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Del Campo J, Carlos-Oliveira M, Čepička I, Hehenberger E, Horák A, Karnkowska A, Kolisko M, Lara E, Lukeš J, Pánek T, Piwosz K, Richter DJ, Škaloud P, Sutak R, Tachezy J, Hampl V. The protist cultural renaissance. Trends Microbiol 2024; 32:128-131. [PMID: 38102035 DOI: 10.1016/j.tim.2023.11.010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 11/20/2023] [Accepted: 11/24/2023] [Indexed: 12/17/2023]
Abstract
Protists are key players in the biosphere. Here, we provide a perspective on integrating protist culturing with omics approaches, imaging, and high-throughput single-cell manipulation strategies, concluding with actions required for a successful return of the golden age of protist culturing.
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Affiliation(s)
- Javier Del Campo
- Biodiversity Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain.
| | - Maria Carlos-Oliveira
- Functional Genomics and Evolution Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Elisabeth Hehenberger
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Warsaw, Poland
| | - Martin Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Enrique Lara
- Department of Mycology, Real Jardín Botánico-CSIC, Madrid, Spain
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic; Department of Molecular Biology, University of South Bohemia, České Budějovice, Czech Republic
| | - Tomáš Pánek
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Kasia Piwosz
- Department of Fisheries Oceanography and Marine Ecology, National Marine Fisheries Research Institute, Gdynia, Poland
| | - Daniel J Richter
- Functional Genomics and Evolution Program, Institut de Biologia Evolutiva (CSIC - Universitat Pompeu Fabra), Barcelona, Catalonia, Spain
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, Prague, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, BIOCEV, Charles University, Vestec, Czech Republic
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Novák T, Žaloudíková M, Smolková P, Kaftanová B, Edlmanová J, Krása K, Hampl V. Hypoxia-inducible factors activator, roxadustat, increases pulmonary vascular resistance in rats. Physiol Res 2023; 72:S587-S592. [PMID: 38165762 PMCID: PMC10861249 DOI: 10.33549/physiolres.935220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Accepted: 09/12/2023] [Indexed: 02/01/2024] Open
Abstract
Activators of hypoxia inducible factors (HIFs), such as roxadustat, are promising agents for anemia treatment. However, since HIFs are also involved in the regulation of the pulmonary circulation, we hypothesized that roxadustat increases pulmonary vascular resistance and vasoconstrictor reactivity. Using isolated, cell-free solution perfused rat lungs, we found perfusion pressure-flow curves to be shifted to higher pressures by 2 weeks of roxadustat treatment (10 mg/kg every other day), although not as much as by chronic hypoxic exposure. Vasoconstrictor reactivity to angiotensin II and acute hypoxic challenges was not altered by roxadustat. Since roxadustat may inhibit angiotensin-converting enzyme 2 (ACE2), we also tested a purported ACE2 activator, diminazene aceturate (DIZE, 0.1 mM). It produced paradoxical, unexplained pulmonary vasoconstriction. We conclude that the risk of serious pulmonary hypertension is not high when roxadustat is given for 14 days, but monitoring is advisable.
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Affiliation(s)
- T Novák
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague 5, Czech Republic.
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Novák LVF, Treitli SC, Pyrih J, Hałakuc P, Pipaliya SV, Vacek V, Brzoň O, Soukal P, Eme L, Dacks JB, Karnkowska A, Eliáš M, Hampl V. Genomics of Preaxostyla Flagellates Illuminates the Path Towards the Loss of Mitochondria. PLoS Genet 2023; 19:e1011050. [PMID: 38060519 PMCID: PMC10703272 DOI: 10.1371/journal.pgen.1011050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2023] [Accepted: 11/03/2023] [Indexed: 12/18/2023] Open
Abstract
The notion that mitochondria cannot be lost was shattered with the report of an oxymonad Monocercomonoides exilis, the first eukaryote arguably without any mitochondrion. Yet, questions remain about whether this extends beyond the single species and how this transition took place. The Oxymonadida is a group of gut endobionts taxonomically housed in the Preaxostyla which also contains free-living flagellates of the genera Trimastix and Paratrimastix. The latter two taxa harbour conspicuous mitochondrion-related organelles (MROs). Here we report high-quality genome and transcriptome assemblies of two Preaxostyla representatives, the free-living Paratrimastix pyriformis and the oxymonad Blattamonas nauphoetae. We performed thorough comparisons among all available genomic and transcriptomic data of Preaxostyla to further decipher the evolutionary changes towards amitochondriality, endobiosis, and unstacked Golgi. Our results provide insights into the metabolic and endomembrane evolution, but most strikingly the data confirm the complete loss of mitochondria for all three oxymonad species investigated (M. exilis, B. nauphoetae, and Streblomastix strix), suggesting the amitochondriate status is common to a large part if not the whole group of Oxymonadida. This observation moves this unique loss to 100 MYA when oxymonad lineage diversified.
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Affiliation(s)
- Lukáš V. F. Novák
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- Université de Bretagne Occidentale, CNRS, Unité Biologie et Ecologie des Ecosystèmes Marins Profonds BEEP, IUEM, Plouzané, France
| | - Sebastian C. Treitli
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Jan Pyrih
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Shweta V. Pipaliya
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- School of Life Sciences, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland; Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Vojtěch Vacek
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Ondřej Brzoň
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Petr Soukal
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
| | - Laura Eme
- Ecology, Systematics, and Evolution Unit, Université Paris-Saclay, CNRS, Orsay, France
| | - Joel B. Dacks
- Division of Infectious Diseases, Department of Medicine, University of Alberta, Edmonton, Canada
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Biological and Chemical Research Centre, Faculty of Biology, University of Warsaw, Poland
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Ostrava, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec, Czech Republic
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Treitli SC, Hanousková P, Beneš V, Brune A, Čepička I, Hampl V. Hydrogenotrophic methanogenesis is the key process in the obligately syntrophic consortium of the anaerobic ameba Pelomyxa schiedti. ISME J 2023; 17:1884-1894. [PMID: 37634049 PMCID: PMC10579272 DOI: 10.1038/s41396-023-01499-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 08/28/2023]
Abstract
Pelomyxa is a genus of anaerobic amoebae that live in consortia with multiple prokaryotic endosymbionts. Although the symbionts represent a large fraction of the cellular biomass, their metabolic roles have not been investigated. Using single-cell genomics and transcriptomics, we have characterized the prokaryotic community associated with P. schiedti, which is composed of two bacteria, Candidatus Syntrophus pelomyxae (class Deltaproteobacteria) and Candidatus Vesiculincola pelomyxae (class Clostridia), and a methanogen, Candidatus Methanoregula pelomyxae. Fluorescence in situ hybridization and electron microscopy showed that Ca. Vesiculincola pelomyxae is localized inside vesicles, whereas the other endosymbionts occur freely in the cytosol, with Ca. Methanoregula pelomyxae enriched around the nucleus. Genome and transcriptome-based reconstructions of the metabolism suggests that the cellulolytic activity of P. schiedti produces simple sugars that fuel its own metabolism and the metabolism of a Ca. Vesiculincola pelomyxae, while Ca. Syntrophus pelomyxae energy metabolism relies on degradation of butyrate and isovalerate from the environment. Both species of bacteria and the ameba use hydrogenases to transfer the electrons from reduced equivalents to hydrogen, a process that requires a low hydrogen partial pressure. This is achieved by the third endosymbiont, Ca. Methanoregula pelomyxae, which consumes H2 and formate for methanogenesis. While the bacterial symbionts can be successfully eliminated by vancomycin treatment without affecting the viability of the amoebae, treatment with 2-bromoethanesulfonate, a specific inhibitor of methanogenesis, killed the amoebae, indicating the essentiality of the methanogenesis for this consortium.
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Affiliation(s)
- Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Beneš
- Genome Biology Unit, European Molecular Biology Laboratory (EMBL), Heidelberg, Germany
| | - Andreas Brune
- RG Insect Gut Microbiology and Symbiosis, Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Viničná 7, 128 00, Prague 2, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42, Vestec, Czech Republic.
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Záhonová K, Füssy Z, Stairs CW, Leger MM, Tachezy J, Čepička I, Roger AJ, Hampl V. Comparative analysis of mitochondrion-related organelles in anaerobic amoebozoans. Microb Genom 2023; 9. [PMID: 37994879 DOI: 10.1099/mgen.0.001143] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [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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6
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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] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Krása K, Vajnerová O, Ďurišová J, Minaříková M, Miková D, Srbová M, Chalupský K, Kaftanová B, Hampl V. Simvastatin and dehydroepiandrosterone sulfate effects against hypoxic pulmonary hypertension are not additive. Physiol Res 2022. [DOI: 10.33549/physiolres.934913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Pulmonary hypertension is a group of disorders characterized by elevated mean pulmonary artery pressure (mPAP) and pulmonary vascular resistance. To test our hypothesis that combining two drugs useful in experimental pulmonary hypertension, statins and dehydroepiandrosterone sulfate (DHEA S), is more effective than either agent alone, we induced pulmonary hypertension in adult male rats by exposing them to hypoxia (10%O2) for 3 weeks. We treated them with simvastatin (60 mg/l) and DHEA S (100 mg/l) in drinking water, either alone or in combination. Both simvastatin and DHEA S reduced mPAP (froma mean±s.d. of 34.4±4.4 to 27.6±5.9 and 26.7±4.8 mmHg, respectively), yet their combination was not more effective (26.7±7.9 mmHg). Differences in the degree of oxidative stress (indicated by malondialdehydeplasma concentration),the rate of superoxide production (electron paramagnetic resonance), or blood nitric oxide levels (chemiluminescence) did not explain the lack of additivity of the effect of DHEA S and simvastatin on pulmonary hypertension. We propose that the main mechanism of both drugs on pulmonary hypertension could be their inhibitory effect on 3-hydroxy-3-methyl-glutaryl-coenzyme A reductase, which could explain their lack of additivity.
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Affiliation(s)
- K Krása
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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8
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Ebenezer TE, Low RS, O'Neill EC, Huang I, DeSimone A, Farrow SC, Field RA, Ginger ML, Guerrero SA, Hammond M, Hampl V, Horst G, Ishikawa T, Karnkowska A, Linton EW, Myler P, Nakazawa M, Cardol P, Sánchez-Thomas R, Saville BJ, Shah MR, Simpson AGB, Sur A, Suzuki K, Tyler KM, Zimba PV, Hall N, Field MC. Euglena International Network (EIN): Driving euglenoid biotechnology for the benefit of a challenged world. Biol Open 2022; 11:bio059561. [PMID: 36412269 PMCID: PMC9836076 DOI: 10.1242/bio.059561] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Euglenoids (Euglenida) are unicellular flagellates possessing exceptionally wide geographical and ecological distribution. Euglenoids combine a biotechnological potential with a unique position in the eukaryotic tree of life. In large part these microbes owe this success to diverse genetics including secondary endosymbiosis and likely additional sources of genes. Multiple euglenoid species have translational applications and show great promise in production of biofuels, nutraceuticals, bioremediation, cancer treatments and more exotically as robotics design simulators. An absence of reference genomes currently limits these applications, including development of efficient tools for identification of critical factors in regulation, growth or optimization of metabolic pathways. The Euglena International Network (EIN) seeks to provide a forum to overcome these challenges. EIN has agreed specific goals, mobilized scientists, established a clear roadmap (Grand Challenges), connected academic and industry stakeholders and is currently formulating policy and partnership principles to propel these efforts in a coordinated and efficient manner.
