migrate outwards, late procyclic forms remain at the inoculation site. Furthermore, trypanosomes respond to exogenously formed pH gradients, with both early and late procyclic forms being attracted to alkali. pH taxis is mediated by multiple cyclic AMP effectors: deletion of one copy of adenylate cyclase ACP5, or both copies of the cyclic AMP response protein CARP3, abrogates the response to acid, while deletion of phosphodiesterase PDEB1 completely abolishes pH taxis. The ability to sense pH is biologically relevant as trypanosomes experience large changes as they migrate through their tsetse host. Supporting this, a CARP3 null mutant is severely compromised in its ability to establish infections in flies. Based on these findings, we propose that the expanded family of adenylate cyclases in trypanosomes might govern other chemotactic responses in their two hosts. African trypanosomes collectively move in a process called social motility. Here, the authors show that procyclic forms acidify their environment as a consequence of glucose metabolism, generating pH gradients by diffusion that are sensed via cyclic AMP signalling. Parasite mutants defective in cAMP signaling are inhibited in fly infection.
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Affiliation(s)
- Sebastian Shaw
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Graduate School of Cellular and Biomedical Sciences, University of Bern, Bern, Switzerland
| | - Sebastian Knüsel
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Daniel Abbühl
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | | | | | | | - Isabel Roditi
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
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12
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Škodová-Sveráková I, Záhonová K, Juricová V, Danchenko M, Moos M, Baráth P, Prokopchuk G, Butenko A, Lukáčová V, Kohútová L, Bučková B, Horák A, Faktorová D, Horváth A, Šimek P, Lukeš J. Highly flexible metabolism of the marine euglenozoan protist Diplonema papillatum. BMC Biol 2021; 19:251. [PMID: 34819072 PMCID: PMC8611851 DOI: 10.1186/s12915-021-01186-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The phylum Euglenozoa is a group of flagellated protists comprising the diplonemids, euglenids, symbiontids, and kinetoplastids. The diplonemids are highly abundant and speciose, and recent tools have rendered the best studied representative, Diplonema papillatum, genetically tractable. However, despite the high diversity of diplonemids, their lifestyles, ecological functions, and even primary energy source are mostly unknown. RESULTS We designed a metabolic map of D. papillatum cellular bioenergetic pathways based on the alterations of transcriptomic, proteomic, and metabolomic profiles obtained from cells grown under different conditions. Comparative analysis in the nutrient-rich and nutrient-poor media, as well as the absence and presence of oxygen, revealed its capacity for extensive metabolic reprogramming that occurs predominantly on the proteomic rather than the transcriptomic level. D. papillatum is equipped with fundamental metabolic routes such as glycolysis, gluconeogenesis, TCA cycle, pentose phosphate pathway, respiratory complexes, β-oxidation, and synthesis of fatty acids. Gluconeogenesis is uniquely dominant over glycolysis under all surveyed conditions, while the TCA cycle represents an eclectic combination of standard and unusual enzymes. CONCLUSIONS The identification of conventional anaerobic enzymes reflects the ability of this protist to survive in low-oxygen environments. Furthermore, its metabolism quickly reacts to restricted carbon availability, suggesting a high metabolic flexibility of diplonemids, which is further reflected in cell morphology and motility, correlating well with their extreme ecological valence.
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Affiliation(s)
- Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia.
| | - Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Valéria Juricová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Maksym Danchenko
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Martin Moos
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Peter Baráth
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Medirex Group Academy n.o., Trnava, Slovakia
| | - Galina Prokopchuk
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | | | - Lenka Kohútová
- Institute of Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Barbora Bučková
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Anton Horváth
- Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Petr Šimek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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13
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Bertsova YV, Oleynikov IP, Bogachev AV. A new water-soluble bacterial NADH: fumarate oxidoreductase. FEMS Microbiol Lett 2021; 367:5941483. [PMID: 33107907 DOI: 10.1093/femsle/fnaa175] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 10/22/2020] [Indexed: 11/12/2022] Open
Abstract
The cytoplasmic fumarate reductase of Klebsiella pneumoniae (FRD) is a monomeric protein which contains three prosthetic groups: noncovalently bound FMN and FAD plus a covalently bound FMN. In the present work, NADH is revealed to be an inherent electron donor for this enzyme. We found that the fumarate reductase activity of FRD significantly exceeds its NADH dehydrogenase activity. During the catalysis of NADH:fumarate oxidoreductase reaction, FRD turnover is limited by a very low rate (∼10/s) of electron transfer between the noncovalently and covalently bound FMN moieties. Induction of FRD synthesis in K. pneumoniae cells was observed only under anaerobic conditions in the presence of fumarate or malate. Enzymes with the FRD-like domain architecture are widely distributed among various bacteria and apparently comprise a new type of water-soluble NADH:fumarate oxidoreductases.
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Affiliation(s)
- Yulia V Bertsova
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Ilya P Oleynikov
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
| | - Alexander V Bogachev
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Vorobievy Gory 1/40, Moscow 119234, Russia
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14
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Michels PAM, Villafraz O, Pineda E, Alencar MB, Cáceres AJ, Silber AM, Bringaud F. Carbohydrate metabolism in trypanosomatids: New insights revealing novel complexity, diversity and species-unique features. Exp Parasitol 2021; 224:108102. [PMID: 33775649 DOI: 10.1016/j.exppara.2021.108102] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Revised: 03/13/2021] [Accepted: 03/18/2021] [Indexed: 12/16/2022]
Abstract
The human pathogenic trypanosomatid species collectively called the "TriTryp parasites" - Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp. - have complex life cycles, with each of these parasitic protists residing in a different niche during their successive developmental stages where they encounter diverse nutrients. Consequently, they adapt their metabolic network accordingly. Yet, throughout the life cycles, carbohydrate metabolism - involving the glycolytic, gluconeogenic and pentose-phosphate pathways - always plays a central role in the biology of these parasites, whether the available carbon and free energy sources are saccharides, amino acids or lipids. In this paper, we provide an updated review of the carbohydrate metabolism of the TriTryps, highlighting new data about this metabolic network, the interconnection of its pathways and the compartmentalisation of its enzymes within glycosomes, cytosol and mitochondrion. Differences in the expression of the branches of the metabolic network between the successive life-cycle stages of each of these parasitic trypanosomatids are discussed, as well as differences between them. Recent structural and kinetic studies have revealed unique regulatory mechanisms for some of the network's key enzymes with important species-specific variations. Furthermore, reports of multiple post-translational modifications of trypanosomal glycolytic enzymes suggest that additional mechanisms for stage- and/or environmental cues that regulate activity are operational in the parasites. The detailed comparison of the carbohydrate metabolism of the TriTryps has thus revealed multiple differences and a greater complexity, including for the reduced metabolic network in bloodstream-form T. brucei, than previously appreciated. Although these parasites are related, share many cytological and metabolic features and are grouped within a single taxonomic family, the differences highlighted in this review reflect their separate evolutionary tracks from a common ancestor to the extant organisms. These differences are indicative of their adaptation to the different insect vectors and niches occupied in their mammalian hosts.
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Affiliation(s)
- Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom.
| | - Oriana Villafraz
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Erika Pineda
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France
| | - Mayke B Alencar
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela.
| | - Ariel M Silber
- Laboratory of Biochemistry of Tryps, Department of Parasitology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, 05508-000, Brazil.
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, France.
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15
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Schenk R, Bachmaier S, Bringaud F, Boshart M. Efficient flavinylation of glycosomal fumarate reductase by its own ApbE domain in Trypanosoma brucei. FEBS J 2021; 288:5430-5445. [PMID: 33755328 DOI: 10.1111/febs.15812] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/08/2021] [Accepted: 03/09/2021] [Indexed: 01/26/2023]
Abstract
A subset of flavoproteins has a covalently attached flavin prosthetic group enzymatically attached via phosphoester bonding. In prokaryotes, this is catalysed by alternative pyrimidine biosynthesis E (ApbE) flavin transferases. ApbE-like domains are present in few eukaryotic taxa, for example the N-terminal domain of fumarate reductase (FRD) of Trypanosoma, a parasitic protist known as a tropical pathogen causing African sleeping sickness. We use the versatile reverse genetic tools available for Trypanosoma to investigate the flavinylation of glycosomal FRD (FRDg) in vivo in the physiological and organellar context. Using direct in-gel fluorescence detection of covalently attached flavin as proxy for activity, we show that the ApbE-like domain of FRDg has flavin transferase activity in vivo. The ApbE domain is preceded by a consensus flavinylation target motif at the extreme N terminus of FRDg, and serine 9 in this motif is essential as flavin acceptor. The preferred mode of flavinylation in the glycosome was addressed by stoichiometric expression and comparison of native and catalytically inactive ApbE domains. In addition to the trans-flavinylation activity, the ApbE domain catalyses the intramolecular cis-flavinylation with at least fivefold higher efficiency. We discuss how the higher efficiency due to unusual fusion of the ApbE domain to its substrate protein FRD may provide a selective advantage by faster FRD biogenesis during rapid metabolic adaptation of trypanosomes. The first 37 amino acids of FRDg, including the consensus motif, are sufficient as flavinylation target upon fusion to other proteins. We propose FRDg(1-37) as 4-kDa heat-stable, detergent-resistant fluorescent protein tag and suggest its use as a new tool to study glycosomal protein import.
