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Springer AL, Agrawal S, Chang EP. Malate dehydrogenase in parasitic protozoans: roles in metabolism and potential therapeutic applications. Essays Biochem 2024:EBC20230075. [PMID: 38938216 DOI: 10.1042/ebc20230075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2024] [Revised: 05/31/2024] [Accepted: 06/18/2024] [Indexed: 06/29/2024]
Abstract
The role of malate dehydrogenase (MDH) in the metabolism of various medically significant protozoan parasites is reviewed. MDH is an NADH-dependent oxidoreductase that catalyzes interconversion between oxaloacetate and malate, provides metabolic intermediates for both catabolic and anabolic pathways, and can contribute to NAD+/NADH balance in multiple cellular compartments. MDH is present in nearly all organisms; isoforms of MDH from apicomplexans (Plasmodium falciparum, Toxoplasma gondii, Cryptosporidium spp.), trypanosomatids (Trypanosoma brucei, T. cruzi) and anaerobic protozoans (Trichomonas vaginalis, Giardia duodenalis) are presented here. Many parasitic species have complex life cycles and depend on the environment of their hosts for carbon sources and other nutrients. Metabolic plasticity is crucial to parasite transition between host environments; thus, the regulation of metabolic processes is an important area to explore for therapeutic intervention. Common themes in protozoan parasite metabolism include emphasis on glycolytic catabolism, substrate-level phosphorylation, non-traditional uses of common pathways like tricarboxylic acid cycle and adapted or reduced mitochondria-like organelles. We describe the roles of MDH isoforms in these pathways, discuss unusual structural or functional features of these isoforms relevant to activity or drug targeting, and review current studies exploring the therapeutic potential of MDH and related genes. These studies show that MDH activity has important roles in many metabolic pathways, and thus in the metabolic transitions of protozoan parasites needed for success as pathogens.
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Affiliation(s)
- Amy L Springer
- Department of Biochemistry and Molecular Biology, University of Massachusetts, Amherst, MA, U.S.A
| | - Swati Agrawal
- Department of Biological Sciences, University of Mary Washington, Fredericksburg, VA, U.S.A
| | - Eric P Chang
- Department of Chemistry and Physical Sciences, Pace University, New York, NY, U.S.A
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Kučerová J, Zdrha A, Shinde A, Harant K, Hrdý I, Tachezy J. The divergent ER-mitochondria encounter structures (ERMES) are conserved in parabasalids but lost in several anaerobic lineages with hydrogenosomes. BMC Biol 2023; 21:259. [PMID: 37968591 PMCID: PMC10648710 DOI: 10.1186/s12915-023-01765-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/09/2023] [Indexed: 11/17/2023] Open
Abstract
BACKGROUND The endoplasmic reticulum (ER)-mitochondria membrane contact sites (MCS) are extensively studied in aerobic eukaryotes; however, little is known about MCS in anaerobes with reduced forms of mitochondria named hydrogenosomes. In several eukaryotic lineages, the direct physical tether between ER and the outer mitochondrial membrane is formed by ER-mitochondria encounter structure (ERMES). The complex consists of four core proteins (Mmm1, Mmm2, Mdm12, and Mdm10) which are involved in phospholipid trafficking. Here we investigated ERMES distribution in organisms bearing hydrogenosomes and employed Trichomonas vaginalis as a model to estimate ERMES cellular localization, structure, and function. RESULTS Homology searches revealed that Parabasalia-Anaeramoebae, anaerobic jakobids, and anaerobic fungi are lineages with hydrogenosomes that retain ERMES, while ERMES components were gradually lost in Fornicata, and are absent in Preaxostyla and Archamoebae. In T. vaginalis and other parabasalids, three ERMES components were found with the expansion of Mmm1. Immunofluorescence microscopy confirmed that Mmm1 localized in ER, while Mdm12 and Mmm2 were partially localized in hydrogenosomes. Pull-down assays and mass spectrometry of the ERMES components identified a parabasalid-specific Porin2 as a substitute for the Mdm10. ERMES modeling predicted a formation of a continuous hydrophobic tunnel of TvMmm1-TvMdm12-TvMmm2 that is anchored via Porin2 to the hydrogenosomal outer membrane. Phospholipid-ERMES docking and Mdm12-phospholipid dot-blot indicated that ERMES is involved in the transport of phosphatidylinositol phosphates. The absence of enzymes involved in hydrogenosomal phospholipid metabolism implies that ERMES is not involved in the exchange of substrates between ER and hydrogenosomes but in the unidirectional import of phospholipids into hydrogenosomal membranes. CONCLUSIONS Our investigation demonstrated that ERMES mediates ER-hydrogenosome interactions in parabasalid T. vaginalis, while the complex was lost in several other lineages with hydrogenosomes.
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Affiliation(s)
- Jitka Kučerová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Alois Zdrha
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Abhishek Shinde
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Karel Harant
- OMICS Proteomics Laboratory, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242, Vestec, Czech Republic.
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2023] Open
Abstract
Archamoebae comprises free-living or endobiotic amoebiform protists that inhabit anaerobic or microaerophilic environments and possess mitochondrion-related organelles (MROs) adapted to function anaerobically. We compared in silico reconstructed MRO proteomes of eight species (six genera) and found that the common ancestor of Archamoebae possessed very few typical components of the protein translocation machinery, electron transport chain and tricarboxylic acid cycle. On the other hand, it contained a sulphate activation pathway and bacterial iron-sulphur (Fe-S) assembly system of MIS-type. The metabolic capacity of the MROs, however, varies markedly within this clade. The glycine cleavage system is widely conserved among Archamoebae, except in Entamoeba, probably owing to its role in catabolic function or one-carbon metabolism. MRO-based pyruvate metabolism was dispensed within subgroups Entamoebidae and Rhizomastixidae, whereas sulphate activation could have been lost in isolated cases of Rhizomastix libera, Mastigamoeba abducta and Endolimax sp. The MIS (Fe-S) assembly system was duplicated in the common ancestor of Mastigamoebidae and Pelomyxidae, and one of the copies took over Fe-S assembly in their MRO. In Entamoebidae and Rhizomastixidae, we hypothesize that Fe-S cluster assembly in both compartments may be facilitated by dual localization of the single system. We could not find evidence for changes in metabolic functions of the MRO in response to changes in habitat; it appears that such environmental drivers do not strongly affect MRO reduction in this group of eukaryotes.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czechia
- Life Science Research Centre, Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czechia
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Courtney W Stairs
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | - Michelle M Leger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Present address: Institute of Evolutionary Biology (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czechia
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, and Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
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Bu XL, Zhao WS, Li ZY, Ma HW, Chen YS, Li WX, Zou H, Li M, Wang GT. The energy metabolism of Balantidium polyvacuolum inhabiting the hindgut of Xenocypris davidi. BMC Genomics 2023; 24:624. [PMID: 37858069 PMCID: PMC10588222 DOI: 10.1186/s12864-023-09706-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 09/29/2023] [Indexed: 10/21/2023] Open
Abstract
Anaerobic parasitic ciliates are a specialized group of ciliates that are adapted to anoxic and oxygen-depleted habitats. Among them, Balantidium polyvacuolum, which inhabits the hindgut of Xenocyprinae fishes, has received very limited scientific attention, so the molecular mechanism of its adaptation to the digestive tract microenvironment is still unclear. In this study, transmission electron microscopy (TEM) and single-cell transcriptome analysis were used to uncover the metabolism of B. polyvacuolum. Starch granules, endosymbiotic bacteria, and multiple specialized mitochondrion-related organelles (MROs) of various shapes were observed. The MROs may have completely lost the electron transport chain (ETC) complexes I, III, IV, and V and only retained succinate dehydrogenase subunit A (SDHA) of complex II. The tricarboxylic acid (TCA) cycle was also incomplete. It can be inferred that the hypoxic intestinal environment has led to the specialization of the mitochondria in B. polyvacuolum. Moreover, carbohydrate-active enzymes (CAZymes), including carbohydrate esterases, enzymes with a carbohydrate-binding module, glycoside hydrolases, and glycosyltransferases, were identified, which may constitute evidence that B. polyvacuolum is able to digest carbohydrates and starch. These findings can improve our knowledge of the energy metabolism and adaptive mechanisms of B. polyvacuolum.
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Affiliation(s)
- Xia-Lian Bu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wei-Shan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Zhong-Yang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Wei Ma
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070, Hubei, China
| | - Yu-Shun Chen
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Wen-Xiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China.
| | - Gui-Tang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, Key Laboratory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, Hubei, China
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Bu X, Zhao W, Li W, Zou H, Li M, Wang G. Comparative Transcriptomics of Chilodonella hexasticha and C. uncinata Provide New Insights into Adaptations to a Parasitic Lifestyle and Mdivi-1 as a Potential Agent for Chilodonellosis Control. Int J Mol Sci 2023; 24:13058. [PMID: 37685862 PMCID: PMC10488290 DOI: 10.3390/ijms241713058] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/09/2023] [Accepted: 08/16/2023] [Indexed: 09/10/2023] Open
Abstract
Chilodonella hexasticha is a harmful parasitic ciliate that can cause severe damage to fish and high mortalities worldwide. Its congeneric species, C. uncinata, is a facultative parasite that not only can be free-living but also can parasitize on fish gills and fins. In this study, single-cell transcriptomes of these two species were assembled and characterized. Numerous enzymes related to energy metabolism and parasitic adaption were identified through annotation in the Non-Redundant (NR), Clusters of Orthologous Genes (COG), Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The expression of isocitrate dehydrogenase (IDH), cytochrome c oxidase subunit 1 (Cox1) and ATP synthase F1, delta subunit (ATP5D) was up-regulated in C. hexasticha compared with C. uncinata. The oxidative phosphorylation process was also enriched in C. hexasticha. The main mitochondrial metabolic pathways in C. hexasticha were depicted and enzymes related to energy metabolism pathways were compared between these two species. More importantly, mitochondrial division inhibitor 1 (mdivi-1) proved to be very effective in killing both C. hexasticha and C. uncinata, which could be a novel drug for Chilodonellosis control. This study can help us better understand the energy metabolisms of C. hexasticha and C. uncinata and provide new insight into novel targets for chilodonellosis control. Meanwhile, the transcriptome data can also facilitate genomic studies of these two species in the future.
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Affiliation(s)
- Xialian Bu
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
- University of Chinese Academy of Sciences, Beijing 100049, China
- Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Weishan Zhao
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
- Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Wenxiang Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
| | - Hong Zou
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
| | - Ming Li
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
- Protist 10,000 Genomics Project (P10K) Consortium, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Guitang Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology, and Key Labatory of Aquaculture Disease Control, Ministry of Agriculture, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; (X.B.); (W.Z.); (W.L.); (H.Z.); (G.W.)
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Cheng WH, Huang PJ, Lee CC, Yeh YM, Ong SC, Lin R, Ku FM, Chiu CH, Tang P. Metabolomics analysis reveals changes related to pseudocyst formation induced by iron depletion in Trichomonas vaginalis. Parasit Vectors 2023; 16:226. [PMID: 37415204 DOI: 10.1186/s13071-023-05842-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 06/18/2023] [Indexed: 07/08/2023] Open
Abstract
BACKGROUND Iron is an essential element for cellular functions, such as energy metabolism. Trichomonas vaginalis, a human urogenital tract pathogen, is capable of surviving in the environment without sufficient iron supplementation. Pseudocysts (cyst-like structures) are an environmentally tolerated stage of this parasite while encountering undesired conditions, including iron deficiency. We previously demonstrated that iron deficiency induces more active glycolysis but a drastic downregulation of hydrogenosomal energy metabolic enzymes. Therefore, the metabolic direction of the end product of glycolysis is still controversial. METHODS In the present work, we conducted an LC‒MS-based metabolomics analysis to obtain accurate insights into the enzymatic events of T. vaginalis under iron-depleted (ID) conditions. RESULTS First, we showed the possible digestion of glycogen, cellulose polymerization, and accumulation of raffinose family oligosaccharides (RFOs). Second, a medium-chain fatty acid (MCFA), capric acid, was elevated, whereas most detected C18 fatty acids were reduced significantly. Third, amino acids were mostly reduced, especially alanine, glutamate, and serine. Thirty-three dipeptides showed significant accumulation in ID cells, which was probably associated with the decrease in amino acids. Our results indicated that glycogen was metabolized as the carbon source, and the structural component cellulose was synthesized at same time. The decrease in C18 fatty acids implied possible incorporation in the membranous compartment for pseudocyst formation. The decrease in amino acids accompanied by an increase in dipeptides implied incomplete proteolysis. These enzymatic reactions (alanine dehydrogenase, glutamate dehydrogenase, and threonine dehydratase) were likely involved in ammonia release. CONCLUSION These findings highlighted the possible glycogen utilization, cellulose biosynthesis, and fatty acid incorporation in pseudocyst formation as well as NO precursor ammonia production induced by iron-depleted stress.
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Affiliation(s)
- Wei-Hung Cheng
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Chi-Ching Lee
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Department of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Yuan-Ming Yeh
- Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taiwan
- Graduate Institute of Health Industry Technology, Chang Gung University of Science and Technology, Taoyuan, Taiwan
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Seow-Chin Ong
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Rose Lin
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Fu-Man Ku
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan
| | - Petrus Tang
- Department of Parasitology, College of Medicine, Chang Gung University, Guishan Dist., Taoyuan City, Taiwan.