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Affiliation(s)
- ThankGod Echezona Ebenezer
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ross S. Low
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
| | | | - Ishuo Huang
- Office of Regulatory Science, United States Food and Drug Administration, Center for Food Safety and Applied Nutrition, College Park, MD 20740, USA
| | - Antonio DeSimone
- The BioRobotics Institute, Scuola Superiore Sant'Anna, Pisa 56127, Italy
| | - Scott C. Farrow
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
- Environmental and Life Sciences Graduate Program, Trent University, Peterborough, Ontario K9L 0G2, Canada
| | - Robert A. Field
- Department of Chemistry and Manchester Institute of Biotechnology, University of Manchester, Manchester M1 7DN, UK
| | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield HD1 3DH, UK
| | - Sergio Adrián Guerrero
- Laboratorio de Enzimología Molecular, Instituto de Agrobiotecnología del Litoral. CCT CONICET Santa Fe, Santa Fe 3000, Argentina
| | - Michael Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
| | - Vladimír Hampl
- Charles University, Faculty of Science, Department of Parasitology, BIOCEV, Vestec 25250, Czech Republic
| | - Geoff Horst
- Kemin Industries, Research and Development, Plymouth, MI 48170, USA
| | - Takahiro Ishikawa
- Institute of Agricultural and Life Sciences, Academic Assembly, Shimane University, Matsue 690-8504, Japan
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Warsaw 02-089, Poland
| | - Eric W. Linton
- Department of Biology, Central Michigan University, Mt. Pleasant, MI 48859, USA
| | - Peter Myler
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Masami Nakazawa
- Department of Applied Biochemistry, Faculty of Agriculture, Osaka Metropolitan University, Sakai, Osaka, 599-8531, Japan
| | - Pierre Cardol
- Department of Life Sciences, Institut de Botanique, Université de Liège, Liège 4000, Belgium
| | | | - Barry J. Saville
- Forensic Science, Environmental and Life Sciences Graduate Program, Trent University, Peterborough K9L 0G2, Canada
| | - Mahfuzur R. Shah
- Discovery Biology, Noblegen Inc., Peterborough, Ontario K9L 1Z8, Canada
| | - Alastair G. B. Simpson
- Department of Biology and Institute for Comparative Genomics, Dalhousie University, Halifax, Nova Scotia B3H 4R2, Canada
| | - Aakash Sur
- Center for Global Infectious Disease Research, Seattle Children's Research Institute and Department of Biomedical Informatics & Medical Education, University of Washington, WA 98109, USA
| | - Kengo Suzuki
- R&D Company, Euglena Co., Ltd., 2F Yokohama Bio Industry Center (YBIC), 1-6 Suehiro, Tsurumi, Yokohama, Kanagawa, 230-0045, Japan
| | - Kevin M. Tyler
- Biomedical Research Centre, Norwich Medical School, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
- Center of Excellence for Bionanoscience Research, King Abdul Aziz University, Jeddah, Saudi Arabia
| | - Paul V. Zimba
- PVZimba, LLC, 12241 Percival St, Chester, VA 23831, USA
- Rice Rivers Center, VA Commonwealth University, Richmond, VA 23284, USA
| | - Neil Hall
- Organisms and Ecosystems, Earlham Institute, Norwich Research Park, Norwich NR4 7UZ, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, Norfolk, UK
| | - Mark C. Field
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice 370 05, Czech Republic
- School of Life Sciences, University of Dundee, Dundee DD1 5EH, UK
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9
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Záhonová K, Treitli SC, Le T, Škodová-Sveráková I, Hanousková P, Čepička I, Tachezy J, Hampl V. Anaerobic derivates of mitochondria and peroxisomes in the free-living amoeba Pelomyxa schiedti revealed by single-cell genomics. BMC Biol 2022; 20:56. [PMID: 35227266 PMCID: PMC8887013 DOI: 10.1186/s12915-022-01247-w] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 02/03/2022] [Indexed: 01/15/2023] Open
Abstract
Background Mitochondria and peroxisomes are the two organelles that are most affected during adaptation to microoxic or anoxic environments. Mitochondria are known to transform into anaerobic mitochondria, hydrogenosomes, mitosomes, and various transition stages in between, collectively called mitochondrion-related organelles (MROs), which vary in enzymatic capacity. Anaerobic peroxisomes were identified only recently, and their putatively most conserved function seems to be the metabolism of inositol. The group Archamoebae includes anaerobes bearing both anaerobic peroxisomes and MROs, specifically hydrogenosomes in free-living Mastigamoeba balamuthi and mitosomes in the human pathogen Entamoeba histolytica, while the organelles within the third lineage represented by Pelomyxa remain uncharacterized. Results We generated high-quality genome and transcriptome drafts from Pelomyxa schiedti using single-cell omics. These data provided clear evidence for anaerobic derivates of mitochondria and peroxisomes in this species, and corresponding vesicles were tentatively identified in electron micrographs. In silico reconstructed MRO metabolism harbors respiratory complex II, electron-transferring flavoprotein, a partial TCA cycle running presumably in the reductive direction, pyruvate:ferredoxin oxidoreductase, [FeFe]-hydrogenases, a glycine cleavage system, a sulfate activation pathway, and an expanded set of NIF enzymes for iron-sulfur cluster assembly. When expressed in the heterologous system of yeast, some of these candidates localized into mitochondria, supporting their involvement in the MRO metabolism. The putative functions of P. schiedti peroxisomes could be pyridoxal 5′-phosphate biosynthesis, amino acid and carbohydrate metabolism, and hydrolase activities. Unexpectedly, out of 67 predicted peroxisomal enzymes, only four were also reported in M. balamuthi, namely peroxisomal processing peptidase, nudix hydrolase, inositol 2-dehydrogenase, and d-lactate dehydrogenase. Localizations in yeast corroborated peroxisomal functions of the latter two. Conclusions This study revealed the presence and partially annotated the function of anaerobic derivates of mitochondria and peroxisomes in P. schiedti using single-cell genomics, localizations in yeast heterologous systems, and transmission electron microscopy. The MRO metabolism resembles that of M. balamuthi and most likely reflects the state in the common ancestor of Archamoebae. The peroxisomal metabolism is strikingly richer in P. schiedti. The presence of myo-inositol 2-dehydrogenase in the predicted peroxisomal proteome corroborates the situation in other Archamoebae, but future experimental evidence is needed to verify additional functions of this organelle. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-022-01247-w.
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Affiliation(s)
- Kristína Záhonová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic. .,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.
| | | | - Tien Le
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ingrid Škodová-Sveráková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Pavla Hanousková
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Čepička
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Jan Tachezy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic.
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10
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Malych R, Füssy Z, Ženíšková K, Arbon D, Hampl V, Hrdý I, Sutak R. The response of Naegleria gruberi to oxidative stress. Metallomics 2022; 14:6527579. [PMID: 35150262 DOI: 10.1093/mtomcs/mfac009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 02/06/2022] [Indexed: 11/14/2022]
Abstract
Aerobic organisms require oxygen for respiration but must simultaneously cope with oxidative damages inherently linked with this molecule. Unicellular amoeboflagellates of the genus Naegleria, containing both free-living species and opportunistic parasite, thrive in aerobic environments. However, they are also known to maintain typical features of anaerobic organisms. Here, we describe the mechanisms of oxidative damage mitigation in Naegleria gruberi and focus on the molecular characteristics of three noncanonical proteins interacting with oxygen and its derived reactive forms. We show that this protist expresses hemerythrin, protoglobin and an aerobic-type rubrerythrin, with spectral properties characteristic of the cofactors they bind. We provide evidence that protoglobin and hemerythrin interact with oxygen in vitro and confirm the mitochondrial localization of rubrerythrin by immunolabeling. Our proteomic analysis and immunoblotting following heavy metal treatment revealed upregulation of hemerythrin, while rotenone treatment resulted in an increase in rubrerythrin protein levels together with vast upregulation of alternative oxidase. Our study provided new insights into the mechanisms employed by N. gruberi to cope with different types of oxidative stress and allowed us to propose specific roles for three unique and understudied proteins: hemerythrin, protoglobin and rubrerythrin.
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Affiliation(s)
- Ronald Malych
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Zoltán Füssy
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Kateřina Ženíšková
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Dominik Arbon
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Ivan Hrdý
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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11
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Abstract
Monocercomonoides exilis is considered the first known eukaryote to completely lack mitochondria. This conclusion is based primarily on a genomic and transcriptomic study which failed to identify any mitochondrial hallmark proteins. However, the available genome assembly has limited contiguity and around 1.5 % of the genome sequence is represented by unknown bases. To improve the contiguity, we re-sequenced the genome and transcriptome of M. exilis using Oxford Nanopore Technology (ONT). The resulting draft genome is assembled in 101 contigs with an N50 value of 1.38 Mbp, almost 20 times higher than the previously published assembly. Using a newly generated ONT transcriptome, we further improve the gene prediction and add high quality untranslated region (UTR) annotations, in which we identify two putative polyadenylation signals present in the 3′UTR regions and characterise the Kozak sequence in the 5′UTR regions. All these improvements are reflected by higher BUSCO genome completeness values. Regardless of an overall more complete genome assembly without missing bases and a better gene prediction, we still failed to identify any mitochondrial hallmark genes, thus further supporting the hypothesis on the absence of mitochondrion.
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Affiliation(s)
- Sebastian Cristian Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Priscila Peña-Diaz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
| | - Paweł Hałakuc
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Průmyslová 595, 252 42 Vestec, Czech Republic
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12
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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13
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Tomečková L, Tomčala A, Oborník M, Hampl V. The Lipid Composition of Euglena gracilis Middle Plastid Membrane Resembles That of Primary Plastid Envelopes. Plant Physiol 2020; 184:2052-2063. [PMID: 33008834 PMCID: PMC7723114 DOI: 10.1104/pp.20.00505] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 09/24/2020] [Indexed: 06/11/2023]
Abstract
Euglena gracilis is a photosynthetic flagellate possessing chlorophyte-derived secondary plastids that are enclosed by only three enveloping membranes, unlike most secondary plastids, which are surrounded by four membranes. It has generally been assumed that the two innermost E. gracilis plastid envelopes originated from the primary plastid, while the outermost is of eukaryotic origin. It was suggested that nucleus-encoded plastid proteins pass through the middle and innermost plastid envelopes of E. gracilis by machinery homologous to the translocons of outer and inner chloroplast membranes, respectively. Although recent genomic, transcriptomic, and proteomic data proved the presence of a reduced form of the translocon of inner membrane, they failed to identify any outer-membrane translocon homologs, which raised the question of the origin of E. gracilis's middle plastid envelope. Here, we compared the lipid composition of whole cells of the pigmented E. gracilis strain Z and two bleached mutants that lack detectable plastid structures, W10BSmL and WgmZOflL We determined the lipid composition of E. gracilis strain Z mitochondria and plastids, and of plastid subfractions (thylakoids and envelopes), using HPLC high-resolution tandem mass spectrometry, thin-layer chromatography, and gas chromatography-flame ionization detection analytical techniques. Phosphoglycerolipids are the main structural lipids in mitochondria, while glycosyldiacylglycerols are the major structural lipids of plastids and also predominate in extracts of whole mixotrophic cells. Glycosyldiacylglycerols were detected in both bleached mutants, indicating that mutant cells retain some plastid remnants. Additionally, we discuss the origin of the E. gracilis middle plastid envelope based on the lipid composition of envelope fraction.
