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Maclean AE, Sloan MA, Renaud EA, Argyle BE, Lewis WH, Ovciarikova J, Demolombe V, Waller RF, Besteiro S, Sheiner L. The Toxoplasma gondii mitochondrial transporter ABCB7L is essential for the biogenesis of cytosolic and nuclear iron-sulfur cluster proteins and cytosolic translation. mBio 2024:e0087224. [PMID: 39207139 DOI: 10.1128/mbio.00872-24] [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: 03/21/2024] [Accepted: 07/26/2024] [Indexed: 09/04/2024] Open
Abstract
Iron-sulfur (Fe-S) clusters are ubiquitous inorganic cofactors required for numerous essential cellular pathways. Since they cannot be scavenged from the environment, Fe-S clusters are synthesized de novo in cellular compartments such as the apicoplast, mitochondrion, and cytosol. The cytosolic Fe-S cluster biosynthesis pathway relies on the transport of an intermediate from the mitochondrial pathway. An ATP-binding cassette (ABC) transporter called ABCB7 is responsible for this role in numerous commonly studied organisms, but its role in the medically important apicomplexan parasites has not yet been studied. Here we identify and characterize a Toxoplasma gondii ABCB7 homolog, which we name ABCB7-like (ABCB7L). Genetic depletion shows that it is essential for parasite growth and that its disruption triggers partial stage conversion. Characterization of the knock-down line highlights a defect in the biogenesis of cytosolic and nuclear Fe-S proteins leading to defects in protein translation and other pathways including DNA and RNA replication and metabolism. Our work provides support for a broad conservation of the connection between mitochondrial and cytosolic pathways in Fe-S cluster biosynthesis and reveals its importance for parasite survival. IMPORTANCE Iron-sulfur (Fe-S) clusters are inorganic cofactors of proteins that play key roles in numerous essential biological processes, for example, respiration and DNA replication. Cells possess dedicated biosynthetic pathways to assemble Fe-S clusters, including a pathway in the mitochondrion and cytosol. A single transporter, called ABCB7, connects these two pathways, allowing an essential intermediate generated by the mitochondrial pathway to be used in the cytosolic pathway. Cytosolic and nuclear Fe-S proteins are dependent on the mitochondrial pathway, mediated by ABCB7, in numerous organisms studied to date. Here, we study the role of a homolog of ABCB7, which we name ABCB7-like (ABCB7L), in the ubiquitous unicellular apicomplexan parasite Toxoplasma gondii. We generated a depletion mutant of Toxoplasma ABCB7L and showed its importance for parasite fitness. Using comparative quantitative proteomic analysis and experimental validation of the mutants, we show that ABCB7L is required for cytosolic and nuclear, but not mitochondrial, Fe-S protein biogenesis. Our study supports the conservation of a protein homologous to ABCB7 and which has a similar function in apicomplexan parasites and provides insight into an understudied aspect of parasite metabolism.
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Affiliation(s)
- Andrew E Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Megan A Sloan
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Eléa A Renaud
- LPHI, Univ Montpellier, CNRS, INSERM, Montpellier, France
| | - Blythe E Argyle
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - William H Lewis
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
| | - Vincent Demolombe
- IPSiM, Univ Montpellier, CNRS, INRAE, Institut Agro, Montpellier, France
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | | | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, United Kingdom
- School of Infection and Immunity, University of Glasgow, Glasgow, United Kingdom
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Williams SK, Jerlström Hultqvist J, Eglit Y, Salas-Leiva DE, Curtis B, Orr RJS, Stairs CW, Atalay TN, MacMillan N, Simpson AGB, Roger AJ. Extreme mitochondrial reduction in a novel group of free-living metamonads. Nat Commun 2024; 15:6805. [PMID: 39122691 PMCID: PMC11316075 DOI: 10.1038/s41467-024-50991-w] [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: 08/11/2023] [Accepted: 07/15/2024] [Indexed: 08/12/2024] Open
Abstract
Metamonads are a diverse group of heterotrophic microbial eukaryotes adapted to living in hypoxic environments. All metamonads but one harbour metabolically altered 'mitochondrion-related organelles' (MROs) with reduced functions, however the degree of reduction varies. Here, we generate high-quality draft genomes, transcriptomes, and predicted proteomes for five recently discovered free-living metamonads. Phylogenomic analyses placed these organisms in a group we name the 'BaSk' (Barthelonids+Skoliomonads) clade, a deeply branching sister group to the Fornicata, a phylum that includes parasitic and free-living flagellates. Bioinformatic analyses of gene models shows that these organisms are predicted to have extremely reduced MRO proteomes in comparison to other free-living metamonads. Loss of the mitochondrial iron-sulfur cluster assembly system in some organisms in this group appears to be linked to the acquisition in their common ancestral lineage of a SUF-like minimal system Fe/S cluster pathway by lateral gene transfer. One of the isolates, Skoliomonas litria, appears to have lost all other known MRO pathways. No proteins were confidently assigned to the predicted MRO proteome of this organism suggesting that the organelle has been lost. The extreme mitochondrial reduction observed within this free-living anaerobic protistan clade demonstrates that mitochondrial functions may be completely lost even in free-living organisms.
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Affiliation(s)
- Shelby K Williams
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Jon Jerlström Hultqvist
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Yana Eglit
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Dayana E Salas-Leiva
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry, Cambridge University, Cambridge, UK
| | - Bruce Curtis
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Russell J S Orr
- Section for Genetics and Evolutionary Biology, Department of Biosciences, University of Oslo, Oslo, Norway
| | | | - Tuğba N Atalay
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Naomi MacMillan
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Alastair G B Simpson
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada
- Department of Biology, Dalhousie University, Halifax, Canada
| | - Andrew J Roger
- Institute for Comparative Genomics, Dalhousie University, Halifax, NS, Canada.
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.
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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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Motyčková A, Voleman L, Najdrová V, Arbonová L, Benda M, Dohnálek V, Janowicz N, Malych R, Šuťák R, Ettema TJG, Svärd S, Stairs CW, Doležal P. Adaptation of the late ISC pathway in the anaerobic mitochondrial organelles of Giardia intestinalis. PLoS Pathog 2023; 19:e1010773. [PMID: 37792908 PMCID: PMC10578589 DOI: 10.1371/journal.ppat.1010773] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/16/2023] [Accepted: 09/17/2023] [Indexed: 10/06/2023] Open
Abstract
Mitochondrial metabolism is entirely dependent on the biosynthesis of the [4Fe-4S] clusters, which are part of the subunits of the respiratory chain. The mitochondrial late ISC pathway mediates the formation of these clusters from simpler [2Fe-2S] molecules and transfers them to client proteins. Here, we characterized the late ISC pathway in one of the simplest mitochondria, mitosomes, of the anaerobic protist Giardia intestinalis that lost the respiratory chain and other hallmarks of mitochondria. In addition to IscA2, Nfu1 and Grx5 we identified a novel BolA1 homologue in G. intestinalis mitosomes. It specifically interacts with Grx5 and according to the high-affinity pulldown also with other core mitosomal components. Using CRISPR/Cas9 we were able to establish full bolA1 knock out, the first cell line lacking a mitosomal protein. Despite the ISC pathway being the only metabolic role of the mitosome no significant changes in the mitosome biology could be observed as neither the number of the mitosomes or their capability to form [2Fe-2S] clusters in vitro was affected. We failed to identify natural client proteins that would require the [2Fe-2S] or [4Fe-4S] cluster within the mitosomes, with the exception of [2Fe-2S] ferredoxin, which is itself part of the ISC pathway. The overall uptake of iron into the cellular proteins remained unchanged as also observed for the grx5 knock out cell line. The pull-downs of all late ISC components were used to build the interactome of the pathway showing specific position of IscA2 due to its interaction with the outer mitosomal membrane proteins. Finally, the comparative analysis across Metamonada species suggested that the adaptation of the late ISC pathway identified in G. intestinalis occurred early in the evolution of this supergroup of eukaryotes.
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Affiliation(s)
- Alžběta Motyčková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Vladimíra Najdrová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Lenka Arbonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Martin Benda
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Vít Dohnálek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Natalia Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Róbert Šuťák
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Staffan Svärd
- Department of Cell and Molecular Biology, Biomedical Center (BMC), Uppsala University, Uppsala, Sweden
| | | | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová Vestec, Czech Republic
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Zítek J, King MS, Peña-Diaz P, Pyrihová E, King AC, Kunji ERS, Hampl V. The free-living flagellate Paratrimastix pyriformis uses a distinct mitochondrial carrier to balance adenine nucleotide pools. Arch Biochem Biophys 2023; 742:109638. [PMID: 37192692 PMCID: PMC10251735 DOI: 10.1016/j.abb.2023.109638] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 05/18/2023]
Abstract
Paratrimastix pyriformis is a free-living flagellate thriving in low-oxygen freshwater sediments. It belongs to the group Metamonada along with human parasites, such as Giardia and Trichomonas. Like other metamonads, P. pyriformis has a mitochondrion-related organelle (MRO) which in this protist is primarily involved in one-carbon folate metabolism. The MRO contains four members of the solute carrier family 25 (SLC25) responsible for the exchange of metabolites across the mitochondrial inner membrane. Here, we characterise the function of the adenine nucleotide carrier PpMC1 by thermostability shift and transport assays. We show that it transports ATP, ADP and, to a lesser extent, AMP, but not phosphate. The carrier is distinct in function and origin from both ADP/ATP carriers and ATP-Mg/phosphate carriers, and it most likely represents a distinct class of adenine nucleotide carriers.
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Affiliation(s)
- Justyna Zítek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Martin S King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Priscila Peña-Diaz
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic
| | - Eva Pyrihová
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom; University of Stavanger, Department of Chemistry, Bioscience, And Environmental Engineering, Richard Johnsens Gate 4, N-4021, Stavanger, Norway
| | - Alannah C King
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom
| | - Edmund R S Kunji
- Medical Research Council Mitochondrial Biology Unit, The Keith Peters Building, Cambridge Biomedical Campus, Hills Road, Cambridge, CB2 0XY, United Kingdom.