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Linkou, Taiwan.
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Carvalho-de-Araújo AD, Carvalho-Kelly LF, Meyer-Fernandes JR. Anaerobic energy metabolism in human microaerophile parasites. Exp Parasitol 2023; 247:108492. [PMID: 36841468 DOI: 10.1016/j.exppara.2023.108492] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 01/30/2023] [Accepted: 02/20/2023] [Indexed: 02/27/2023]
Abstract
Mucosal-associated parasites, such as Giardia intestinalis, Entamoeba histolytica, and Trichomonas vaginalis, have significant clinical relevance. The pathologies associated with infection by these parasites are among those with the highest incidence of gastroenteritis (giardiasis and amoebiasis) and sexually transmitted infections (trichomoniasis). The treatment of these diseases is based on drugs that act on the anaerobic metabolism of these parasites, such as nitroimidazole and benzimidazole derivatives. One interesting feature of parasites is their ability to produce ATP under anaerobic conditions. Due to the absence of enzymes capable of producing ATP under anaerobic conditions in the vertebrate host, they have become interesting therapeutic targets. This review discusses anaerobic energy metabolism in mucosal-associated parasites, focusing on the anaerobic metabolism of pyruvate, the importance of these enzymes as therapeutic targets, and the importance of treating their infections.
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Affiliation(s)
- Ayra Diandra Carvalho-de-Araújo
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bloco H, 2 andar, sala 13. Ilha do Fundão, Rio de Janeiro, 21941-902, Brazil; Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, Ilha do Fundão, Rio de Janeiro, 21941-902, Brazil
| | - Luiz Fernando Carvalho-Kelly
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bloco H, 2 andar, sala 13. Ilha do Fundão, Rio de Janeiro, 21941-902, Brazil
| | - José Roberto Meyer-Fernandes
- Instituto de Bioquímica Médica Leopoldo de Meis, Universidade Federal do Rio de Janeiro, Av. Carlos Chagas Filho, 373, CCS, Bloco H, 2 andar, sala 13. Ilha do Fundão, Rio de Janeiro, 21941-902, Brazil; Instituto Nacional de Ciência a Tecnologia em Biologia Estrutural e Bioimagem (INCTBEB), Cidade Universitária, Ilha do Fundão, 21941-902, Rio de Janeiro, RJ, Brazil.
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Rubio-Sánchez R, Ríos-Reina R, Ubeda C. Identification of volatile biomarkers of Trichomonas vaginalis infection in vaginal discharge and urine. Appl Microbiol Biotechnol 2023; 107:3057-3069. [PMID: 37000228 PMCID: PMC10106345 DOI: 10.1007/s00253-023-12484-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 03/07/2023] [Accepted: 03/12/2023] [Indexed: 04/01/2023]
Abstract
Trichomoniasis, a disease caused by Trichomonas vaginalis, is the most common non-viral sexually transmitted infection worldwide. The importance of its diagnosis lies in its ease of transmission and the absence of symptoms in most cases, as occurs in men, which have a significant role as asymptomatic carriers. The most widely used diagnostic methods are the fresh examination of vaginal or urethral secretions and molecular techniques. However, as they have some disadvantages and, sometimes, low sensitivity, new trichomoniasis diagnostic methods are necessary. Volatile organic compounds in clinical samples are effective in the diagnosis of different diseases. This work aimed to study, for the first time, those present in vaginal discharge and urine of patients with Trichomonas vaginalis infection to look for volatile biomarkers. The results showed that volatile compounds such as 2-methyl-1-propanol and cyclohexanone could serve as biomarkers in vaginal discharge samples, as well as 2-octen-1-ol and 3-nonanone in urine. Moreover, 3-hydroxy-2,4,4-trimethylpentyl 2-methylpropanoate found in vaginal discharge, highly correlated to positive patients, is also highly related to urines of patients with trichomoniasis. The biomarkers described in this study might be a promising diagnostic tool. KEY POINTS: • The incidence of Trichomonas vaginalis infection is increasing • Trichomonas vaginalis VOC study in vaginal discharge and urine was performed • The identification of volatile biomarkers could allow a new diagnostic method.
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Affiliation(s)
- Ricardo Rubio-Sánchez
- Servicio de Análisis Clínicos, Hospital Universitario Virgen de Valme, 41014, Seville, Spain
| | - Rocío Ríos-Reina
- Área de Nutrición y Bromatología, Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain.
| | - Cristina Ubeda
- Área de Nutrición y Bromatología, Departamento de Nutrición y Bromatología, Toxicología y Medicina Legal, Facultad de Farmacia, Universidad de Sevilla, 41012, Seville, Spain
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Fang YK, Vaitová Z, Hampl V. A mitochondrion-free eukaryote contains proteins capable of import into an exogenous mitochondrion-related organelle. Open Biol 2023; 13:220238. [PMID: 36629021 PMCID: PMC9832562 DOI: 10.1098/rsob.220238] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The endobiotic flagellate Monocercomonoides exilis is the only known eukaryote to have lost mitochondria and all its associated proteins in its evolutionary past. This final stage of the mitochondrial evolutionary pathway may serve as a model to explain events at their very beginning such as the initiation of protein import. We have assessed the capability of proteins from this eukaryote to enter emerging mitochondria using a specifically designed in vitro assay. Hydrogenosomes (reduced mitochondria) of Trichomonas vaginalis were incubated with a soluble protein pool derived from a cytosolic fraction of M. exilis, and proteins entering hydrogenosomes were subsequently detected by mass spectrometry. The assay detected 19 specifically and reproducibly imported proteins, and in 14 cases the import was confirmed by the overexpression of their tagged version in T. vaginalis. In most cases, only a small portion of the signal reached the hydrogenosomes, suggesting specific but inefficient transport. Most of these proteins represent enzymes of carbon metabolism, and none exhibited clear signatures of proteins targeted to hydrogenosomes or mitochondria, which is consistent with their inefficient import. The observed phenomenon may resemble a primaeval type of protein import which might play a role in the establishment of the organelle and shaping of its proteome in the initial stages of endosymbiosis.
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Affiliation(s)
- Yi-Kai Fang
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Zuzana Vaitová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Prague 160 00, Czech Republic
| | - Vladimir Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
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Reduced mitochondria provide an essential function for the cytosolic methionine cycle. Curr Biol 2022; 32:5057-5068.e5. [PMID: 36347252 PMCID: PMC9746703 DOI: 10.1016/j.cub.2022.10.028] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 08/15/2022] [Accepted: 10/14/2022] [Indexed: 11/09/2022]
Abstract
The loss of mitochondria in oxymonad protists has been associated with the redirection of the essential Fe-S cluster assembly to the cytosol. Yet as our knowledge of diverse free-living protists broadens, the list of functions of their mitochondrial-related organelles (MROs) expands. We revealed another such function in the closest oxymonad relative, Paratrimastix pyriformis, after we solved the proteome of its MRO with high accuracy, using localization of organelle proteins by isotope tagging (LOPIT). The newly assigned enzymes connect to the glycine cleavage system (GCS) and produce folate derivatives with one-carbon units and formate. These are likely to be used by the cytosolic methionine cycle involved in S-adenosyl methionine recycling. The data provide consistency with the presence of the GCS in MROs of free-living species and its absence in most endobionts, which typically lose the methionine cycle and, in the case of oxymonads, the mitochondria.
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11
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Benchimol M, Gadelha AP, de Souza W. Unusual Cell Structures and Organelles in Giardia intestinalis and Trichomonas vaginalis Are Potential Drug Targets. Microorganisms 2022; 10:2176. [PMID: 36363768 PMCID: PMC9698047 DOI: 10.3390/microorganisms10112176] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 10/28/2022] [Accepted: 10/31/2022] [Indexed: 09/29/2023] Open
Abstract
This review presents the main cell organelles and structures of two important protist parasites, Giardia intestinalis, and Trichomonas vaginalis; many are unusual and are not found in other eukaryotic cells, thus could be good candidates for new drug targets aimed at improvement of the chemotherapy of diseases caused by these eukaryotic protists. For example, in Giardia, the ventral disc is a specific structure to this parasite and is fundamental for the adhesion and pathogenicity to the host. In Trichomonas, the hydrogenosome, a double membrane-bounded organelle that produces ATP, also can be a good target. Other structures include mitosomes, ribosomes, and proteasomes. Metronidazole is the most frequent compound used to kill many anaerobic organisms, including Giardia and Trichomonas. It enters the cell by passive diffusion and needs to find a highly reductive environment to be reduced to the nitro radicals to be active. However, it provokes several side effects, and some strains present metronidazole resistance. Therefore, to improve the quality of the chemotherapy against parasitic protozoa is important to invest in the development of highly specific compounds that interfere with key steps of essential metabolic pathways or in the functional macromolecular complexes which are most often associated with cell structures and organelles.
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Affiliation(s)
- Marlene Benchimol
- Laboratorio de Ultraestrutura Celular Hertha Meyer, Centro de Ciêcias da Saúde, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Cidade Universitaria, Rio de Janeiro 96200-000, Brazil
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
| | - Ana Paula Gadelha
- Diretoria de Metrologia Aplicada as Ciências da Vida, Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Rio de Janeiro 25250-020, Brazil
| | - Wanderley de Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens e Centro Nacional de Biologia Estrutural e Bioimagens, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-901, Brazil
- CMABio, Escola Superior de Saúde, Universidade do Estado do Amazonas-UEA, Manaus 69850-000, Brazil
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12
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Lorenzo-Benito S, Rivera-Rivas LA, Sánchez-Ayala L, Ortega-López J, Montes-Flores O, Talamás-Lara D, Arroyo R. Omics Analyses of Trichomonas vaginalis Actin and Tubulin and Their Participation in Intercellular Interactions and Cytokinesis. Genes (Basel) 2022; 13:genes13061067. [PMID: 35741829 PMCID: PMC9222396 DOI: 10.3390/genes13061067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Revised: 06/04/2022] [Accepted: 06/07/2022] [Indexed: 02/01/2023] Open
Abstract
Actin and tubulin proteins from Trichomonas vaginalis are crucial for morphogenesis and mitosis. This parasite has 10 and 11 genes coding bonafide actin and tubulin proteins, respectively. Hence, the goal of this work was to analyze these actin and tubulin genes, their expression at the mRNA and protein levels, and their parasite localization in intercellular interaction and cytokinesis. Representative bonafide actin (tvact1) and tubulin (tvtubα1) genes were cloned into and expressed in Escherichia coli. The recombinant proteins TvACT1r and TvTUBα1r were affinity purified and used as antigens to produce polyclonal antibodies. These antibodies were used in 1DE and 2DE WB and indirect immunofluorescence assays (IFA). By IFA, actin was detected as a ring on the periphery of ameboid, ovoid, and cold-induced cyst-like parasites, on pseudopods of amoeboid parasites, and in cytoplasmic extensions (filopodia) in cell–cell interactions. Tubulin was detected in the axostyle, flagellum, undulating membrane, and paradesmose during mitosis. Paradesmose was observed by IFA mainly during cytokinesis. By scanning electron microscopy, a tubulin-containing nanotubular structure similar to the tunneling nanotubes (TNTs) was also detected in the last stage of cytokinesis. In conclusion, actin and tubulin are multigene families differentially expressed that play important roles in intercellular interactions and cytokinesis.
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Affiliation(s)
- Sebastián Lorenzo-Benito
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (S.L.-B.); (L.A.R.-R.); (L.S.-A.); (D.T.-L.)
| | - Luis Alberto Rivera-Rivas
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (S.L.-B.); (L.A.R.-R.); (L.S.-A.); (D.T.-L.)
| | - Lizbeth Sánchez-Ayala
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (S.L.-B.); (L.A.R.-R.); (L.S.-A.); (D.T.-L.)
| | - Jaime Ortega-López
- Departamento de Biotecnología y Bioingeniería, CINVESTAV-IPN. Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (J.O.-L.); (O.M.-F.)
| | - Octavio Montes-Flores
- Departamento de Biotecnología y Bioingeniería, CINVESTAV-IPN. Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (J.O.-L.); (O.M.-F.)
| | - Daniel Talamás-Lara
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (S.L.-B.); (L.A.R.-R.); (L.S.-A.); (D.T.-L.)
| | - Rossana Arroyo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Av. IPN #2508, Col. San Pedro Zacatenco, Alcaldía Gustavo A. Madero, Mexico City CP 07360, Mexico; (S.L.-B.); (L.A.R.-R.); (L.S.-A.); (D.T.-L.)