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Affiliation(s)
- Lucia Tomečková
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- University of South Bohemia, Faculty of Fisheries and Protection of Water, CENAKVA, Institute of Aquaculture and Protection of Waters, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, 252 50 Vestec, Czech Republic
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14
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Faktorová D, Nisbet RER, Fernández Robledo JA, Casacuberta E, Sudek L, Allen AE, Ares M, Aresté C, Balestreri C, Barbrook AC, Beardslee P, Bender S, Booth DS, Bouget FY, Bowler C, Breglia SA, Brownlee C, Burger G, Cerutti H, Cesaroni R, Chiurillo MA, Clemente T, Coles DB, Collier JL, Cooney EC, Coyne K, Docampo R, Dupont CL, Edgcomb V, Einarsson E, Elustondo PA, Federici F, Freire-Beneitez V, Freyria NJ, Fukuda K, García PA, Girguis PR, Gomaa F, Gornik SG, Guo J, Hampl V, Hanawa Y, Haro-Contreras ER, Hehenberger E, Highfield A, Hirakawa Y, Hopes A, Howe CJ, Hu I, Ibañez J, Irwin NAT, Ishii Y, Janowicz NE, Jones AC, Kachale A, Fujimura-Kamada K, Kaur B, Kaye JZ, Kazana E, Keeling PJ, King N, Klobutcher LA, Lander N, Lassadi I, Li Z, Lin S, Lozano JC, Luan F, Maruyama S, Matute T, Miceli C, Minagawa J, Moosburner M, Najle SR, Nanjappa D, Nimmo IC, Noble L, Novák Vanclová AMG, Nowacki M, Nuñez I, Pain A, Piersanti A, Pucciarelli S, Pyrih J, Rest JS, Rius M, Robertson D, Ruaud A, Ruiz-Trillo I, Sigg MA, Silver PA, Slamovits CH, Jason Smith G, Sprecher BN, Stern R, Swart EC, Tsaousis AD, Tsypin L, Turkewitz A, Turnšek J, Valach M, Vergé V, von Dassow P, von der Haar T, Waller RF, Wang L, Wen X, Wheeler G, Woods A, Zhang H, Mock T, Worden AZ, Lukeš J. Publisher Correction: Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:551. [PMID: 32296171 PMCID: PMC7200595 DOI: 10.1038/s41592-020-0828-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Drahomíra Faktorová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
| | - R Ellen R Nisbet
- Department of Biochemistry, University of Cambridge, Cambridge, UK.,School of Biosciences, University of Nottingham, Sutton Bonington, UK
| | | | - Elena Casacuberta
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Lisa Sudek
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA
| | - Andrew E Allen
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Manuel Ares
- Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Cristina Aresté
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Cecilia Balestreri
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | | | - Patrick Beardslee
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Sara Bender
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - David S Booth
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - François-Yves Bouget
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Chris Bowler
- Institut de Biologie de l'Ecole Normale Supérieure (IBENS), Ecole Normale Supérieure, CNRS, INSERM, Université PSL, Paris, France
| | - Susana A Breglia
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Colin Brownlee
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Heriberto Cerutti
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Rachele Cesaroni
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Miguel A Chiurillo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Thomas Clemente
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Duncan B Coles
- Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jackie L Collier
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | - Elizabeth C Cooney
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kathryn Coyne
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Roberto Docampo
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Christopher L Dupont
- Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | | | - Elin Einarsson
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Pía A Elustondo
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada.,AGADA Biosciences Inc., Halifax, Nova Scotia, Canada
| | - Fernan Federici
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Veronica Freire-Beneitez
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | | | - Kodai Fukuda
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Paulo A García
- Department of Mechanical Engineering, Massachusetts Institute of Technology, Boston, MA, USA
| | - Peter R Girguis
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Fatma Gomaa
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Sebastian G Gornik
- Centre for Organismal Studies, University of Heidelberg, Heidelberg, Germany
| | - Jian Guo
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA.,Molecular, Cell and Developmental Biology, University of California, Santa Cruz, CA, USA
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Yutaka Hanawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Esteban R Haro-Contreras
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Elisabeth Hehenberger
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Andrea Highfield
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Ibaraki, Japan
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich, UK
| | | | - Ian Hu
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jorge Ibañez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Nicholas A T Irwin
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Yuu Ishii
- Graduate School of Life Sciences, Tohoku University, Sendai, Miyagi, Japan
| | - Natalia Ewa Janowicz
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Adam C Jones
- Gordon and Betty Moore Foundation, Palo Alto, CA, USA
| | - Ambar Kachale
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | - Konomi Fujimura-Kamada
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Binnypreet Kaur
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic
| | | | - Eleanna Kazana
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nicole King
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | | | - Noelia Lander
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Imen Lassadi
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Zhuhong Li
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, GA, USA
| | - Senjie Lin
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Jean-Claude Lozano
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Fulei Luan
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | | | - Tamara Matute
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Cristina Miceli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jun Minagawa
- Division of Environmental Photobiology, National Institute for Basic Biology, Okazaki, Aichi, Japan.,Department of Basic Biology, School of Life Science, Graduate University for Advanced Studies, Okazaki, Aichi, Japan
| | - Mark Moosburner
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA
| | - Sebastián R Najle
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Instituto de Biología Molecular y Celular, CONICET, and Facultad de Ciencias Bioquímicas y Farmacéuticas, Universidad Nacional de Rosario, Rosario, Argentina
| | - Deepak Nanjappa
- University of Delaware College of Earth, Ocean and Environment, Lewes, DE, USA
| | - Isabel C Nimmo
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Luke Noble
- Center for Genomics and Systems Biology, New York University, New York, NY, USA.,Institute de Biologie de l'ENS, Département de biologie, École Normale Supérieure, CNRS, INSERM, Paris, France
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Mariusz Nowacki
- Institute of Cell Biology, University of Bern, Bern, Switzerland
| | - Isaac Nuñez
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile
| | - Arnab Pain
- Biological and Environmental Science and Engineering Division, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Center for Zoonosis Control, Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan
| | - Angela Piersanti
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Sandra Pucciarelli
- School of Biosciences and Veterinary Medicine, University of Camerino, Camerino, Italy
| | - Jan Pyrih
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Joshua S Rest
- Department of Ecology and Evolution, Stony Brook University, Stony Brook, NY, USA
| | - Mariana Rius
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, NY, USA
| | | | - Albane Ruaud
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva, CSIC-Universitat Pompeu Fabra, Barcelona, Spain.,Departament de Genètica Microbiologia i Estadıśtica, Universitat de Barcelona, Barcelona, Spain.,Catalan Institution for Research and Advanced Studies, Barcelona, Spain
| | - Monika A Sigg
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, USA
| | - Pamela A Silver
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Claudio H Slamovits
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G Jason Smith
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | | | - Rowena Stern
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - Estienne C Swart
- Institute of Cell Biology, University of Bern, Bern, Switzerland.,Max Planck Institute for Developmental Biology, Tübingen, Germany
| | - Anastasios D Tsaousis
- School of Biosciences, University of Kent, Canterbury, Kent, UK.,Laboratory of Molecular and Evolutionary Parasitology, University of Kent, Kent, UK
| | - Lev Tsypin
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA.,Department of Biology, California Institute of Technology, Pasadena, CA, USA
| | - Aaron Turkewitz
- Department of Molecular Genetics and Cell Biology, University of Chicago, Chicago, IL, USA
| | - Jernej Turnšek
- Integrative Oceanography Division, Scripps Institution of Oceanography, University of California, San Diego, CA, USA.,Microbial and Environmental Genomics, J. Craig Venter Institute, La Jolla, CA, USA.,Department of Systems Biology, Harvard Medical School, Boston, MA, USA.,Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Quebec, Canada
| | - Valérie Vergé
- Sorbonne Université, CNRS UMR7621, Observatoire Océanologique, Banyuls sur Mer, France
| | - Peter von Dassow
- Facultad Ciencias Biológicas, Pontificia Universidad Católica de Chile, Fondo de Desarrollo de Areas Prioritarias, Center for Genome Regulation and Millennium Institute for Integrative Biology (iBio), Santiago de Chile, Chile.,Instituto Milenio de Oceanografia de Chile, Concepción, Chile
| | | | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Lu Wang
- Institute of Oceanography, Minjiang University, Fuzhou, China
| | - Xiaoxue Wen
- School of Biological Sciences, University of Nebraska, Lincoln, NE, USA
| | - Glen Wheeler
- The Marine Biological Association, Plymouth and School of Ocean and Earth Sciences, University of Southampton, Southampton, UK
| | - April Woods
- Department of Environmental Biotechnology, Moss Landing Marine Laboratories, Moss Landing, CA, USA
| | - Huan Zhang
- Department of Marine Sciences, University of Connecticut, Groton, CT, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich, UK.
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute, Moss Landing, CA, USA. .,Ocean EcoSystems Biology Unit, Marine Ecology Division, Helmholtz Centre for Ocean Research, Kiel, Germany.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences and Faculty of Sciences, University of South Bohemia, České Budějovice, Czech Republic.
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15
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Butenko A, Opperdoes FR, Flegontova O, Horák A, Hampl V, Keeling P, Gawryluk RMR, Tikhonenkov D, Flegontov P, Lukeš J. Evolution of metabolic capabilities and molecular features of diplonemids, kinetoplastids, and euglenids. BMC Biol 2020; 18:23. [PMID: 32122335 PMCID: PMC7052976 DOI: 10.1186/s12915-020-0754-1] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2019] [Accepted: 02/17/2020] [Indexed: 12/24/2022] Open
Abstract
Background The Euglenozoa are a protist group with an especially rich history of evolutionary diversity. They include diplonemids, representing arguably the most species-rich clade of marine planktonic eukaryotes; trypanosomatids, which are notorious parasites of medical and veterinary importance; and free-living euglenids. These different lifestyles, and particularly the transition from free-living to parasitic, likely require different metabolic capabilities. We carried out a comparative genomic analysis across euglenozoan diversity to see how changing repertoires of enzymes and structural features correspond to major changes in lifestyles. Results We find a gradual loss of genes encoding enzymes in the evolution of kinetoplastids, rather than a sudden decrease in metabolic capabilities corresponding to the origin of parasitism, while diplonemids and euglenids maintain more metabolic versatility. Distinctive characteristics of molecular machines such as kinetochores and the pre-replication complex that were previously considered specific to parasitic kinetoplastids were also identified in their free-living relatives. Therefore, we argue that they represent an ancestral rather than a derived state, as thought until the present. We also found evidence of ancient redundancy in systems such as NADPH-dependent thiol-redox. Only the genus Euglena possesses the combination of trypanothione-, glutathione-, and thioredoxin-based systems supposedly present in the euglenozoan common ancestor, while other representatives of the phylum have lost one or two of these systems. Lastly, we identified convergent losses of specific metabolic capabilities between free-living kinetoplastids and ciliates. Although this observation requires further examination, it suggests that certain eukaryotic lineages are predisposed to such convergent losses of key enzymes or whole pathways. Conclusions The loss of metabolic capabilities might not be associated with the switch to parasitic lifestyle in kinetoplastids, and the presence of a highly divergent (or unconventional) kinetochore machinery might not be restricted to this protist group. The data derived from the transcriptomes of free-living early branching prokinetoplastids suggests that the pre-replication complex of Trypanosomatidae is a highly divergent version of the conventional machinery. Our findings shed light on trends in the evolution of metabolism in protists in general and open multiple avenues for future research.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Fred R Opperdoes
- de Duve Institute, Université Catholique de Louvain, Brussels, Belgium
| | - Olga Flegontova
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Vladimír Hampl
- Faculty of Science, Charles University, Biocev, Vestec, Czech Republic
| | - Patrick Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | | | - Denis Tikhonenkov
- Department of Botany, University of British Columbia, Vancouver, Canada.,Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Pavel Flegontov
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of Ostrava, Ostrava, Czech Republic. .,Present address: Department of Genetics, Harvard Medical School, Boston, USA.
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
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16
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Novák Vanclová AMG, Zoltner M, Kelly S, Soukal P, Záhonová K, Füssy Z, Ebenezer TE, Lacová Dobáková E, Eliáš M, Lukeš J, Field MC, Hampl V. Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid. New Phytol 2020; 225:1578-1592. [PMID: 31580486 DOI: 10.1111/nph.16237] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 05/20/2023]
Abstract
Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.
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Affiliation(s)
| | - Martin Zoltner
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Petr Soukal
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
| | - Kristína Záhonová
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Eva Lacová Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Marek Eliáš
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czechia
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Vladimír Hampl
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
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17
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Lukešová S, Karlicki M, Tomečková Hadariová L, Szabová J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. Environ Microbiol Rep 2020; 12:78-91. [PMID: 31845515 DOI: 10.1111/1758-2229.12817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/23/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high-throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low-abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.