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, 252 50, Czech Republic.
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Benchimol M, Gadelha AP, de Souza W. Ultrastructural Alterations of the Human Pathogen Giardia intestinalis after Drug Treatment. Pathogens 2023; 12:810. [PMID: 37375500 DOI: 10.3390/pathogens12060810] [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: 04/07/2023] [Revised: 06/04/2023] [Accepted: 06/05/2023] [Indexed: 06/29/2023] Open
Abstract
This review presents the main cell characteristics altered after in vitro incubation of the parasite with commercial drugs used to treat the disease caused by Giardia intestinalis. This important intestinal parasite primarily causes diarrhea in children. Metronidazole and albendazole are the primary compounds used in therapy against Giardia intestinalis. However, they provoke significant side effects, and some strains have developed resistance to metronidazole. Benzimidazole carbamates, such as albendazole and mebendazole, have shown the best activity against Giardia. Despite their in vitro efficacy, clinical treatment with benzimidazoles has yielded conflicting results, demonstrating lower cure rates. Recently, nitazoxanide has been suggested as an alternative to these drugs. Therefore, to enhance the quality of chemotherapy against this parasite, it is important to invest in developing other compounds that can interfere with key steps of metabolic pathways or cell structures and organelles. For example, Giardia exhibits a unique cell structure called the ventral disc, which is crucial for host adhesion and pathogenicity. Thus, drugs that can disrupt the adhesion process hold promise for future therapy against Giardia. Additionally, this review discusses new drugs and strategies that can be employed, as well as suggestions for developing novel drugs to control the infection caused by this parasite.
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Affiliation(s)
- Marlene Benchimol
- BIOTRANS-CAXIAS, Universidade do Grande Rio. UNIGRANRIO, 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 Científica, Instituto Nacional de Metrologia, Qualidade e Tecnologia (INMETRO), Rio de Janeiro 25259-020, 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
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Wu JH, Lee JC, Ho CC, Chiu PW, Sun CH. A myeloid leukemia factor homolog is involved in tolerance to stresses and stress-induced protein metabolism in Giardia lamblia. Biol Direct 2023; 18:20. [PMID: 37095576 PMCID: PMC10127389 DOI: 10.1186/s13062-023-00378-6] [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: 01/04/2023] [Accepted: 04/17/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND The eukaryotic membrane vesicles contain specific sets of proteins that determine vesicle function and shuttle with specific destination. Giardia lamblia contains unknown cytosolic vesicles that are related to the identification of a homolog of human myeloid leukemia factor (MLF) named MLF vesicles (MLFVs). Previous studies suggest that MLF also colocalized with two autophagy machineries, FYVE and ATG8-like protein, and that MLFVs are stress-induced compartments for substrates of the proteasome or autophagy in response to rapamycin, MG132, and chloroquine treatment. A mutant protein of cyclin-dependent kinase 2, CDK2m3, was used to understand whether the aberrant proteins are targeted to degradative compratments. Interestingly, MLF was upregulated by CDK2m3 and they both colocalized within the same vesicles. Autophagy is a self-digestion process that is activated to remove damaged proteins for preventing cell death in response to various stresses. Because of the absence of some autophagy machineries, the mechanism of autophagy is unclear in G. lamblia. RESULTS In this study, we tested the six autophagosome and stress inducers in mammalian cells, including MG132, rapamycin, chloroquine, nocodazole, DTT, and G418, and found that their treatment increased reactive oxygen species production and vesicle number and level of MLF, FYVE, and ATG8-like protein in G. lamblia. Five stress inducers also increased the CDK2m3 protein levels and vesicles. Using stress inducers and knockdown system for MLF, we identified that stress induction of CDK2m3 was positively regulated by MLF. An autophagosome-reducing agent, 3-methyl adenine, can reduce MLF and CDK2m3 vesicles and proteins. In addition, knockdown of MLF with CRISPR/Cas9 system reduced cell survival upon treatment with stress inducers. Our newly developed complementation system for CRISPR/Cas9 indicated that complementation of MLF restored cell survival in response to stress inducers. Furthermore, human MLF2, like Giardia MLF, can increase cyst wall protein expression and cyst formation in G. lamblia, and it can colocalize with MLFVs and interact with MLF. CONCLUSIONS Our results suggest that MLF family proteins are functionally conserved in evolution. Our results also suggest an important role of MLF in survival in stress conditions and that MLFVs share similar stress-induced characteristics with autophagy compartments.
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Affiliation(s)
- Jui-Hsuan Wu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, Republic of China
| | - Jen-Chi Lee
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, Republic of China
| | - Chun-Che Ho
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, Republic of China
| | - Pei-Wei Chiu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, Republic of China
| | - Chin-Hung Sun
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei, 100, Taiwan, Republic of China.
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9
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Onuț-Brännström I, Stairs CW, Campos KIA, Thorén MH, Ettema TJG, Keeling PJ, Bass D, Burki F. A Mitosome With Distinct Metabolism in the Uncultured Protist Parasite Paramikrocytos canceri (Rhizaria, Ascetosporea). Genome Biol Evol 2023; 15:7039708. [PMID: 36790104 PMCID: PMC9998036 DOI: 10.1093/gbe/evad022] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/13/2023] [Accepted: 02/07/2023] [Indexed: 02/16/2023] Open
Abstract
Ascetosporea are endoparasites of marine invertebrates that include economically important pathogens of aquaculture species. Owing to their often-minuscule cell sizes, strict intracellular lifestyle, lack of cultured representatives and minimal availability of molecular data, these unicellular parasites remain poorly studied. Here, we sequenced and assembled the genome and transcriptome of Paramikrocytos canceri, an endoparasite isolated from the European edible crab Cancer pagurus. Using bioinformatic predictions, we show that P. canceri likely possesses a mitochondrion-related organelle (MRO) with highly reduced metabolism, resembling the mitosomes of other parasites but with key differences. Like other mitosomes, this MRO is predicted to have reduced metabolic capacity and lack an organellar genome and function in iron-sulfur cluster (ISC) pathway-mediated Fe-S cluster biosynthesis. However, the MRO in P. canceri is uniquely predicted to produce ATP via a partial glycolytic pathway and synthesize phospholipids de novo through the CDP-DAG pathway. Heterologous gene expression confirmed that proteins from the ISC and CDP-DAG pathways retain mitochondrial targeting sequences that are recognized by yeast mitochondria. This represents a unique combination of metabolic pathways in an MRO, including the first reported case of a mitosome-like organelle able to synthesize phospholipids de novo. Some of these phospholipids, such as phosphatidylserine, are vital in other protist endoparasites that invade their host through apoptotic mimicry.
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Affiliation(s)
- Ioana Onuț-Brännström
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Microbiology Research Group, Department of Biology, Lund University, Lund, Sweden
| | | | - Markus Hiltunen Thorén
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
| | - Thijs J G Ettema
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, The Netherlands
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - David Bass
- International Centre of Excellence for Aquatic Animal Health, Centre for Environment, Fisheries and Aquaculture Science (Cefas), Weymouth, United Kingdom.,Department of Life Sciences, The Natural History Museum, London, United Kingdom.,Sustainable Aquaculture Futures, Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.,Science for Life Laboratory, Uppsala University, Uppsala, Sweden
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10
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Essential Oils and Terpenic Compounds as Potential Hits for Drugs against Amitochondriate Protists. Trop Med Infect Dis 2023; 8:tropicalmed8010037. [PMID: 36668944 PMCID: PMC9865018 DOI: 10.3390/tropicalmed8010037] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2022] [Revised: 12/26/2022] [Accepted: 01/03/2023] [Indexed: 01/06/2023] Open
Abstract
The human anaerobic or microaerophilic protists Giardia duodenalis, Entamoeba histolytica, and Trichomonas vaginalis are classified as amitochondriate parasites, a group of unicellular organisms that lack canonical mitochondria organelles. These microorganisms suffered adaptations to survive in hostile microenvironments and together represent an increasing threat to public health in developing countries. Nevertheless, the current therapeutic drugs to manage the infections are scarce and often cause several side effects. Furthermore, refractory cases associated with the emergence of parasitic resistance are concerns that guide the search for new pharmacological targets and treatment alternatives. Herein, essential oils and terpenic compounds with activity against amitochondriate parasites with clinical relevance are summarized and insights into possible mechanisms of action are made. This review aims to contribute with future perspectives for research with these natural products as potential alternatives for the acquisition of new molecules for the treatment of amitochondriate protists.
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11
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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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12
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Application of Proteomics to the Study of the Therapeutics and Pathogenicity of Giardia duodenalis. Diagnostics (Basel) 2022; 12:diagnostics12112744. [DOI: 10.3390/diagnostics12112744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/21/2022] [Accepted: 11/03/2022] [Indexed: 11/12/2022] Open
Abstract
Giardia duodenalis remains a neglected tropical disease. A key feature of the sustained transmission of Giardia is the ability to form environmentally resistant cysts. For the last 38 years, proteomics has been utilised to study various aspects of the parasite across different life cycle stages. Thirty-one articles have been published in PubMed from 2012 to 2022 related to the proteomics of G. duodenalis. Currently, mass spectrometry with LC-MS/MS and MALDI-TOF/TOF has been commonly utilised in proteomic analyses of Giardia, which enables researchers to determine potential candidates for diagnostic biomarkers as well as vaccine and drug targets, in addition to allowing them to investigate the virulence of giardiasis, the pathogenicity mechanisms of G. duodenalis, and the post-translational modifications of Giardia proteins throughout encystation. Over the last decade, valuable information from proteomics analyses of G. duodenalis has been discovered in terms of the pathogenesis and virulence of Giardia, which may provide guidance for the development of better means with which to prevent and reduce the impacts of giardiasis. Nonetheless, there is room for improving proteomics analyses of G. duodenalis, since genomic sequences for additional assemblages of Giardia have uncovered previously unknown proteins associated with the Giardia proteome. Therefore, this paper aims to review the applications of proteomics for the characterisation of G. duodenalis pathogenicity and the discovery of novel vaccine as well as drug targets, in addition to proposing some general directions for future Giardia proteomic research.