- Correspondence: ; Tel.: +52-55-5747-3342
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13
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Tachezy J, Makki A, Hrdý I. The hydrogenosomes of Trichomonas vaginalis. J Eukaryot Microbiol 2022; 69:e12922. [PMID: 35567536 DOI: 10.1111/jeu.12922] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
This review is dedicated to the 50th anniversary of the discovery of hydrogenosomes by Miklós Müller and Donald Lindmark, which we will celebrate the following year. It was a long journey from the first observation of enigmatic rows of granules in trichomonads at the end of the 19th century to their first biochemical characterization in 1973. The key experiments by Müller and Lindmark revealed that the isolated granules contain hydrogen-producing hydrogenase, similar to some anaerobic bacteria-a discovery that gave birth to the field of hydrogenosomes. It is also important to acknowledge the parallel work of the team of Apolena Čerkasovová, Jiří Čerkasov, and Jaroslav Kulda, who demonstrated that these granules, similar to mitochondria, produce ATP. However, the evolutionary origin of hydrogenosomes remained enigmatic until the turn of the millennium, when it was finally accepted that hydrogenosomes and mitochondria evolved from a common ancestor. After a historical introduction, the review provides an overview of hydrogenosome biogenesis, hydrogenosomal protein import, and the relationship between the peculiar structure of membrane translocases and its low inner membrane potential due to the lack of respiratory complexes. Next, it summarizes the current state of knowledge on energy metabolism, the oxygen defense system, and iron/sulfur cluster assembly.
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Affiliation(s)
- Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 25242 Vestec, Czech Republic
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14
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Ma J, Zhong P, Li Y, Sun Z, Sun X, Aung M, Hao L, Cheng Y, Zhu W. Hydrogenosome, Pairing Anaerobic Fungi and H2-Utilizing Microorganisms Based on Metabolic Ties to Facilitate Biomass Utilization. J Fungi (Basel) 2022; 8:jof8040338. [PMID: 35448569 PMCID: PMC9026988 DOI: 10.3390/jof8040338] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 03/21/2022] [Accepted: 03/22/2022] [Indexed: 02/04/2023] Open
Abstract
Anaerobic fungi, though low in abundance in rumen, play an important role in the degradation of forage for herbivores. When only anaerobic fungi exist in the fermentation system, the continuous accumulation of metabolites (e.g., hydrogen (H2) and formate) generated from their special metabolic organelles—the hydrogenosome—inhibits the enzymatic reactions in the hydrogenosome and reduces the activity of the anaerobic fungi. However, due to interspecific H2 transfer, H2 produced by the hydrogenosome can be used by other microorganisms to form valued bioproducts. This symbiotic interaction between anaerobic fungi and other microorganisms can be used to improve the nutritional value of animal feeds and produce value-added products that are normally in low concentrations in the fermentation system. Because of the important role in the generation and further utilization of H2, the study of the hydrogensome is increasingly becoming an important part of the development of anaerobic fungi as model organisms that can effectively improve the utilization value of roughage. Here, we summarize and discuss the classification and the process of biomass degradation of anaerobic fungi and the metabolism and function of anaerobic fungal hydrogensome, with a focus on the potential role of the hydrogensome in the efficient utilization of biomass.
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Affiliation(s)
- Jing Ma
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Pei Zhong
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Yuqi Li
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Zhanying Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Xiaoni Sun
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
| | - Min Aung
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
- Department of Animal Nutrition, University of Veterinary Science, Nay Pyi Taw 15013, Myanmar
| | - Lizhuang Hao
- Key Laboratory of Plateau Grazing Animal Nutrition and Feed Science of Qinghai Province, State Key Laboratory of Plateau Ecology and Agriculture, Qinghai Plateau Yak Research Center, Qinghai Academy of Science and Veterinary Medicine of Qinghai University, Xining 810016, China;
| | - Yanfen Cheng
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
- Correspondence: ; Tel.: +86-25-8439-5523
| | - Weiyun Zhu
- Laboratory of Gastrointestinal Microbiology, National Center for International Research on Animal Gut Nutrition, Nanjing Agricultural University, Nanjing 210095, China; (J.M.); (P.Z.); (Y.L.); (Z.S.); (X.S.); (M.A.); (W.Z.)
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15
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Hammond M, Dorrell RG, Speijer D, Lukeš J. Eukaryotic cellular intricacies shape mitochondrial proteomic complexity. Bioessays 2022; 44:e2100258. [PMID: 35318703 DOI: 10.1002/bies.202100258] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/08/2022] [Accepted: 03/09/2022] [Indexed: 12/17/2022]
Abstract
Mitochondria have been fundamental to the eco-physiological success of eukaryotes since the last eukaryotic common ancestor (LECA). They contribute essential functions to eukaryotic cells, above and beyond classical respiration. Mitochondria interact with, and complement, metabolic pathways occurring in other organelles, notably diversifying the chloroplast metabolism of photosynthetic organisms. Here, we integrate existing literature to investigate how mitochondrial metabolism varies across the landscape of eukaryotic evolution. We illustrate the mitochondrial remodelling and proteomic changes undergone in conjunction with major evolutionary transitions. We explore how the mitochondrial complexity of the LECA has been remodelled in specific groups to support subsequent evolutionary transitions, such as the acquisition of chloroplasts in photosynthetic species and the emergence of multicellularity. We highlight the versatile and crucial roles played by mitochondria during eukaryotic evolution, extending from its huge contribution to the development of the LECA itself to the dynamic evolution of individual eukaryote groups, reflecting both their current ecologies and evolutionary histories.
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Affiliation(s)
- Michael Hammond
- 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
| | - Richard G Dorrell
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Dave Speijer
- Medical Biochemistry, UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - 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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16
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Krakovka S, Ribacke U, Miyamoto Y, Eckmann L, Svärd S. Characterization of Metronidazole-Resistant Giardia intestinalis Lines by Comparative Transcriptomics and Proteomics. Front Microbiol 2022; 13:834008. [PMID: 35222342 PMCID: PMC8866875 DOI: 10.3389/fmicb.2022.834008] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Accepted: 01/13/2022] [Indexed: 12/13/2022] Open
Abstract
Metronidazole (MTZ) is a clinically important antimicrobial agent that is active against both bacterial and protozoan organisms. MTZ has been used extensively for more than 60 years and until now resistance has been rare. However, a recent and dramatic increase in the number of MTZ resistant bacteria and protozoa is of great concern since there are few alternative drugs with a similarly broad activity spectrum. To identify key factors and mechanisms underlying MTZ resistance, we utilized the protozoan parasite Giardia intestinalis, which is commonly treated with MTZ. We characterized two in vitro selected, metronidazole resistant parasite lines, as well as one revertant, by analyzing fitness aspects associated with increased drug resistance and transcriptomes and proteomes. We also conducted a meta-analysis using already existing data from additional resistant G. intestinalis isolates. The combined data suggest that in vitro generated MTZ resistance has a substantial fitness cost to the parasite, which may partly explain why resistance is not widespread despite decades of heavy use. Mechanistically, MTZ resistance in Giardia is multifactorial and associated with complex changes, yet a core set of pathways involving oxidoreductases, oxidative stress responses and DNA repair proteins, is central to MTZ resistance in both bacteria and protozoa.
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Affiliation(s)
- Sascha Krakovka
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden
| | - Ulf Ribacke
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Stockholm, Sweden
| | - Yukiko Miyamoto
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Lars Eckmann
- Department of Medicine, University of California, San Diego, La Jolla, CA, United States
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden.,SciLifeLab, Uppsala University, Uppsala, Sweden
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17
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Oxygen levels are key to understanding "Anaerobic" protozoan pathogens with micro-aerophilic lifestyles. Adv Microb Physiol 2021; 79:163-240. [PMID: 34836611 DOI: 10.1016/bs.ampbs.2021.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Publications abound on the physiology, biochemistry and molecular biology of "anaerobic" protozoal parasites as usually grown under "anaerobic" culture conditions. The media routinely used are poised at low redox potentials using techniques that remove O2 to "undetectable" levels in sealed containers. However there is growing understanding that these culture conditions do not faithfully resemble the O2 environments these organisms inhabit. Here we review for protists lacking oxidative energy metabolism, the oxygen cascade from atmospheric to intracellular concentrations and relevant methods of measurements of O2, some well-studied parasitic or symbiotic protozoan lifestyles, their homeodynamic metabolic and redox balances, organism-drug-oxygen interactions, and the present and future prospects for improved drugs and treatment regimes.
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18
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Smutná T, Dohnálková A, Sutak R, Narayanasamy RK, Tachezy J, Hrdý I. A cytosolic ferredoxin-independent hydrogenase possibly mediates hydrogen uptake in Trichomonas vaginalis. Curr Biol 2021; 32:124-135.e5. [PMID: 34762819 DOI: 10.1016/j.cub.2021.10.050] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/30/2021] [Accepted: 10/22/2021] [Indexed: 11/16/2022]
Abstract
Trichomonads, represented by the highly prevalent sexually transmitted human parasite Trichomonas vaginalis, are anaerobic eukaryotes with hydrogenosomes in the place of the standard mitochondria. Hydrogenosomes form indispensable FeS-clusters, synthesize ATP, and release molecular hydrogen as a waste product. Hydrogen formation is catalyzed by [FeFe] hydrogenase, the hallmark enzyme of all hydrogenosomes found in various eukaryotic anaerobes. Eukaryotic hydrogenases were originally thought to be exclusively localized within organelles, but today few eukaryotic anaerobes are known that possess hydrogenase in their cytosol. We identified a thus-far unknown hydrogenase in T. vaginalis cytosol that cannot use ferredoxin as a redox partner but can use cytochrome b5 as an electron acceptor. Trichomonads overexpressing the cytosolic hydrogenase, while maintaining the carbon flux through hydrogenosomes, show decreased excretion of hydrogen and increased excretion of methylated alcohols, suggesting that the cytosolic hydrogenase uses the hydrogen gas as a source of reducing power for the reactions occurring in the cytoplasm and thus accounts for the overall redox balance. This is the first evidence of hydrogen uptake in a eukaryote, although further work is needed to confirm it. Assembly of the catalytic center of [FeFe] hydrogenases (H-cluster) requires the activity of three dedicated maturases, and these proteins in T. vaginalis are exclusively localized in hydrogenosomes, where they participate in the maturation of organellar hydrogenases. Despite the different subcellular localization of cytosolic hydrogenase and maturases, the H-cluster is present in the cytosolic enzyme, suggesting the existence of an alternative mechanism of H-cluster assembly.
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Affiliation(s)
- Tamara Smutná
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Alena Dohnálková
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Róbert Sutak
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Ravi Kumar Narayanasamy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Jan Tachezy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic
| | - Ivan Hrdý
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 252 50, Czech Republic.
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19
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Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biol 2021; 19:142. [PMID: 34294116 PMCID: PMC8296547 DOI: 10.1186/s12915-021-01078-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.
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Affiliation(s)
- Emily K Herman
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Alex Greninger
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
- Department of Laboratory Medicine, University of Washington Medical Center, Montlake, USA
| | - Mark van der Giezen
- Centre for Organelle Research, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Michael L Ginger
- School of Applied Sciences, Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK
| | - Inmaculada Ramirez-Macias
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Department of Cardiology, Hospital Clinico Universitario Virgen de la Arrixaca. Instituto Murciano de Investigación Biosanitaria. Centro de Investigación Biomedica en Red-Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Haylea C Miller
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
- CSIRO, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Matthew J Morgan
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | | | - Katrina Velle
- Department of Biology, University of Massachusetts, Amherst, UK
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristína Záhonová
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Sebastian Rodrigo Najle
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Catalonia, Spain
| | - Georgina MacIntyre
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Norbert Muller
- Institute of Parasitology, Vetsuisse Faculty Bern, University of Bern, Bern, Switzerland
| | - Mattias Wittwer
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | | | - Francine Marciano-Cabral
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Geoffrey J Puzon
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | - Charles Chiu
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Life Sciences, The Natural History Museum, London, UK.
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20
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Natto MJ, Hulpia F, Kalkman ER, Baillie S, Alhejeli A, Miyamoto Y, Eckmann L, Van Calenbergh S, de Koning HP. Deazapurine Nucleoside Analogues for the Treatment of Trichomonas vaginalis. ACS Infect Dis 2021; 7:1752-1764. [PMID: 33974405 DOI: 10.1021/acsinfecdis.1c00075] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Trichomoniasis is the most common nonviral sexually transmitted disease in humans, but treatment options are limited. Here, we report a resorufin-based drug sensitivity assay for high-throughput microplate-based screening under hypoxic conditions. A 5203-compound enamine kinase library and several specialized compound series were tested for the inhibition of Trichomonas growth at 10 μM with Z' values of >0.5. Hits were rescreened in serial dilution to establish an IC50 concentration. A series of 7-substituted 7-deazaadenosine analogues emerged as highly potent anti-T. vaginalis agents, with EC50 values in the low double digit nanomolar range. These analogues exhibited excellent selectivity indices. Follow-up medicinal chemistry efforts identified an optimal ribofuranose and C7 substituent. Several nucleosides rapidly cleared cultures of T. vaginalis at a concentrations of just 2 × EC50. Preliminary in vivo evaluation in a murine trichomoniasis model (Tritrichomonas foetus) revealed promising activity upon topical administration, validating purine nucleoside analogues as a new class of antitrichomonal agents.