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Affiliation(s)
- Soňa Lukešová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Michał Karlicki
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Lucia Tomečková Hadariová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Jana Szabová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Anna Karnkowska
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Vladimír Hampl
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
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18
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Karnkowska A, Treitli SC, Brzoň O, Novák L, Vacek V, Soukal P, Barlow LD, Herman EK, Pipaliya SV, Pánek T, Žihala D, Petrželková R, Butenko A, Eme L, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Hampl V. The Oxymonad Genome Displays Canonical Eukaryotic Complexity in the Absence of a Mitochondrion. Mol Biol Evol 2019; 36:2292-2312. [PMID: 31387118 PMCID: PMC6759080 DOI: 10.1093/molbev/msz147] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
The discovery that the protist Monocercomonoides exilis completely lacks mitochondria demonstrates that these organelles are not absolutely essential to eukaryotic cells. However, the degree to which the metabolism and cellular systems of this organism have adapted to the loss of mitochondria is unknown. Here, we report an extensive analysis of the M. exilis genome to address this question. Unexpectedly, we find that M. exilis genome structure and content is similar in complexity to other eukaryotes and less "reduced" than genomes of some other protists from the Metamonada group to which it belongs. Furthermore, the predicted cytoskeletal systems, the organization of endomembrane systems, and biosynthetic pathways also display canonical eukaryotic complexity. The only apparent preadaptation that permitted the loss of mitochondria was the acquisition of the SUF system for Fe-S cluster assembly and the loss of glycine cleavage system. Changes in other systems, including in amino acid metabolism and oxidative stress response, were coincident with the loss of mitochondria but are likely adaptations to the microaerophilic and endobiotic niche rather than the mitochondrial loss per se. Apart from the lack of mitochondria and peroxisomes, we show that M. exilis is a fully elaborated eukaryotic cell that is a promising model system in which eukaryotic cell biology can be investigated in the absence of mitochondria.
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Affiliation(s)
- Anna Karnkowska
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
- Department of Molecular Phylogenetics and Evolution, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Sebastian C Treitli
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Ondřej Brzoň
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lukáš Novák
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Vojtěch Vacek
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Petr Soukal
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
| | - Lael D Barlow
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Emily K Herman
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Shweta V Pipaliya
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Tomáš Pánek
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - David Žihala
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Anzhelika Butenko
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Canada
| | - Vladimír Hampl
- Department of Parasitology, BIOCEV, Faculty of Science, Charles University, Vestec, Czech Republic
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19
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Vacek V, Novák LVF, Treitli SC, Táborský P, Cepicka I, Kolísko M, Keeling PJ, Hampl V. Fe-S Cluster Assembly in Oxymonads and Related Protists. Mol Biol Evol 2019; 35:2712-2718. [PMID: 30184127 PMCID: PMC6231488 DOI: 10.1093/molbev/msy168] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
The oxymonad Monocercomonoides exilis was recently reported to be the first eukaryote that has completely lost the mitochondrial compartment. It was proposed that an important prerequisite for such a radical evolutionary step was the acquisition of the SUF Fe–S cluster assembly pathway from prokaryotes, making the mitochondrial ISC pathway dispensable. We have investigated genomic and transcriptomic data from six oxymonad species and their relatives, composing the group Preaxostyla (Metamonada, Excavata), for the presence and absence of enzymes involved in Fe–S cluster biosynthesis. None possesses enzymes of mitochondrial ISC pathway and all apparently possess the SUF pathway, composed of SufB, C, D, S, and U proteins, altogether suggesting that the transition from ISC to SUF preceded their last common ancestor. Interestingly, we observed that SufDSU were fused in all three oxymonad genomes, and in the genome of Paratrimastix pyriformis. The donor of the SUF genes is not clear from phylogenetic analyses, but the enzyme composition of the pathway and the presence of SufDSU fusion suggests Firmicutes, Thermotogae, Spirochaetes, Proteobacteria, or Chloroflexi as donors. The inventory of the downstream CIA pathway enzymes is consistent with that of closely related species that retain ISC, indicating that the switch from ISC to SUF did not markedly affect the downstream process of maturation of cytosolic and nuclear Fe–S proteins.
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Affiliation(s)
- Vojtech Vacek
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Lukáš V F Novák
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Petr Táborský
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Ivan Cepicka
- Department of Zoology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Martin Kolísko
- Institute of Parasitology, Biology Centre, Czech Academy of Science, České Budějovice, Czech Republic.,Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
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20
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Adl SM, Bass D, Lane CE, Lukeš J, Schoch CL, Smirnov A, Agatha S, Berney C, Brown MW, Burki F, Cárdenas P, Čepička I, Chistyakova L, del Campo J, Dunthorn M, Edvardsen B, Eglit Y, Guillou L, Hampl V, Heiss AA, Hoppenrath M, James TY, Karnkowska A, Karpov S, Kim E, Kolisko M, Kudryavtsev A, Lahr DJ, Lara E, Le Gall L, Lynn DH, Mann DG, Massana R, Mitchell EA, Morrow C, Park JS, Pawlowski JW, Powell MJ, Richter DJ, Rueckert S, Shadwick L, Shimano S, Spiegel FW, Torruella G, Youssef N, Zlatogursky V, Zhang Q. Revisions to the Classification, Nomenclature, and Diversity of Eukaryotes. J Eukaryot Microbiol 2019; 66:4-119. [PMID: 30257078 PMCID: PMC6492006 DOI: 10.1111/jeu.12691] [Citation(s) in RCA: 563] [Impact Index Per Article: 112.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2018] [Accepted: 09/04/2018] [Indexed: 12/22/2022]
Abstract
This revision of the classification of eukaryotes follows that of Adl et al., 2012 [J. Euk. Microbiol. 59(5)] and retains an emphasis on protists. Changes since have improved the resolution of many nodes in phylogenetic analyses. For some clades even families are being clearly resolved. As we had predicted, environmental sampling in the intervening years has massively increased the genetic information at hand. Consequently, we have discovered novel clades, exciting new genera and uncovered a massive species level diversity beyond the morphological species descriptions. Several clades known from environmental samples only have now found their home. Sampling soils, deeper marine waters and the deep sea will continue to fill us with surprises. The main changes in this revision are the confirmation that eukaryotes form at least two domains, the loss of monophyly in the Excavata, robust support for the Haptista and Cryptista. We provide suggested primer sets for DNA sequences from environmental samples that are effective for each clade. We have provided a guide to trophic functional guilds in an appendix, to facilitate the interpretation of environmental samples, and a standardized taxonomic guide for East Asian users.
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Affiliation(s)
- Sina M. Adl
- Department of Soil SciencesCollege of Agriculture and Bioresources, University of SaskatchewanSaskatoonS7N 5A8SKCanada
| | - David Bass
- Department of Life SciencesThe Natural History MuseumCromwell RoadLondonSW7 5BDUnited Kingdom
- Centre for Environment, Fisheries and Aquaculture Science (CEFAS)Barrack Road, The NotheWeymouthDorsetDT4 8UBUnited Kingdom
| | - Christopher E. Lane
- Department of Biological SciencesUniversity of Rhode IslandKingstonRhode Island02881USA
| | - Julius Lukeš
- Institute of Parasitology, Biology CentreCzech Academy of SciencesČeské Budějovice37005Czechia
- Faculty of ScienceUniversity of South BohemiaČeské Budějovice37005Czechia
| | - Conrad L. Schoch
- National Institute for Biotechnology Information, National Library of Medicine, National Institutes of HealthBethesdaMaryland20892USA
| | - Alexey Smirnov
- Department of Invertebrate ZoologyFaculty of BiologySaint Petersburg State UniversitySaint Petersburg199034Russia
| | - Sabine Agatha
- Department of BiosciencesUniversity of SalzburgHellbrunnerstrasse 34SalzburgA‐5020Austria
| | - Cedric Berney
- CNRS, UMR 7144 (AD2M), Groupe Evolution des Protistes et Ecosystèmes PélagiquesStation Biologique de RoscoffPlace Georges TeissierRoscoff29680France
| | - Matthew W. Brown
- Department of Biological SciencesMississippi State UniversityStarkville39762MississippiUSA
- Institute for Genomics, Biocomputing & BiotechnologyMississippi State UniversityStarkville39762MississippiUSA
| | - Fabien Burki
- Department of Organismal BiologyProgram in Systematic BiologyScience for Life LaboratoryUppsala UniversityUppsala75236Sweden
| | - Paco Cárdenas
- Pharmacognosy, Department of Medicinal ChemistryUppsala UniversityBMC Box 574UppsalaSE‐75123Sweden
| | - Ivan Čepička
- Department of ZoologyFaculty of ScienceCharles UniversityVinicna 7Prague128 44Czechia
| | - Lyudmila Chistyakova
- Core Facility Centre for Culture Collection of MicroorganismsSaint Petersburg State UniversitySaint Petersburg198504Russia
| | - Javier del Campo
- Institut de Ciències del Mar, CSICPasseig Marítim de la Barceloneta, 37‐49Barcelona08003CataloniaSpain
| | - Micah Dunthorn
- Department of EcologyUniversity of KaiserslauternErwin‐Schroedinger StreetKaiserslauternD‐67663Germany
- Department of Eukaryotic MicrobiologyUniversity of Duisburg‐EssenUniversitätsstrasse 5EssenD‐45141Germany
| | - Bente Edvardsen
- Department of BiosciencesUniversity of OsloP.O. Box 1066 BlindernOslo0316Norway
| | - Yana Eglit
- Department of BiologyDalhousie UniversityHalifaxB3H 4R2NSCanada
| | - Laure Guillou