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Affiliation(s)
- Robin Schenk
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Sabine Bachmaier
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
| | - Frédéric Bringaud
- CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Université de Bordeaux, France
| | - Michael Boshart
- Biozentrum, Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München (LMU), Martinsried, Germany
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16
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Wargnies M, Plazolles N, Schenk R, Villafraz O, Dupuy JW, Biran M, Bachmaier S, Baudouin H, Clayton C, Boshart M, Bringaud F. Metabolic selection of a homologous recombination-mediated gene loss protects Trypanosoma brucei from ROS production by glycosomal fumarate reductase. J Biol Chem 2021; 296:100548. [PMID: 33741344 PMCID: PMC8065229 DOI: 10.1016/j.jbc.2021.100548] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 03/08/2021] [Accepted: 03/15/2021] [Indexed: 11/23/2022] Open
Abstract
The genome of trypanosomatids rearranges by using repeated sequences as platforms for amplification or deletion of genomic segments. These stochastic recombination events have a direct impact on gene dosage and foster the selection of adaptive traits in response to environmental pressure. We provide here such an example by showing that the phosphoenolpyruvate carboxykinase (PEPCK) gene knockout (Δpepck) leads to the selection of a deletion event between two tandemly arranged fumarate reductase (FRDg and FRDm2) genes to produce a chimeric FRDg-m2 gene in the Δpepck∗ cell line. FRDg is expressed in peroxisome-related organelles, named glycosomes, expression of FRDm2 has not been detected to date, and FRDg-m2 is nonfunctional and cytosolic. Re-expression of FRDg significantly impaired growth of the Δpepck∗ cells, but FRD enzyme activity was not required for this negative effect. Instead, glycosomal localization as well as the covalent flavinylation motif of FRD is required to confer growth retardation and intracellular accumulation of reactive oxygen species (ROS). The data suggest that FRDg, similar to Escherichia coli FRD, can generate ROS in a flavin-dependent process by transfer of electrons from NADH to molecular oxygen instead of fumarate when the latter is unavailable, as in the Δpepck background. Hence, growth retardation is interpreted as a consequence of increased production of ROS, and rearrangement of the FRD locus liberates Δpepck∗ cells from this obstacle. Interestingly, intracellular production of ROS has been shown to be required to complete the parasitic cycle in the insect vector, suggesting that FRDg may play a role in this process.
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Affiliation(s)
- Marion Wargnies
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Bordeaux, France; Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB), UMR 5536, Bordeaux, France
| | - Nicolas Plazolles
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Bordeaux, France
| | - Robin Schenk
- Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Oriana Villafraz
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Bordeaux, France
| | | | - Marc Biran
- Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB), UMR 5536, Bordeaux, France
| | - Sabine Bachmaier
- Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München, Martinsried, Germany
| | - Hélène Baudouin
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Bordeaux, France; Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB), UMR 5536, Bordeaux, France
| | - Christine Clayton
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZBMH), Universität Heidelberg, Heidelberg, Germany
| | - Michael Boshart
- Fakultät für Biologie, Genetik, Ludwig-Maximilians-Universität München, Martinsried, Germany.
| | - Frédéric Bringaud
- Univ. Bordeaux, CNRS, Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234, Bordeaux, France; Univ. Bordeaux, CNRS, Centre de Résonance Magnétique des Systèmes Biologiques (CRMSB), UMR 5536, Bordeaux, France.
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17
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Cardoso IA, de Souza AKL, Burgess AMG, Chalmers IW, Hoffmann KF, Nonato MC. Characterization of class II fumarase from Schistosoma mansoni provides the molecular basis for selective inhibition. Int J Biol Macromol 2021; 175:406-421. [PMID: 33549669 DOI: 10.1016/j.ijbiomac.2021.01.180] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 01/20/2021] [Accepted: 01/28/2021] [Indexed: 01/01/2023]
Abstract
Schistosomiasis is a neglected tropical disease that affects more than 250 million people worldwide. The only drug available for its treatment undergoes first-pass hepatic metabolism and is not capable of preventing reinfection, which makes the search of new therapies urgently needed. Due to the essential role of fumarases in metabolism, these enzymes represent potential targets for developing novel schistosomiasis treatments. Here, we evaluate the expression profiles for class I and class II fumarases from Schistosoma mansoni (SmFHI and SmFHII, respectively), and report the complete characterization of SmFHII. The first SmFHII structure in complex with L-malate was determined at 1.85 Å resolution. The significant thermoshift observed for SmFHII in the presence of identified ligands makes the differential scanning fluorimetry an adequate technique for ligand screening. A complete kinetic characterization of SmFHII was performed, and comparison with the human fumarase (HsFH) revealed differences regarding the turnover number (kcat). Structural characterization allowed us to identify differences between SmFHII and HsFH that could be explored to design new selective inhibitors. This work represents the very first step towards validate the fumarases as drug targets to treat schistosomiasis. Our results provide the structural basis to rational search for selective ligands.
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Affiliation(s)
- Iara Aimê Cardoso
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Aline Kusumota Luiz de Souza
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil
| | - Adam Muslem George Burgess
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Iain Wyllie Chalmers
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Karl Francis Hoffmann
- The Institute of Biological, Environmental and Rural Sciences (IBERS), Aberystwyth University, Wales, United Kingdom
| | - Maria Cristina Nonato
- Laboratório de Cristalografia de Proteínas, Departamento de Ciências BioMoleculares, Faculdade de Ciências Farmacêuticas de Ribeirão Preto, Universidade de São Paulo, Ribeirão Preto, SP, Brazil.
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18
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Jinich A, Sanchez-Lengeling B, Ren H, Goldford JE, Noor E, Sanders JN, Segrè D, Aspuru-Guzik A. A thermodynamic atlas of carbon redox chemical space. Proc Natl Acad Sci U S A 2020; 117:32910-8. [PMID: 33376214 DOI: 10.1073/pnas.2005642117] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Carbon redox chemistry plays a fundamental role in biology. However, the thermodynamic and physicochemical principles underlying the rise of metabolites involved in redox biochemistry remain poorly understood. Our work introduces the theory and techniques that allow us to quantify and understand the global energy landscape of carbon redox biochemistry. We analyze the space of all possible oxidation states of linear-chain molecules with two to five carbon atoms and generate a detailed atlas of the thermodynamic stability of metabolites in comparison to nonbiological molecules. Although the emergence of life required the underlying chemistry to bootstrap itself out of equilibrium, a quantitative understanding of the environment-dependent thermodynamic landscape of prebiotic molecules will be extremely valuable for future origins of life models. Redox biochemistry plays a key role in the transduction of chemical energy in living systems. However, the compounds observed in metabolic redox reactions are a minuscule fraction of chemical space. It is not clear whether compounds that ended up being selected as metabolites display specific properties that distinguish them from nonbiological compounds. Here, we introduce a systematic approach for comparing the chemical space of all possible redox states of linear-chain carbon molecules to the corresponding metabolites that appear in biology. Using cheminformatics and quantum chemistry, we analyze the physicochemical and thermodynamic properties of the biological and nonbiological compounds. We find that, among all compounds, aldose sugars have the highest possible number of redox connections to other molecules. Metabolites are enriched in carboxylic acid functional groups and depleted of ketones and aldehydes and have higher solubility than nonbiological compounds. Upon constructing the energy landscape for the full chemical space as a function of pH and electron-donor potential, we find that metabolites tend to have lower Gibbs energies than nonbiological molecules. Finally, we generate Pourbaix phase diagrams that serve as a thermodynamic atlas to indicate which compounds are energy minima in redox chemical space across a set of pH values and electron-donor potentials. While escape from thermodynamic equilibrium toward kinetically driven states is a hallmark of life and its origin, we envision that a deeper quantitative understanding of the environment-dependent thermodynamic landscape of putative prebiotic molecules will provide a crucial reference for future origins-of-life models.
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Yang L, Henriksen MM, Hansen RS, Lübeck M, Vang J, Andersen JE, Bille S, Lübeck PS. Metabolic engineering of Aspergillus niger via ribonucleoprotein-based CRISPR-Cas9 system for succinic acid production from renewable biomass. Biotechnol Biofuels 2020; 13:206. [PMID: 33317620 PMCID: PMC7737382 DOI: 10.1186/s13068-020-01850-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 12/04/2020] [Indexed: 05/02/2023]
Abstract
BACKGROUND Succinic acid has great potential to be a new bio-based building block for deriving a number of value-added chemicals in industry. Bio-based succinic acid production from renewable biomass can provide a feasible approach to partially alleviate the dependence of global manufacturing on petroleum refinery. To improve the economics of biological processes, we attempted to explore possible solutions with a fungal cell platform. In this study, Aspergillus niger, a well-known industrial production organism for bio-based organic acids, was exploited for its potential for succinic acid production. RESULTS With a ribonucleoprotein (RNP)-based CRISPR-Cas9 system, consecutive genetic manipulations were realized in engineering of the citric acid-producing strain A. niger ATCC 1015. Two genes involved in production of two byproducts, gluconic acid and oxalic acid, were disrupted. In addition, an efficient C4-dicarboxylate transporter and a soluble NADH-dependent fumarate reductase were overexpressed. The resulting strain SAP-3 produced 17 g/L succinic acid while there was no succinic acid detected at a measurable level in the wild-type strain using a synthetic substrate. Furthermore, two cultivation parameters, temperature and pH, were investigated for their effects on succinic acid production. The highest amount of succinic acid was obtained at 35 °C after 3 days, and low culture pH had inhibitory effects on succinic acid production. Two types of renewable biomass were explored as substrates for succinic acid production. After 6 days, the SAP-3 strain was capable of producing 23 g/L and 9 g/L succinic acid from sugar beet molasses and wheat straw hydrolysate, respectively. CONCLUSIONS In this study, we have successfully applied the RNP-based CRISPR-Cas9 system in genetic engineering of A. niger and significantly improved the succinic acid production in the engineered strain. The studies on cultivation parameters revealed the impacts of pH and temperature on succinic acid production and the future challenges in strain development. The feasibility of using renewable biomass for succinic acid production by A. niger has been demonstrated with molasses and wheat straw hydrolysate.