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Affiliation(s)
- Manal J. Natto
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U.K
| | - Fabian Hulpia
- Laboratory for Medicinal Chemistry, Campus Heymans (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Eric R. Kalkman
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U.K
| | - Susan Baillie
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U.K
| | - Amani Alhejeli
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U.K
| | | | | | - Serge Van Calenbergh
- Laboratory for Medicinal Chemistry, Campus Heymans (FFW), Ghent University, Ottergemsesteenweg 460, B-9000 Gent, Belgium
| | - Harry P. de Koning
- Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, U.K
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21
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Graf JS, Schorn S, Kitzinger K, Ahmerkamp S, Woehle C, Huettel B, Schubert CJ, Kuypers MMM, Milucka J. Anaerobic endosymbiont generates energy for ciliate host by denitrification. Nature 2021; 591:445-450. [PMID: 33658719 PMCID: PMC7969357 DOI: 10.1038/s41586-021-03297-6] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 01/27/2021] [Indexed: 11/27/2022]
Abstract
Mitochondria are specialized eukaryotic organelles that have a dedicated function in oxygen respiration and energy production. They evolved about 2 billion years ago from a free-living bacterial ancestor (probably an alphaproteobacterium), in a process known as endosymbiosis1,2. Many unicellular eukaryotes have since adapted to life in anoxic habitats and their mitochondria have undergone further reductive evolution3. As a result, obligate anaerobic eukaryotes with mitochondrial remnants derive their energy mostly from fermentation4. Here we describe 'Candidatus Azoamicus ciliaticola', which is an obligate endosymbiont of an anaerobic ciliate and has a dedicated role in respiration and providing energy for its eukaryotic host. 'Candidatus A. ciliaticola' contains a highly reduced 0.29-Mb genome that encodes core genes for central information processing, the electron transport chain, a truncated tricarboxylic acid cycle, ATP generation and iron-sulfur cluster biosynthesis. The genome encodes a respiratory denitrification pathway instead of aerobic terminal oxidases, which enables its host to breathe nitrate instead of oxygen. 'Candidatus A. ciliaticola' and its ciliate host represent an example of a symbiosis that is based on the transfer of energy in the form of ATP, rather than nutrition. This discovery raises the possibility that eukaryotes with mitochondrial remnants may secondarily acquire energy-providing endosymbionts to complement or replace functions of their mitochondria.
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Affiliation(s)
- Jon S Graf
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
| | - Sina Schorn
- Max Planck Institute for Marine Microbiology, Bremen, Germany
| | - Katharina Kitzinger
- Max Planck Institute for Marine Microbiology, Bremen, Germany
- Division of Microbial Ecology, Centre for Microbiology and Environmental Systems Science, University of Vienna, Vienna, Austria
| | | | - Christian Woehle
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Bruno Huettel
- Max Planck Genome Centre Cologne, Max Planck Institute for Plant Breeding Research, Cologne, Germany
| | - Carsten J Schubert
- Surface Waters - Research and Management, Eawag, Kastanienbaum, Switzerland
| | | | - Jana Milucka
- Max Planck Institute for Marine Microbiology, Bremen, Germany.
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22
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Experimentally Validated Reconstruction and Analysis of a Genome-Scale Metabolic Model of an Anaerobic Neocallimastigomycota Fungus. mSystems 2021; 6:6/1/e00002-21. [PMID: 33594000 PMCID: PMC8561657 DOI: 10.1128/msystems.00002-21] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Anaerobic gut fungi in the phylum Neocallimastigomycota typically inhabit the digestive tracts of large mammalian herbivores, where they play an integral role in the decomposition of raw lignocellulose into its constitutive sugar monomers. However, quantitative tools to study their physiology are lacking, partially due to their complex and unresolved metabolism that includes the largely uncharacterized fungal hydrogenosome. Modern omics approaches combined with metabolic modeling can be used to establish an understanding of gut fungal metabolism and develop targeted engineering strategies to harness their degradation capabilities for lignocellulosic bioprocessing. Here, we introduce a high-quality genome of the anaerobic fungus Neocallimastix lanati from which we constructed the first genome-scale metabolic model of an anaerobic fungus. Relative to its size (200 Mbp, sequenced at 62× depth), it is the least fragmented publicly available gut fungal genome to date. Of the 1,788 lignocellulolytic enzymes annotated in the genome, 585 are associated with the fungal cellulosome, underscoring the powerful lignocellulolytic potential of N. lanati. The genome-scale metabolic model captures the primary metabolism of N. lanati and accurately predicts experimentally validated substrate utilization requirements. Additionally, metabolic flux predictions are verified by 13C metabolic flux analysis, demonstrating that the model faithfully describes the underlying fungal metabolism. Furthermore, the model clarifies key aspects of the hydrogenosomal metabolism and can be used as a platform to quantitatively study these biotechnologically important yet poorly understood early-branching fungi. IMPORTANCE Recent genomic analyses have revealed that anaerobic gut fungi possess both the largest number and highest diversity of lignocellulolytic enzymes of all sequenced fungi, explaining their ability to decompose lignocellulosic substrates, e.g., agricultural waste, into fermentable sugars. Despite their potential, the development of engineering methods for these organisms has been slow due to their complex life cycle, understudied metabolism, and challenging anaerobic culture requirements. Currently, there is no framework that can be used to combine multi-omic data sets to understand their physiology. Here, we introduce a high-quality PacBio-sequenced genome of the anaerobic gut fungus Neocallimastix lanati. Beyond identifying a trove of lignocellulolytic enzymes, we use this genome to construct the first genome-scale metabolic model of an anaerobic gut fungus. The model is experimentally validated and sheds light on unresolved metabolic features common to gut fungi. Model-guided analysis will pave the way for deepening our understanding of anaerobic gut fungi and provides a systematic framework to guide strain engineering efforts of these organisms for biotechnological use.
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Adherence of Trichomonas vaginalis to SiHa Cells is Inhibited by Diphenyleneiodonium. Microorganisms 2020; 8:microorganisms8101570. [PMID: 33066000 PMCID: PMC7600062 DOI: 10.3390/microorganisms8101570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 11/16/2022] Open
Abstract
Microbial adhesion is critical for parasitic infection and colonization of host cells. To study the host–parasite interaction in vitro, we established a flow cytometry-based assay to measure the adherence of Trichomonas vaginalis to epithelial cell line SiHa. SiHa cells and T. vaginalis were detected as clearly separated, quantifiable populations by flow cytometry. We found that T. vaginalis attached to SiHa cells as early as 30 min after infection and the binding remained stable up to several hours, allowing for analysis of drug treatment efficacy. Importantly, NADPH oxidase inhibitor DPI treatment induced the detachment of T. vaginalis from SiHa cells in a dose-dependent manner without affecting host cell viability. Thus, this study may provide an understanding for the potential development of therapies against T. vaginalis and other parasite infections.
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24
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Hammond MJ, Nenarokova A, Butenko A, Zoltner M, Dobáková EL, Field MC, Lukeš J. A Uniquely Complex Mitochondrial Proteome from Euglena gracilis. Mol Biol Evol 2020; 37:2173-2191. [PMID: 32159766 PMCID: PMC7403612 DOI: 10.1093/molbev/msaa061] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
Euglena gracilis is a metabolically flexible, photosynthetic, and adaptable free-living protist of considerable environmental importance and biotechnological value. By label-free liquid chromatography tandem mass spectrometry, a total of 1,786 proteins were identified from the E. gracilis purified mitochondria, representing one of the largest mitochondrial proteomes so far described. Despite this apparent complexity, protein machinery responsible for the extensive RNA editing, splicing, and processing in the sister clades diplonemids and kinetoplastids is absent. This strongly suggests that the complex mechanisms of mitochondrial gene expression in diplonemids and kinetoplastids occurred late in euglenozoan evolution, arising independently. By contrast, the alternative oxidase pathway and numerous ribosomal subunits presumed to be specific for parasitic trypanosomes are present in E. gracilis. We investigated the evolution of unexplored protein families, including import complexes, cristae formation proteins, and translation termination factors, as well as canonical and unique metabolic pathways. We additionally compare this mitoproteome with the transcriptome of Eutreptiella gymnastica, illuminating conserved features of Euglenida mitochondria as well as those exclusive to E. gracilis. This is the first mitochondrial proteome of a free-living protist from the Excavata and one of few available for protists as a whole. This study alters our views of the evolution of the mitochondrion and indicates early emergence of complexity within euglenozoan mitochondria, independent of parasitism.
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Affiliation(s)
- Michael J Hammond
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice, Budweis, Czech Republic
| | - Anzhelika Butenko
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Eva Lacová Dobáková
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
| | - Mark C Field
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, České Budějovice, Budweis, Czech Republic
- School of Life Sciences, University of Dundee, Dundee, United Kingdom
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, 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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25
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Morales-Luna L, Hernández-Ochoa B, Ramírez-Nava EJ, Martínez-Rosas V, Ortiz-Ramírez P, Fernández-Rosario F, González-Valdez A, Cárdenas-Rodríguez N, Serrano-Posada H, Centeno-Leija S, Arreguin-Espinosa R, Cuevas-Cruz M, Ortega-Cuellar D, Pérez de la Cruz V, Rocha-Ramírez LM, Sierra-Palacios E, Castillo-Rodríguez RA, Vega-García V, Rufino-González Y, Marcial-Quino J, Gómez-Manzo S. Characterizing the Fused TvG6PD::6PGL Protein from the Protozoan Trichomonas vaginalis, and Effects of the NADP + Molecule on Enzyme Stability. Int J Mol Sci 2020; 21:ijms21144831. [PMID: 32650494 PMCID: PMC7402283 DOI: 10.3390/ijms21144831] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/03/2020] [Accepted: 07/04/2020] [Indexed: 12/30/2022] Open
Abstract
This report describes a functional and structural analysis of fused glucose-6-phosphate dehydrogenase dehydrogenase-phosphogluconolactonase protein from the protozoan Trichomonas vaginalis (T. vaginalis). The glucose-6-phosphate dehydrogenase (g6pd) gene from T. vaginalis was isolated by PCR and the sequence of the product showed that is fused with 6pgl gene. The fused Tvg6pd::6pgl gene was cloned and overexpressed in a heterologous system. The recombinant protein was purified by affinity chromatography, and the oligomeric state of the TvG6PD::6PGL protein was found as tetramer, with an optimal pH of 8.0. The kinetic parameters for the G6PD domain were determined using glucose-6-phosphate (G6P) and nicotinamide adenine dinucleotide phosphate (NADP+) as substrates. Biochemical assays as the effects of temperature, susceptibility to trypsin digestion, and analysis of hydrochloride of guanidine on protein stability in the presence or absence of NADP+ were performed. These results revealed that the protein becomes more stable in the presence of the NADP+. In addition, we determined the dissociation constant for the binding (Kd) of NADP+ in the protein and suggests the possible structural site in the fused TvG6PD::6PGL protein. Finally, computational modeling studies were performed to obtain an approximation of the structure of TvG6PD::6PGL. The generated model showed differences with the GlG6PD::6PGL protein (even more so with human G6PD) despite both being fused.
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Affiliation(s)
- Laura Morales-Luna
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Beatriz Hernández-Ochoa
- Laboratorio de Inmunoquímica, Hospital Infantil de México Federico Gómez, Secretaría de Salud, 06720 Ciudad de México, Mexico;
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Edson Jiovany Ramírez-Nava
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Posgrado en Ciencias Biológicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico
| | - Víctor Martínez-Rosas
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Programa de Posgrado en Biomedicina y Biotecnología Molecular, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, 11340 Ciudad de México, Mexico
| | - Paulina Ortiz-Ramírez
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Fabiola Fernández-Rosario
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
| | - Abigail González-Valdez
- Departamento de Biología Molecular y Biotecnología, Instituto de Investigaciones Biomédicas, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Noemí Cárdenas-Rodríguez
- Laboratorio de Neurociencias, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Hugo Serrano-Posada
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Sara Centeno-Leija
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Laboratorio de Agrobiotecnología, Tecnoparque CLQ, Universidad de Colima, Carretera los Limones-Loma de Juárez, 28629 Colima, Mexico; (H.S.-P.); (S.C.-L.)
| | - Roberto Arreguin-Espinosa
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Miguel Cuevas-Cruz
- Departamento de Química de Biomacromoléculas, Instituto de Química, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico; (R.A.-E.); (M.C.-C.)
| | - Daniel Ortega-Cuellar
- Laboratorio de Nutrición Experimental, Instituto Nacional de Pediatría, 04530 Secretaría de Salud, Mexico;
| | - Verónica Pérez de la Cruz
- Departamento de Neuroquímica, Instituto Nacional de Neurología y Neurocirugía Manuel Velasco Suárez, Secretaria de Salud, 14269 Ciudad de México, Mexico;
| | - Luz María Rocha-Ramírez
- Unidad de Investigación en Enfermedades Infecciosas, Hospital Infantil de México Federico Gómez, Dr. Márquez No. 162, Col Doctores, 06720 Delegación Cuauhtémoc, Mexico;
| | - Edgar Sierra-Palacios
- Colegio de Ciencias y Humanidades, Plantel Casa Libertad, Universidad Autónoma de la Ciudad de México, 09620 Ciudad de México, Mexico;
| | - Rosa Angélica Castillo-Rodríguez
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Vanesa Vega-García
- Facultad de Ciencias, Universidad Nacional Autónoma de México, 04510 Ciudad de México, Mexico;
| | - Yadira Rufino-González
- Laboratorio de Parasitología Experimental, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
| | - Jaime Marcial-Quino
- Consejo Nacional de Ciencia y Tecnología (CONACYT), Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico;
- Correspondence: (J.M.-Q.); (S.G.-M.); Tel.: +52-55-1084-0900 (ext. 1442) (J.M.-Q. & S.G.-M.)
| | - Saúl Gómez-Manzo
- Laboratorio de Bioquímica Genética, Instituto Nacional de Pediatría, Secretaría de Salud, 04530 Ciudad de México, Mexico; (L.M.-L.); (E.J.R.-N.); (V.M.-R.); (P.O.-R.); (F.F.-R.)