- Sorbonne Université, Université Pierre et Marie Curie ‐ Paris 6, CNRS, UMR 7144 (AD2M)Station Biologique de RoscoffPlace Georges Teissier, CS90074Roscoff29688France
| | - Vladimír Hampl
- Department of ParasitologyFaculty of ScienceCharles University, BIOCEVPrůmyslová 595Vestec252 42Czechia
| | - Aaron A. Heiss
- Department of Invertebrate ZoologyAmerican Museum of Natural HistoryNew York CityNew York10024USA
| | - Mona Hoppenrath
- Senckenberg am Meer, DZMB – German Centre for Marine Biodiversity ResearchWilhelmshaven26382Germany
| | - Timothy Y. James
- Department of Ecology and Evolutionary BiologyUniversity of MichiganAnn ArborMichigan48109USA
| | - Anna Karnkowska
- Department of Molecular Phylogenetics and EvolutionUniversity of WarsawWarsaw02‐089Poland
| | - Sergey Karpov
- Department of Invertebrate ZoologyFaculty of BiologySaint Petersburg State UniversitySaint Petersburg199034Russia
- Department of Molecular Phylogenetics and EvolutionUniversity of WarsawWarsaw02‐089Poland
| | - Eunsoo Kim
- Department of Invertebrate ZoologyAmerican Museum of Natural HistoryNew York CityNew York10024USA
| | - Martin Kolisko
- Institute of Parasitology, Biology CentreCzech Academy of SciencesČeské Budějovice37005Czechia
| | - Alexander Kudryavtsev
- Department of Invertebrate ZoologyFaculty of BiologySaint Petersburg State UniversitySaint Petersburg199034Russia
- Laboratory of Parasitic Worms and ProtistologyZoological Institute RASSaint Petersburg199034Russia
| | - Daniel J.G. Lahr
- Department of ZoologyInstitute of BiosciencesUniversity of Sao PauloMatao Travessa 14 Cidade UniversitariaSao Paulo05508‐090Sao PauloBrazil
| | - Enrique Lara
- Laboratory of Soil BiodiversityUniversity of NeuchâtelRue Emile‐Argand 11Neuchâtel2000Switzerland
- Real Jardín Botánico, CSICPlaza de Murillo 2Madrid28014Spain
| | - Line Le Gall
- Institut de Systématique, Évolution, Biodiversité, Muséum National d'Histoire NaturelleSorbonne Universités57 rue Cuvier, CP 39Paris75005France
| | - Denis H. Lynn
- Department of Integrative BiologyUniversity of GuelphSummerlee Science ComplexGuelphONN1G 2W1Canada
- Department of ZoologyUniversity of British Columbia4200‐6270 University Blvd.VancouverBCV6T 1Z4Canada
| | - David G. Mann
- Royal Botanic GardenEdinburghEH3 5LRUnited Kingdom
- Institute for Agrifood Research and TechnologyC/Poble Nou km 5.5Sant Carles de La RàpitaE‐43540Spain
| | - Ramon Massana
- Institut de Ciències del Mar, CSICPasseig Marítim de la Barceloneta, 37‐49Barcelona08003CataloniaSpain
| | - Edward A.D. Mitchell
- Laboratory of Soil BiodiversityUniversity of NeuchâtelRue Emile‐Argand 11Neuchâtel2000Switzerland
- Jardin Botanique de NeuchâtelChemin du Perthuis‐du‐Sault 58Neuchâtel2000Switzerland
| | - Christine Morrow
- Department of Natural SciencesNational Museums Northern Ireland153 Bangor RoadHolywoodBT18 OEUUnited Kingdom
| | - Jong Soo Park
- Department of Oceanography and Kyungpook Institute of OceanographySchool of Earth System SciencesKyungpook National UniversityDaeguKorea
| | - Jan W. Pawlowski
- Department of Genetics and EvolutionUniversity of Geneva1211Geneva 4Switzerland
| | - Martha J. Powell
- Department of Biological SciencesThe University of AlabamaTuscaloosaAlabama35487USA
| | - Daniel J. Richter
- Institut de Biologia Evolutiva (CSIC‐Universitat Pompeu Fabra)Passeig Marítim de la Barceloneta 37‐49Barcelona08003CataloniaSpain
| | - Sonja Rueckert
- School of Applied SciencesEdinburgh Napier UniversityEdinburghEH11 4BNUnited Kingdom
| | - Lora Shadwick
- Department of Biological SciencesUniversity of ArkansasFayettevilleArkansasAR 72701USA
| | - Satoshi Shimano
- Science Research CentreHosei University2‐17‐1 FujimiChiyoda‐kuTokyo102‐8160Japan
| | - Frederick W. Spiegel
- Department of Biological SciencesUniversity of ArkansasFayettevilleArkansasAR 72701USA
| | - Guifré Torruella
- Laboratoire Evolution et Systématique, Université Paris‐XIOrsay91405France
| | - Noha Youssef
- Department of Microbiology and Molecular GeneticsOklahoma State UniversityStillwaterOklahoma74074USA
| | - Vasily Zlatogursky
- Department of Invertebrate ZoologyFaculty of BiologySaint Petersburg State UniversitySaint Petersburg199034Russia
- Department of Organismal BiologySystematic Biology ProgramUppsala UniversityUppsalaSE‐752 36Sweden
| | - Qianqian Zhang
- Yantai Institute of Coastal Zone ResearchChinese Academy of ScienceYantai264003China
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Jakoubek V, Hampl V. Alcohol and fetoplacental vasoconstrictor reactivity. Physiol Res 2018. [PMID: 29527911 DOI: 10.33549/physiolres.933609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Alcohol abuse during pregnancy is a well-known factor in fetal morbidity, including smaller fetal size. We have shown that chronic hypoxia, considered the main pathogenetic factor in intrauterine growth restriction, elevates fetoplacental vascular resistance (and vasoconstrictor reactivity) and thus, presumably, reduces placental blood flow. We thus hypothesized that alcohol may affect the fetus - in addition to other mechanisms - by altering fetoplacental vascular resistance and/or reactivity. Using isolated, double-perfused rat placenta model, we found that maternal alcohol intake in the last third of gestation doubled the vasoconstrictor responses to angiotensin II but did not affect resting vascular resistance. Reactivity to acute hypoxic challenges was unchanged. Chronic maternal alcohol intake in a rat model alters fetoplacental vasculature reactivity; nevertheless, these changes do not appear as serious as other detrimental effects of alcohol on the fetus.
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Affiliation(s)
- V Jakoubek
- Department of Physiology Second Medical School, Charles University in Prague, Prague 5, Czech Republic.
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22
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Záhonová K, Petrželková R, Valach M, Yazaki E, Tikhonenkov DV, Butenko A, Janouškovec J, Hrdá Š, Klimeš V, Burger G, Inagaki Y, Keeling PJ, Hampl V, Flegontov P, Yurchenko V, Eliáš M. Extensive molecular tinkering in the evolution of the membrane attachment mode of the Rheb GTPase. Sci Rep 2018; 8:5239. [PMID: 29588502 PMCID: PMC5869587 DOI: 10.1038/s41598-018-23575-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Accepted: 03/15/2018] [Indexed: 02/07/2023] Open
Abstract
Rheb is a conserved and widespread Ras-like GTPase involved in cell growth regulation mediated by the (m)TORC1 kinase complex and implicated in tumourigenesis in humans. Rheb function depends on its association with membranes via prenylated C-terminus, a mechanism shared with many other eukaryotic GTPases. Strikingly, our analysis of a phylogenetically rich sample of Rheb sequences revealed that in multiple lineages this canonical and ancestral membrane attachment mode has been variously altered. The modifications include: (1) accretion to the N-terminus of two different phosphatidylinositol 3-phosphate-binding domains, PX in Cryptista (the fusion being the first proposed synapomorphy of this clade), and FYVE in Euglenozoa and the related undescribed flagellate SRT308; (2) acquisition of lipidic modifications of the N-terminal region, namely myristoylation and/or S-palmitoylation in seven different protist lineages; (3) acquisition of S-palmitoylation in the hypervariable C-terminal region of Rheb in apusomonads, convergently to some other Ras family proteins; (4) replacement of the C-terminal prenylation motif with four transmembrane segments in a novel Rheb paralog in the SAR clade; (5) loss of an evident C-terminal membrane attachment mechanism in Tremellomycetes and some Rheb paralogs of Euglenozoa. Rheb evolution is thus surprisingly dynamic and presents a spectacular example of molecular tinkering.
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Affiliation(s)
- Kristína Záhonová
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matus Valach
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Euki Yazaki
- Institute for Biological Sciences, University of Tsukuba, Tsukuba, Japan
| | - Denis V Tikhonenkov
- Laboratory of Microbiology, Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, Borok, Russia
| | - Anzhelika Butenko
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jan Janouškovec
- Department of Genetics, Evolution and Environment, University College London, London, United Kingdom
| | - Štěpánka Hrdá
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Vladimír Klimeš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Gertraud Burger
- Department of Biochemistry and Robert-Cedergren Centre for Bioinformatics and Genomics, Université de Montréal, Montreal, Canada
| | - Yuji Inagaki
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | - Patrick J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic
| | - Pavel Flegontov
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vyacheslav Yurchenko
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Marek Eliáš
- Department of Biology and Ecology & Institute of Environmental Technologies, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.
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23
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Beitl E, Baňasová A, Miková D, Hampl V. Nitric oxide elevation in polytrauma is driven by oxygen radicals. Physiol Res 2017; 66:S561-S565. [PMID: 29355385 DOI: 10.33549/physiolres.933793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
A common problem in management of polytrauma - a simultaneous injury to more than one organ or organ system, at least one of them lethal without intervention - is a discrepancy between a relatively good initial state and a serious subsequent development. Since nitric oxide (NO) is produced in high quantities during tissue injury, we assumed that serum levels of NO (and its oxidation products, NOx) might serve as a prognostic marker of polytrauma severity. However, we found recently that NOx was increased in polytrauma, but not in the most severe cases. The present study was undertaken to test the hypothesis that serum NOx is reduced in severe polytrauma by concomitant overproduction of reactive oxygen species (ROS). Polytrauma was induced in rats under anesthesia by bilateral fracture of femurs and tibiae plus incision of the right liver lobe through laparotomy. Serum NOx was measured by chemiluminescence after hot acidic reduction. The role of ROS was assessed by treatment with an antioxidant, N-acetyl-L-cysteine (NAC). Experimental polytrauma elevated NOx from 11.0+/-0.7 to 23.8+/-4.5 ppb. This was completely prevented by NAC treatment (9.1+/-2.2 ppb). Serum NOx is elevated in severe polytrauma, and this is not reduced by ROS. On the contrary, ROS are necessary for the NOx elevation, probably because ROS produced by inflammatory cells activated by the polytrauma induce massive NO production.