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13
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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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14
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Pech-Santiago EO, Argüello-García R, Vázquez C, Saavedra E, González-Hernández I, Jung-Cook H, Rafferty SP, Ortega-Pierres MG. Giardia duodenalis: Flavohemoglobin is involved in drug biotransformation and resistance to albendazole. PLoS Pathog 2022; 18:e1010840. [PMID: 36166467 PMCID: PMC9514659 DOI: 10.1371/journal.ppat.1010840] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Accepted: 08/28/2022] [Indexed: 12/12/2022] Open
Abstract
Giardia duodenalis causes giardiasis, a major diarrheal disease in humans worldwide whose treatment relies mainly on metronidazole (MTZ) and albendazole (ABZ). The emergence of ABZ resistance in this parasite has prompted studies to elucidate the molecular mechanisms underlying this phenomenon. G. duodenalis trophozoites convert ABZ into its sulfoxide (ABZSO) and sulfone (ABZSOO) forms, despite lacking canonical enzymes involved in these processes, such as cytochrome P450s (CYP450s) and flavin-containing monooxygenases (FMOs). This study aims to identify the enzyme responsible for ABZ metabolism and its role in ABZ resistance in G. duodenalis. We first determined that the iron-containing cofactor heme induces higher mRNA expression levels of flavohemoglobin (gFlHb) in Giardia trophozoites. Molecular docking analyses predict favorable interactions of gFlHb with ABZ, ABZSO and ABZSOO. Spectral analyses of recombinant gFlHb in the presence of ABZ, ABZSO and ABZSOO showed high affinities for each of these compounds with Kd values of 22.7, 19.1 and 23.8 nM respectively. ABZ and ABZSO enhanced gFlHb NADH oxidase activity (turnover number 14.5 min-1), whereas LC-MS/MS analyses of the reaction products showed that gFlHb slowly oxygenates ABZ into ABZSO at a much lower rate (turnover number 0.01 min-1). Further spectroscopic analyses showed that ABZ is indirectly oxidized to ABZSO by superoxide generated from the NADH oxidase activity of gFlHb. In a similar manner, the superoxide-generating enzyme xanthine oxidase was able to produce ABZSO in the presence of xanthine and ABZ. Interestingly, we find that gFlHb mRNA expression is lower in albendazole-resistant clones compared to those that are sensitive to this drug. Furthermore, all albendazole-resistant clones transfected to overexpress gFlHb displayed higher susceptibility to the drug than the parent clones. Collectively these findings indicate a role for gFlHb in ABZ conversion to its sulfoxide and that gFlHb down-regulation acts as a passive pharmacokinetic mechanism of resistance in this parasite.
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Affiliation(s)
- Edar O. Pech-Santiago
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Raúl Argüello-García
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
| | - Citlali Vázquez
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Emma Saavedra
- Departamento de Bioquímica, Instituto Nacional de Cardiología Ignacio Chávez, Mexico City, Mexico
| | - Iliana González-Hernández
- Laboratorio de Neuropsicofarmacología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Ciudad de México, México
| | - Helgi Jung-Cook
- Laboratorio de Neuropsicofarmacología, Instituto Nacional de Neurología y Neurocirugía, Manuel Velasco Suárez, Ciudad de México, México
| | | | - M. Guadalupe Ortega-Pierres
- Departamento de Genética y Biología Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, Mexico City, Mexico
- * E-mail:
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15
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Chowdhury SR, Bhoumik A, Gupta VK, Majumder HK. Type II DNA Topoisomerases in trypanosomatid and apicomplexan parasites. Acta Trop 2022; 234:106613. [PMID: 35905776 DOI: 10.1016/j.actatropica.2022.106613] [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: 03/06/2022] [Revised: 07/14/2022] [Accepted: 07/18/2022] [Indexed: 11/01/2022]
Abstract
Diseases caused by trypanosomatid parasites have no commercially available vaccines for human application. Treatment modalities completely rely on chemotherapeutics strategies that often exhibit clinical drawbacks, like host toxicity, side effects and treatment failure for drug resistance. These, in many instances, are costly, making them unaffordable for certain groups of beneficiaries. To find reasonable solutions, researchers are attempting to identify and validate new drug targets that would offer parasite specificity. DNA topoisomerases in parasites present a consolidated class of drug targets due to their multiple structural and functional differences with host homologs. Type II DNA topoisomerases in these parasites, in particular, have been attracting interest of scientific community attributable to their pivotal role in the replication of the atypical DNA. In this article, we present a detailed review of structural and functional features of type II DNA topoisomerases of clinically-relevant trypanosomatid and apicomplexan parasites. Also, we provide up-to-date information on different molecules that target these enzymes. Altogether, the review will largely help in understanding the rationale for exploiting type II DNA topoisomerases in these groups of parasites as drug targets.
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Affiliation(s)
- Somenath Roy Chowdhury
- Institut für Physikalische Chemie, Westfälische Wilhelms-Universität Münster, Correnstrasse 28, 48149, Münster.
| | - Arpita Bhoumik
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700 032
| | - Vivek Kumar Gupta
- Organic and Medicinal Chemistry Division, CSIR-Indian Institute of Chemical Biology, Kolkata 700 032
| | - Hemanta K Majumder
- Infectious Diseases & Immunology Division, CSIR-Indian Institute of Chemical Biology, Kolkata, 700 032
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16
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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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17
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Benchimol M, de Souza W. Giardia intestinalis and its Endomembrane System. J Eukaryot Microbiol 2022; 69:e12893. [PMID: 35148450 DOI: 10.1111/jeu.12893] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Revised: 02/08/2022] [Accepted: 02/08/2022] [Indexed: 11/29/2022]
Abstract
Giardia intestinalis has unique characteristics, even in the absence of certain organelles. For instance, Golgi and mitochondria are not found. On the other hand, there is a network of peripheral vacuoles (PVs) and mitosomes. The endoplasmic reticulum (ER), nuclear membrane, peroxisomes, and lipid bodies are present. The peripheral vacuole system seems to play several simultaneous roles. It is involved in the endocytic activity of the trophozoite but also has characteristics of early and late endosomes and even lysosomes, establishing a connection with the ER. Some of the PVs contain small vesicles, acting as multivesicular bodies, including the release of exosomes. The mitosomes are surrounded by two membranes, divide during mitosis, and are distributed throughout the cell. They do not contain DNA, enzymes involved in the citric acid cycle, respiratory chain, or ATP synthesis. However, they contain the iron-sulfur complex and transporters as TOM and TIM. Some mitosomes are linked to flagellar axonemes through a fibrillar connection. During encystation, two types of larger cytoplasmic vesicles appear. One originating from the ER contains the cyst wall proteins. Another contains carbohydrates. Both migrate to the cell periphery and fuse with plasma membrane secreting their contents to give rise to the cell wall.
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Affiliation(s)
- Marlene Benchimol
- Universidade do Grande Rio (UNIGRANRIO), Rio de Janeiro Duque de Caxias, RJ, Brazil.,Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro Nacional de Biologia Estrutural e Bioimagens, CENABIO-Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Wanderley de Souza
- Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil.,Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Bioimagens, Centro Nacional de Biologia Estrutural e Bioimagens, CENABIO-Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
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18
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Santos HJ, Nozaki T. The mitosome of the anaerobic parasitic protist Entamoeba histolytica: A peculiar and minimalist mitochondrion-related organelle. J Eukaryot Microbiol 2022; 69:e12923. [PMID: 35588086 PMCID: PMC9796589 DOI: 10.1111/jeu.12923] [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] [Indexed: 01/01/2023]
Abstract
The simplest class of mitochondrion-related organelles (MROs) is the mitosome, an organelle present in a few anaerobic protozoan parasites such as Entamoeba histolytica, Giardia intestinalis, and Cryptosporidium parvum. E. histolytica causes amoebiasis in humans, deemed as one of the important, yet neglected tropical infections in the world. Much of the enigma of the E. histolytica mitosome circles around the obvious lack of a majority of known mitochondrial components and functions exhibited in other organisms. The identification of enzymes responsible for sulfate activation (AS, IPP, and APSK) and a number of lineage-specific proteins such as the outer membrane beta-barrel protein (MBOMP30), and transmembrane domain-containing proteins that bind to various organellar proteins (ETMP1, ETMP30, EHI_170120, and EHI_099350) showcased the remarkable divergence of this organelle compared to the other MROs of anaerobic protozoa. Here, we summarize the findings regarding the biology of the mitosomes in E. histolytica, from their discovery up to the present understanding of its roles and interactions. We also include current advances and future perspectives on the biology, biochemistry, and evolution of the mitosomes of E. histolytica.