- Correspondence: (J.M.-Q.); (S.G.-M.); Tel.: +52-55-1084-0900 (ext. 1442) (J.M.-Q. & S.G.-M.)
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26
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Lin HC, Chu LJ, Huang PJ, Cheng WH, Zheng YH, Huang CY, Hong SW, Chen LC, Lin HA, Wang JY, Chen RM, Lin WN, Tang P, Huang KY. Proteomic signatures of metronidazole-resistant Trichomonas vaginalis reveal novel proteins associated with drug resistance. Parasit Vectors 2020; 13:274. [PMID: 32487244 PMCID: PMC7268490 DOI: 10.1186/s13071-020-04148-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2020] [Accepted: 05/25/2020] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Trichomoniasis is the most common non-viral sexually transmitted disease caused by the protozoan parasite Trichomonas vaginalis. Metronidazole (MTZ) is a widely used drug for the treatment of trichomoniasis; however, increased resistance of the parasite to MTZ has emerged as a highly problematic public health issue. METHODS We conducted iTRAQ-based analysis to profile the proteomes of MTZ-sensitive (MTZ-S) and MTZ-resistant (MTZ-R) parasites. STRING and gene set enrichment analysis (GESA) were utilized to explore the protein-protein interaction networks and enriched pathways of the differentially expressed proteins, respectively. Proteins potentially related to MTZ resistance were selected for functional validation. RESULTS A total of 3123 proteins were identified from the MTZ-S and MTZ-R proteomes in response to drug treatment. Among the identified proteins, 304 proteins were differentially expressed in the MTZ-R proteome, including 228 upregulated and 76 downregulated proteins. GSEA showed that the amino acid-related metabolism, including arginine, proline, alanine, aspartate, and glutamate are the most upregulated pathways in the MTZ-R proteome, whereas oxidative phosphorylation is the most downregulated pathway. Ten proteins categorized into the gene set of oxidative phosphorylation were ATP synthase subunit-related proteins. Drug resistance was further examined in MTZ-S parasites pretreated with the ATP synthase inhibitors oligomycin and bafilomycin A1, showing enhanced MTZ resistance and potential roles of ATP synthase in drug susceptibility. CONCLUSIONS We provide novel insights into previously unidentified proteins associated with MTZ resistance, paving the way for future development of new drugs against MTZ-refractory trichomoniasis.
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Affiliation(s)
- Hsin-Chung Lin
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Lichieh Julie Chu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan City, 333, Taiwan.,Liver Research Center, Chang Gung Memorial Hospital, Linkou, Taoyuan City, 333, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan City, 333, Taiwan.,Genomic Medicine Core Laboratory, Chang Gung Memorial Hospital, Linkou, Taoyuan City, 333, Taiwan
| | - Wei-Hung Cheng
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan City, 333, Taiwan
| | - Yu-Hsing Zheng
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Ching-Yun Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Shu-Wen Hong
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Lih-Chyang Chen
- Department of Medicine, Mackay Medical College, New Taipei City, 252, Taiwan
| | - Hsin-An Lin
- Division of Infection, Department of Medicine, Tri-Service General Hospital SongShan Branch, Taipei City, 105, Taiwan
| | - Jui-Yang Wang
- Division of Family Medicine, Tri-Service General Hospital Songshan Branch, Taipei City, 105, Taiwan
| | - Ruei-Min Chen
- Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taipei City, 114, Taiwan
| | - Wei-Ning Lin
- Graduate Institute of Biomedical and Pharmaceutical Science, Fu Jen Catholic University, New Taipei City, 242, Taiwan
| | - Petrus Tang
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan City, 333, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei City, 114, Taiwan.
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27
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Jiménez-González A, Xu F, Andersson JO. Lateral Acquisitions Repeatedly Remodel the Oxygen Detoxification Pathway in Diplomonads and Relatives. Genome Biol Evol 2020; 11:2542-2556. [PMID: 31504492 PMCID: PMC6934886 DOI: 10.1093/gbe/evz188] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/19/2019] [Indexed: 12/13/2022] Open
Abstract
Oxygen and reactive oxygen species (ROS) are important stress factors for cells because they can oxidize many large molecules. Fornicata, a group of flagellated protists that includes diplomonads, have anaerobic metabolism but are still able to tolerate fluctuating levels of oxygen. We identified 25 protein families putatively involved in detoxification of oxygen and ROS in this group using a bioinformatics approach and propose how these interact in an oxygen detoxification pathway. These protein families were divided into a central oxygen detoxification pathway and accessory pathways for the synthesis of nonprotein thiols. We then used a phylogenetic approach to investigate the evolutionary origin of the components of this putative pathway in Diplomonadida and other Fornicata species. Our analyses suggested that the diplomonad ancestor was adapted to low-oxygen levels, was able to reduce O2 to H2O in a manner similar to extant diplomonads, and was able to synthesize glutathione and l-cysteine. Several genes involved in the pathway have complex evolutionary histories and have apparently been repeatedly acquired through lateral gene transfer and subsequently lost. At least seven genes were acquired independently in different Fornicata lineages, leading to evolutionary convergences. It is likely that acquiring these oxygen detoxification proteins helped anaerobic organisms (like the parasitic Giardia intestinalis) adapt to low-oxygen environments (such as the digestive tract of aerobic hosts).
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Affiliation(s)
- Alejandro Jiménez-González
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Molecular Evolution Program, Uppsala University, Sweden
| | - Feifei Xu
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Microbiology Program, Uppsala University, Sweden
| | - Jan O Andersson
- Uppsala Biomedicine Centre, Department of Cell and Molecular Biology, Molecular Evolution Program, Uppsala University, Sweden
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Gray MW, Burger G, Derelle R, Klimeš V, Leger MM, Sarrasin M, Vlček Č, Roger AJ, Eliáš M, Lang BF. The draft nuclear genome sequence and predicted mitochondrial proteome of Andalucia godoyi, a protist with the most gene-rich and bacteria-like mitochondrial genome. BMC Biol 2020; 18:22. [PMID: 32122349 PMCID: PMC7050145 DOI: 10.1186/s12915-020-0741-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/21/2020] [Indexed: 01/02/2023] Open
Abstract
Background Comparative analyses have indicated that the mitochondrion of the last eukaryotic common ancestor likely possessed all the key core structures and functions that are widely conserved throughout the domain Eucarya. To date, such studies have largely focused on animals, fungi, and land plants (primarily multicellular eukaryotes); relatively few mitochondrial proteomes from protists (primarily unicellular eukaryotic microbes) have been examined. To gauge the full extent of mitochondrial structural and functional complexity and to identify potential evolutionary trends in mitochondrial proteomes, more comprehensive explorations of phylogenetically diverse mitochondrial proteomes are required. In this regard, a key group is the jakobids, a clade of protists belonging to the eukaryotic supergroup Discoba, distinguished by having the most gene-rich and most bacteria-like mitochondrial genomes discovered to date. Results In this study, we assembled the draft nuclear genome sequence for the jakobid Andalucia godoyi and used a comprehensive in silico approach to infer the nucleus-encoded portion of the mitochondrial proteome of this protist, identifying 864 candidate mitochondrial proteins. The A. godoyi mitochondrial proteome has a complexity that parallels that of other eukaryotes, while exhibiting an unusually large number of ancestral features that have been lost particularly in opisthokont (animal and fungal) mitochondria. Notably, we find no evidence that the A. godoyi nuclear genome has or had a gene encoding a single-subunit, T3/T7 bacteriophage-like RNA polymerase, which functions as the mitochondrial transcriptase in all eukaryotes except the jakobids. Conclusions As genome and mitochondrial proteome data have become more widely available, a strikingly punctuate phylogenetic distribution of different mitochondrial components has been revealed, emphasizing that the pathways of mitochondrial proteome evolution are likely complex and lineage-specific. Unraveling this complexity will require comprehensive comparative analyses of mitochondrial proteomes from a phylogenetically broad range of eukaryotes, especially protists. The systematic in silico approach described here offers a valuable adjunct to direct proteomic analysis (e.g., via mass spectrometry), particularly in cases where the latter approach is constrained by sample limitation or other practical considerations.
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Affiliation(s)
- Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.
| | - Gertraud Burger
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, Birmingham, B15 2TT, UK
| | - Vladimír Klimeš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Michelle M Leger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada.,Institute of Evolutionary Biology (CSIC-UPF), Barcelona, Spain
| | - Matt Sarrasin
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
| | - Čestmír Vlček
- Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Sir Charles Tupper Medical Building, Dalhousie University, 5850 College Street, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - B Franz Lang
- Département de Biochimie and Robert-Cedergren Center for Bioinformatics and Genomics, Université de Montréal, Montréal, QC, Canada
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29
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Benoit SL, Maier RJ, Sawers RG, Greening C. Molecular Hydrogen Metabolism: a Widespread Trait of Pathogenic Bacteria and Protists. Microbiol Mol Biol Rev 2020; 84:e00092-19. [PMID: 31996394 PMCID: PMC7167206 DOI: 10.1128/mmbr.00092-19] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Pathogenic microorganisms use various mechanisms to conserve energy in host tissues and environmental reservoirs. One widespread but often overlooked means of energy conservation is through the consumption or production of molecular hydrogen (H2). Here, we comprehensively review the distribution, biochemistry, and physiology of H2 metabolism in pathogens. Over 200 pathogens and pathobionts carry genes for hydrogenases, the enzymes responsible for H2 oxidation and/or production. Furthermore, at least 46 of these species have been experimentally shown to consume or produce H2 Several major human pathogens use the large amounts of H2 produced by colonic microbiota as an energy source for aerobic or anaerobic respiration. This process has been shown to be critical for growth and virulence of the gastrointestinal bacteria Salmonella enterica serovar Typhimurium, Campylobacter jejuni, Campylobacter concisus, and Helicobacter pylori (including carcinogenic strains). H2 oxidation is generally a facultative trait controlled by central regulators in response to energy and oxidant availability. Other bacterial and protist pathogens produce H2 as a diffusible end product of fermentation processes. These include facultative anaerobes such as Escherichia coli, S Typhimurium, and Giardia intestinalis, which persist by fermentation when limited for respiratory electron acceptors, as well as obligate anaerobes, such as Clostridium perfringens, Clostridioides difficile, and Trichomonas vaginalis, that produce large amounts of H2 during growth. Overall, there is a rich literature on hydrogenases in growth, survival, and virulence in some pathogens. However, we lack a detailed understanding of H2 metabolism in most pathogens, especially obligately anaerobic bacteria, as well as a holistic understanding of gastrointestinal H2 transactions overall. Based on these findings, we also evaluate H2 metabolism as a possible target for drug development or other therapies.
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Affiliation(s)
- Stéphane L Benoit
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - Robert J Maier
- Department of Microbiology, University of Georgia, Athens, Georgia, USA
| | - R Gary Sawers
- Institute of Microbiology, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Chris Greening
- School of Biological Sciences, Monash University, Clayton, VIC, Australia
- Department of Microbiology, Monash Biomedicine Discovery Institute, Clayton, VIC, Australia
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Hsu HM, Huang YH, Aryal S, Liu HW, Chen C, Chen SH, Chu CH, Tai JH. Endomembrane Protein Trafficking Regulated by a TvCyP2 Cyclophilin in the Protozoan Parasite, Trichomonas vaginalis. Sci Rep 2020; 10:1275. [PMID: 31988345 PMCID: PMC6985235 DOI: 10.1038/s41598-020-58270-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Accepted: 01/10/2020] [Indexed: 01/08/2023] Open
Abstract
In Trichomonas vaginalis, the TvCyP1-catalyzed conformational switches of two glycinyl-prolyl imide bonds in Myb3 were previously shown to regulate the trafficking of Myb3 from cytoplasmic membrane compartments towards the nucleus. In this study, TvCyP2 was identified as a second cyclophilin that binds to Myb3 at the same dipeptide motifs. The enzymatic proficiency of TvCyP2, but not its binding to Myb3, was aborted by a mutation of Arg75 in the catalytic domain. TvCyP2 was localized to the endoplasmic reticulum with a weak signal that extensively extends into the cytoplasm as well as to the plasma membrane according to an immunofluorescence assay. Moreover, TvCyP2 was co-enriched with TvCyP1 and Myb3 in various membrane fractions purified by differential and gradient centrifugation. TvCyP2 was found to proficiently enzymatically regulate the distribution of TvCyP1 and Myb3 among purified membrane fractions, and to localize TvCyP1 in hydrogenosomes and on plasma membranes. Protein complexes immunoprecipitated from lysates of cells overexpressing TvCyP1 and TvCyP2 were found to share some common components, like TvCyP1, TvCyP2, TvBip, Myb3, TvHSP72, and the hydrogenosomal heat shock protein 70 (HSP70). Direct interaction between TvCyP1 and TvCyP2 was confirmed by a GST pull-down assay. Fusion of vesicles with hydrogenosomes was observed by transmission electron microscopy, whereas TvCyP1, TvCyP2, and Myb3 were each detected at the fusion junction by immunoelectron microscopy. These observations suggest that T. vaginalis may have evolved a novel protein trafficking pathway to deliver proteins among the endomembrane compartments, hydrogenosomes and plasma membranes.