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Affiliation(s)
- E Beitl
- First Orthopaedic Clinic, First Faculty of Medicine, Charles University, Prague, Czech Republic, Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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24
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Egea J, Fabregat I, Frapart YM, Ghezzi P, Görlach A, Kietzmann T, Kubaichuk K, Knaus UG, Lopez MG, Olaso-Gonzalez G, Petry A, Schulz R, Vina J, Winyard P, Abbas K, Ademowo OS, Afonso CB, Andreadou I, Antelmann H, Antunes F, Aslan M, Bachschmid MM, Barbosa RM, Belousov V, Berndt C, Bernlohr D, Bertrán E, Bindoli A, Bottari SP, Brito PM, Carrara G, Casas AI, Chatzi A, Chondrogianni N, Conrad M, Cooke MS, Costa JG, Cuadrado A, My-Chan Dang P, De Smet B, Debelec-Butuner B, Dias IHK, Dunn JD, Edson AJ, El Assar M, El-Benna J, Ferdinandy P, Fernandes AS, Fladmark KE, Förstermann U, Giniatullin R, Giricz Z, Görbe A, Griffiths H, Hampl V, Hanf A, Herget J, Hernansanz-Agustín P, Hillion M, Huang J, Ilikay S, Jansen-Dürr P, Jaquet V, Joles JA, Kalyanaraman B, Kaminskyy D, Karbaschi M, Kleanthous M, Klotz LO, Korac B, Korkmaz KS, Koziel R, Kračun D, Krause KH, Křen V, Krieg T, Laranjinha J, Lazou A, Li H, Martínez-Ruiz A, Matsui R, McBean GJ, Meredith SP, Messens J, Miguel V, Mikhed Y, Milisav I, Milković L, Miranda-Vizuete A, Mojović M, Monsalve M, Mouthuy PA, Mulvey J, Münzel T, Muzykantov V, Nguyen ITN, Oelze M, Oliveira NG, Palmeira CM, Papaevgeniou N, Pavićević A, Pedre B, Peyrot F, Phylactides M, Pircalabioru GG, Pitt AR, Poulsen HE, Prieto I, Rigobello MP, Robledinos-Antón N, Rodríguez-Mañas L, Rolo AP, Rousset F, Ruskovska T, Saraiva N, Sasson S, Schröder K, Semen K, Seredenina T, Shakirzyanova A, Smith GL, Soldati T, Sousa BC, Spickett CM, Stancic A, Stasia MJ, Steinbrenner H, Stepanić V, Steven S, Tokatlidis K, Tuncay E, Turan B, Ursini F, Vacek J, Vajnerova O, Valentová K, Van Breusegem F, Varisli L, Veal EA, Yalçın AS, Yelisyeyeva O, Žarković N, Zatloukalová M, Zielonka J, Touyz RM, Papapetropoulos A, Grune T, Lamas S, Schmidt HHHW, Di Lisa F, Daiber A. Corrigendum to "European contribution to the study of ROS: A summary of the findings and prospects for the future from the COST action BM1203 (EU-ROS)" [Redox Biol. 13 (2017) 94-162]. Redox Biol 2017; 14:694-696. [PMID: 29107648 PMCID: PMC5975209 DOI: 10.1016/j.redox.2017.10.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Affiliation(s)
- J Egea
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine, Univerisdad Autonoma de Madrid, Spain
| | - I Fabregat
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - Y M Frapart
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - P Ghezzi
- Brighton & Sussex Medical School, Brighton, UK
| | - A Görlach
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany; DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich, Germany
| | - T Kietzmann
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - K Kubaichuk
- Faculty of Biochemistry and Molecular Medicine, and Biocenter Oulu, University of Oulu, Oulu, Finland
| | - U G Knaus
- Conway Institute, School of Medicine, University College Dublin, Dublin, Ireland
| | - M G Lopez
- Institute Teofilo Hernando, Department of Pharmacology, School of Medicine, Univerisdad Autonoma de Madrid, Spain
| | | | - A Petry
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - R Schulz
- Institute of Physiology, JLU Giessen, Giessen, Germany
| | - J Vina
- Department of Physiology, University of Valencia, Spain
| | - P Winyard
- University of Exeter Medical School, St Luke's Campus, Exeter EX1 2LU, UK
| | - K Abbas
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France
| | - O S Ademowo
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - C B Afonso
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - I Andreadou
- Laboratory of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - H Antelmann
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - F Antunes
- Departamento de Química e Bioquímica and Centro de Química e Bioquímica, Faculdade de Ciências, Portugal
| | - M Aslan
- Department of Medical Biochemistry, Faculty of Medicine, Akdeniz University, Antalya, Turkey
| | - M M Bachschmid
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - R M Barbosa
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - V Belousov
- Molecular technologies laboratory, Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry, Miklukho-Maklaya 16/10, Moscow 117997, Russia
| | - C Berndt
- Department of Neurology, Medical Faculty, Heinrich-Heine University, Düsseldorf, Germany
| | - D Bernlohr
- Department of Biochemistry, Molecular Biology and Biophysics, University of Minnesota - Twin Cities, USA
| | - E Bertrán
- Bellvitge Biomedical Research Institute (IDIBELL) and University of Barcelona (UB), L'Hospitalet, Barcelona, Spain
| | - A Bindoli
- Institute of Neuroscience (CNR), Padova, Italy
| | - S P Bottari
- GETI, Institute for Advanced Biosciences, INSERM U1029, CNRS UMR 5309, Grenoble-Alpes University and Radio-analysis Laboratory, CHU de Grenoble, Grenoble, France
| | - P M Brito
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; Faculdade de Ciências da Saúde, Universidade da Beira Interior, Covilhã, Portugal
| | - G Carrara
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - A I Casas
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - A Chatzi
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - N Chondrogianni
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - M Conrad
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - M S Cooke
- Helmholtz Center Munich, Institute of Developmental Genetics, Neuherberg, Germany
| | - J G Costa
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal; CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - A Cuadrado
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - P My-Chan Dang
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - B De Smet
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy; Pharmahungary Group, Szeged, Hungary
| | - B Debelec-Butuner
- Department of Pharmaceutical Biotechnology, Faculty of Pharmacy, Ege University, Bornova, Izmir 35100, Turkey
| | - I H K Dias
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - J D Dunn
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - A J Edson
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - M El Assar
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain
| | - J El-Benna
- Université Paris Diderot, Sorbonne Paris Cité, INSERM-U1149, CNRS-ERL8252, Centre de Recherche sur l'Inflammation, Laboratoire d'Excellence Inflamex, Faculté de Médecine Xavier Bichat, Paris, France
| | - P Ferdinandy
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - A S Fernandes
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - K E Fladmark
- Department of Molecular Biology, University of Bergen, Bergen, Norway
| | - U Förstermann
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - R Giniatullin
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - Z Giricz
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - A Görbe
- Department of Pharmacology and Pharmacotherapy, Medical Faculty, Semmelweis University, Budapest, Hungary; Pharmahungary Group, Szeged, Hungary
| | - H Griffiths
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK; Faculty of Health and Medical Sciences, University of Surrey, Guildford GU2 7XH, UK
| | - V Hampl
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - A Hanf
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - J Herget
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - P Hernansanz-Agustín
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Departamento de Bioquímica, Facultad de Medicina, Universidad Autónoma de Madrid (UAM) and Instituto de Investigaciones Biomédicas Alberto Sols, Madrid, Spain
| | - M Hillion
- Institute for Biology-Microbiology, Freie Universität Berlin, Berlin, Germany
| | - J Huang
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - S Ilikay
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - P Jansen-Dürr
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - V Jaquet
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - J A Joles
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | | | - D Kaminskyy
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - M Karbaschi
- Oxidative Stress Group, Dept. Environmental & Occupational Health, Florida International University, Miami, FL 33199, USA
| | - M Kleanthous
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - L O Klotz
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - B Korac
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - K S Korkmaz
- Department of Bioengineering, Cancer Biology Laboratory, Faculty of Engineering, Ege University, Bornova, 35100 Izmir, Turkey
| | - R Koziel
- Institute for Biomedical Aging Research, University of Innsbruck, Innsbruck, Austria
| | - D Kračun
- Experimental and Molecular Pediatric Cardiology, German Heart Center Munich at the Technical University Munich, Munich, Germany
| | - K H Krause
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - V Křen
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - T Krieg
- Department of Medicine, University of Cambridge, UK
| | - J Laranjinha
- Center for Neurosciences and Cell Biology, University of Coimbra and Faculty of Pharmacy, University of Coimbra, Coimbra, Portugal
| | - A Lazou
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki 54124, Greece
| | - H Li
- Department of Pharmacology, Johannes Gutenberg University Medical Center, Mainz, Germany
| | - A Martínez-Ruiz
- Servicio de Immunología, Hospital Universitario de La Princesa, Instituto de Investigación Sanitaria Princesa (IIS-IP), Madrid, Spain; Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - R Matsui
- Vascular Biology Section & Whitaker Cardiovascular Institute, Boston University School of Medicine, Boston, MA, USA
| | - G J McBean
- School of Biomolecular and Biomedical Science, Conway Institute, University College Dublin, Dublin, Ireland
| | - S P Meredith
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - J Messens
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - V Miguel
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - Y Mikhed
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - I Milisav
- University of Ljubljana, Faculty of Medicine, Institute of Pathophysiology and Faculty of Health Sciences, Ljubljana, Slovenia
| | - L Milković
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - A Miranda-Vizuete
- Instituto de Biomedicina de Sevilla, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, Sevilla, Spain
| | - M Mojović
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - M Monsalve
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - P A Mouthuy
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - J Mulvey
- Department of Medicine, University of Cambridge, UK
| | - T Münzel
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - V Muzykantov
- Department of Pharmacology, Center for Targeted Therapeutics & Translational Nanomedicine, ITMAT/CTSA Translational Research Center University of Pennsylvania The Perelman School of Medicine, Philadelphia, PA, USA
| | - I T N Nguyen
- Department of Nephrology & Hypertension, University Medical Center Utrecht, The Netherlands
| | - M Oelze
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - N G Oliveira
- Research Institute for Medicines (iMed.ULisboa), Faculty of Pharmacy, Universidade de Lisboa, Lisboa, Portugal
| | - C M Palmeira
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - N Papaevgeniou
- National Hellenic Research Foundation, Institute of Biology, Medicinal Chemistry and Biotechnology, 48 Vas. Constantinou Ave., 116 35 Athens, Greece
| | - A Pavićević
- University of Belgrade, Faculty of Physical Chemistry, Studentski trg 12-16, 11000 Belgrade, Serbia
| | - B Pedre
- Structural Biology Research Center, VIB, 1050 Brussels, Belgium; Brussels Center for Redox Biology, Structural Biology Brussels, Vrije Universiteit Brussel, 1050 Brussels, Belgium
| | - F Peyrot
- LCBPT, UMR 8601 CNRS - Paris Descartes University, Sorbonne Paris Cité, Paris, France; ESPE of Paris, Paris Sorbonne University, Paris, France
| | - M Phylactides
- Molecular Genetics Thalassaemia Department, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - G G Pircalabioru
- The Research Institute of University of Bucharest, Bucharest, Romania
| | - A R Pitt
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - H E Poulsen
- Laboratory of Clinical Pharmacology, Rigshospitalet, University Hospital Copenhagen, Denmark; Department of Clinical Pharmacology, Bispebjerg Frederiksberg Hospital, University Hospital Copenhagen, Denmark; Department Q7642, Rigshospitalet, Blegdamsvej 9, DK-2100 Copenhagen, Denmark
| | - I Prieto
- Instituto de Investigaciones Biomédicas "Alberto Sols" (CSIC-UAM), Madrid, Spain
| | - M P Rigobello
- Department of Biomedical Sciences, University of Padova, via Ugo Bassi 58/b, 35131 Padova, Italy
| | - N Robledinos-Antón
- Instituto de Investigaciones Biomédicas "Alberto Sols" UAM-CSIC, Instituto de Investigación Sanitaria La Paz (IdiPaz), Department of Biochemistry, Faculty of Medicine, Autonomous University of Madrid, Centro de Investigación Biomédica en Red sobre Enfermedades Neurodegenerativas (CIBERNED), Madrid, Spain
| | - L Rodríguez-Mañas
- Fundación para la Investigación Biomédica del Hospital Universitario de Getafe, Getafe, Spain; Servicio de Geriatría, Hospital Universitario de Getafe, Getafe, Spain
| | - A P Rolo
- Center for Neurosciences & Cell Biology of the University of Coimbra, Coimbra, Portugal; Department of Life Sciences of the Faculty of Sciences & Technology of the University of Coimbra, Coimbra, Portugal
| | - F Rousset
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - T Ruskovska
- Faculty of Medical Sciences, Goce Delcev University, Stip, Republic of Macedonia
| | - N Saraiva
- CBIOS, Universidade Lusófona Research Center for Biosciences & Health Technologies, Lisboa, Portugal
| | - S Sasson
- Institute for Drug Research, Section of Pharmacology, Diabetes Research Unit, The Hebrew University Faculty of Medicine, Jerusalem, Israel
| | - K Schröder
- Institute for Cardiovascular Physiology, Goethe-University, Frankfurt, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany
| | - K Semen
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - T Seredenina
- Dept. of Pathology and Immunology, Centre Médical Universitaire, Geneva, Switzerland
| | - A Shakirzyanova
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, Finland
| | - G L Smith
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - T Soldati
- Department of Biochemistry, Science II, University of Geneva, 30 quai Ernest-Ansermet, 1211 Geneva-4, Switzerland
| | - B C Sousa
- School of Life & Health Sciences, Aston University, Aston Triangle, Birmingham B47ET, UK
| | - C M Spickett
- Life & Health Sciences and Aston Research Centre for Healthy Ageing, Aston University, Aston Triangle, Birmingham B4 7ET, UK
| | - A Stancic
- University of Belgrade, Institute for Biological Research "Sinisa Stankovic" and Faculty of Biology, Belgrade, Serbia
| | - M J Stasia
- Université Grenoble Alpes, CNRS, Grenoble INP, CHU Grenoble Alpes, TIMC-IMAG, F38000 Grenoble, France; CDiReC, Pôle Biologie, CHU de Grenoble, Grenoble F-38043, France
| | - H Steinbrenner
- Institute of Nutrition, Department of Nutrigenomics, Friedrich Schiller University, Jena, Germany
| | - V Stepanić
- Ruđer Bošković Institute, Division of Molecular Medicine, Zagreb, Croatia
| | - S Steven
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany
| | - K Tokatlidis
- Institute of Molecular Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow, University Avenue, Glasgow, UK
| | - E Tuncay
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - B Turan
- Department of Biophysics, Ankara University, Faculty of Medicine, 06100 Ankara, Turkey
| | - F Ursini
- Department of Molecular Medicine, University of Padova, Padova, Italy
| | - J Vacek
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - O Vajnerova
- Department of Physiology, 2nd Faculty of Medicine, Charles University, Prague, Czech Republic
| | - K Valentová
- Institute of Microbiology, Laboratory of Biotransformation, Czech Academy of Sciences, Videnska 1083, CZ-142 20 Prague, Czech Republic
| | - F Van Breusegem
- Department of Plant Systems Biology, VIB, 9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
| | - L Varisli
- Harran University, Arts and Science Faculty, Department of Biology, Cancer Biology Lab, Osmanbey Campus, Sanliurfa, Turkey
| | - E A Veal
- Institute for Cell and Molecular Biosciences, and Institute for Ageing, Newcastle University, Framlington Place, Newcastle upon Tyne, UK
| | - A S Yalçın
- Department of Biochemistry, School of Medicine, Marmara University, Istanbul, Turkey
| | - O Yelisyeyeva
- Danylo Halytsky Lviv National Medical University, Lviv, Ukraine
| | - N Žarković
- Laboratory for Oxidative Stress, Rudjer Boskovic Institute, Bijenicka 54, 10000 Zagreb, Croatia
| | - M Zatloukalová
- Department of Medical Chemistry and Biochemistry, Faculty of Medicine and Dentistry, Palacký University, Hnevotinska 3, Olomouc 77515, Czech Republic
| | - J Zielonka
- Medical College of Wisconsin, Milwaukee, USA
| | - R M Touyz
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, UK
| | - A Papapetropoulos
- Laboratoty of Pharmacology, Faculty of Pharmacy, National and Kapodistrian University of Athens, Greece
| | - T Grune
- German Institute of Human Nutrition, Department of Toxicology, Arthur-Scheunert-Allee 114-116, 14558 Nuthetal, Germany
| | - S Lamas
- Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Madrid, Spain
| | - H H H W Schmidt
- Department of Pharmacology & Personalized Medicine, Cardiovascular Research Institute Maastricht (CARIM), Maastricht University, Maastricht, The Netherlands
| | - F Di Lisa
- Department of Biomedical Sciences and CNR Institute of Neuroscience, University of Padova, Padova, Italy.