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Affiliation(s)
- Lei Yang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark.
| | - Mikkel Møller Henriksen
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Rasmus Syrach Hansen
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Mette Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
| | - Jesper Vang
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
- Disease Data Intelligence, Department of Health Technology Bioinformatics, Technical University of Denmark, Bldg. 208, 2800, KemitorvetKgs. Lyngby, Denmark
| | - Julie Egelund Andersen
- Section of Microbiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Signe Bille
- Section of Cell and Neurobiology, Department of Biology, University of Copenhagen, Universitetsparken 15, 2100, Copenhagen, Denmark
| | - Peter Stephensen Lübeck
- Section for Sustainable Biotechnology, Department of Chemistry and Bioscience, Aalborg University Copenhagen, A. C. Meyers Vænge 15, 2450, Copenhagen SV, Denmark
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Martínez-Flórez A, Galizzi M, Izquierdo L, Bustamante JM, Rodriguez A, Rodriguez F, Rodríguez-Cortés A, Alberola J. Repurposing bioenergetic modulators against protozoan parasites responsible for tropical diseases. Int J Parasitol Drugs Drug Resist 2020; 14:17-27. [PMID: 32829099 DOI: 10.1016/j.ijpddr.2020.07.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 07/17/2020] [Accepted: 07/20/2020] [Indexed: 12/30/2022]
Abstract
Malaria, leishmaniasis and trypanosomiasis are arthropod-borne, parasitic diseases that constitute a major global health problem. They are generally found in developing countries, where lack of access to preventive tools and treatment hinders their management. Because these parasites share an increased demand on glucose consumption with most cancer cells, six compounds used in anti-tumoral research were selected to be tested as antiparasitic agents in in vitro models of Leishmania infantum, Trypanosoma brucei, T. cruzi, and Plasmodium falciparum: dichloroacetic acid (DCA), 3-bromopyruvic acid (3BP), 2-deoxy-D-glucose (2DG), lonidamine (LND), metformin (MET), and sirolimus (SIR). No parasite-killing activity was found in L. infantum promastigotes, whereas DCA and 3BP reduced the burden of intra-macrophagic amastigotes. For T. brucei all selected compounds, but 2DG, decreased parasite survival. DCA, 2DG, LND and MET showed parasite-killing activity in T. cruzi. Finally, anti-plasmodial activity was found for DCA, 2DG, LND, MET and SIR. These results reinforce the hypothesis that drugs with proven efficacy in the treatment of cancer by interfering with ATP production, proliferation, and survival cell strategies might be useful in treating threatening parasitic diseases and provide new opportunities for their repurposing. Parasitic diseases are prevalent among the poorest of the poor. Some parasitic protists degrade glucose into CO2 even aerobically making this a target. Degrading glucose into CO2 (Warburg effect) is also characteristic for cancer cells. Repurposing cancer glycolysis blockers may provide cost-effective treatments for the poorest.
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21
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Paes MC, Saraiva FMS, Nogueira NP, Vieira CSD, Dias FA, Rossini A, Coelho VL, Pane A, Sang F, Alcocer M. Gene expression profiling of Trypanosoma cruzi in the presence of heme points to glycosomal metabolic adaptation of epimastigotes inside the vector. PLoS Negl Trop Dis 2020; 14:e0007945. [PMID: 31895927 PMCID: PMC6959606 DOI: 10.1371/journal.pntd.0007945] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2019] [Revised: 01/14/2020] [Accepted: 11/22/2019] [Indexed: 11/18/2022] Open
Abstract
Chagas disease, also known as American trypanosomiasis, is a potentially life-threatening illness caused by the protozoan parasite, Trypanosoma cruzi, and is transmitted by triatomine insects during its blood meal. Proliferative epimastigotes forms thrive inside the insects in the presence of heme (iron protoporphyrin IX), an abundant product of blood digestion, however little is known about the metabolic outcome of this signaling molecule in the parasite. Trypanosomatids exhibit unusual gene transcription employing a polycistronic transcription mechanism through trans-splicing that regulates its life cycle. Using the Deep Seq transcriptome sequencing we characterized the heme induced transcriptome of epimastigotes and determined that most of the upregulated genes were related to glucose metabolism inside the glycosomes. These results were supported by the upregulation of glycosomal isoforms of PEPCK and fumarate reductase of heme-treated parasites, implying that the fermentation process was favored. Moreover, the downregulation of mitochondrial gene enzymes in the presence of heme also supported the hypothesis that heme shifts the parasite glycosomal glucose metabolism towards aerobic fermentation. These results are examples of the environmental metabolic plasticity inside the vector supporting ATP production, promoting epimastigotes proliferation and survival.
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Affiliation(s)
- Marcia C. Paes
- Laboratório de Interação Tripanossomatídeos e Vetores—Departamento de Bioquímica, IBRAG–UERJ–Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia—Entomologia Molecular (INCT-EM)–Brazil
- * E-mail: (MCP); (MA)
| | - Francis M. S. Saraiva
- Laboratório de Interação Tripanossomatídeos e Vetores—Departamento de Bioquímica, IBRAG–UERJ–Rio de Janeiro, Brazil
| | - Natália P. Nogueira
- Laboratório de Interação Tripanossomatídeos e Vetores—Departamento de Bioquímica, IBRAG–UERJ–Rio de Janeiro, Brazil
- Instituto Nacional de Ciência e Tecnologia—Entomologia Molecular (INCT-EM)–Brazil
| | - Carolina S. D. Vieira
- Laboratório de Interação Tripanossomatídeos e Vetores—Departamento de Bioquímica, IBRAG–UERJ–Rio de Janeiro, Brazil
| | - Felipe A. Dias
- Instituto Nacional de Ciência e Tecnologia—Entomologia Molecular (INCT-EM)–Brazil
- Laboratório de Bioquímica de Artrópodes Hematófagos, Instituto de Bioquímica Médica, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Ana Rossini
- Laboratório de Toxicologia e Biologia Molecular, Departamento de Bioquímica, IBRAG- UERJ- Rio de Janeiro, Brazil
| | - Vitor Lima Coelho
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Attilio Pane
- Instituto de Ciências Biomédicas, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fei Sang
- Deep Seq, School of Life Sciences, University of Nottingham, Nottingham, United Kingdom
| | - Marcos Alcocer
- School of Biosciences, University of Nottingham, United Kingdom
- * E-mail: (MCP); (MA)
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Hennig K, Abi-Ghanem J, Bunescu A, Meniche X, Biliaut E, Ouattara AD, Lewis MD, Kelly JM, Braillard S, Courtemanche G, Chatelain E, Béquet F. Metabolomics, lipidomics and proteomics profiling of myoblasts infected with Trypanosoma cruzi after treatment with different drugs against Chagas disease. Metabolomics 2019; 15:117. [PMID: 31440849 DOI: 10.1007/s11306-019-1583-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2019] [Accepted: 08/17/2019] [Indexed: 01/11/2023]
Abstract
INTRODUCTION Chagas disease, the most important parasitic infection in Latin America, is caused by the intracellular protozoan Trypanosoma cruzi. To treat this disease, only two nitroheterocyclic compounds with toxic side effects exist and frequent treatment failures are reported. Hence there is an urgent need to develop new drugs. Recently, metabolomics has become an efficient and cost-effective strategy for dissecting drug mode of action, which has been applied to bacteria as well as parasites, such as different Trypanosome species and forms. OBJECTIVES We assessed if the metabolomics approach can be applied to study drug action of the intracellular amastigote form of T. cruzi in a parasite-host cell system. METHODS We applied a metabolic fingerprinting approach (DI-MS and NMR) to evaluate metabolic changes induced by six different (candidate) drugs in a parasite-host cell system. In a second part of our study, we analyzed the impact of two drugs on polar metabolites, lipid and proteins to evaluate if affected pathways can be identified. RESULTS Metabolic signatures, obtained by the fingerprinting approach, resulted in three different clusters. Two can be explained by already known of mode actions, whereas the three experimental drugs formed a separate cluster. Significant changes induced by drug action were observed in all the three metabolic fractions (polar metabolites, lipids and proteins). We identified a general impact on the TCA cycle, but no specific pathways could be attributed to drug action, which might be caused by a high percentage of common metabolome between a eukaryotic host cell and a eukaryotic parasite. Additionally, ion suppression effects due to differences in abundance between host cells and parasites may have occurred. CONCLUSION We validated the metabolic fingerprinting approach to a complex host-cell parasite system. This technique can potentially be applied in the early stage of drug discovery and could help to prioritize early leads or reconfirmed hits for further development.
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Affiliation(s)
- K Hennig
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - J Abi-Ghanem
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - A Bunescu
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - X Meniche
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - E Biliaut
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - A D Ouattara
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France
| | - M D Lewis
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - J M Kelly
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - S Braillard
- Drugs for Neglected Diseases Initiative (DNDi), 15 Chemin Louis-Dunant, 1202, Geneva, Switzerland
| | | | - E Chatelain
- Drugs for Neglected Diseases Initiative (DNDi), 15 Chemin Louis-Dunant, 1202, Geneva, Switzerland
| | - F Béquet
- BIOASTER, 40 avenue Tony Garnier, 69007, Lyon, France.
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Acosta H, Burchmore R, Naula C, Gualdrón-López M, Quintero-Troconis E, Cáceres AJ, Michels PAM, Concepción JL, Quiñones W. Proteomic analysis of glycosomes from Trypanosoma cruzi epimastigotes. Mol Biochem Parasitol 2019; 229:62-74. [PMID: 30831156 PMCID: PMC7082770 DOI: 10.1016/j.molbiopara.2019.02.008] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/25/2019] [Accepted: 02/27/2019] [Indexed: 12/20/2022]
Abstract
In Trypanosoma cruzi, the causal agent of Chagas disease, the first seven steps of glycolysis are compartmentalized in glycosomes, which are authentic but specialized peroxisomes. Besides glycolysis, activity of enzymes of other metabolic processes have been reported to be present in glycosomes, such as β-oxidation of fatty acids, purine salvage, pentose-phosphate pathway, gluconeogenesis and biosynthesis of ether-lipids, isoprenoids, sterols and pyrimidines. In this study, we have purified glycosomes from T. cruzi epimastigotes, collected the soluble and membrane fractions of these organelles, and separated peripheral and integral membrane proteins by Na2CO3 treatment and osmotic shock. Proteomic analysis was performed on each of these fractions, allowing us to confirm the presence of enzymes involved in various metabolic pathways as well as identify new components of this parasite's glycosomes.
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Affiliation(s)
- Héctor Acosta
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Richard Burchmore
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Christina Naula
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Melisa Gualdrón-López
- Instituto Salud Global, Hospital Clinic-Universitat de Barcelona, and Institute for Health Sciences Trias i Pujol, Barcelona, Spain
| | - Ender Quintero-Troconis
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, The University of Edinburgh, Edinburgh, EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, Mérida, 5101, Venezuela.