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Affiliation(s)
- Hong-Ming Hsu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, Taiwan
| | - Yu-Hsin Huang
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Sarita Aryal
- Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Hsing-Wei Liu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Chinpan Chen
- Structural Biology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan
| | - Shu-Hui Chen
- Department of Chemistry, National Cheng Kung University, Tainan, Taiwan
| | - Chien-Hsin Chu
- Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
| | - Jung-Hsiang Tai
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, Taiwan. .,Division of Infectious Diseases and Immunology, Institute of Biomedical Sciences, Academia Sinica, Taipei, Taiwan.
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31
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Feng JM, Jiang CQ, Sun ZY, Hua CJ, Wen JF, Miao W, Xiong J. Single-cell transcriptome sequencing of rumen ciliates provides insight into their molecular adaptations to the anaerobic and carbohydrate-rich rumen microenvironment. Mol Phylogenet Evol 2019; 143:106687. [PMID: 31740334 DOI: 10.1016/j.ympev.2019.106687] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2019] [Revised: 11/11/2019] [Accepted: 11/13/2019] [Indexed: 01/26/2023]
Abstract
Rumen ciliates are a specialized group of ciliates exclusively found in the anaerobic, carbohydrate-rich rumen microenvironment. However, the molecular and mechanistic basis of the physiological and behavioral adaptation of ciliates to the rumen microenvironment is undefined. We used single-cell transcriptome sequencing to explore the adaptive evolution of three rumen ciliates: two entodiniomorphids, Entodinium furca and Diplodinium dentatum; and one vestibuliferid, Isotricha intestinalis. We found that all three species are members of monophyletic orders within the class Litostomatea, with E. furca and D. dentatum in Entodiniomorphida and I. intestinalis in Vestibuliferida. The two entodiniomorphids might use H2-producing mitochondria and the vestibuliferid might use anaerobic mitochondria to survive under strictly anaerobic conditions. Moreover, carbohydrate-active enzyme (CAZyme) genes were identified in all three species, including cellulases, hemicellulases, and pectinases. The evidence that all three species have acquired prokaryote-derived genes by horizontal gene transfer (HGT) to digest plant biomass includes a significant enrichment of gene ontology categories such as cell wall macromolecule catabolic process and carbohydrate catabolic process and the identification of genes in common between CAZyme and HGT groups. These findings suggest that HGT might be an important mechanism in the adaptive evolution of ciliates to the rumen microenvironment.
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Affiliation(s)
- Jin-Mei Feng
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Chuan-Qi Jiang
- Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China; Guangdong Provincial Engineering Research Center for Aquatic Animal Health Assessment, Shenzhen 518120, China; Shenzhen Dapeng New District Science and Technology Innovation Service Center, Shenzhen 518119, China; Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zong-Yi Sun
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Cong-Jie Hua
- Department of Pathogenic Biology, School of Medicine, Jianghan University, Wuhan 430056, China
| | - Jian-Fan Wen
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Wei Miao
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China; State Key Laboratory of Freshwater Ecology and Biotechnology of China, Wuhan 430072, China; CAS Center for Excellence in Animal Evolution and Genetics, Kunming 650223, China.
| | - Jie Xiong
- Key Laboratory of Aquatic Biodiversity and Conservation, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China.
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32
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Rada P, Kellerová P, Verner Z, Tachezy J. Investigation of the Secretory Pathway inTrichomonas vaginalisArgues against a Moonlighting Function of Hydrogenosomal Enzymes. J Eukaryot Microbiol 2019; 66:899-910. [DOI: 10.1111/jeu.12741] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 05/01/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Petr Rada
- Department of Parasitology Faculty of Science Charles University, BIOCEV Průmyslová 595 Vestec 25242 Czech Republic
| | - Pavlína Kellerová
- Department of Parasitology Faculty of Science Charles University, BIOCEV Průmyslová 595 Vestec 25242 Czech Republic
| | - Zdeněk Verner
- Department of Parasitology Faculty of Science Charles University, BIOCEV Průmyslová 595 Vestec 25242 Czech Republic
| | - Jan Tachezy
- Department of Parasitology Faculty of Science Charles University, BIOCEV Průmyslová 595 Vestec 25242 Czech Republic
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33
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Rada P, Makki A, Žárský V, Tachezy J. Targeting of tail-anchored proteins to Trichomonas vaginalis hydrogenosomes. Mol Microbiol 2019; 111:588-603. [PMID: 30506591 DOI: 10.1111/mmi.14175] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/25/2018] [Indexed: 01/17/2023]
Abstract
Tail-anchored (TA) proteins are membrane proteins that are found in all domains of life. They consist of an N-terminal domain that performs various functions and a single transmembrane domain (TMD) near the C-terminus. In eukaryotes, TA proteins are targeted to the membranes of mitochondria, the endoplasmic reticulum (ER), peroxisomes and in plants, chloroplasts. The targeting of these proteins to their specific destinations correlates with the properties of the C-terminal domain, mainly the TMD hydrophobicity and the net charge of the flanking regions. Trichomonas vaginalis is a human parasite that has adapted to oxygen-poor environment. This adaptation is reflected by the presence of highly modified mitochondria (hydrogenosomes) and the absence of peroxisomes. The proteome of hydrogenosomes is considerably reduced; however, our bioinformatic analysis predicted 120 putative hydrogenosomal TA proteins. Seven proteins were selected to prove their localization. The elimination of the net positive charge in the C-tail of the hydrogenosomal TA4 protein resulted in its dual localization to hydrogenosomes and the ER, causing changes in ER morphology. Domain mutation and swap experiments with hydrogenosomal (TA4) and ER (TAPDI) proteins indicated that the general principles for specific targeting are conserved across eukaryotic lineages, including T. vaginalis; however, there are also significant lineage-specific differences.
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Affiliation(s)
- Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, Vestec, 25242, Czech Republic
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34
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Makki A, Rada P, Žárský V, Kereïche S, Kováčik L, Novotný M, Jores T, Rapaport D, Tachezy J. Triplet-pore structure of a highly divergent TOM complex of hydrogenosomes in Trichomonas vaginalis. PLoS Biol 2019; 17:e3000098. [PMID: 30608924 PMCID: PMC6334971 DOI: 10.1371/journal.pbio.3000098] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Revised: 01/16/2019] [Accepted: 12/11/2018] [Indexed: 11/30/2022] Open
Abstract
Mitochondria originated from proteobacterial endosymbionts, and their transition to organelles was tightly linked to establishment of the protein import pathways. The initial import of most proteins is mediated by the translocase of the outer membrane (TOM). Although TOM is common to all forms of mitochondria, an unexpected diversity of subunits between eukaryotic lineages has been predicted. However, experimental knowledge is limited to a few organisms, and so far, it remains unsettled whether the triplet-pore or the twin-pore structure is the generic form of TOM complex. Here, we analysed the TOM complex in hydrogenosomes, a metabolically specialised anaerobic form of mitochondria found in the excavate Trichomonas vaginalis. We demonstrate that the highly divergent β-barrel T. vaginalis TOM (TvTom)40-2 forms a translocation channel to conduct hydrogenosomal protein import. TvTom40-2 is present in high molecular weight complexes, and their analysis revealed the presence of four tail-anchored (TA) proteins. Two of them, Tom36 and Tom46, with heat shock protein (Hsp)20 and tetratricopeptide repeat (TPR) domains, can bind hydrogenosomal preproteins and most likely function as receptors. A third subunit, Tom22-like protein, has a short cis domain and a conserved Tom22 transmembrane segment but lacks a trans domain. The fourth protein, hydrogenosomal outer membrane protein 19 (Homp19) has no known homology. Furthermore, our data indicate that TvTOM is associated with sorting and assembly machinery (Sam)50 that is involved in β-barrel assembly. Visualisation of TvTOM by electron microscopy revealed that it forms three pores and has an unconventional skull-like shape. Although TvTOM seems to lack Tom7, our phylogenetic profiling predicted Tom7 in free-living excavates. Collectively, our results suggest that the triplet-pore TOM complex, composed of three conserved subunits, was present in the last common eukaryotic ancestor (LECA), while receptors responsible for substrate binding evolved independently in different eukaryotic lineages. The highly divergent outer membrane translocase (TOM) from the Trichomonas hydrogenosome (an organelle related to mitochondria) is composed of conserved core and lineage-specific subunits, and has an unconventional skull-like triplet-pore structure. Mitochondria carry out many vital functions in the eukaryotic cells, from energy metabolism to programmed cell death. These organelles descended from bacterial endosymbionts, and during their evolution, the cell established a mechanism to transport nuclear-encoded proteins into mitochondria. Embedded in the mitochondrial outer membrane is a molecular machine, known as the translocase of the outer membrane (TOM) complex, that plays a key role in protein import and biogenesis of the organelle. Here, we provide evidence that the TOM complex of hydrogenosomes, a metabolically specialised anaerobic form of mitochondria in Trichomonas vaginalis, is composed of highly divergent core subunits and lineage-specific peripheral subunits. Despite the evolutionary distance, the T. vaginalis TOM (TvTOM) complex has a conserved triplet-pore structure but with a unique skull-like shape suggesting that the TOM in the early mitochondrion could have formed three pores. Our results contribute to a better understanding of the evolution and adaptation of protein import machinery in anaerobic forms of mitochondria.
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Affiliation(s)
- Abhijith Makki
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Petr Rada
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Sami Kereïche
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Lubomír Kováčik
- Institute of Biology and Medical Genetics, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Marian Novotný
- Department of Cell Biology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Tobias Jores
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Doron Rapaport
- Interfaculty Institute of Biochemistry, University of Tübingen, Tübingen, Germany
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- * E-mail:
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Kume K, Amagasa T, Hashimoto T, Kitagawa H. NommPred: Prediction of Mitochondrial and Mitochondrion-Related Organelle Proteins of Nonmodel Organisms. Evol Bioinform Online 2018; 14:1176934318819835. [PMID: 30626996 PMCID: PMC6305954 DOI: 10.1177/1176934318819835] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 11/07/2018] [Indexed: 01/11/2023] Open
Abstract
To estimate the functions of mitochondria of diverse eukaryotic nonmodel organisms in which the mitochondrial proteomes are not available, it is necessary to predict the protein sequence features of the mitochondrial proteins computationally. Various prediction methods that are trained using the proteins of model organisms belonging particularly to animals, plants, and fungi exist. However, such methods may not be suitable for predicting the proteins derived from nonmodel organisms because the sequence features of the mitochondrial proteins of diversified nonmodel organisms can differ from those of model organisms that are present only in restricted parts of the tree of eukaryotes. Here, we proposed NommPred, which predicts the mitochondrial proteins of nonmodel organisms that are widely distributed over eukaryotes. We used a gradient boosting machine to develop 2 predictors-one for predicting the proteins of mitochondria and the other for predicting the proteins of mitochondrion-related organelles that are highly reduced mitochondria. The performance of both predictors was found to be better than that of the best method available.
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Affiliation(s)
- Keitaro Kume
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Toshiyuki Amagasa
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Hiroyuki Kitagawa
- Graduate School of Systems and Information Engineering, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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36
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Dias-Lopes G, Wiśniewski JR, de Souza NP, Vidal VE, Padrón G, Britto C, Cuervo P, De Jesus JB. In-Depth Quantitative Proteomic Analysis of Trophozoites and Pseudocysts of Trichomonas vaginalis. J Proteome Res 2018; 17:3704-3718. [PMID: 30239205 DOI: 10.1021/acs.jproteome.8b00343] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Trichomonas vaginalis is a sexually transmitted anaerobic parasite that infects humans causing trichomoniasis, a common and ubiquitous sexually transmitted disease. The life cycle of this parasite possesses a trophozoite form without a cystic stage. However, the presence of nonproliferative and nonmotile, yet viable and reversible spherical forms with internalized flagella, denominated pseudocysts, has been commonly observed for this parasite. To understand the mechanisms involved in the formation of pseudocysts, we performed a mass spectrometry-based high-throughput quantitative proteomics study using a label-free approach and functional assays by biochemical and flow cytometric methods. We observed that the morphological transformation of trophozoite to pseudocysts is coupled to (i) a metabolic shift toward a less glycolytic phenotype; (ii) alterations in the abundance of hydrogenosomal iron-sulfur cluster (ISC) assembly machinery; (iii) increased abundance of regulatory particles of the ubiquitin-proteasome system; (iv) significant alterations in proteins involved in adhesion and cytoskeleton reorganization; and (v) arrest in G2/M phase associated with alterations in the abundance of regulatory proteins of the cell cycle. These data demonstrate that pseudocysts experience important physiological and structural alterations for survival under unfavorable environmental conditions.