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Affiliation(s)
- Herbert J. Santos
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
| | - Tomoyoshi Nozaki
- Department of Biomedical Chemistry, Graduate School of MedicineThe University of TokyoTokyoJapan
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19
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van Esveld SL, Meerstein‐Kessel L, Boshoven C, Baaij JF, Barylyuk K, Coolen JPM, van Strien J, Duim RAJ, Dutilh BE, Garza DR, Letterie M, Proellochs NI, de Ridder MN, Venkatasubramanian PB, de Vries LE, Waller RF, Kooij TWA, Huynen MA. A Prioritized and Validated Resource of Mitochondrial Proteins in Plasmodium Identifies Unique Biology. mSphere 2021; 6:e0061421. [PMID: 34494883 PMCID: PMC8550323 DOI: 10.1128/msphere.00614-21] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 08/23/2021] [Indexed: 11/20/2022] Open
Abstract
Plasmodium species have a single mitochondrion that is essential for their survival and has been successfully targeted by antimalarial drugs. Most mitochondrial proteins are imported into this organelle, and our picture of the Plasmodium mitochondrial proteome remains incomplete. Many data sources contain information about mitochondrial localization, including proteome and gene expression profiles, orthology to mitochondrial proteins from other species, coevolutionary relationships, and amino acid sequences, each with different coverage and reliability. To obtain a comprehensive, prioritized list of Plasmodium falciparum mitochondrial proteins, we rigorously analyzed and integrated eight data sets using Bayesian statistics into a predictive score per protein for mitochondrial localization. At a corrected false discovery rate of 25%, we identified 445 proteins with a sensitivity of 87% and a specificity of 97%. They include proteins that have not been identified as mitochondrial in other eukaryotes but have characterized homologs in bacteria that are involved in metabolism or translation. Mitochondrial localization of seven Plasmodium berghei orthologs was confirmed by epitope labeling and colocalization with a mitochondrial marker protein. One of these belongs to a newly identified apicomplexan mitochondrial protein family that in P. falciparum has four members. With the experimentally validated mitochondrial proteins and the complete ranked P. falciparum proteome, which we have named PlasmoMitoCarta, we present a resource to study unique proteins of Plasmodium mitochondria. IMPORTANCE The unique biology and medical relevance of the mitochondrion of the malaria parasite Plasmodium falciparum have made it the subject of many studies. However, we actually do not have a comprehensive assessment of which proteins reside in this organelle. Many omics data are available that are predictive of mitochondrial localization, such as proteomics data and expression data. Individual data sets are, however, rarely complete and can provide conflicting evidence. We integrated a wide variety of available omics data in a manner that exploits the relative strengths of the data sets. Our analysis gave a predictive score for the mitochondrial localization to each nuclear encoded P. falciparum protein and identified 445 likely mitochondrial proteins. We experimentally validated the mitochondrial localization of seven of the new mitochondrial proteins, confirming the quality of the complete list. These include proteins that have not been observed mitochondria before, adding unique mitochondrial functions to P. falciparum.
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Affiliation(s)
- Selma L. van Esveld
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
| | - Lisette Meerstein‐Kessel
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Institute for Health Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Cas Boshoven
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Jochem F. Baaij
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Konstantin Barylyuk
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Jordy P. M. Coolen
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Joeri van Strien
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ronald A. J. Duim
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Bas E. Dutilh
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Theoretical Biology and Bioinformatics, Science for Life, Utrecht University, Utrecht, the Netherlands
| | - Daniel R. Garza
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Laboratory of Molecular Bacteriology (Rega Institute), Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Marijn Letterie
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Nicholas I. Proellochs
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Michelle N. de Ridder
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | | | - Laura E. de Vries
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Ross F. Waller
- Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Taco W. A. Kooij
- Department of Medical Microbiology, Radboudumc Center for Infectious Diseases, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
| | - Martijn A. Huynen
- Center for Molecular and Biomolecular Informatics, Radboud Institute for Molecular Life Sciences, Radboudumc, Nijmegen, the Netherlands
- Radboud Center for Mitochondrial Medicine, Radboudumc, Nijmegen, the Netherlands
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20
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Tůmová P, Voleman L, Klingl A, Nohýnková E, Wanner G, Doležal P. Inheritance of the reduced mitochondria of Giardia intestinalis is coupled to the flagellar maturation cycle. BMC Biol 2021; 19:193. [PMID: 34493257 PMCID: PMC8422661 DOI: 10.1186/s12915-021-01129-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 08/20/2021] [Indexed: 01/13/2023] Open
Abstract
Background The presence of mitochondria is a distinguishing feature between prokaryotic and eukaryotic cells. It is currently accepted that the evolutionary origin of mitochondria coincided with the formation of eukaryotes and from that point control of mitochondrial inheritance was required. Yet, the way the mitochondrial presence has been maintained throughout the eukaryotic cell cycle remains a matter of study. Eukaryotes control mitochondrial inheritance mainly due to the presence of the genetic component; still only little is known about the segregation of mitochondria to daughter cells during cell division. Additionally, anaerobic eukaryotic microbes evolved a variety of genomeless mitochondria-related organelles (MROs), which could be theoretically assembled de novo, providing a distinct mechanistic basis for maintenance of stable mitochondrial numbers. Here, we approach this problem by studying the structure and inheritance of the protist Giardia intestinalis MROs known as mitosomes. Results We combined 2D stimulated emission depletion (STED) microscopy and focused ion beam scanning electron microscopy (FIB/SEM) to show that mitosomes exhibit internal segmentation and conserved asymmetric structure. From a total of about forty mitosomes, a small, privileged population is harnessed to the flagellar apparatus, and their life cycle is coordinated with the maturation cycle of G. intestinalis flagella. The orchestration of mitosomal inheritance with the flagellar maturation cycle is mediated by a microtubular connecting fiber, which physically links the privileged mitosomes to both axonemes of the oldest flagella pair and guarantees faithful segregation of the mitosomes into the daughter cells. Conclusion Inheritance of privileged Giardia mitosomes is coupled to the flagellar maturation cycle. We propose that the flagellar system controls segregation of mitochondrial organelles also in other members of this supergroup (Metamonada) of eukaryotes and perhaps reflects the original strategy of early eukaryotic cells to maintain this key organelle before mitochondrial fusion-fission dynamics cycle as observed in Metazoa was established. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01129-7.
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Affiliation(s)
- Pavla Tůmová
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic.
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Andreas Klingl
- Plant Development and Electron Microscopy, Department of Biology I, Biocenter of Ludwig-Maximilians University, Munich, Germany
| | - Eva Nohýnková
- Institute of Immunology and Microbiology, First Faculty of Medicine, Charles University, Prague, Czech Republic
| | - Gerhard Wanner
- Department of Biology I, Biocenter of Ludwig-Maximilians University, Munich, Germany
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
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21
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Pipaliya SV, Santos R, Salas-Leiva D, Balmer EA, Wirdnam CD, Roger AJ, Hehl AB, Faso C, Dacks JB. Unexpected organellar locations of ESCRT machinery in Giardia intestinalis and complex evolutionary dynamics spanning the transition to parasitism in the lineage Fornicata. BMC Biol 2021; 19:167. [PMID: 34446013 PMCID: PMC8394649 DOI: 10.1186/s12915-021-01077-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 06/23/2021] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Comparing a parasitic lineage to its free-living relatives is a powerful way to understand how that evolutionary transition to parasitism occurred. Giardia intestinalis (Fornicata) is a leading cause of gastrointestinal disease world-wide and is famous for its unusual complement of cellular compartments, such as having peripheral vacuoles instead of typical endosomal compartments. Endocytosis plays an important role in Giardia's pathogenesis. Endosomal sorting complexes required for transport (ESCRT) are membrane-deforming proteins associated with the late endosome/multivesicular body (MVB). MVBs are ill-defined in G. intestinalis, and roles for identified ESCRT-related proteins are not fully understood in the context of its unique endocytic system. Furthermore, components thought to be required for full ESCRT functionality have not yet been documented in this species. RESULTS We used genomic and transcriptomic data from several Fornicata species to clarify the evolutionary genome streamlining observed in Giardia, as well as to detect any divergent orthologs of the Fornicata ESCRT subunits. We observed differences in the ESCRT machinery complement between Giardia strains. Microscopy-based investigations of key components of ESCRT machinery such as GiVPS36 and GiVPS25 link them to peripheral vacuoles, highlighting these organelles as simplified MVB equivalents. Unexpectedly, we show ESCRT components associated with the endoplasmic reticulum and, for the first time, mitosomes. Finally, we identified the rare ESCRT component CHMP7 in several fornicate representatives, including Giardia and show that contrary to current understanding, CHMP7 evolved from a gene fusion of VPS25 and SNF7 domains, prior to the last eukaryotic common ancestor, over 1.5 billion years ago. CONCLUSIONS Our findings show that ESCRT machinery in G. intestinalis is far more varied and complete than previously thought, associates to multiple cellular locations, and presents changes in ESCRT complement which pre-date adoption of a parasitic lifestyle.
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Affiliation(s)
- Shweta V Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada
| | - Rui Santos
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Dayana Salas-Leiva
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Erina A Balmer
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Corina D Wirdnam
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Andrew J Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Faculty of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Adrian B Hehl
- Institute of Parasitology, University of Zurich, Zurich, Switzerland
| | - Carmen Faso
- Institute of Cell Biology, University of Bern, Bern, Switzerland.
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland.
| | - Joel B Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Alberta, Canada.
- Institute of Parasitology, Biology Centre, CAS, v.v.i. Branisovska 31, 370 05, Ceske Budejovice, Czech Republic.
- Centre for Life's Origin and Evolution, Department of Genetics, Evolution and Environment, University College of London, London, UK.
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22
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Abstract
Giardia duodenalis captured the attention of Leeuwenhoek in 1681 while he was examining his own diarrheal stool, but, ironically, it did not really gain attention as a human pathogen until the 1960s, when outbreaks were reported. Key technological advances, including in vitro cultivation, genomic and proteomic databases, and advances in microscopic and molecular approaches, have led to an understanding that this is a eukaryotic organism with a reduced genome rather than a truly premitochondriate eukaryote. This has included the discovery of mitosomes (vestiges of mitochondria), a transport system with many of the features of the Golgi apparatus, and even evidence for a sexual or parasexual cycle. Cell biology approaches have led to a better understanding of how Giardia survives with two nuclei and how it goes through its life cycle as a noninvasive organism in the hostile environment of the lumen of the host intestine. Studies of its immunology and pathogenesis have moved past the general understanding of the importance of the antibody response in controlling infection to determining the key role of the Th17 response. This work has led to understanding of the requirement for a balanced host immune response that avoids the extremes of an excessive response with collateral damage or one that is unable to clear the organism. This understanding is especially important in view of the remarkable ranges of early manifestations, which range from asymptomatic to persistent diarrhea and weight loss, and longer-term sequelae that include growth stunting in children who had no obvious symptoms and a high frequency of postinfectious irritable bowel syndrome (IBS).