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Wargnies M, Bertiaux E, Cahoreau E, Ziebart N, Crouzols A, Morand P, Biran M, Allmann S, Hubert J, Villafraz O, Millerioux Y, Plazolles N, Asencio C, Rivière L, Rotureau B, Boshart M, Portais JC, Bringaud F. Gluconeogenesis is essential for trypanosome development in the tsetse fly vector. PLoS Pathog 2018; 14:e1007502. [PMID: 30557412 DOI: 10.1371/journal.ppat.1007502] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 12/31/2018] [Accepted: 12/04/2018] [Indexed: 11/19/2022] Open
Abstract
In the glucose-free environment that is the midgut of the tsetse fly vector, the procyclic form of Trypanosoma brucei primarily uses proline to feed its central carbon and energy metabolism. In these conditions, the parasite needs to produce glucose 6-phosphate (G6P) through gluconeogenesis from metabolism of non-glycolytic carbon source(s). We showed here that two phosphoenolpyruvate-producing enzymes, PEP carboxykinase (PEPCK) and pyruvate phosphate dikinase (PPDK) have a redundant function for the essential gluconeogenesis from proline. Indeed, incorporation of 13C-enriched proline into G6P was abolished in the PEPCK/PPDK null double mutant (Δppdk/Δpepck), but not in the single Δppdk and Δpepck mutant cell lines. The procyclic trypanosome also uses the glycerol conversion pathway to feed gluconeogenesis, since the death of the Δppdk/Δpepck double null mutant in glucose-free conditions is only observed after RNAi-mediated down-regulation of the expression of the glycerol kinase, the first enzyme of the glycerol conversion pathways. Deletion of the gene encoding fructose-1,6-bisphosphatase (Δfbpase), a key gluconeogenic enzyme irreversibly producing fructose 6-phosphate from fructose 1,6-bisphosphate, considerably reduced, but not abolished, incorporation of 13C-enriched proline into G6P. In addition, the Δfbpase cell line is viable in glucose-free conditions, suggesting that an alternative pathway can be used for G6P production in vitro. However, FBPase is essential in vivo, as shown by the incapacity of the Δfbpase null mutant to colonise the fly vector salivary glands, while the parental phenotype is restored in the Δfbpase rescued cell line re-expressing FBPase. The essential role of FBPase for the development of T. brucei in the tsetse was confirmed by taking advantage of an in vitro differentiation assay based on the RNA-binding protein 6 over-expression, in which the procyclic forms differentiate into epimastigote forms but not into mammalian-infective metacyclic parasites. In total, morphology, immunofluorescence and cytometry analyses showed that the differentiation of the epimastigote stages into the metacyclic forms is abolished in the Δfbpase mutant.
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Kim S, Kim CM, Son YJ, Choi JY, Siegenthaler RK, Lee Y, Jang TH, Song J, Kang H, Kaiser CA, Park HH. Molecular basis of maintaining an oxidizing environment under anaerobiosis by soluble fumarate reductase. Nat Commun 2018; 9:4867. [PMID: 30451826 PMCID: PMC6242907 DOI: 10.1038/s41467-018-07285-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 10/22/2018] [Indexed: 11/09/2022] Open
Abstract
Osm1 and Frd1 are soluble fumarate reductases from yeast that are critical for allowing survival under anaerobic conditions. Although they maintain redox balance during anaerobiosis, the underlying mechanism is not understood. Here, we report the crystal structure of a eukaryotic soluble fumarate reductase, which is unique among soluble fumarate reductases as it lacks a heme domain. Structural and enzymatic analyses indicate that Osm1 has a specific binding pocket for flavin molecules, including FAD, FMN, and riboflavin, catalyzing their oxidation while reducing fumarate to succinate. Moreover, ER-resident Osm1 can transfer electrons from the Ero1 FAD cofactor to fumarate either by free FAD or by a direct interaction, allowing de novo disulfide bond formation in the absence of oxygen. We conclude that soluble eukaryotic fumarate reductases can maintain an oxidizing environment under anaerobic conditions, either by oxidizing cellular flavin cofactors or by a direct interaction with flavoenzymes such as Ero1.
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Affiliation(s)
- Sunghwan Kim
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea. .,R&D Center, Polus Inc., 9 Songdomirae-ro, Yeonsu-gu, Incheon, 21984, South Korea.
| | - Chang Min Kim
- College of Pharmacy, Chung-Ang University, 06974, Seoul, South Korea
| | - Young-Jin Son
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Jae Young Choi
- Department of Biochemistry, Yeungnam University, Gyeongsan, 38541, South Korea
| | - Rahel K Siegenthaler
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Younho Lee
- College of Pharmacy and Yonsei, Institute of Pharmaceutical Sciences, Yonsei University, 85 Songdogwahak-ro, Yeonsu-gu, Incheon, 21983, Republic of Korea
| | - Tae-Ho Jang
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Jaeyoung Song
- New Drug Development Center, Daegu-Gyeongbuk Medical Innovation Foundation, Daegu, 41061, South Korea
| | - Hara Kang
- Division of Life Sciences, College of Life Science and Bioengineering, Incheon National University, Incheon, 22012, Republic of Korea
| | - Chris A Kaiser
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, 02139, USA
| | - Hyun Ho Park
- College of Pharmacy, Chung-Ang University, 06974, Seoul, South Korea.
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Jinich A, Flamholz A, Ren H, Kim SJ, Sanchez-Lengeling B, Cotton CAR, Noor E, Aspuru-Guzik A, Bar-Even A. Quantum chemistry reveals thermodynamic principles of redox biochemistry. PLoS Comput Biol 2018; 14:e1006471. [PMID: 30356318 PMCID: PMC6218094 DOI: 10.1371/journal.pcbi.1006471] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Revised: 11/05/2018] [Accepted: 08/29/2018] [Indexed: 01/28/2023] Open
Abstract
Thermodynamics dictates the structure and function of metabolism. Redox reactions drive cellular energy and material flow. Hence, accurately quantifying the thermodynamics of redox reactions should reveal design principles that shape cellular metabolism. However, only few redox potentials have been measured, and mostly with inconsistent experimental setups. Here, we develop a quantum chemistry approach to calculate redox potentials of biochemical reactions and demonstrate our method predicts experimentally measured potentials with unparalleled accuracy. We then calculate the potentials of all redox pairs that can be generated from biochemically relevant compounds and highlight fundamental trends in redox biochemistry. We further address the question of why NAD/NADP are used as primary electron carriers, demonstrating how their physiological potential range fits the reactions of central metabolism and minimizes the concentration of reactive carbonyls. The use of quantum chemistry can revolutionize our understanding of biochemical phenomena by enabling fast and accurate calculation of thermodynamic values. Redox reactions define the energetic constraints within which life can exist. However, measurements of reduction potentials are scarce and unstandardized, and current prediction methods fall short of desired accuracy and coverage. Here, we harness quantum chemistry tools to enable the high-throughput prediction of reduction potentials with unparalleled accuracy. We calculate the reduction potentials of all redox pairs that can be generated using known biochemical compounds. This high-resolution dataset enables us to uncover global trends in metabolism, including the differences between and within oxidoreductase groups. We further demonstrate that the redox potential of NAD(P) optimally satisfies two constraints: reversibly reducing and oxidizing the vast majority of redox reactions in central metabolism while keeping the concentration of reactive carbonyl intermediates in check.
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Affiliation(s)
- Adrian Jinich
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
- Division of Infectious Diseases, Weill Department of Medicine, Weill-Cornell Medical College, New York, New York, United States of America
| | - Avi Flamholz
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Haniu Ren
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | - Sung-Jin Kim
- Center for Systems Biology, Massachusetts General Hospital, Boston, Massachusetts, United States of America
- Department of Biomedical Engineering, Worcester Polytechnic Institute, Worcester, Massachusetts, United States of America
| | - Benjamin Sanchez-Lengeling
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts, United States of America
| | | | - Elad Noor
- Institute of Molecular Systems Biology, ETH Zurich, Zürich, Switzerland
| | - Alán Aspuru-Guzik
- Department of Chemistry and Department of Computer Science, University of Toronto, Ontario, Canada
- Vector Institute, Toronto, Ontario, Canada
- Biologically-Inspired Solar Energy Program, Canadian Institute for Advanced Research (CIFAR), Toronto, Ontario, Canada
| | - Arren Bar-Even
- Max Planck Institute of Molecular Plant Physiology, Potsdam-Golm, Germany
- * E-mail:
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27
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Serebryakova MV, Bertsova YV, Sokolov SS, Kolesnikov AA, Baykov AA, Bogachev AV. Catalytically important flavin linked through a phosphoester bond in a eukaryotic fumarate reductase. Biochimie 2018; 149:34-40. [DOI: 10.1016/j.biochi.2018.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 03/28/2018] [Indexed: 02/03/2023]
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28
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Millerioux Y, Mazet M, Bouyssou G, Allmann S, Kiema TR, Bertiaux E, Fouillen L, Thapa C, Biran M, Plazolles N, Dittrich-Domergue F, Crouzols A, Wierenga RK, Rotureau B, Moreau P, Bringaud F. De novo biosynthesis of sterols and fatty acids in the Trypanosoma brucei procyclic form: Carbon source preferences and metabolic flux redistributions. PLoS Pathog 2018; 14:e1007116. [PMID: 29813135 PMCID: PMC5993337 DOI: 10.1371/journal.ppat.1007116] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 06/08/2018] [Accepted: 05/22/2018] [Indexed: 12/27/2022] Open
Abstract
De novo biosynthesis of lipids is essential for Trypanosoma brucei, a protist responsible for the sleeping sickness. Here, we demonstrate that the ketogenic carbon sources, threonine, acetate and glucose, are precursors for both fatty acid and sterol synthesis, while leucine only contributes to sterol production in the tsetse fly midgut stage of the parasite. Degradation of these carbon sources into lipids was investigated using a combination of reverse genetics and analysis of radio-labelled precursors incorporation into lipids. For instance, (i) deletion of the gene encoding isovaleryl-CoA dehydrogenase, involved in the leucine degradation pathway, abolished leucine incorporation into sterols, and (ii) RNAi-mediated down-regulation of the SCP2-thiolase gene expression abolished incorporation of the three ketogenic carbon sources into sterols. The SCP2-thiolase is part of a unidirectional two-step bridge between the fatty acid precursor, acetyl-CoA, and the precursor of the mevalonate pathway leading to sterol biosynthesis, 3-hydroxy-3-methylglutaryl-CoA. Metabolic flux through this bridge is increased either in the isovaleryl-CoA dehydrogenase null mutant or when the degradation of the ketogenic carbon sources is affected. We also observed a preference for fatty acids synthesis from ketogenic carbon sources, since blocking acetyl-CoA production from both glucose and threonine abolished acetate incorporation into sterols, while incorporation of acetate into fatty acids was increased. Interestingly, the growth of the isovaleryl-CoA dehydrogenase null mutant, but not that of the parental cells, is interrupted in the absence of ketogenic carbon sources, including lipids, which demonstrates the essential role of the mevalonate pathway. We concluded that procyclic trypanosomes have a strong preference for fatty acid versus sterol biosynthesis from ketogenic carbon sources, and as a consequence, that leucine is likely to be the main source, if not the only one, used by trypanosomes in the infected insect vector digestive tract to feed the mevalonate pathway.