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Affiliation(s)
| | - Jacek R Wiśniewski
- Department of Proteomics and Signal Transduction , Max-Planck-Institute for Biochemistry , 82152 Martinsried , Germany
| | | | | | | | | | | | - José Batista De Jesus
- Departamento de Medicina , Universidade Federal de São João del Rei , 36301-160 São João del Rei , Minas Gerais Brazil
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37
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Santos HJ, Makiuchi T, Nozaki T. Reinventing an Organelle: The Reduced Mitochondrion in Parasitic Protists. Trends Parasitol 2018; 34:1038-1055. [PMID: 30201278 DOI: 10.1016/j.pt.2018.08.008] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2018] [Revised: 08/10/2018] [Accepted: 08/10/2018] [Indexed: 12/18/2022]
Abstract
Mitochondria originated from the endosymbiotic event commencing from the engulfment of an ancestral α-proteobacterium by the first eukaryotic ancestor. Establishment of niches has led to various adaptations among eukaryotes. In anaerobic parasitic protists, the mitochondria have undergone modifications by combining features shared from the aerobic mitochondria with lineage-specific components and mechanisms; a diversified class of organelles emerged and are generally called mitochondrion-related organelles (MROs). In this review we summarize and discuss the recent advances in the knowledge of MROs from parasitic protists, particularly the themes such as metabolic functions, contribution to parasitism, dynamics, protein targeting, and novel lineage- specific proteins, with emphasis on the diversity among these organelles.
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Affiliation(s)
- Herbert J Santos
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Takashi Makiuchi
- Department of Infectious Diseases, Tokai University School of Medicine, 143 Shimokasuya, Isehara, Kanagawa 259-1193, Japan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
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Kameshwar AKS, Qin W. Genome Wide Analysis Reveals the Extrinsic Cellulolytic and Biohydrogen Generating Abilities of Neocallimastigomycota Fungi. J Genomics 2018; 6:74-87. [PMID: 29928466 PMCID: PMC6004548 DOI: 10.7150/jgen.25648] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 04/25/2018] [Indexed: 11/26/2022] Open
Abstract
Ruminating animals, especially cattle lack the carbohydrate active enzyme encoding genes which are required for the degradation of the glycosidic linkages of plant cell wall carbohydrates (such as cellulose, hemicellulose, lignin and pectin). Thus, ruminating animals are completely dependent on the microorganisms (anaerobic bacteria and fungi, methanogenic archaea and protozoa) residing in their rumen (hindgut). In this study, we have retrieved and analyzed the complete genome wide annotations of the Neocallimastigomycota division fungi such as Anaeromyces robustus, Neocallismatix californiae, Orpinomyces sp, Piromyces finnis, Piromyces sp E2. We have retrieved the InterPro, CAZy, KOG, KEGG, SM Clusters and MEROPS genome level data of these anaerobic fungi from JGI-MycoCosm database. Results obtained in our study reveals that, the genomes of anaerobic fungi completely lack genes encoding for lignin degrading auxiliary activity enzymes. Contrastingly, these fungi outnumbered other fungi by having highest number of CAZyme encoding genes. The genes encoding for dockerins and carbohydrate binding modules exaggerated other CAZymes which are involved in the structure and functioning of cellulosomes. Presence of cellulosomes and higher number of carbohydrate transport and metabolism genes also endorses the plant cell wall carbohydrate degrading abilities of these fungi. We also reported the tentative total cellulolytic, hemicellulolytic and pectinolytic abilities. And we have explicitly reported the genes, enzymes and the mechanisms involved in structure and functioning of the cellulosomes and hydrogenosomes. Our present work reveals the genomic machinery underlying the extrinsic plant cell wall degrading abilities of the anaerobic fungi. Results obtained in our study can be significantly applied in improving the gut health of cattle and especially in the fields of biofuel, biorefining and bioremediation-based industries.
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Affiliation(s)
| | - Wensheng Qin
- Department of Biology, Lakehead University, 955 Oliver Road, Thunder Bay, Ontario, P7B 5E1, Canada
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Leitsch D, Williams CF, Hrdý I. Redox Pathways as Drug Targets in Microaerophilic Parasites. Trends Parasitol 2018; 34:576-589. [PMID: 29807758 DOI: 10.1016/j.pt.2018.04.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2018] [Revised: 04/27/2018] [Accepted: 04/28/2018] [Indexed: 01/06/2023]
Abstract
The microaerophilic parasites Entamoeba histolytica, Trichomonas vaginalis, and Giardia lamblia jointly cause hundreds of millions of infections in humans every year. Other microaerophilic parasites such as Tritrichomonas foetus and Spironucleus spp. pose a relevant health problem in veterinary medicine. Unfortunately, vaccines against these pathogens are unavailable, but their microaerophilic lifestyle opens opportunities for specifically developed chemotherapeutics. In particular, their high sensitivity towards oxygen can be exploited by targeting redox enzymes. This review focusses on the redox pathways of microaerophilic parasites and on drugs, either already in use or currently in the state of development, which target these pathways.
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Affiliation(s)
- David Leitsch
- Institute for Specific Prophylaxis and Tropical Medicine, Center for Pathophysiology, Infectiology, and Immunology, Medical University of Vienna, Austria.
| | - Catrin F Williams
- School of Engineering, Cardiff University, Cardiff, Wales, United Kingdom
| | - Ivan Hrdý
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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Peña-Diaz P, Lukeš J. Fe-S cluster assembly in the supergroup Excavata. J Biol Inorg Chem 2018; 23:521-541. [PMID: 29623424 PMCID: PMC6006210 DOI: 10.1007/s00775-018-1556-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2018] [Accepted: 03/29/2018] [Indexed: 12/21/2022]
Abstract
The majority of established model organisms belong to the supergroup Opisthokonta, which includes yeasts and animals. While enlightening, this focus has neglected protists, organisms that represent the bulk of eukaryotic diversity and are often regarded as primitive eukaryotes. One of these is the “supergroup” Excavata, which comprises unicellular flagellates of diverse lifestyles and contains species of medical importance, such as Trichomonas, Giardia, Naegleria, Trypanosoma and Leishmania. Excavata exhibits a continuum in mitochondrial forms, ranging from classical aerobic, cristae-bearing mitochondria to mitochondria-related organelles, such as hydrogenosomes and mitosomes, to the extreme case of a complete absence of the organelle. All forms of mitochondria house a machinery for the assembly of Fe–S clusters, ancient cofactors required in various biochemical activities needed to sustain every extant cell. In this review, we survey what is known about the Fe–S cluster assembly in the supergroup Excavata. We aim to bring attention to the diversity found in this group, reflected in gene losses and gains that have shaped the Fe–S cluster biogenesis pathways.
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Affiliation(s)
- Priscila Peña-Diaz
- Institute of Parasitology, 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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Westrop GD, Wang L, Blackburn GJ, Zhang T, Zheng L, Watson DG, Coombs GH. Metabolomic profiling and stable isotope labelling of Trichomonas vaginalis and Tritrichomonas foetus reveal major differences in amino acid metabolism including the production of 2-hydroxyisocaproic acid, cystathionine and S-methylcysteine. PLoS One 2017; 12:e0189072. [PMID: 29267346 PMCID: PMC5739422 DOI: 10.1371/journal.pone.0189072] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2017] [Accepted: 11/17/2017] [Indexed: 11/19/2022] Open
Abstract
Trichomonas vaginalis and Tritrichomonas foetus are pathogens that parasitise, respectively, human and bovine urogenital tracts causing disease. Using LC-MS, reference metabolomic profiles were obtained for both species and stable isotope labelling with D-[U-13C6] glucose was used to analyse central carbon metabolism. This facilitated a comparison of the metabolic pathways of T. vaginalis and T. foetus, extending earlier targeted biochemical studies. 43 metabolites, whose identities were confirmed by comparison of their retention times with authentic standards, occurred at more than 3-fold difference in peak intensity between T. vaginalis and T. foetus. 18 metabolites that were removed from or released into the medium during growth also showed more than 3-fold difference between the species. Major differences were observed in cysteine and methionine metabolism in which homocysteine, produced as a bi-product of trans-methylation, is catabolised by methionine γ-lyase in T. vaginalis but converted to cystathionine in T. foetus. Both species synthesise methylthioadenosine by an unusual mechanism, but it is not used as a substrate for methionine recycling. T. vaginalis also produces and exports high levels of S-methylcysteine, whereas only negligible levels were found in T. foetus which maintains significantly higher intracellular levels of cysteine. 13C-labeling confirmed that both cysteine and S-methylcysteine are synthesised by T. vaginalis; S-methylcysteine can be generated by recombinant T. vaginalis cysteine synthase using phosphoserine and methanethiol. T. foetus contained higher levels of ornithine and citrulline than T. vaginalis and exported increased levels of putrescine, suggesting greater flux through the arginine dihydrolase pathway. T. vaginalis produced and exported hydroxy acid derivatives of certain amino acids, particularly 2-hydroxyisocaproic acid derived from leucine, whereas negligible levels of these metabolites occurred in T. foetus.
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Affiliation(s)
- Gareth D. Westrop
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
- * E-mail:
| | - Lijie Wang
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
| | | | - Tong Zhang
- Institute of Cancer Sciences, University of Glasgow, Glasgow, United Kingdom
| | - Liang Zheng
- Pediatric Translational Medicine Institute, Shanghai Children’s Medical Center, Shanghai, China
| | - David G. Watson
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
| | - Graham H. Coombs
- Strathclyde Institute of Pharmacy and Biomedical Science, Strathclyde University, Glasgow, United Kingdom
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Huang KY, Ong SC, Wu CC, Hsu CW, Lin HC, Fang YK, Cheng WH, Huang PJ, Chiu CH, Tang P. Metabolic reprogramming of hydrogenosomal amino acids in Trichomonas vaginalis under glucose restriction. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 52:630-637. [PMID: 29198954 DOI: 10.1016/j.jmii.2017.10.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2017] [Revised: 06/12/2017] [Accepted: 10/29/2017] [Indexed: 12/13/2022]
Abstract
BACKGROUND Glucose is the major energy source that is converted to pyruvate for ATP generation in the trichomonad hydrogenosome. Under glucose restriction (GR), the regulation of amino acids metabolism is crucial for trichomonad growth and survival. RNA-sequencing (RNA-seq) analysis has been used to identify differentially expressed genes in Trichomonas vaginalis under GR, leading to significant advances in understanding adaptive responses of amino acid metabolism to GR. However, the levels of amino acid metabolites modulated by GR are unknown in T. vaginalis. METHODS Herein, we describe a comprehensive metabolomic analysis of amino acid metabolites in the hydrogenosome using liquid chromatography Fourier transform ion cyclotron resonance mass spectrometry (LC-FT MS). The relative abundance of 17 hydrogenosomal amino acids was analyzed under GR and high-glucose (HG) conditions. RESULTS Levels of most amino acids were higher in GR culture. Arginine was not detectable in either HG or GR cultures; however, its metabolic end-product proline was slightly increased under GR, suggesting that the arginine dihydrolase pathway was more activated by GR. Additionally, methionine catabolism was less stimulated under GR because of greater methionine accumulation. Furthermore, branched chain amino acids (BCAA), including leucine, isoleucine and valine, as well as phenylalanine and alanine, markedly accumulated under GR, indicating that glutamate-related metabolic pathways were remarkably enhanced in this setting. Our metabolomic analysis combined with previous RNA-seq data confirm the existence of several amino acid metabolic pathways in the hydrogenosome and highlight their potentially important roles in T. vaginalis under glucose deprivation.
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Affiliation(s)
- Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Seow-Chin Ong
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chih-Ching Wu
- Graduate Institute of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Chia-Wei Hsu
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Hsin-Chung Lin
- Graduate Institute of Medical Sciences, National Defense Medical Center, Taipei, Taiwan; Division of Clinical Pathology, Department of Pathology, Tri-Service General Hospital, Taipei, Taiwan
| | - Yi-Kai Fang
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Wei-Hung Cheng
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan
| | - Po-Jung Huang
- Department of Biomedical Sciences, Chang Gung University, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Petrus Tang
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Taoyuan, Taiwan; Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan.
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Fang YK, Chien KY, Huang KY, Cheng WH, Ku FM, Lin R, Chen TW, Huang PJ, Chiu CH, Tang P. Responding to a Zoonotic Emergency with Multi-omics Research: Pentatrichomonas hominis Hydrogenosomal Protein Characterization with Use of RNA Sequencing and Proteomics. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2017; 20:662-669. [PMID: 27828770 DOI: 10.1089/omi.2016.0111] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Pentatrichomonas hominis is an anaerobic flagellated protist that colonizes the large intestine of a number of mammals, including cats, dogs, nonhuman primates, and humans. The wide host range of this organism is alarming and suggests a rising zoonotic emergency. However, knowledge on in-depth biology of this protist is still limited. Similar to the human pathogen, Trichomonas vaginalis, P. hominis possesses hydrogenosomes instead of mitochondria. Studies in T. vaginalis indicated that hydrogenosome is essential for cell survival and associated with numerous pivotal biological functions, including drug resistance. To further decipher the biology of this important organelle, we undertook proteomic research in P. hominis hydrogenosomes. Lacking a decoded P. hominis genome, we utilized an RNA sequencing (RNA-seq) data set generated from P. hominis axenic culture as the reference for proteome analysis. Using this in-house reference data set and mass spectrometry (MS), we identified 442 putative hydrogenosomal proteins. Interestingly, the composition of the P. hominis hydrogenosomal proteins is very similar to that of T. vaginalis, but proteins such as Hmp36, Pam16, Pam18, and Isd11 are absent based on both MS and the RNA-seq. Our data underscore that P. hominis expresses different homologs of multiple gene families from T. vaginalis. To the best of our knowledge, we present here the first hydrogenosome proteome in a protist other than T. vaginalis that offers crucial new scholarship for global health, therapeutics, diagnostics, and veterinary medicine research. In addition, the research strategy used here using RNA sequencing and proteomics might inform future multi-omics research in other understudied organisms without decoded genomes.