| | - A Daiber
- Molecular Cardiology, Center for Cardiology, Cardiology 1, University Medical Center Mainz, Mainz, Germany; DZHK (German Centre for Cardiovascular Research), partner site Rhine-Main, Mainz, Germany.
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Hermanns C, Hampl V, Holzer K, Aigner A, Penkava J, Frank N, Martin DE, Maier KC, Waldburger N, Roessler S, Goppelt-Struebe M, Akrap I, Thavamani A, Singer S, Nordheim A, Gudermann T, Muehlich S. The novel MKL target gene myoferlin modulates expansion and senescence of hepatocellular carcinoma. Oncogene 2017; 36:3464-3476. [DOI: 10.1038/onc.2016.496] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Revised: 10/23/2016] [Accepted: 11/22/2016] [Indexed: 12/20/2022]
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Kafka P, Vajnerova O, Hampl V. Chronic hypoxia increases fetoplacental vascular resistance in rat placenta perfused with blood. BRATISL MED J 2016; 117:583-586. [PMID: 27826973 DOI: 10.4149/bll_2016_113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Chronic hypoxia elevates vascular resistance on the fetal side of the placenta. However, when a low-viscosity perfusate is used, the increase in resistance caused by chronic hypoxia is relatively small (12 mmHg). In the present study, we tested the hypothesis that perfusion with more viscous fluid (blood) will reveal more substantial effect of chronic hypoxia. METHODS Using an isolated, dually perfused rat placenta perfused at a constant flow rate with homologous blood, perfusion pressure on the fetal side was measured. Then, the relationship between perfusion pressure and flow (P/Q) was determined. RESULTS Fetoplacental vascular resistance was increased by chronic hypoxia (10 % O2) during the last third of gestation. This was observed when the placentas were perfused with a low viscosity Krebs solution and more enhanced when perfused with blood. Nevertheless, we found no clear advantage for using blood instead of Krebs solution to study the effects of hypoxia on the fetoplacental vasculature. The elevation of fetoplacental vascular resistance caused by chronic hypoxia was at least partly resistant to acute reoxygenation. CONCLUSION Using blood for the perfusion of the isolated rat placenta does not confer any clear methodological advantage over using Krebs solution (Tab. 2, Fig. 2, Ref. 21).
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Hrdá Š, Hroudová M, Vlček Č, Hampl V. Mitochondrial Genome of Prasinophyte Alga Pyramimonas parkeae. J Eukaryot Microbiol 2016; 64:360-369. [PMID: 27678215 DOI: 10.1111/jeu.12371] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2016] [Revised: 09/07/2016] [Accepted: 09/14/2016] [Indexed: 01/18/2023]
Abstract
Prasinophytes are a paraphyletic assemblage of nine heterogeneous lineages in the Chlorophyta clade of Archaeplastida. Until now, seven complete mitochondrial genomes have been sequenced from four prasinophyte lineages. Here, we report the mitochondrial genome of Pyramimonas parkeae, the first representative of the prasinophyte clade I. The circular-mapping molecule is 43,294 bp long, AT rich (68.8%), very compact and it comprises two 6,671 bp long inverted repeat regions. The gene content is slightly smaller than the gene-richest prasinophyte mitochondrial genomes. The single identified intron is located in the cytochrome c oxidase subunit 1 gene (cox1). Interestingly, two exons of cox1 are encoded on the same strand of DNA in the reverse order and the mature mRNA is formed by trans-splicing. The phylogenetic analysis using the data set of 6,037 positions assembled from 34 mtDNA-encoded proteins of 48 green algae and plants is not in compliance with the branching order of prasinophyte clades revealed on the basis of 18S rRNA genes and cpDNA-encoded proteins. However, the phylogenetic analyses based on all three genomic elements support the sister position of prasinophyte clades Pyramimonadales and Mamiellales.
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Affiliation(s)
- Štěpánka Hrdá
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 43, Czech Republic
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, 142 20, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, 142 20, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, Prague, 128 43, Czech Republic
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Novák L, Zubáčová Z, Karnkowska A, Kolisko M, Hroudová M, Stairs CW, Simpson AGB, Keeling PJ, Roger AJ, Čepička I, Hampl V. Arginine deiminase pathway enzymes: evolutionary history in metamonads and other eukaryotes. BMC Evol Biol 2016; 16:197. [PMID: 27716026 PMCID: PMC5052871 DOI: 10.1186/s12862-016-0771-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2015] [Accepted: 09/28/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiple prokaryotic lineages use the arginine deiminase (ADI) pathway for anaerobic energy production by arginine degradation. The distribution of this pathway among eukaryotes has been thought to be very limited, with only two specialized groups living in low oxygen environments (Parabasalia and Diplomonadida) known to possess the complete set of all three enzymes. We have performed an extensive survey of available sequence data in order to map the distribution of these enzymes among eukaryotes and to reconstruct their phylogenies. RESULTS We have found genes for the complete pathway in almost all examined representatives of Metamonada, the anaerobic protist group that includes parabasalids and diplomonads. Phylogenetic analyses indicate the presence of the complete pathway in the last common ancestor of metamonads and heterologous transformation experiments suggest its cytosolic localization in the metamonad ancestor. Outside Metamonada, the complete pathway occurs rarely, nevertheless, it was found in representatives of most major eukaryotic clades. CONCLUSIONS Phylogenetic relationships of complete pathways are consistent with the presence of the Archaea-derived ADI pathway in the last common ancestor of all eukaryotes, although other evolutionary scenarios remain possible. The presence of the incomplete set of enzymes is relatively common among eukaryotes and it may be related to the fact that these enzymes are involved in other cellular processes, such as the ornithine-urea cycle. Single protein phylogenies suggest that the evolutionary history of all three enzymes has been shaped by frequent gene losses and horizontal transfers, which may sometimes be connected with their diverse roles in cellular metabolism.
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Affiliation(s)
- Lukáš Novák
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Anna Karnkowska
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Martin Kolisko
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Courtney W. Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | | | | | - Andrew J. Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Canada
| | - Ivan Čepička
- Department of Zoology, Charles University, Faculty of Science, Prague, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Faculty of Science, Prague, Czech Republic
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Abstract
Due to their involvement in the energy metabolism, mitochondria are essential for most eukaryotic cells. Microbial eukaryotes living in low oxygen environments possess reduced forms of mitochondria, namely mitochondrion-related organelles (MROs). These do not produce ATP by oxidative phosphorylation on their membranes and some do not produce ATP at all. Still, they are indispensable because of other essential functions such as iron-sulphur (Fe-S) cluster assembly. Recently, the first microbial eukaryote with neither mitochondrion nor MRO was characterized - Monocercomonoides sp. Genome and transcriptome sequencing of Monocercomonoides revealed that it lacks all hallmark mitochondrial proteins. Crucially, the essential mitochondrial pathway for the Fe-S cluster assembly (ISC) was replaced by a bacterial sulphur mobilization (SUF) system. The discovery of such bona fide amitochondriate eukaryote broadens our knowledge about the diversity and plasticity of eukaryotic cells and provides a substantial contribution to our understanding of eukaryotic cell evolution.
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Affiliation(s)
- Anna Karnkowska
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada V6T 1Z4
| | - Vladimír Hampl
- Department of Parasitology, Charles University, Prague, Czech Republic
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Abstract
BACKGROUND Patients with injuries to multiple organs or organ systems are in a serious risk of shock, multiorgan failure and death. Although there are scoring systems available to assess the extent of polytrauma and guide the prognosis, their usefulness is limited by their considerably subjective nature. As the production of nitric oxide (NO) by many cell types is elevated in tissue injury, we hypothesized that serum concentration of NO (and its oxidation products, NOx) represents a suitable marker of polytrauma correlating with prognosis. We wanted to prove that nitric oxide could serve as an indicator for severity of injury in polytrauma. METHODS We measured serum NOx and standard biochemical parameters in 93 patients with various degrees of polytrauma, 15 patients with minor injuries and 20 healthy volunteers. RESULTS On admission, serum NOx was higher in patients with moderate polytrauma than both in controls and patients with minor injury, and it was even higher in patients with severe polytrauma. Surprisingly, NOx on admission was normal in the group of patients that required cardiopulmonary resuscitation or died within 48 hours after admission. In the groups, where it was elevated on admission, serum NOx dropped to normal values within 12 hours. Blood lactate levels on admission were elevated in proportion to the severity of subsequent clinical course. CONCLUSION Elevated serum NOx and blood lactate in patients with polytrauma are markers of serious clinical course, while normal NOx combined with a very high lactate may signal a fatal prognosis (Fig. 4, Ref. 8).
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Žaloudíková M, Vytášek R, Vajnerová O, Hniličková O, Vízek M, Hampl V, Herget J. Depletion of alveolar macrophages attenuates hypoxic pulmonary hypertension but not hypoxia-induced increase in serum concentration of MCP-1. Physiol Res 2016; 65:763-768. [PMID: 27429111 DOI: 10.33549/physiolres.933187] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Exposure to hypoxia, leading to hypoxic pulmonary hypertension (HPH), is associated with activation of alveolar macrophages (AM). However, it remains unclear how AM participate in this process. There are studies which imply that the AM product monocyte chemoattractant protein-1 (MCP-1) plays an important role. Thus we tested: 1. if the selective elimination of AM attenuates HPH in rats, 2. the correlation of MCP-1 plasmatic concentrations with the presence and absence of AM during exposure to hypoxia, 3. the direct influence of hypoxia on MCP-1 production in isolated AM. We found that experimental depletion of AM attenuated the chronic hypoxia-induced increase in mean pulmonary arterial pressure, but did not affect the serum MCP-1 concentrations. Furthermore, the MCP-1 production by AM in vitro was unaffected by hypoxia. Thus we conclude that AM play a significant role in the mechanism of HPH, but MCP-1 release from these cells is most likely not involved in this process. The increase of MCP-1 accompanying the development of HPH probably originates from other sources than AM.