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Affiliation(s)
- Yoann Millerioux
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Muriel Mazet
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Guillaume Bouyssou
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Stefan Allmann
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Tiila-Riikka Kiema
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Eloïse Bertiaux
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Laetitia Fouillen
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
- Metabolome Facility of Bordeaux, Functional Genomics Center, Villenave d'Ornon
| | - Chandan Thapa
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
| | - Nicolas Plazolles
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
| | - Franziska Dittrich-Domergue
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Aline Crouzols
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Rik K. Wierenga
- Faculty of Biochemistry and Molecular Medicine, Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Brice Rotureau
- Trypanosome Transmission Group, Trypanosome Cell Biology Unit, Department of Parasites and Insect Vectors, INSERM U1201, Institut Pasteur, Paris, France
| | - Patrick Moreau
- Membrane Biogenesis Laboratory, CNRS-University of Bordeaux, UMR-5200, INRA Bordeaux Aquitaine, Villenave d'Ornon, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
- Centre de Résonance Magnétique des Systèmes Biologiques (RMSB), Université de Bordeaux, CNRS UMR-5536, Bordeaux, France
- * E-mail:
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Abstract
How mitochondria came to reside within the cytosol of their host has been debated for 50 years. Though current data indicate that the last eukaryote common ancestor possessed mitochondria and was a complex cell, whether mitochondria or complexity came first in eukaryotic evolution is still discussed. In autogenous models (complexity first), the origin of phagocytosis poses the limiting step at eukaryote origin, with mitochondria coming late as an undigested growth substrate. In symbiosis-based models (mitochondria first), the host was an archaeon, and the origin of mitochondria was the limiting step at eukaryote origin, with mitochondria providing bacterial genes, ATP synthesis on internalized bioenergetic membranes, and mitochondrion-derived vesicles as the seed of the eukaryote endomembrane system. Metagenomic studies are uncovering new host-related archaeal lineages that are reported as complex or phagocytosing, although images of such cells are lacking. Here we review the physiology and components of phagocytosis in eukaryotes, critically inspecting the concept of a phagotrophic host. From ATP supply and demand, a mitochondrion-lacking phagotrophic archaeal fermenter would have to ingest about 34 times its body weight in prokaryotic prey to obtain enough ATP to support one cell division. It would lack chemiosmotic ATP synthesis at the plasma membrane, because phagocytosis and chemiosmosis in the same membrane are incompatible. It would have lived from amino acid fermentations, because prokaryotes are mainly protein. Its ATP yield would have been impaired relative to typical archaeal amino acid fermentations, which involve chemiosmosis. In contrast, phagocytosis would have had great physiological benefit for a mitochondrion-bearing cell.
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Affiliation(s)
- William F Martin
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Aloysius G M Tielens
- Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Bratislava, Slovakia
| | - Sriram G Garg
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
| | - Sven B Gould
- Institute for Molecular Evolution, Heinrich Heine University Düsseldorf, Düsseldorf, Germany
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Neal SE, Dabir DV, Wijaya J, Boon C, Koehler CM. Osm1 facilitates the transfer of electrons from Erv1 to fumarate in the redox-regulated import pathway in the mitochondrial intermembrane space. Mol Biol Cell 2017; 28:2773-2785. [PMID: 28814504 PMCID: PMC5638582 DOI: 10.1091/mbc.e16-10-0712] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 08/10/2017] [Accepted: 08/10/2017] [Indexed: 11/18/2022] Open
Abstract
Osm1 transfers electrons from fumarate to succinate and functions with Mia40 and Erv1 in the redox-regulated import pathway for proteins that form disulfide bonds in the mitochondrial intermembrane space. Expression of Osm1 and cytochrome c is reciprocally regulated, indicating that the cell has strategies to coordinate expression of terminal electron acceptors. Prokaryotes have aerobic and anaerobic electron acceptors for oxidative folding of periplasmic proteins. The mitochondrial intermembrane space has an analogous pathway with the oxidoreductase Mia40 and sulfhydryl oxidase Erv1, termed the mitochondrial intermembrane space assembly (MIA) pathway. The aerobic electron acceptors include oxygen and cytochrome c, but an acceptor that can function under anaerobic conditions has not been identified. Here we show that the fumarate reductase Osm1, which facilitates electron transfer from fumarate to succinate, fills this gap as a new electron acceptor. In addition to microsomes, Osm1 localizes to the mitochondrial intermembrane space and assembles with Erv1 in a complex. In reconstitution studies with reduced Tim13, Mia40, and Erv1, the addition of Osm1 and fumarate completes the disulfide exchange pathway that results in Tim13 oxidation. From in vitro import assays, mitochondria lacking Osm1 display decreased import of MIA substrates, Cmc1 and Tim10. Comparative reconstitution assays support that the Osm1/fumarate couple accepts electrons with similar efficiency to cytochrome c and that the cell has strategies to coordinate expression of the terminal electron acceptors. Thus Osm1/fumarate is a new electron acceptor couple in the mitochondrial intermembrane space that seems to function in both aerobic and anaerobic conditions.
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Affiliation(s)
- Sonya E Neal
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095
| | - Deepa V Dabir
- Department of Biology, Loyola Marymount University, Los Angeles, CA 90045
| | - Juwina Wijaya
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Cennyana Boon
- Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095
| | - Carla M Koehler
- Molecular Biology Institute, University of California, Los Angeles, Los Angeles, CA 90095 .,Department of Chemistry and Biochemistry, University of California, Los Angeles, Los Angeles, CA 90095.,Jonsson Comprehensive Cancer Center, University of California, Los Angeles, Los Angeles, CA 90095
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31
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Rondón-Mercado R, Acosta H, Cáceres AJ, Quiñones W, Concepción JL. Subcellular localization of glycolytic enzymes and characterization of intermediary metabolism of Trypanosoma rangeli. Mol Biochem Parasitol 2017. [PMID: 28645481 DOI: 10.1016/j.molbiopara.2017.06.007] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Trypanosoma rangeli is a hemoflagellate protist that infects wild and domestic mammals as well as humans in Central and South America. Although this parasite is not pathogenic for human, it is being studied because it shares with Trypanosoma cruzi, the etiological agent of Chagas' disease, biological characteristics, geographic distribution, vectors and vertebrate hosts. Several metabolic studies have been performed with T. cruzi epimastigotes, however little is known about the metabolism of T. rangeli. In this work we present the subcellular distribution of the T. rangeli enzymes responsible for the conversion of glucose to pyruvate, as determined by epifluorescense immunomicroscopy and subcellular fractionation involving either selective membrane permeabilization with digitonin or differential and isopycnic centrifugation. We found that in T. rangeli epimastigotes the first six enzymes of the glycolytic pathway, involved in the conversion of glucose to 1,3-bisphosphoglycerate are located within glycosomes, while the last four steps occur in the cytosol. In contrast with T. cruzi, where three isoenzymes (one cytosolic and two glycosomal) of phosphoglycerate kinase are expressed simultaneously, only one enzyme with this activity is detected in T. rangeli epimastigotes, in the cytosol. Consistent with this latter result, we found enzymes involved in auxiliary pathways to glycolysis needed to maintain adenine nucleotide and redox balances within glycosomes such as phosphoenolpyruvate carboxykinase, malate dehydrogenase, fumarate reductase, pyruvate phosphate dikinase and glycerol-3-phosphate dehydrogenase. Glucokinase, galactokinase and the first enzyme of the pentose-phosphate pathway, glucose-6-phosphate dehydrogenase, were also located inside glycosomes. Furthermore, we demonstrate that T. rangeli epimastigotes growing in LIT medium only consume glucose and do not excrete ammonium; moreover, they are unable to survive in partially-depleted glucose medium. The velocity of glucose consumption is about 40% higher than that of procyclic Trypanosoma brucei, and four times faster than by T. cruzi epimastigotes under the same culture conditions.
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Affiliation(s)
- Rocío Rondón-Mercado
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Héctor Acosta
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela.
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32
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Wang X, Inaoka DK, Shiba T, Balogun EO, Allmann S, Watanabe YI, Boshart M, Kita K, Harada S. Expression, purification, and crystallization of type 1 isocitrate dehydrogenase from Trypanosoma brucei brucei. Protein Expr Purif 2017; 138:56-62. [PMID: 28642005 DOI: 10.1016/j.pep.2017.06.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Isocitrate dehydrogenases (IDHs) are metabolic enzymes that catalyze the oxidative decarboxylation of isocitrate to α-ketoglutarate. Depending on the electron acceptor and subcellular localization, these enzymes are classified as NADP+-dependent IDH1 in the cytosol or peroxisomes, NADP+-dependent IDH2 and NAD+-dependent IDH3 in mitochondria. Trypanosoma brucei is a protozoan parasite that causes African sleeping sickness in humans and Nagana disease in animals. Here, for the first time, a putative glycosomal T. brucei type 1 IDH (TbIDH1) was expressed in Escherichia coli and purified for crystallographic study. Surprisingly, the putative NADP+-dependent TbIDH1 has higher activity with NAD+ compared with NADP+ as electron acceptor, a unique characteristic among known eukaryotic IDHs which encouraged us to crystallize TbIDH1 for future biochemical and structural studies. Methods of expression and purification of large amounts of recombinant TbIDH1 with improved solubility to facilitate protein crystallization are presented.