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Affiliation(s)
- Yi-Kai Fang
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Kun-Yi Chien
- 3 Proteomics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Kuo-Yang Huang
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Wei-Hung Cheng
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Fu-Mann Ku
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Rose Lin
- 2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan
| | - Ting-Wen Chen
- 4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Po-Jung Huang
- 4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- 5 Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital , Taoyuan, Taiwan
| | - Petrus Tang
- 1 Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University , Taoyuan, Taiwan .,2 Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, Chang Gung University , Taoyuan, Taiwan .,4 Bioinformatics Core Laboratory, Chang Gung University , Taoyuan, Taiwan .,5 Molecular Infectious Diseases Research Center, Chang Gung Memorial Hospital , Taoyuan, Taiwan
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Cheng WH, Huang KY, Huang PJ, Lee CC, Yeh YM, Ku FM, Lin R, Cheng ML, Chiu CH, Tang P. γ-Carboxymuconolactone decarboxylase: a novel cell cycle-related basal body protein in the early branching eukaryote Trichomonas vaginalis. Parasit Vectors 2017; 10:443. [PMID: 28950916 PMCID: PMC5615479 DOI: 10.1186/s13071-017-2381-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 09/14/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND γ-Carboxymuconolactone decarboxylase (CMD) participates in the β-ketoadipate pathway, which catalyzes aromatic compounds to produce acetyl- or succinyl-CoA, in prokaryotes and yeast. Our previous study demonstrated that expression of a CMD homologue that contains two signatures (dualCMD) is negatively regulated by iron in Trichomonas vaginalis. However, we were not able to identify the components of the β-ketoadipate pathway in the parasite's genome. These observations prompted us to investigate the biological functions of this novel CMD homologue in T. vaginalis. METHODS The specific anti-TvCMD1 antibody was generated, and the expression of TvCMD1 in T. vaginalis cultured under iron-rich and iron-deficient were evaluated. Phylogenetic, metabolomic and substrate induction (protocatechuate and benzoate) analysis were conducted to clarify the function of dualCMD in trichomonad cells. Subcellular localization of TvCMD1 was observed by confocal microscopy. The cell cycle-related role of TvCMD1 was assessed by treating cells with G2/M inhibitor nocodazole. RESULTS We confirmed that T. vaginalis is not able to catabolize the aromatic compounds benzoate and protocatechuate, which are known substrates of the β-ketoadipate pathway. Using immunofluorescence microscopy, we found that TvCMD1 is spatially associated with the basal body, a part of the cytoskeletal organizing center in T. vaginalis. TvCMD1 accumulated upon treatment with the G2/M inhibitor nocodazole. Additionally, TvCMD1 was expressed and transported to/from the basal body during cytokinesis, suggesting that TvCMD1 plays a role in cell division. CONCLUSION We demonstrated that TvCMD1 is unlikely to participate in the β-ketoadipate pathway and demonstrated that it is a novel basal body-localizing (associated) protein. This model sheds light on the importance of genes that are acquired laterally in the coevolution of ancient protists, which surprisingly functions in cell cycle regulation of T. vaginalis.
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Affiliation(s)
- Wei-Hung Cheng
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Kuo-Yang Huang
- Graduate Institute of Pathology and Parasitology, National Defense Medical Center, Taipei, Taiwan
| | - Po-Jung Huang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Chi-Ching Lee
- Department and Graduate Institute of Computer Science and Information Engineering, College of Engineering, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Yuan-Ming Yeh
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Fu-Man Ku
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Rose Lin
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Mei-Ling Cheng
- Department of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
| | - Cheng-Hsun Chiu
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
| | - Petrus Tang
- Graduate Institute of Biomedical Sciences, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Regulation and Bioinformatics Laboratory, Department of Parasitology, College of Medicine, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Bioinformatics Core Laboratory, Molecular Medicine Research Center, Chang Gung University, Kweishan, Taoyuan, Taiwan
- Molecular Infectious Disease Research Center, Chang Gung Memorial Hospital, Kweishan, Taoyuan, Taiwan
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FunctionAnnotator, a versatile and efficient web tool for non-model organism annotation. Sci Rep 2017; 7:10430. [PMID: 28874813 PMCID: PMC5585236 DOI: 10.1038/s41598-017-10952-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2017] [Accepted: 08/17/2017] [Indexed: 02/07/2023] Open
Abstract
Along with the constant improvement in high-throughput sequencing technology, an increasing number of transcriptome sequencing projects are carried out in organisms without decoded genome information and even on environmental biological samples. To study the biological functions of novel transcripts, the very first task is to identify their potential functions. We present a web-based annotation tool, FunctionAnnotator, which offers comprehensive annotations, including GO term assignment, enzyme annotation, domain/motif identification and predictions for subcellular localization. To accelerate the annotation process, we have optimized the computation processes and used parallel computing for all annotation steps. Moreover, FunctionAnnotator is designed to be versatile, and it generates a variety of useful outputs for facilitating other analyses. Here, we demonstrate how FunctionAnnotator can be helpful in annotating non-model organisms. We further illustrate that FunctionAnnotator can estimate the taxonomic composition of environmental samples and assist in the identification of novel proteins by combining RNA-Seq data with proteomics technology. In summary, FunctionAnnotator can efficiently annotate transcriptomes and greatly benefits studies focusing on non-model organisms or metatranscriptomes. FunctionAnnotator, a comprehensive annotation web-service tool, is freely available online at: http://fa.cgu.edu.tw/. This new web-based annotator will shed light on field studies involving organisms without a reference genome.
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Giardia intestinalis mitosomes undergo synchronized fission but not fusion and are constitutively associated with the endoplasmic reticulum. BMC Biol 2017; 15:27. [PMID: 28372543 DOI: 10.1186/s12915-017-0361-y] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Mitochondria of opisthokonts undergo permanent fission and fusion throughout the cell cycle. Here, we investigated the dynamics of the mitosomes, the simplest forms of mitochondria, in the anaerobic protist parasite Giardia intestinalis, a member of the Excavata supergroup of eukaryotes. The mitosomes have abandoned typical mitochondrial traits such as the mitochondrial genome and aerobic respiration and their single role known to date is the formation of iron-sulfur clusters. RESULTS In live experiments, no fusion events were observed between the mitosomes in G. intestinalis. Moreover, the organelles were highly prone to becoming heterogeneous. This suggests that fusion is either much less frequent or even absent in mitosome dynamics. Unlike in mitochondria, division of the mitosomes was absolutely synchronized and limited to mitosis. The association of the nuclear and the mitosomal division persisted during the encystation of the parasite. During the segregation of the divided mitosomes, the subset of the organelles between two G. intestinalis nuclei had a prominent role. Surprisingly, the sole dynamin-related protein of the parasite seemed not to be involved in mitosomal division. However, throughout the cell cycle, mitosomes associated with the endoplasmic reticulum (ER), although none of the known ER-tethering complexes was present. Instead, the ER-mitosome interface was occupied by the lipid metabolism enzyme long-chain acyl-CoA synthetase 4. CONCLUSIONS This study provides the first report on the dynamics of mitosomes. We show that together with the loss of metabolic complexity of mitochondria, mitosomes of G. intestinalis have uniquely streamlined their dynamics by harmonizing their division with mitosis. We propose that this might be a strategy of G. intestinalis to maintain a stable number of organelles during cell propagation. The lack of mitosomal fusion may also be related to the secondary reduction of the organelles. However, as there are currently no reports on mitochondrial fusion in the whole Excavata supergroup, it is possible that the absence of mitochondrial fusion is an ancestral trait common to all excavates.
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Leger MM, Kolisko M, Kamikawa R, Stairs CW, Kume K, Čepička I, Silberman JD, Andersson JO, Xu F, Yabuki A, Eme L, Zhang Q, Takishita K, Inagaki Y, Simpson AGB, Hashimoto T, Roger AJ. Organelles that illuminate the origins of Trichomonas hydrogenosomes and Giardia mitosomes. Nat Ecol Evol 2017; 1:0092. [PMID: 28474007 PMCID: PMC5411260 DOI: 10.1038/s41559-017-0092] [Citation(s) in RCA: 66] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
- Michelle M Leger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Graduate School of Global Environmental Studies, Kyoto University, Kyoto, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Keitaro Kume
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, USA
| | - Jan O Andersson
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Feifei Xu
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai, Shandong, People's Republic of China
| | - Kiyotaka Takishita
- Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Kanagawa, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | | | - Tetsuo Hashimoto
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
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Isolation of Mitochondria, Their Sub-Organellar Compartments, and Membranes. Methods Mol Biol 2016. [PMID: 27730604 DOI: 10.1007/978-1-4939-6533-5_7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
Abstract
Mitochondria are the sites of a diverse set of essential biochemical processes in plants. In order to facilitate the analysis of these functions, this chapter presents protocols for the isolation of intact mitochondria from a range of plant tissues as well two workflows for fractionation into their four subcompartments; the inner and outer membranes and the two aqueous compartments, the inter membrane space and matrix. Protocols for the assessment of mitochondrial integrity and purity through enzymatic function and suggestions of commercially available compartment marker antibodies are provided.
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Richardson E, Zerr K, Tsaousis A, Dorrell RG, Dacks JB. Evolutionary cell biology: functional insight from "endless forms most beautiful". Mol Biol Cell 2016; 26:4532-8. [PMID: 26668171 PMCID: PMC4678011 DOI: 10.1091/mbc.e14-10-1433] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
In animal and fungal model organisms, the complexities of cell biology have been analyzed in exquisite detail and much is known about how these organisms function at the cellular level. However, the model organisms cell biologists generally use include only a tiny fraction of the true diversity of eukaryotic cellular forms. The divergent cellular processes observed in these more distant lineages are still largely unknown in the general scientific community. Despite the relative obscurity of these organisms, comparative studies of them across eukaryotic diversity have had profound implications for our understanding of fundamental cell biology in all species and have revealed the evolution and origins of previously observed cellular processes. In this Perspective, we will discuss the complexity of cell biology found across the eukaryotic tree, and three specific examples of where studies of divergent cell biology have altered our understanding of key functional aspects of mitochondria, plastids, and membrane trafficking.
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Affiliation(s)
| | - Kelly Zerr
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7 Canada
| | - Anastasios Tsaousis
- Laboratory of Molecular and Evolutionary Parasitology, School of Biosciences, University of Kent, Canterbury CT2 7NJ, UK
| | | | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7 Canada
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Gawryluk RMR, Kamikawa R, Stairs CW, Silberman JD, Brown MW, Roger AJ. The Earliest Stages of Mitochondrial Adaptation to Low Oxygen Revealed in a Novel Rhizarian. Curr Biol 2016; 26:2729-2738. [PMID: 27666965 DOI: 10.1016/j.cub.2016.08.025] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Revised: 07/21/2016] [Accepted: 08/09/2016] [Indexed: 12/26/2022]
Abstract
Mitochondria exist on a functional and evolutionary continuum that includes anaerobic mitochondrion-related organelles (MROs), such as hydrogenosomes. Hydrogenosomes lack many classical mitochondrial features, including conspicuous cristae, mtDNA, the tricarboxylic acid (TCA) cycle, and ATP synthesis powered by an electron transport chain (ETC); instead, they produce ATP anaerobically, liberating H2 and CO2 gas in the process. However, our understanding of the evolutionary transformation from aerobic mitochondria to various MRO types remains incomplete. Here we describe a novel MRO from a cercomonad (Brevimastigomonas motovehiculus n. sp.; Rhizaria). We have sequenced its 30,608-bp mtDNA and characterized organelle function through a combination of transcriptomic, genomic, and cell biological approaches. B. motovehiculus MROs are metabolically versatile, retaining mitochondrial metabolic pathways, such as a TCA cycle and ETC-driven ATP synthesis, but also possessing hydrogenosomal-type pyruvate metabolism and substrate-level phosphorylation. Notably, the B. motovehiculus ETC is degenerate and appears to be losing cytochrome-based electron transport (complexes III and IV). Furthermore, the F1Fo ATP synthase (complex V) is unique, with the highly conserved Atpα subunit fragmented into four separate pieces. The B. motovehiculus MRO appears to be in the process of losing aerobic metabolic capacities. Our findings shed light on the transition between organelle types, specifically the early stages of mitochondrial adaptation to anaerobiosis.
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Affiliation(s)
- Ryan M R Gawryluk
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto 606-8501, Japan; Graduate School of Global Environmental Studies, Kyoto University, Kyoto 606-8501, Japan
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Jeffrey D Silberman
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Matthew W Brown
- Department of Biological Sciences, Mississippi State University, Mississippi State, MS 39762, USA; Institute for Genomics, Biocomputing and Biotechnology, Mississippi State University, Mississippi State, MS 39762, USA
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada; Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Halifax, NS B3H 4R2, Canada.
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