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23
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Multimodal regulation of encystation in Giardia duodenalis revealed by deep proteomics. Int J Parasitol 2021; 51:809-824. [PMID: 34331939 DOI: 10.1016/j.ijpara.2021.01.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 12/24/2020] [Accepted: 01/07/2021] [Indexed: 12/21/2022]
Abstract
Cyst formation in the parasitic protist Giardia duodenalis is critical to its transmission. Existing proteomic data quantifies only 17% of coding genes transcribed during encystation and does not cover the complete process from trophozoite to mature cyst. Using high-resolution mass spectrometry, we have quantified proteomic changes across encystation and compared this with published transcriptomic data. We reproducibly identified 3863 (64.5% of Giardia proteins) and quantified 3382 proteins (56.5% of Giardia proteins) over standard trophozoite growth (TY), during low-bile encystation priming (LB), 16 h into encystation (EC), and at cyst maturation (C). This work provides the first known expanded observation of encystation at the proteomic level and triples the coverage of previous encystation proteomes. One-third (1169 proteins) of the quantified proteome is differentially expressed in the mature cyst relative to the trophozoite, including proteasomal machinery, metabolic pathways, and secretory proteins. Changes in lipid metabolism indicated a shift in lipid species dependency during encystation. Consistent with this, we identified the first, putative lipid transporters in this species, representing the steroidogenic acute regulatory protein-related lipid transfer (StARkin), oxysterol binding protein related protein (ORP/Osh) and glycosphingolipid transfer protein (GLTP) families, and follow their differential expression over cyst formation. Lastly, we undertook correlation analyses of the transcriptome and proteome of trophozoites and cysts, and found evidence of post-transcriptional regulation of key protein classes (RNA binding proteins) and stage-specific genes (encystation markers) implicating translation-repression in encystation. We provide the most extensive proteomic analysis of encystation in Giardia to date and the first known exploration across its complete duration. This work identifies encystation as highly coordinated, involving major changes in proteostasis, metabolism and membrane dynamics, and indicates a potential role for post-transcriptional regulation, mediated through RNA-binding proteins. Together our work provides a valuable resource for Giardia research and the development of transmission-blocking anti-giardials.
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24
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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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25
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Applied Proteomics in 'One Health'. Proteomes 2021; 9:proteomes9030031. [PMID: 34208880 PMCID: PMC8293331 DOI: 10.3390/proteomes9030031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 06/24/2021] [Accepted: 06/25/2021] [Indexed: 12/19/2022] Open
Abstract
‘One Health’ summarises the idea that human health and animal health are interdependent and bound to the health of ecosystems. The purpose of proteomics methodologies and studies is to determine proteins present in samples of interest and to quantify changes in protein expression during pathological conditions. The objectives of this paper are to review the application of proteomics technologies within the One Health concept and to appraise their role in the elucidation of diseases and situations relevant to One Health. The paper develops in three sections. Proteomics Applications in Zoonotic Infections part discusses proteomics applications in zoonotic infections and explores the use of proteomics for studying pathogenetic pathways, transmission dynamics, diagnostic biomarkers and novel vaccines in prion, viral, bacterial, protozoan and metazoan zoonotic infections. Proteomics Applications in Antibiotic Resistance part discusses proteomics applications in mechanisms of resistance development and discovery of novel treatments for antibiotic resistance. Proteomics Applications in Food Safety part discusses the detection of allergens, exposure of adulteration, identification of pathogens and toxins, study of product traits and characterisation of proteins in food safety. Sensitive analysis of proteins, including low-abundant ones in complex biological samples, will be achieved in the future, thus enabling implementation of targeted proteomics in clinical settings, shedding light on biomarker research and promoting the One Health concept.
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26
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Horváthová L, Žárský V, Pánek T, Derelle R, Pyrih J, Motyčková A, Klápšťová V, Vinopalová M, Marková L, Voleman L, Klimeš V, Petrů M, Vaitová Z, Čepička I, Hryzáková K, Harant K, Gray MW, Chami M, Guilvout I, Francetic O, Franz Lang B, Vlček Č, Tsaousis AD, Eliáš M, Doležal P. Analysis of diverse eukaryotes suggests the existence of an ancestral mitochondrial apparatus derived from the bacterial type II secretion system. Nat Commun 2021; 12:2947. [PMID: 34011950 PMCID: PMC8134430 DOI: 10.1038/s41467-021-23046-7] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Accepted: 03/22/2021] [Indexed: 12/14/2022] Open
Abstract
The type 2 secretion system (T2SS) is present in some Gram-negative eubacteria and used to secrete proteins across the outer membrane. Here we report that certain representative heteroloboseans, jakobids, malawimonads and hemimastigotes unexpectedly possess homologues of core T2SS components. We show that at least some of them are present in mitochondria, and their behaviour in biochemical assays is consistent with the presence of a mitochondrial T2SS-derived system (miT2SS). We additionally identified 23 protein families co-occurring with miT2SS in eukaryotes. Seven of these proteins could be directly linked to the core miT2SS by functional data and/or sequence features, whereas others may represent different parts of a broader functional pathway, possibly also involving the peroxisome. Its distribution in eukaryotes and phylogenetic evidence together indicate that the miT2SS-centred pathway is an ancestral eukaryotic trait. Our findings thus have direct implications for the functional properties of the early mitochondrion. Bacteria use the type 2 secretion system to secrete enzymes and toxins across the outer membrane to the environment. Here the authors analyse the T2SS pathway in three protist lineages and suggest that the early mitochondrion may have been capable of secreting proteins into the cytosol.
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Affiliation(s)
- Lenka Horváthová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vojtěch Žárský
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Tomáš Pánek
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Romain Derelle
- School of Biosciences, University of Birmingham, Edgbaston, UK
| | - Jan Pyrih
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Alžběta Motyčková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Veronika Klápšťová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Martina Vinopalová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lenka Marková
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Luboš Voleman
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Klimeš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic
| | - Markéta Petrů
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zuzana Vaitová
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Čepička
- Faculty of Science, Department of Zoology, Charles University, Prague 2, Czech Republic
| | - Klára Hryzáková
- Faculty of Science, Department of Genetics and Microbiology, Charles University, Prague 2, Czech Republic
| | - Karel Harant
- Faculty of Science, Proteomic core facility, Charles University, BIOCEV, Vestec, Czech Republic
| | - Michael W Gray
- Department of Biochemistry and Molecular Biology and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Mohamed Chami
- Center for Cellular Imaging and NanoAnalytics, University of Basel, Basel, Switzerland
| | - Ingrid Guilvout
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - Olivera Francetic
- Biochemistry of Macromolecular Interactions Unit, Department of Structural Biology and Chemistry, Institut Pasteur, CNRS UMR3528, Paris, France
| | - B Franz Lang
- Robert Cedergren Centre for Bioinformatics and Genomics, Département de Biochimie, Université de Montréal, Montreal, QC, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Prague 4, Czech Republic
| | - Anastasios D Tsaousis
- Laboratory of Molecular & Evolutionary Parasitology, RAPID group, School of Biosciences, University of Kent, Canterbury, UK
| | - Marek Eliáš
- Faculty of Science, Department of Biology and Ecology, University of Ostrava, Ostrava, Czech Republic.
| | - Pavel Doležal
- Faculty of Science, Department of Parasitology, Charles University, BIOCEV, Vestec, Czech Republic.
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27
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Ca 2+-regulated mitochondrial carriers of ATP-Mg 2+/Pi: Evolutionary insights in protozoans. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2021; 1868:119038. [PMID: 33839167 DOI: 10.1016/j.bbamcr.2021.119038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/30/2021] [Accepted: 03/31/2021] [Indexed: 11/23/2022]
Abstract
In addition to its uptake across the Ca2+ uniporter, intracellular calcium signals can stimulate mitochondrial metabolism activating metabolite exchangers of the inner mitochondrial membrane belonging to the mitochondrial carrier family (SLC25). One of these Ca2+-regulated mitochondrial carriers (CaMCs) are the reversible ATP-Mg2+/Pi transporters, or SCaMCs, required for maintaining optimal adenine nucleotide (AdN) levels in the mitochondrial matrix representing an alternative transporter to the ADP/ATP translocases (AAC). This CaMC has a distinctive Calmodulin-like (CaM-like) domain fused to the carrier domain that makes its transport activity strictly dependent on cytosolic Ca2+ signals. Here we investigate about its origin analysing its distribution and features in unicellular eukaryotes. Unexpectedly, we find two types of ATP-Mg2+/Pi carriers, the canonical ones and shortened variants lacking the CaM-like domain. Phylogenetic analysis shows that both SCaMC variants have a common origin, unrelated to AACs, suggesting in turn that recurrent losses of the regulatory module have occurred in the different phyla. They are excluding variants that show a more limited distribution and less conservation than AACs. Interestingly, these truncated variants of SCaMC are found almost exclusively in parasitic protists, such as apicomplexans, kinetoplastides or animal-patogenic oomycetes, and in green algae, suggesting that its lost could be related to certain life-styles. In addition, we find an intricate structural diversity in these variants that may be associated with their pathogenicity. The consequences on SCaMC functions of these new SCaMC-b variants are discussed.