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33
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Abstract
Cellular metabolic activity is a highly complex, dynamic, regulated process that is influenced by numerous factors, including extracellular environmental signals, nutrient availability and the physiological and developmental status of the cell. The causative agent of sleeping sickness,
Trypanosoma brucei, is an exclusively extracellular protozoan parasite that encounters very different extracellular environments during its life cycle within the mammalian host and tsetse fly insect vector. In order to meet these challenges, there are significant alterations in the major energetic and metabolic pathways of these highly adaptable parasites. This review highlights some of these metabolic changes in this early divergent eukaryotic model organism.
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Affiliation(s)
- Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, Fife, UK
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234 CNRS, Université de Bordeaux, Bordeaux, France
| | - Derek P Nolan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Luisa M Figueiredo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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34
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Abstract
Cellular metabolic activity is a highly complex, dynamic, regulated process that is influenced by numerous factors, including extracellular environmental signals, nutrient availability and the physiological and developmental status of the cell. The causative agent of sleeping sickness, Trypanosoma brucei, is an exclusively extracellular protozoan parasite that encounters very different extracellular environments during its life cycle within the mammalian host and tsetse fly insect vector. In order to meet these challenges, there are significant alterations in the major energetic and metabolic pathways of these highly adaptable parasites. This review highlights some of these metabolic changes in this early divergent eukaryotic model organism.
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Affiliation(s)
- Terry K Smith
- Biomedical Sciences Research Complex, University of St Andrews, Fife, UK
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), UMR 5234 CNRS, Université de Bordeaux, Bordeaux, France
| | - Derek P Nolan
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin, Ireland
| | - Luisa M Figueiredo
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisboa, Portugal
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35
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Allmann S, Bringaud F. Glycosomes: A comprehensive view of their metabolic roles in T. brucei. Int J Biochem Cell Biol 2017; 85:85-90. [PMID: 28179189 DOI: 10.1016/j.biocel.2017.01.015] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Revised: 01/27/2017] [Accepted: 01/29/2017] [Indexed: 11/28/2022]
Abstract
Peroxisomes are single-membrane cellular organelles, present in most eukaryotic cells and organisms from human to yeast, fulfilling essential metabolic functions in lipid metabolism, free radical detoxification, differentiation, development, morphogenesis, etc. Interestingly, the protozoan parasite species Trypanosoma contains peroxisome-like organelles named glycosomes, which lack hallmark peroxisomal pathways and enzymes, such as catalase. Glycosomes are the only peroxisome-like organelles containing most enzymatic steps of the glycolytic pathway as well as enzymes of pyrimidine biosynthesis, purine salvage and biosynthesis of nucleotide sugars. We present here an overview of the glycosomal metabolic peculiarities together with the current view of the raison d'être of this unique metabolic peroxisomal sequestration.
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Affiliation(s)
- Stefan Allmann
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France
| | - Frédéric Bringaud
- Laboratoire de Microbiologie Fondamentale et Pathogénicité (MFP), Université de Bordeaux, CNRS UMR-5234, Bordeaux, France.
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36
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Li J, Li Y, Cui Z, Liang Q, Qi Q. Enhancement of succinate yield by manipulating NADH/NAD + ratio and ATP generation. Appl Microbiol Biotechnol 2017; 101:3153-61. [PMID: 28108762 DOI: 10.1007/s00253-017-8127-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Revised: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
We previously engineered Escherichia coli YL104 to efficiently produce succinate from glucose. In this study, we investigated the relationships between the NADH/NAD+ ratio, ATP level, and overall yield of succinate production by using glucose as the carbon source in YL104. First, the use of sole NADH dehydrogenases increased the overall yield of succinate by 7% and substantially decreased the NADH/NAD+ ratio. Second, the soluble fumarate reductase from Saccharomyces cerevisiae was overexpressed to manipulate the anaerobic NADH/NAD+ ratio and ATP level. Third, another strategy for reducing the ATP level was applied by introducing ATP futile cycling for improving succinate production. Finally, a combination of these methods exerted a synergistic effect on improving the overall yield of succinate, which was 39% higher than that of the previously engineered strain YL104. The study results indicated that regulation of the NADH/NAD+ ratio and ATP level is an efficient strategy for succinate production.
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Jardim-Messeder D, Cabreira-Cagliari C, Rauber R, Turchetto-Zolet AC, Margis R, Margis-Pinheiro M. Fumarate reductase superfamily: A diverse group of enzymes whose evolution is correlated to the establishment of different metabolic pathways. Mitochondrion 2017; 34:56-66. [PMID: 28088649 DOI: 10.1016/j.mito.2017.01.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Revised: 12/21/2016] [Accepted: 01/10/2017] [Indexed: 11/21/2022]
Abstract
Fumarate and succinate are known to be present in prebiotic systems essential for the origin of life. The fumarate and succinate interconversion reactions have been conserved throughout evolution and are found in all living organisms. The fumarate and succinate interconversion is catalyzed by the enzymes succinate dehydrogenase (SDH) and fumarate reductase (FRD). In this work we show that SDH and FRD are part of a group of enzymes that we propose to designate "fumarate reductase superfamily". Our results demonstrate that these enzymes emerged from a common ancestor and were essential in the development of metabolic pathways involved in energy transduction.
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Dutra FL, Oliveira MM, Santos RS, Silva WS, Alviano DS, Vieira DP, Lopes AH. Effects of linalool and eugenol on the survival of Leishmania (L.) infantum chagasi within macrophages. Acta Trop 2016; 164:69-76. [PMID: 27591136 DOI: 10.1016/j.actatropica.2016.08.026] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2015] [Revised: 08/12/2016] [Accepted: 08/29/2016] [Indexed: 12/14/2022]
Abstract
The most commonly used drugs against visceral leishmaniasis are based on pentavalent antimonial compounds, which have played a fundamental role in therapy for over 70 years. However, the treatment is painful and has severe toxic side effects that can be fatal. Antimonial resistance is spreading and reaching alarming proportions. Linalool and eugenol have been shown to kill Leishmania (L.) amazonensis and Trypanosoma cruzi at low doses. In the present study, we demonstrate the effects of linalool and eugenol, components of essential oils, on Leishmania (L.) infantum chagasi, one of the causative agents of visceral leishmaniasis. We compared the effects of those compounds to the effects of glucantime, a positive control. In L. infantum chagasi killing assays, the LD50 for eugenol was 220μg/ml, and that for linalool was 550μg/ml. L. infantum chagasi was added to cultures of peritoneal mouse macrophages for four hours prior to drug treatment. Eugenol and linalool significantly decreased the number of parasites within the macrophages. Eugenol and linalool enhanced the activities of the L. infantum chagasi protein kinases PKA and PKC. Linalool also decreased L. infantum chagasi oxygen consumption. In conclusion, both linalool and eugenol promoted a decrease in the proliferation and viability of L. infantum chagasi. These effects were more pronounced during the interaction between the parasites and peritoneal mouse macrophages.
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González-Marcano E, Acosta H, Mijares A, Concepción JL. Kinetic and molecular characterization of the pyruvate phosphate dikinase from Trypanosoma cruzi. Exp Parasitol 2016; 165:81-7. [PMID: 27003459 DOI: 10.1016/j.exppara.2016.03.023] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 03/14/2016] [Accepted: 03/18/2016] [Indexed: 11/18/2022]
Abstract
Trypanosoma cruzi, like other trypanosomatids analyzed so far, can use both glucose and amino acids as carbon and energy source. In these parasites, glycolysis is compartmentalized in glycosomes, authentic but specialized peroxisomes. The major part of this pathway, as well as a two-branched glycolytic auxiliary system, are present in these organelles. The first enzyme of one branch of this auxiliary system is the PPi-dependent pyruvate phosphate dikinase (PPDK) that converts phosphoenolpyruvate (PEP), inorganic pyrophosphate (PPi) and AMP into pyruvate, inorganic phosphate (Pi) and ATP, thus contributing to the ATP/ADP balance within the glycosomes. In this work we cloned, expressed and purified the T. cruzi PPDK. It kinetic parameters were determined, finding KM values for PEP, PPi and AMP of 320, 70 and 17 μM, respectively. Using molecular exclusion chromatography, two native forms of the enzyme were found with estimated molecular weights of 200 and 100 kDa, corresponding to a homodimer and monomer, respectively. It was established that T. cruzi PPDK's specific activity can be enhanced up to 2.6 times by the presence of ammonium in the assay mixture. During growth of epimastigotes in batch culture an apparent decrease in the specific activity of PPDK was observed. However, when its activity is normalized for the presence of ammonium in the medium, no significant modification of the enzyme activity per cell in time was found.
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Affiliation(s)
- Eglys González-Marcano
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, La Hechicera, Mérida 5101, Venezuela.
| | - Héctor Acosta
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, La Hechicera, Mérida 5101, Venezuela.
| | - Alfredo Mijares
- Laboratorio de Fisiología de Parásitos, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas, Caracas 1020-A, Venezuela.
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Facultad de Ciencias, Universidad de Los Andes, La Hechicera, Mérida 5101, Venezuela.
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Rivero LA, Concepción JL, Quintero-Troconis E, Quiñones W, Michels PA, Acosta H. Trypanosoma evansi contains two auxiliary enzymes of glycolytic metabolism: Phosphoenolpyruvate carboxykinase and pyruvate phosphate dikinase. Exp Parasitol 2016; 165:7-15. [PMID: 26968775 DOI: 10.1016/j.exppara.2016.03.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 02/11/2016] [Accepted: 03/03/2016] [Indexed: 11/22/2022]
Abstract
Trypanosoma evansi is a monomorphic protist that can infect horses and other animal species of economic importance for man. Like the bloodstream form of the closely related species Trypanosoma brucei, T. evansi depends exclusively on glycolysis for its free-energy generation. In T. evansi as in other kinetoplastid organisms, the enzymes of the major part of the glycolytic pathway are present within organelles called glycosomes, which are authentic but specialized peroxisomes. Since T. evansi does not undergo stage-dependent differentiations, it occurs only as bloodstream forms, it has been assumed that the metabolic pattern of this parasite is identical to that of the bloodstream form of T. brucei. However, we report here the presence of two additional enzymes, phosphoenolpyruvate carboxykinase and PPi-dependent pyruvate phosphate dikinase in T. evansi glycosomes. Their colocalization with glycolytic enzymes within the glycosomes of this parasite has not been reported before. Both enzymes can make use of PEP for contributing to the production of ATP within the organelles. The activity of these enzymes in T. evansi glycosomes drastically changes the model assumed for the oxidation of glucose by this parasite.
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Abstract
Representatives of all major lineages of eukaryotes contain peroxisomes with similar morphology and mode of biogenesis, indicating a monophyletic origin of the organelles within the common ancestor of all eukaryotes. Peroxisomes originated from the endoplasmic reticulum, but despite a common origin and shared morphological features, peroxisomes from different organisms show a remarkable diversity of enzyme content and the metabolic processes present can vary dependent on nutritional or developmental conditions. A common characteristic and probable evolutionary driver for the origin of the organelle is an involvement in lipid metabolism, notably H2O2-dependent fatty-acid oxidation. Subsequent evolution of the organelle in different lineages involved multiple acquisitions of metabolic processes-often involving retargeting enzymes from other cell compartments-and losses. Information about peroxisomes in protists is still scarce, but available evidence, including new bioinformatics data reported here, indicate striking diversity amongst free-living and parasitic protists from different phylogenetic supergroups. Peroxisomes in only some protists show major involvement in H2O2-dependent metabolism, as in peroxisomes of mammalian, plant and fungal cells. Compartmentalization of glycolytic and gluconeogenic enzymes inside peroxisomes is characteristic of kinetoplastids and diplonemids, where the organelles are hence called glycosomes, whereas several other excavate parasites (Giardia, Trichomonas) have lost peroxisomes. Amongst alveolates and amoebozoans patterns of peroxisome loss are more complicated. Often, a link is apparent between the niches occupied by the parasitic protists, nutrient availability, and the absence of the organelles or their presence with a specific enzymatic content. In trypanosomatids, essentiality of peroxisomes may be considered for use in anti-parasite drug discovery.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Michael L Ginger
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK; Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, UK; Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, UK; Laboratorio de Enzimología de Parásitos, Departamento de Biología, Universidad de Los Andes, Mérida, Venezuela.
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Yang L, Lübeck M, Ahring BK, Lübeck PS. Enhanced succinic acid production in Aspergillus saccharolyticus by heterologous expression of fumarate reductase from Trypanosoma brucei. Appl Microbiol Biotechnol 2016; 100:1799-809. [PMID: 26521243 DOI: 10.1007/s00253-015-7086-z] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Revised: 10/04/2015] [Accepted: 10/13/2015] [Indexed: 10/22/2022]
Abstract
Aspergillus saccharolyticus exhibits great potential as a cell factory for industrial production of dicarboxylic acids. In the analysis of the organic acid profile, A. saccharolyticus was cultivated in an acid production medium using two different pH conditions. The specific activities of the enzymes, pyruvate carboxylase (PYC), malate dehydrogenase (MDH), and fumarase (FUM), involved in the reductive tricarboxylic acid (rTCA) branch, were examined and compared in cells harvested from the acid production medium and a complete medium. The results showed that ambient pH had a significant impact on the pattern and the amount of organic acids produced by A. saccharolyticus. The wild-type strain produced higher amount of malic acid and succinic acid in the pH buffered condition (pH 6.5) compared with the pH non-buffered condition. The enzyme assays showed that the rTCA branch was active in the acid production medium as well as the complete medium, but the measured enzyme activities were different depending on the media. Furthermore, a soluble NADH-dependent fumarate reductase gene (frd) from Trypanosoma brucei was inserted and expressed in A. saccharolyticus. The expression of the frd gene led to an enhanced production of succinic acid in frd transformants compared with the wild-type in both pH buffered and pH non-buffered conditions with highest amount produced in the pH buffered condition (16.2 ± 0.5 g/L). This study demonstrates the feasibility of increasing succinic acid production through the cytosolic reductive pathway by genetic engineering in A. saccharolyticus.
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Moreno SA, Nava M. Trypanosoma evansi is alike to Trypanosoma brucei brucei in the subcellular localisation of glycolytic enzymes. Mem Inst Oswaldo Cruz 2015; 110:468-75. [PMID: 26061149 PMCID: PMC4501409 DOI: 10.1590/0074-02760150024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2015] [Accepted: 04/01/2015] [Indexed: 01/17/2023] Open
Abstract
Trypanosoma evansi, which causes surra, is descended from
Trypanosoma brucei brucei, which causes nagana. Although both
parasites are presumed to be metabolically similar, insufficient knowledge of
T. evansi precludes a full comparison. Herein, we provide the
first report on the subcellular localisation of the glycolytic enzymes in T.
evansi, which is a alike to that of the bloodstream form (BSF) of
T. b. brucei: (i) fructose-bisphosphate aldolase,
glyceraldehyde-3-phosphate dehydrogenase (GAPDH), hexokinase, phosphofructokinase,
glucose-6-phosphate isomerase, phosphoglycerate kinase, triosephosphate isomerase
(glycolytic enzymes) and glycerol-3-phosphate dehydrogenase (a glycolysis-auxiliary
enzyme) in glycosomes, (ii) enolase, phosphoglycerate mutase, pyruvate kinase
(glycolytic enzymes) and a GAPDH isoenzyme in the cytosol, (iii) malate dehydrogenase
in cytosol and (iv) glucose-6-phosphate dehydrogenase in both glycosomes and the
cytosol. Specific enzymatic activities also suggest that T. evansi
is alike to the BSF of T. b. brucei in glycolytic flux, which is
much faster than the pentose phosphate pathway flux, and in the involvement of
cytosolic GAPDH in the NAD+/NADH balance. These similarities were expected
based on the close phylogenetic relationship of both parasites.
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Affiliation(s)
- S Andrea Moreno
- Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Mérida, Venezuela
| | - Mayerly Nava
- Departamento de Biología, Facultad Experimental de Ciencias, Universidad del Zulia, Maracaibo, Zulia, Venezuela
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Deka RK, Brautigam CA, Liu WZ, Tomchick DR, Norgard MV. Evidence for Posttranslational Protein Flavinylation in the Syphilis Spirochete Treponema pallidum: Structural and Biochemical Insights from the Catalytic Core of a Periplasmic Flavin-Trafficking Protein. mBio 2015; 6:e00519-15. [PMID: 25944861 DOI: 10.1128/mBio.00519-15] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
The syphilis spirochete Treponema pallidum is an important human pathogen but a highly enigmatic bacterium that cannot be cultivated in vitro. T. pallidum lacks many biosynthetic pathways and therefore has evolved the capability to exploit host-derived metabolites via its periplasmic lipoprotein repertoire. We recently reported a flavin-trafficking protein in T. pallidum (Ftp_Tp; TP0796) as the first bacterial metal-dependent flavin adenine dinucleotide (FAD) pyrophosphatase that hydrolyzes FAD into AMP and flavin mononucleotide (FMN) in the spirochete’s periplasm. However, orthologs of Ftp_Tp from other bacteria appear to lack this hydrolytic activity; rather, they bind and flavinylate subunits of a cytoplasmic membrane redox system (Nqr/Rnf). To further explore this dichotomy, biochemical analyses, protein crystallography, and structure-based mutagenesis were used to show that a single amino acid change (N55Y) in Ftp_Tp converts it from an Mg2+-dependent FAD pyrophosphatase to an FAD-binding protein. We also demonstrated that Ftp_Tp has a second enzymatic activity (Mg2+-FMN transferase); it flavinylates protein(s) covalently with FMN on a threonine side chain of an appropriate sequence motif using FAD as the substrate. Moreover, mutation of a metal-binding residue (D284A) eliminates Ftp_Tp’s dual activities, thereby underscoring the role of Mg2+ in the enzyme-catalyzed reactions. The posttranslational flavinylation activity that can target a periplasmic lipoprotein (TP0171) has not previously been described. The observed activities reveal the catalytic flexibility of a treponemal protein to perform multiple functions. Together, these findings imply mechanisms by which a dynamic pool of flavin cofactor is maintained and how flavoproteins are generated by Ftp_Tp locally in the T. pallidum periplasm. Treponema pallidum, the syphilis spirochete, exploits its periplasmic lipoproteins for a number of essential physiologic processes. One of these, flavin-trafficking protein (Ftp), not only exploits its catalytic center to mediate posttranslational flavinylation of proteins (to create flavoproteins) but also likely maintains the periplasmic flavin pool via its unique ability to hydrolyze FAD. This functional diversity within a single lipoprotein is quite remarkable and reflects the enzymatic versatility of the treponemal lipoproteins, as well as molecular parsimony in an organism with a limited genome. Ftp-mediated protein flavinylation in the periplasm also likely is a key aspect of a predicted flavin-dependent Rnf-based redox homeostasis system at the cytoplasmic membrane of T. pallidum. In addition to its importance in T. pallidum physiology, Ftp homologs exist in other bacteria, thereby expanding our understanding of the bacterial periplasm as a metabolically active subcellular compartment for flavoprotein biogenesis as well as flavin homeostasis.