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28
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Füssy Z, Vinopalová M, Treitli SC, Pánek T, Smejkalová P, Čepička I, Doležal P, Hampl V. Retortamonads from vertebrate hosts share features of anaerobic metabolism and pre-adaptations to parasitism with diplomonads. Parasitol Int 2021; 82:102308. [PMID: 33626397 PMCID: PMC7985675 DOI: 10.1016/j.parint.2021.102308] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 01/26/2021] [Accepted: 02/11/2021] [Indexed: 12/17/2022]
Abstract
Although the mitochondria of extant eukaryotes share a single origin, functionally these organelles diversified to a great extent, reflecting lifestyles of the organisms that host them. In anaerobic protists of the group Metamonada, mitochondria are present in reduced forms (also termed hydrogenosomes or mitosomes) and a complete loss of mitochondrion in Monocercomonoides exilis (Metamonada:Preaxostyla) has also been reported. Within metamonads, retortamonads from the gastrointestinal tract of vertebrates form a sister group to parasitic diplomonads (e.g. Giardia and Spironucleus) and have also been hypothesized to completely lack mitochondria. We obtained transcriptomic data from Retortamonas dobelli and R. caviae and searched for enzymes of the core metabolism as well as mitochondrion- and parasitism-related proteins. Our results indicate that retortamonads have a streamlined metabolism lacking pathways for metabolites they are probably capable of obtaining from prey bacteria or their environment, reminiscent of the biochemical arrangement in other metamonads. Retortamonads were surprisingly found do encode homologs of components of Giardia's remarkable ventral disk, as well as homologs of regulatory NEK kinases and secreted lytic enzymes known for involvement in host colonization by Giardia. These can be considered pre-adaptations of these intestinal microorganisms to parasitism. Furthermore, we found traces of the mitochondrial metabolism represented by iron‑sulfur cluster assembly subunits, subunits of mitochondrial translocation and chaperone machinery and, importantly, [FeFe]‑hydrogenases and hydrogenase maturases (HydE, HydF and HydG). Altogether, our results strongly suggest that a remnant mitochondrion is still present.
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Affiliation(s)
- Zoltán Füssy
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
| | - Martina Vinopalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | | | - Tomáš Pánek
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavla Smejkalová
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic; Charles University, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Ivan Čepička
- Charles University, Faculty of Science, Department of Zoology, Prague, Czech Republic
| | - Pavel Doležal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic.
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Wu JH, Tung SY, Ho CC, Su LH, Gan SW, Liao JY, Cho CC, Lin BC, Chiu PW, Pan YJ, Kao YY, Liu YC, Sun CH. A myeloid leukemia factor homolog involved in encystation-induced protein metabolism in Giardia lamblia. Biochim Biophys Acta Gen Subj 2021; 1865:129859. [PMID: 33581251 DOI: 10.1016/j.bbagen.2021.129859] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2020] [Revised: 01/14/2021] [Accepted: 01/25/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND Giardia lamblia differentiates into resistant cysts as an established model for dormancy. Myeloid leukemia factor (MLF) proteins are important regulators of cell differentiation. Giardia possesses a MLF homolog which was up-regulated during encystation and localized to unknown cytosolic vesicles named MLF vesicles (MLFVs). METHODS We used double staining for visualization of potential factors with role in protein metabolism pathway and a strategy that employed a deletion mutant, CDK2m3, to test the protein degradation pathway. We also explored whether autophagy or proteasomal degradation are regulators of Giardia encystation by treatment with MG132, rapamycin, or chloroquine. RESULTS Double staining of MLF and ISCU or CWP1 revealed no overlap between their vesicles. The aberrant CDK2m3 colocalized with MLFVs and formed complexes with MLF. MG132 increased the number of CDK2m3-localized vesicles and its protein level. We further found that MLF colocalized and interacted with a FYVE protein and an ATG8-like (ATG8L) protein, which were up-regulated during encystation and their expression induced Giardia encystation. The addition of MG132, rapamycin, or chloroquine, increased their levels and the number of their vesicles, and inhibited the cyst formation. MLF and FYVE were detected in exosomes released from culture. CONCLUSIONS The MLFVs are not mitosomes or encystation-specific vesicles, but are related with degradative pathway for CDK2m3. MLF, FYVE, and ATG8L play a positive role in encystation and function in protein clearance pathway, which is important for encystation and coordinated with Exosomes. GENERAL SIGNIFICANCE MLF, FYVE, and ATG8L may be involved an encystation-induced protein metabolism during Giardia differentiation.
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Affiliation(s)
- Jui-Hsuan Wu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Szu-Yu Tung
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Chun-Che Ho
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Li-Hsin Su
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Soo-Wah Gan
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Jo-Yu Liao
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Chao-Cheng Cho
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Bo-Chi Lin
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Pei-Wei Chiu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Yu-Jiao Pan
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Yu-Yun Kao
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Yu-Chen Liu
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC
| | - Chin-Hung Sun
- Department of Tropical Medicine and Parasitology, College of Medicine, National Taiwan University, Taipei 100, Taiwan, ROC.
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Chhuon C, Zhang SY, Jung V, Lewandowski D, Lipecka J, Pawlak A, Sahali D, Ollero M, Guerrera IC. A sensitive S-Trap-based approach to the analysis of T cell lipid raft proteome. J Lipid Res 2020; 61:1512-1523. [PMID: 32769147 PMCID: PMC7604723 DOI: 10.1194/jlr.d120000672] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The analysis of T cell lipid raft proteome is challenging due to the highly dynamic nature of rafts and the hydrophobic character of raft-resident proteins. We explored an innovative strategy for bottom-up lipid raftomics based on suspension-trapping (S-Trap) sample preparation. Mouse T cells were prepared from splenocytes by negative immunoselection, and rafts were isolated by a detergent-free method and OptiPrep gradient ultracentrifugation. Microdomains enriched in flotillin-1, LAT, and cholesterol were subjected to proteomic analysis through an optimized protocol based on S-Trap and high pH fractionation, followed by nano-LC-MS/MS. Using this method, we identified 2,680 proteins in the raft-rich fraction and established a database of 894 T cell raft proteins. We then performed a differential analysis on the raft-rich fraction from nonstimulated versus anti-CD3/CD28 T cell receptor (TCR)-stimulated T cells. Our results revealed 42 proteins present in one condition and absent in the other. For the first time, we performed a proteomic analysis on rafts from ex vivo T cells obtained from individual mice, before and after TCR activation. This work demonstrates that the proposed method utilizing an S-Trap-based approach for sample preparation increases the specificity and sensitivity of lipid raftomics.
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Affiliation(s)
- Cerina Chhuon
- Proteomic Platform Necker, Structure Fédérative de Recherche SFR Necker US24, Paris, France
- Institut Mondor de Recherche Biomédicale, INSERM, U955, Créteil, France
| | - Shao-Yu Zhang
- Institut Mondor de Recherche Biomédicale, INSERM, U955, Créteil, France
| | - Vincent Jung
- Proteomic Platform Necker, Structure Fédérative de Recherche SFR Necker US24, Paris, France
| | - Daniel Lewandowski
- CEA/DRF/IBFJ/iRCM/LRTS, Fontenay-aux-Roses Cedex, France
- CEA/DRF/IBFJ/iRCM/LRTS, Fontenay-aux-Roses Cedex, France
- CEA/DRF/IBFJ/iRCM/LRTS, Fontenay-aux-Roses Cedex, France
- Université Paris-Sud, Paris, France
| | - Joanna Lipecka
- Proteomic Platform Necker, Structure Fédérative de Recherche SFR Necker US24, Paris, France
| | - André Pawlak
- Institut Mondor de Recherche Biomédicale, INSERM, U955, Créteil, France
| | - Dil Sahali
- Institut Mondor de Recherche Biomédicale, INSERM, U955, Créteil, France
- AP-HP (Assistance Publique des Hôpitaux de Paris), Department of Nephrology and Renal Transplantation, Groupe Hospitalier Henri-Mondor, Créteil, France
- Université Paris Est Créteil, Créteil, France
| | - Mario Ollero
- Institut Mondor de Recherche Biomédicale, INSERM, U955, Créteil, France
- Université Paris Est Créteil, Créteil, France
| | - Ida Chiara Guerrera
- Proteomic Platform Necker, Structure Fédérative de Recherche SFR Necker US24, Paris, France
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Pick E. The necessity of NEDD8/Rub1 for vitality and its association with mitochondria-derived oxidative stress. Redox Biol 2020; 37:101765. [PMID: 33099217 PMCID: PMC7582104 DOI: 10.1016/j.redox.2020.101765] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Revised: 10/12/2020] [Accepted: 10/16/2020] [Indexed: 01/04/2023] Open
Abstract
Access of molecular oxygen to the respiratory electron transport chain at the mitochondria costs in the generation of reactive oxygen-derived species (ROS). ROS induces progressive damage to macromolecules in all living cells, hence, rapid defense mechanisms to maintain cellular redox homeostasis are vital. NEDD8/Rub1 is a highly conserved ubiquitin-like modifier that has recently been identified as a key regulator of cellular redox homeostasis. In this review, I will present NEDD8/Rub1, its modification cascade of enzymes, substrates and hydrolases. After introduction, I will show that the NEDD8/Rub1 pathway is linked with mitochondria physiology, namely, oxidative stress. In the rest of the review, I will approach the Ascomycota phylum of the kingdom fungi instrumentally, to present existing links between NEDD8/Rub1 vitality and the aerobic lifestyle of model species belonging to three subphyla: Saccharomycotina (S. cerevisiae and C. albicans), Pezizomycotina (A. nidulans and N. crassa), and Taphrinomycotina (S. pombe). NEDD8/Rub1 is a key regulator of cellular redox homeostasis. Ascomycota species that produce mitochondria-derived ROS during glycolysis require NEDD8/Rub1for viability. NEDD8/Rub1 essentiality correlates with the existence of NEDP1 in the organism genome.
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Affiliation(s)
- Elah Pick
- Department of Biology and Environment, Faculty of Natural Sciences, University of Haifa, Oranim, Tivon, 3600600, Israel.