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Bringaud F, Biran M, Millerioux Y, Wargnies M, Allmann S, Mazet M. Combining reverse genetics and nuclear magnetic resonance-based metabolomics unravels trypanosome-specific metabolic pathways. Mol Microbiol 2015; 96:917-26. [PMID: 25753950 DOI: 10.1111/mmi.12990] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2015] [Indexed: 01/20/2023]
Abstract
Numerous eukaryotes have developed specific metabolic traits that are not present in extensively studied model organisms. For instance, the procyclic insect form of Trypanosoma brucei, a parasite responsible for sleeping sickness in its mammalian-specific bloodstream form, metabolizes glucose into excreted succinate and acetate through pathways with unique features. Succinate is primarily produced from glucose-derived phosphoenolpyruvate in peroxisome-like organelles, also known as glycosomes, by a soluble NADH-dependent fumarate reductase only described in trypanosomes so far. Acetate is produced in the mitochondrion of the parasite from acetyl-CoA by a CoA-transferase, which forms an ATP-producing cycle with succinyl-CoA synthetase. The role of this cycle in ATP production was recently demonstrated in procyclic trypanosomes and has only been proposed so far for anaerobic organisms, in addition to trypanosomatids. We review how nuclear magnetic resonance spectrometry can be used to analyze the metabolic network perturbed by deletion (knockout) or downregulation (RNAi) of the candidate genes involved in these two particular metabolic pathways of procyclic trypanosomes. The role of succinate and acetate production in trypanosomes is discussed, as well as the connections between the succinate and acetate branches, which increase the metabolic flexibility probably required by the parasite to deal with environmental changes such as oxidative stress.
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Affiliation(s)
- Frédéric Bringaud
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Marc Biran
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Yoann Millerioux
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Marion Wargnies
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Stefan Allmann
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
| | - Muriel Mazet
- Centre de Résonance Magnétique des Systèmes Biologiques, UMR-5536 Université de Bordeaux, CNRS, 146 rue Léo Saignat, 33076, Bordeaux, France
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Quiñones W, Cáceres AJ, Ruiz MT, Concepción JL. Glycosomal membrane proteins and lipids from Leishmania mexicana. Comp Biochem Physiol B Biochem Mol Biol 2015; 182:27-36. [DOI: 10.1016/j.cbpb.2014.11.012] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2014] [Revised: 11/18/2014] [Accepted: 11/29/2014] [Indexed: 11/29/2022]
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Rodriguez-Contreras D, Hamilton N. Gluconeogenesis in Leishmania mexicana: contribution of glycerol kinase, phosphoenolpyruvate carboxykinase, and pyruvate phosphate dikinase. J Biol Chem 2014; 289:32989-3000. [PMID: 25288791 DOI: 10.1074/jbc.m114.569434] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Gluconeogenesis is an active pathway in Leishmania amastigotes and is essential for their survival within the mammalian cells. However, our knowledge about this pathway in trypanosomatids is very limited. We investigated the role of glycerol kinase (GK), phosphoenolpyruvate carboxykinase (PEPCK), and pyruvate phosphate dikinase (PPDK) in gluconeogenesis by generating the respective Leishmania mexicana Δgk, Δpepck, and Δppdk null mutants. Our results demonstrated that indeed GK, PEPCK, and PPDK are key players in the gluconeogenesis pathway in Leishmania, although stage-specific differences in their contribution to this pathway were found. GK participates in the entry of glycerol in promastigotes and amastigotes; PEPCK participates in the entry of aspartate in promastigotes, and PPDK is involved in the entry of alanine in amastigotes. Furthermore, the majority of alanine enters into the pathway via decarboxylation of pyruvate in promastigotes, whereas pathway redundancy is suggested for the entry of aspartate in amastigotes. Interestingly, we also found that l-lactate, an abundant glucogenic precursor in mammals, was used by Leishmania amastigotes to synthesize mannogen, entering the pathway through PPDK. On the basis of these new results, we propose a revision in the current model of gluconeogenesis in Leishmania, emphasizing the differences between amastigotes and promastigotes. This work underlines the importance of studying the trypanosomatid intracellular life cycle stages to gain a better understanding of the pathologies caused in humans.
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Affiliation(s)
- Dayana Rodriguez-Contreras
- From the Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239
| | - Nicklas Hamilton
- From the Department of Molecular Microbiology and Immunology, Oregon Health and Science University, Portland, Oregon 97239
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48
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Deramchia K, Morand P, Biran M, Millerioux Y, Mazet M, Wargnies M, Franconi JM, Bringaud F. Contribution of pyruvate phosphate dikinase in the maintenance of the glycosomal ATP/ADP balance in the Trypanosoma brucei procyclic form. J Biol Chem 2014; 289:17365-78. [PMID: 24794874 DOI: 10.1074/jbc.m114.567230] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Trypanosoma brucei belongs to a group of protists that sequester the first six or seven glycolytic steps inside specialized peroxisomes, named glycosomes. Because of the glycosomal membrane impermeability to nucleotides, ATP molecules consumed by the first glycolytic steps need to be regenerated in the glycosomes by kinases, such as phosphoenolpyruvate carboxykinase (PEPCK). The glycosomal pyruvate phosphate dikinase (PPDK), which reversibly converts phosphoenolpyruvate into pyruvate, could also be involved in this process. To address this question, we analyzed the metabolism of the main carbon sources used by the procyclic trypanosomes (glucose, proline, and threonine) after deletion of the PPDK gene in the wild-type (Δppdk) and PEPCK null (Δppdk/Δpepck) backgrounds. The rate of acetate production from glucose is 30% reduced in the Δppdk mutant, whereas threonine-derived acetate production is not affected, showing that PPDK function in the glycolytic direction with production of ATP in the glycosomes. The Δppdk/Δpepck mutant incubated in glucose as the only carbon source showed a 3.8-fold reduction of the glycolytic rate compared with the Δpepck mutant, as a consequence of the imbalanced glycosomal ATP/ADP ratio. The role of PPDK in maintenance of the ATP/ADP balance was confirmed by expressing the glycosomal phosphoglycerate kinase (PGKC) in the Δppdk/Δpepck cell line, which restored the glycolytic flux. We also observed that expression of PGKC is lethal for procyclic trypanosomes, as a consequence of ATP depletion, due to glycosomal relocation of cytosolic ATP production. This illustrates the key roles played by glycosomal and cytosolic kinases, including PPDK, to maintain the cellular ATP/ADP homeostasis.
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Affiliation(s)
- Kamel Deramchia
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Pauline Morand
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Marc Biran
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Yoann Millerioux
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Muriel Mazet
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Marion Wargnies
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Jean-Michel Franconi
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
| | - Frédéric Bringaud
- From the Centre de Résonance Magnétique des Systèmes Biologiques, Université de Bordeaux, CNRS UMR-5536, 146 rue Léo Saignat, 33076 Bordeaux Cedex, France
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Cao Y, Zhang R, Sun C, Cheng T, Liu Y, Xian M. Fermentative succinate production: an emerging technology to replace the traditional petrochemical processes. Biomed Res Int 2013; 2013:723412. [PMID: 24396827 DOI: 10.1155/2013/723412] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2013] [Revised: 10/13/2013] [Accepted: 11/01/2013] [Indexed: 11/17/2022]
Abstract
Succinate is a valuable platform chemical for multiple applications. Confronted with the exhaustion of fossil energy resources, fermentative succinate production from renewable biomass to replace the traditional petrochemical process is receiving an increasing amount of attention. During the past few years, the succinate-producing process using microbial fermentation has been made commercially available by the joint efforts of researchers in different fields. In this review, recent attempts and experiences devoted to reduce the production cost of biobased succinate are summarized, including strain improvement, fermentation engineering, and downstream processing. The key limitations and challenges faced in current microbial production systems are also proposed.
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Merlino A, Vieites M, Gambino D, Coitiño EL. Homology modeling of T. cruzi and L. major NADH-dependent fumarate reductases: ligand docking, molecular dynamics validation, and insights on their binding modes. J Mol Graph Model 2013; 48:47-59. [PMID: 24370672 DOI: 10.1016/j.jmgm.2013.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Revised: 11/16/2013] [Accepted: 12/03/2013] [Indexed: 11/26/2022]
Abstract
Leishmania major and Trypanosoma cruzi are the main causes of leishmaniasis and Chagas disease, two endemic parasitosis identified as neglected diseases by the World Health Organization. Fumarate reductase (FR) is a central enzyme in the conversion of fumarate to succinate, an energy releasing path essential for the survival of these protozoans which is also absent in their mammalian hosts. FR can thus be considered as a good candidate for targeting specific inhibition by new drugs designed against L. major and T. cruzi. The lack of tertiary structures available for LmFR and TcFR has limited until now the possibility of performing structure-based drug design. Here we used homology modeling combined with enzyme-cofactor docking to propose tertiary structures for NADH-dependent LmFR and TcFR using an homologous X-ray crystallographic structure of flavine-adenine dinucleotide (FAD) dependent FR from Shewanella frigidimarina (PDB ID: 1QO8) as template. These models were refined and stabilized with/without substrate in the active site using classical molecular dynamics simulations under quasi-physiological conditions. Structural features relevant for understanding the mechanism of action of the enzyme were also analyzed, with special attention to the hydrogen bond network involving the cofactor and water molecules present at the binding sites. A small set of compounds previously synthesized and assayed for their inhibitory capacity against TcFR ([M(mpo)₂] metal complexes with M=Pt(II), Pd(II) and V(IV)O and mpo=2-mercaptopyridine N-oxide) and LmFR (licochalcone A) were screened by protein-ligand docking using the NADH-LmFR and NADH-TcFR models here proposed and validated, gaining insight into their binding modes in each enzyme.
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Affiliation(s)
- Alicia Merlino
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
| | - Marisol Vieites
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, C. C. 1157, 11800 Montevideo, Uruguay
| | - Dinorah Gambino
- Cátedra de Química Inorgánica, Facultad de Química, Universidad de la República, Gral. Flores 2124, C. C. 1157, 11800 Montevideo, Uruguay
| | - E Laura Coitiño
- Laboratorio de Química Teórica y Computacional, Instituto de Química Biológica, Facultad de Ciencias, Universidad de la República, Iguá 4225, 11400 Montevideo, Uruguay.
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