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Braymer JJ, Freibert SA, Rakwalska-Bange M, Lill R. Mechanistic concepts of iron-sulfur protein biogenesis in Biology. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2020; 1868:118863. [PMID: 33007329 DOI: 10.1016/j.bbamcr.2020.118863] [Citation(s) in RCA: 98] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 09/14/2020] [Accepted: 09/17/2020] [Indexed: 02/08/2023]
Abstract
Iron-sulfur (Fe/S) proteins are present in virtually all living organisms and are involved in numerous cellular processes such as respiration, photosynthesis, metabolic reactions, nitrogen fixation, radical biochemistry, protein synthesis, antiviral defense, and genome maintenance. Their versatile functions may go back to the proposed role of their Fe/S cofactors in the origin of life as efficient catalysts and electron carriers. More than two decades ago, it was discovered that the in vivo synthesis of cellular Fe/S clusters and their integration into polypeptide chains requires assistance by complex proteinaceous machineries, despite the fact that Fe/S proteins can be assembled chemically in vitro. In prokaryotes, three Fe/S protein biogenesis systems are known; ISC, SUF, and the more specialized NIF. The former two systems have been transferred by endosymbiosis from bacteria to mitochondria and plastids, respectively, of eukaryotes. In their cytosol, eukaryotes use the CIA machinery for the biogenesis of cytosolic and nuclear Fe/S proteins. Despite the structural diversity of the protein constituents of these four machineries, general mechanistic concepts underlie the complex process of Fe/S protein biogenesis. This review provides a comprehensive and comparative overview of the various known biogenesis systems in Biology, and summarizes their common or diverging molecular mechanisms, thereby illustrating both the conservation and diverse adaptions of these four machineries during evolution and under different lifestyles. Knowledge of these fundamental biochemical pathways is not only of basic scientific interest, but is important for the understanding of human 'Fe/S diseases' and can be used in biotechnology.
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Affiliation(s)
- Joseph J Braymer
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | - Sven A Freibert
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany
| | | | - Roland Lill
- Institut für Zytobiologie, Philipps-Universität Marburg, Robert-Koch-Str. 6, 35032 Marburg, Germany; SYNMIKRO Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Strasse, 35043 Marburg, Germany.
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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: 20] [Impact Index Per Article: 5.0] [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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Schneider A. Evolution of mitochondrial protein import – lessons from trypanosomes. Biol Chem 2020; 401:663-676. [DOI: 10.1515/hsz-2019-0444] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Accepted: 03/02/2020] [Indexed: 01/02/2023]
Abstract
AbstractThe evolution of mitochondrial protein import and the systems that mediate it marks the boundary between the endosymbiotic ancestor of mitochondria and a true organelle that is under the control of the nucleus. Protein import has been studied in great detail inSaccharomyces cerevisiae. More recently, it has also been extensively investigated in the parasitic protozoanTrypanosoma brucei, making it arguably the second best studied system. A comparative analysis of the protein import complexes of yeast and trypanosomes is provided. Together with data from other systems, this allows to reconstruct the ancestral features of import complexes that were present in the last eukaryotic common ancestor (LECA) and to identify which subunits were added later in evolution. How these data can be translated into plausible scenarios is discussed, providing insights into the evolution of (i) outer membrane protein import receptors, (ii) proteins involved in biogenesis of α-helically anchored outer membrane proteins, and (iii) of the intermembrane space import and assembly system. Finally, it is shown that the unusual presequence-associated import motor of trypanosomes suggests a scenario of how the two ancestral inner membrane protein translocases present in LECA evolved into the single bifunctional one found in extant trypanosomes.
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Affiliation(s)
- André Schneider
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland
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35
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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: 32] [Impact Index Per Article: 8.0] [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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Abstract
The shape and number of mitochondria respond to the metabolic needs during the cell cycle of the eukaryotic cell. In the best-studied model systems of animals and fungi, the cells contain many mitochondria, each carrying its own nucleoid. The organelles, however, mostly exist as a dynamic network, which undergoes constant cycles of division and fusion. These mitochondrial dynamics are driven by intricate protein machineries centered around dynamin-related proteins (DRPs). Here, we review recent advances on the dynamics of mitochondria and mitochondrion-related organelles (MROs) of parasitic protists. In contrast to animals and fungi, many parasitic protists from groups of Apicomplexa or Kinetoplastida carry only a single mitochondrion with a single nucleoid. In these groups, mitochondrial division is strictly coupled to the cell cycle, and the morphology of the organelle responds to the cell differentiation during the parasite life cycle. On the other hand, anaerobic parasitic protists such as Giardia, Entamoeba, and Trichomonas contain multiple MROs that have lost their organellar genomes. We discuss the function of DRPs, the occurrence of mitochondrial fusion, and mitophagy in the parasitic protists from the perspective of eukaryote evolution.
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Affiliation(s)
- Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- * E-mail:
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Lalle M, Fiorillo A. The protein 14-3-3: A functionally versatile molecule in Giardia duodenalis. ADVANCES IN PARASITOLOGY 2019; 106:51-103. [PMID: 31630760 DOI: 10.1016/bs.apar.2019.08.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Giardia duodenalis is a cosmopolitan zoonotic protozoan parasite causing giardiasis, one of the most common diarrhoeal diseases in human and animals. Beyond its public health relevance, Giardia represents a valuable and fascinating model microorganism. The deep-branching phylogenetic position of Giardia, its simple life cycle and its minimalistic genomic and cellular organization provide a unique opportunity to define basal and "ancestral" eukaryotic functions. The eukaryotic 14-3-3 protein family represents a distinct example of phosphoserine/phosphothreonine-binding proteins. The extended network of protein-protein interactions established by 14-3-3 proteins place them at the crossroad of multiple signalling pathways that regulate physiological and pathological cellular processes. Despite the remarkable insight on 14-3-3 protein in different organisms, from yeast to humans, so far little attention was given to the study of this protein in protozoan parasites. However, in the last years, research efforts have provided evidences on unique properties of the single 14-3-3 protein of Giardia and on its association in key aspects of Giardia life cycle. In the first part of this chapter, a general overview of the features commonly shared among 14-3-3 proteins in different organisms (i.e. structure, target recognition, mode of action and regulatory mechanisms) is included. The second part focus on the current knowledge on the biochemistry and biology of the Giardia 14-3-3 protein and on the possibility to use this protein as target to propose new strategies for developing innovative antigiardial therapy.
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Affiliation(s)
- Marco Lalle
- Department of Infectious Diseases, European Union Reference Laboratory for Parasites, Istituto Superiore di Sanità, Rome, Italy.
| | - Annarita Fiorillo
- Department of Biochemical Sciences "A. Rossi Fanelli", Sapienza University of Rome, Rome, Italy
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Zimorski V, Mentel M, Tielens AGM, Martin WF. Energy metabolism in anaerobic eukaryotes and Earth's late oxygenation. Free Radic Biol Med 2019; 140:279-294. [PMID: 30935869 PMCID: PMC6856725 DOI: 10.1016/j.freeradbiomed.2019.03.030] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 03/21/2019] [Accepted: 03/26/2019] [Indexed: 01/09/2023]
Abstract
Eukaryotes arose about 1.6 billion years ago, at a time when oxygen levels were still very low on Earth, both in the atmosphere and in the ocean. According to newer geochemical data, oxygen rose to approximately its present atmospheric levels very late in evolution, perhaps as late as the origin of land plants (only about 450 million years ago). It is therefore natural that many lineages of eukaryotes harbor, and use, enzymes for oxygen-independent energy metabolism. This paper provides a concise overview of anaerobic energy metabolism in eukaryotes with a focus on anaerobic energy metabolism in mitochondria. We also address the widespread assumption that oxygen improves the overall energetic state of a cell. While it is true that ATP yield from glucose or amino acids is increased in the presence of oxygen, it is also true that the synthesis of biomass costs thirteen times more energy per cell in the presence of oxygen than in anoxic conditions. This is because in the reaction of cellular biomass with O2, the equilibrium lies very far on the side of CO2. The absence of oxygen offers energetic benefits of the same magnitude as the presence of oxygen. Anaerobic and low oxygen environments are ancient. During evolution, some eukaryotes have specialized to life in permanently oxic environments (life on land), other eukaryotes have remained specialized to low oxygen habitats. We suggest that the Km of mitochondrial cytochrome c oxidase of 0.1-10 μM for O2, which corresponds to about 0.04%-4% (avg. 0.4%) of present atmospheric O2 levels, reflects environmental O2 concentrations that existed at the time that the eukaryotes arose.
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Affiliation(s)
- Verena Zimorski
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University in Bratislava, 851 04, Bratislava, Slovakia.
| | - Aloysius G M Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus Medical Center Rotterdam, The Netherlands; Department of Biochemistry and Cell Biology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands.
| | - William F Martin
- Institute of Molecular Evolution, Heinrich-Heine-University, 40225, Düsseldorf, Germany.
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Vickman O, Erives A. Episodic evolution of a eukaryotic NADK repertoire of ancient provenance. PLoS One 2019; 14:e0220447. [PMID: 31369599 PMCID: PMC6675116 DOI: 10.1371/journal.pone.0220447] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 07/16/2019] [Indexed: 12/02/2022] Open
Abstract
NAD kinase (NADK) is the sole enzyme that phosphorylates nicotinamide adenine dinucleotide (NAD+/NADH) into NADP+/NADPH, which provides the chemical reducing power in anabolic (biosynthetic) pathways. While prokaryotes typically encode a single NADK, eukaryotes encode multiple NADKs. How these different NADK genes are all related to each other and those of prokaryotes is not known. Here we conduct phylogenetic analysis of NADK genes and identify major clade-defining patterns of NADK evolution. First, almost all eukaryotic NADK genes belong to one of two ancient eukaryotic sister clades corresponding to cytosolic (“cyto”) and mitochondrial (“mito”) clades. Secondly, we find that the cyto-clade NADK gene is duplicated in connection with loss of the mito-clade NADK gene in several eukaryotic clades or with acquisition of plastids in Archaeplastida. Thirdly, we find that horizontal gene transfers from proteobacteria have replaced mitochondrial NADK genes in only a few rare cases. Last, we find that the eukaryotic cyto and mito paralogs are unrelated to independent duplications that occurred in sporulating bacteria, once in mycelial Actinobacteria and once in aerobic endospore-forming Firmicutes. Altogether these findings show that the eukaryotic NADK gene repertoire is ancient and evolves episodically with major evolutionary transitions.
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Affiliation(s)
- Oliver Vickman
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
| | - Albert Erives
- Department of Biology, University of Iowa, Iowa City, IA, United States of America
- * E-mail:
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Development of CRISPR/Cas9-mediated gene disruption systems in Giardia lamblia. PLoS One 2019; 14:e0213594. [PMID: 30856211 PMCID: PMC6411161 DOI: 10.1371/journal.pone.0213594] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2018] [Accepted: 02/25/2019] [Indexed: 12/26/2022] Open
Abstract
Giardia lamblia becomes dormant by differentiation into a water-resistant cyst that can infect a new host. Synthesis of three cyst wall proteins (CWPs) is the fundamental feature of this differentiation. Myeloid leukemia factor (MLF) proteins are involved in cell differentiation, and tumorigenesis in mammals, but little is known about its role in protozoan parasites. We developed a CRISPR/Cas9 system to understand the role of MLF in Giardia. Due to the tetraploid genome in two nuclei of Giardia, it could be hard to disrupt a gene completely in Giardia. We only generated knockdown but not knockout mutants. We found that knockdown of the mlf gene resulted in a significant decrease of cwp gene expression and cyst formation, suggesting a positive role of MLF in encystation. We further used mlf as a model gene to improve the system. The addition of an inhibitor for NHEJ, Scr7, or combining all cassettes for gRNA and Cas9 expression into one plasmid resulted in improved gene disruption efficiencies and a significant decrease in cwp gene expression. Our results provide insights into a positive role of MLF in inducing Giardia differentiation and a useful tool for studies in Giardia.
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Faso C, Hehl AB. A cytonaut's guide to protein trafficking in Giardia lamblia. ADVANCES IN PARASITOLOGY 2019; 106:105-127. [PMID: 31630756 DOI: 10.1016/bs.apar.2019.08.001] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Over the past years, the subcellular organization of the Excavata member Giardia lamblia (syn. duodenalis, intestinalis) has been investigated in considerable detail. There are several reasons for this endeavour which go beyond this parasite's medical importance and are mostly concerned with its reduced subcellular complexity and debated evolutionary status. One may say that simplification has emerged as a paradigm for the evolution of Giardia's subcellular architecture. However, a complete appreciation of the evolutionary and ecological significance of this phenomenon is far from complete. In this chapter, we present and discuss the most recent data on the main trafficking pathways in G. lamblia which include endo- and exo-cytosis, organellar import and function. We provide perspectives on open questions concerning organelle replication and inheritance and include a technical outlook on methods and approaches to genetic manipulations in G. lamblia. A better understanding of G. lamblia subcellular organization at the morphological and molecular level complements any effort aimed at elucidating this parasitic species' evolutionary status and could provide us with the basis for novel strategies to interfere with parasite transmission and/or pathogenesis.
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Affiliation(s)
- Carmen Faso
- Laboratory of Molecular Parasitology, Institute of Parasitology, University of Zurich (ZH), Zürich, Switzerland
| | - Adrian B Hehl
- Laboratory of Molecular Parasitology, Institute of Parasitology, University of Zurich (ZH), Zürich, Switzerland.
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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: 15] [Impact Index Per Article: 2.5] [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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Pyrihová E, Motycková A, Voleman L, Wandyszewska N, Fišer R, Seydlová G, Roger A, Kolísko M, Doležal P. A Single Tim Translocase in the Mitosomes of Giardia intestinalis Illustrates Convergence of Protein Import Machines in Anaerobic Eukaryotes. Genome Biol Evol 2018; 10:2813-2822. [PMID: 30265292 PMCID: PMC6200312 DOI: 10.1093/gbe/evy215] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/27/2018] [Indexed: 11/14/2022] Open
Abstract
Mitochondria have evolved diverse forms across eukaryotic diversity in adaptation to anoxia. Mitosomes are the simplest and the least well-studied type of anaerobic mitochondria. Transport of proteins via TIM complexes, composed of three proteins of the Tim17 protein family (Tim17/22/23), is one of the key unifying aspects of mitochondria and mitochondria-derived organelles. However, multiple experimental and bioinformatic attempts have so far failed to identify the nature of TIM in mitosomes of the anaerobic metamonad protist, Giardia intestinalis, one of the few experimental models for mitosome biology. Here, we present the identification of a single G. intestinalis Tim17 protein (GiTim17), made possible only by the implementation of a metamonad-specific hidden Markov model. While very divergent in primary sequence and in predicted membrane topology, experimental data suggest that GiTim17 is an inner membrane mitosomal protein, forming a disulphide-linked dimer. We suggest that the peculiar GiTim17 sequence reflects adaptation to the unusual, detergent resistant, inner mitosomal membrane. Specific pull-down experiments indicate interaction of GiTim17 with mitosomal Tim44, the tethering component of the import motor complex. Analysis of TIM complexes across eukaryote diversity suggests that a "single Tim" translocase is a convergent adaptation of mitosomes in anaerobic protists, with Tim22 and Tim17 (but not Tim23), providing the protein backbone.
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Affiliation(s)
- Eva Pyrihová
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Alžbeta Motycková
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Natalia Wandyszewska
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Radovan Fišer
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Gabriela Seydlová
- Department of Genetics and Microbiology, Charles University, Praha 2, Czech Republic
| | - Andrew Roger
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Martin Kolísko
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada.,Biology Centre CAS, České Budějovice, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, Vestec, Czech Republic
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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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Biochemical Characterization and Structural Modeling of Fused Glucose-6-Phosphate Dehydrogenase-Phosphogluconolactonase from Giardia lamblia. Int J Mol Sci 2018; 19:ijms19092518. [PMID: 30149622 PMCID: PMC6165198 DOI: 10.3390/ijms19092518] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 08/18/2018] [Accepted: 08/22/2018] [Indexed: 11/17/2022] Open
Abstract
Glucose-6-phosphate dehydrogenase (G6PD) is the first enzyme in the pentose phosphate pathway and is highly relevant in the metabolism of Giardialamblia. Previous reports suggested that the G6PD gene is fused with the 6-phosphogluconolactonase (6PGL) gene (6pgl). Therefore, in this work, we decided to characterize the fused G6PD-6PGL protein in Giardialamblia. First, the gene of g6pd fused with the 6pgl gene (6gpd::6pgl) was isolated from trophozoites of Giardialamblia and the corresponding G6PD::6PGL protein was overexpressed and purified in Escherichia coli. Then, we characterized the native oligomeric state of the G6PD::6PGL protein in solution and we found a catalytic dimer with an optimum pH of 8.75. Furthermore, we determined the steady-state kinetic parameters for the G6PD domain and measured the thermal stability of the protein in both the presence and absence of guanidine hydrochloride (Gdn-HCl) and observed that the G6PD::6PGL protein showed alterations in the stability, secondary structure, and tertiary structure in the presence of Gdn-HCl. Finally, computer modeling studies revealed unique structural and functional features, which clearly established the differences between G6PD::6PGL protein from G. lamblia and the human G6PD enzyme, proving that the model can be used for the design of new drugs with antigiardiasic activity. These results broaden the perspective for future studies of the function of the protein and its effect on the metabolism of this parasite as a potential pharmacological target.
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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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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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Giardia's primitive GPL biosynthesis pathways with parasitic adaptation 'patches': implications for Giardia's evolutionary history and for finding targets against Giardiasis. Sci Rep 2017; 7:9507. [PMID: 28842650 PMCID: PMC5573378 DOI: 10.1038/s41598-017-10054-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 08/02/2017] [Indexed: 11/23/2022] Open
Abstract
Giardia is a worldwide spread protozoan parasite colonizing in small intestines of vertebrates, causing Giardiasis. The controversy about whether it is an extremely primitive eukaryote or just a highly evolved parasite has become a fetter to its uses as a model for both evolutionary and parasitological studies for years. Glycerophospholipid (GPL) synthesis is a conserved essential cellular process, and thus may retain some original features reflecting its evolutionary position, and this process should also have undergone parasitic adaptation to suit Giardia’s dietary lipid-rich environment. Thus, GPL synthesis pathways may be a perfect object to examine the controversy over Giardia. Here, we first clarified Giardia’s previously confusing GPL synthesis by re-identifying a reliable set of GPL synthesis genes/enzymes. Then using phylogenetic and comparative genomic analyses, we revealed that these pathways turn out to be evolutionarily primitive ones, but with many secondary parasitic adaptation ‘patches’ including gene loss, rapid evolution, product relocation, and horizontal gene transfer. Therefore, modern Giardia should be a mosaic of ‘primary primitivity’ and ‘secondary parasitic adaptability’, and to make a distinction between the two categories of features would restart the studies of eukaryotic evolution and parasitic adaptation using Giardia as a model system.
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50
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Touz MC, Zamponi N. Sorting without a Golgi complex. Traffic 2017; 18:637-645. [DOI: 10.1111/tra.12500] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2017] [Revised: 07/01/2017] [Accepted: 07/06/2017] [Indexed: 12/22/2022]
Affiliation(s)
- Maria C. Touz
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
| | - Nahuel Zamponi
- Instituto de Investigación Médica Mercedes y Martín Ferreyra, INIMEC - CONICET; Universidad Nacional de Córdoba; Córdoba Argentina
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