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Affiliation(s)
- M Žaloudíková
- Department of Pathophysiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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Karnkowska A, Vacek V, Zubáčová Z, Treitli SC, Petrželková R, Eme L, Novák L, Žárský V, Barlow LD, Herman EK, Soukal P, Hroudová M, Doležal P, Stairs CW, Roger AJ, Eliáš M, Dacks JB, Vlček Č, Hampl V. A Eukaryote without a Mitochondrial Organelle. Curr Biol 2016; 26:1274-84. [PMID: 27185558 DOI: 10.1016/j.cub.2016.03.053] [Citation(s) in RCA: 218] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 03/05/2016] [Accepted: 03/23/2016] [Indexed: 11/28/2022]
Abstract
The presence of mitochondria and related organelles in every studied eukaryote supports the view that mitochondria are essential cellular components. Here, we report the genome sequence of a microbial eukaryote, the oxymonad Monocercomonoides sp., which revealed that this organism lacks all hallmark mitochondrial proteins. Crucially, the mitochondrial iron-sulfur cluster assembly pathway, thought to be conserved in virtually all eukaryotic cells, has been replaced by a cytosolic sulfur mobilization system (SUF) acquired by lateral gene transfer from bacteria. In the context of eukaryotic phylogeny, our data suggest that Monocercomonoides is not primitively amitochondrial but has lost the mitochondrion secondarily. This is the first example of a eukaryote lacking any form of a mitochondrion, demonstrating that this organelle is not absolutely essential for the viability of a eukaryotic cell.
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Affiliation(s)
- Anna Karnkowska
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic; Department of Molecular Phylogenetics and Evolution, University of Warsaw, Warsaw 00478, Poland.
| | - Vojtěch Vacek
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Zuzana Zubáčová
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Sebastian C Treitli
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Romana Petrželková
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Laura Eme
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Lukáš Novák
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Lael D Barlow
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Emily K Herman
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Petr Soukal
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Miluše Hroudová
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic
| | - Courtney W Stairs
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Andrew J Roger
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Marek Eliáš
- Department of Biology and Ecology, University of Ostrava, Ostrava 710 00, Czech Republic
| | - Joel B Dacks
- Department of Cell Biology, University of Alberta, Edmonton, AB T6G 2H7, Canada
| | - Čestmír Vlček
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Prague 14220, Czech Republic
| | - Vladimír Hampl
- Department of Parasitology, Charles University in Prague, Prague 12843, Czech Republic.
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Zíková A, Hampl V, Paris Z, Týč J, Lukeš J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. Mol Biochem Parasitol 2016; 209:46-57. [PMID: 26906976 DOI: 10.1016/j.molbiopara.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 02/08/2023]
Abstract
In this review the main features of the mitochondria of aerobic parasitic protists are discussed. While the best characterized organelles are by far those of kinetoplastid flagellates and Plasmodium, we also consider amoebae Naegleria and Acanthamoeba, a ciliate Ichthyophthirius and related lineages. The simplistic view of the mitochondrion as just a power house of the cell has already been abandoned in multicellular organisms and available data indicate that this also does not apply for protists. We discuss in more details the following mitochondrial features: genomes, post-transcriptional processing, translation, biogenesis of iron-sulfur complexes, heme metabolism and the electron transport chain. Substantial differences in all these core mitochondrial features between lineages are compatible with the view that aerobic protists harbor organelles that are more complex and flexible than previously appreciated.
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Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic.
| | - Vladimír Hampl
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada.
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Červenka L, Bíbová J, Husková Z, Vaňourková Z, Kramer HJ, Herget J, Jíchová Š, Sadowski J, Hampl V. Combined suppression of the intrarenal and circulating vasoconstrictor renin-ACE-ANG II axis and augmentation of the vasodilator ACE2-ANG 1-7-Mas axis attenuates the systemic hypertension in Ren-2 transgenic rats exposed to chronic hypoxia. Physiol Res 2014; 64:11-24. [PMID: 25194129 DOI: 10.33549/physiolres.932842] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The aim of the present study was to test the hypothesis that chronic hypoxia would aggravate hypertension in Ren-2 transgenic rats (TGR), a well-defined monogenetic model of hypertension with increased activity of endogenous renin-angiotensin system (RAS). Systolic blood pressure (SBP) in conscious rats and mean arterial pressure (MAP) in anesthetized TGR and normotensive Hannover Sprague-Dawley (HanSD) rats were determined under normoxia that was either continuous or interrupted by two weeks´ hypoxia. Expression, activities and concentrations of individual components of RAS were studied in plasma and kidney of TGR and HanSD rats under normoxic conditions and after exposure to chronic hypoxia. In HanSD rats two weeks´ exposure to chronic hypoxia did not alter SBP and MAP. Surprisingly, in TGR it decreased markedly SBP and MAP; this was associated with substantial reduction in plasma and kidney renin activities and also of angiotensin II (ANG II) levels, without altering angiotensin-converting enzyme (ACE) activities. Simultaneously, in TGR the exposure to hypoxia increased kidney ACE type 2 (ACE2) activity and angiotensin 1-7 (ANG 1-7) concentrations as compared with TGR under continuous normoxia. Based on these results, we propose that suppression of the hypertensiogenic ACE-ANG II axis in the circulation and kidney tissue, combined with augmentation of the intrarenal vasodilator ACE2-ANG 1-7 axis, is the main mechanism responsible for the blood pressure-lowering effects of chronic hypoxia in TGR.
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Affiliation(s)
- L Červenka
- Department of Pathophysiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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Pánek T, Simpson AG, Hampl V, Čepička I. Creneis carolina gen. et sp. nov. (Heterolobosea), a Novel Marine Anaerobic Protist with Strikingly Derived Morphology and Life Cycle. Protist 2014; 165:542-67. [DOI: 10.1016/j.protis.2014.05.005] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 05/05/2014] [Accepted: 05/28/2014] [Indexed: 11/29/2022]
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Szabová J, Yubuki N, Leander BS, Triemer RE, Hampl V. The evolution of paralogous enzymes MAT and MATX within the Euglenida and beyond. BMC Evol Biol 2014; 14:25. [PMID: 24517416 PMCID: PMC3923989 DOI: 10.1186/1471-2148-14-25] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2013] [Accepted: 12/30/2013] [Indexed: 11/10/2022] Open
Abstract
Background Methionine adenosyltransferase (MAT) is a ubiquitous essential enzyme that, in eukaryotes, occurs in two relatively divergent paralogues: MAT and MATX. MATX has a punctate distribution across the tree of eukaryotes and, except for a few cases, is mutually exclusive with MAT. This phylogenetic pattern could have arisen by either differential loss of old paralogues or the spread of one of these paralogues by horizontal gene transfer. Our aim was to map the distribution of MAT/MATX genes within the Euglenida in order to more comprehensively characterize the evolutionary history of MATX. Results We generated 26 new sequences from 23 different lineages of euglenids and one prasinophyte alga Pyramimonas parkeae. MATX was present only in photoautotrophic euglenids. The mixotroph Rapaza viridis and the prasinophyte alga Pyramimonas parkeae, which harbors chloroplasts that are most closely related to the chloroplasts in photoautotrophic euglenids, both possessed only the MAT paralogue. We found both the MAT and MATX paralogues in two photoautotrophic species (Phacus orbicularis and Monomorphina pyrum). The significant conflict between eukaryotic phylogenies inferred from MATX and SSU rDNA data represents strong evidence that MATX paralogues have undergone horizontal gene transfer across the tree of eukaryotes. Conclusions Our results suggest that MATX entered the euglenid lineage in a single horizontal gene transfer event that took place after the secondary endosymbiotic origin of the euglenid chloroplast. The origin of the MATX paralogue is unclear, and it cannot be excluded that it arose by a gene duplication event before the most recent common ancestor of eukaryotes.
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Affiliation(s)
- Jana Szabová
- Department of Parasitology, Charles University in Prague, Faculty of Science, Vinicna 7, Prague 2 128 44, Czech Republic.
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Kafka P, Vajnerová O, Herget J, Hampl V. Rho-kinase inhibition attenuates acute hypoxic fetoplacental vasoconstriction in the rat. Physiol Res 2013; 61 Suppl 2:S43-8. [PMID: 23130902 DOI: 10.33549/physiolres.932398] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The vessels on the fetal side of the placenta differ from most other vascular beds except the lungs in that they respond to acute hypoxia by vasoconstriction. An essential role of calcium influx in the mechanism of this hypoxic fetoplacental vasoconstriction (HFPV) has been shown previously. That finding does not, however, exclude the possible involvement of other mechanisms of vascular tone regulation. In this study we tested the hypothesis that Rho-kinase-mediated calcium sensitization is involved in HFPV. We used a model of isolated rat placenta dually perfused (from both the maternal and fetal side) with Krebs salt solution saturated with normoxic and hypoxic gas mixture respectively at constant flow rate. Rho-kinase pathway was inhibited by fasudil (10 microM). We found that fasudil reduced basal normoxic fetoplacental vascular resistance and completely prevented HFPV. This suggests that the activity of Rho-kinase signaling pathway is essential for HFPV.
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Affiliation(s)
- P Kafka
- Department of Physiology, Second Faculty of Medicine, Charles University, Prague, Czech Republic.
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Zubáčová Z, Novák L, Bublíková J, Vacek V, Fousek J, Rídl J, Tachezy J, Doležal P, Vlček Č, Hampl V. The mitochondrion-like organelle of Trimastix pyriformis contains the complete glycine cleavage system. PLoS One 2013; 8:e55417. [PMID: 23516392 PMCID: PMC3596361 DOI: 10.1371/journal.pone.0055417] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2012] [Accepted: 12/22/2012] [Indexed: 11/19/2022] Open
Abstract
All eukaryotic organisms contain mitochondria or organelles that evolved from the same endosymbiotic event like classical mitochondria. Organisms inhabiting low oxygen environments often contain mitochondrial derivates known as hydrogenosomes, mitosomes or neutrally as mitochondrion-like organelles. The detailed investigation has shown unexpected evolutionary plasticity in the biochemistry and protein composition of these organelles in various protists. We investigated the mitochondrion-like organelle in Trimastix pyriformis, a free-living member of one of the three lineages of anaerobic group Metamonada. Using 454 sequencing we have obtained 7 037 contigs from its transcriptome and on the basis of sequence homology and presence of N-terminal extensions we have selected contigs coding for proteins that putatively function in the organelle. Together with the results of a previous transcriptome survey, the list now consists of 23 proteins - mostly enzymes involved in amino acid metabolism, transporters and maturases of proteins and transporters of metabolites. We have no evidence of the production of ATP in the mitochondrion-like organelle of Trimastix but we have obtained experimental evidence for the presence of enzymes of the glycine cleavage system (GCS), which is part of amino acid metabolism. Using homologous antibody we have shown that H-protein of GCS localizes into vesicles in the cell of Trimastix. When overexpressed in yeast, H- and P-protein of GCS and cpn60 were transported into mitochondrion. In case of H-protein we have demonstrated that the first 16 amino acids are necessary for this transport. Glycine cleavage system is at the moment the only experimentally localized pathway in the mitochondrial derivate of Trimastix pyriformis.
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Affiliation(s)
- Zuzana Zubáčová
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Lukáš Novák
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Jitka Bublíková
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Vojtěch Vacek
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Jan Fousek
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jakub Rídl
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Jan Tachezy
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Pavel Doležal
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics of the Academy of Sciences of the Czech Republic, Prague, Czech Republic
| | - Vladimír Hampl
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
- * E-mail:
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Hrdá Š, Fousek J, Szabová J, Hampl V, Hampl V, Vlček Č. The plastid genome of Eutreptiella provides a window into the process of secondary endosymbiosis of plastid in euglenids. PLoS One 2012; 7:e33746. [PMID: 22448269 PMCID: PMC3308993 DOI: 10.1371/journal.pone.0033746] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2011] [Accepted: 02/16/2012] [Indexed: 11/18/2022] Open
Abstract
Euglenids are a group of protists that comprises species with diverse feeding modes. One distinct and diversified clade of euglenids is photoautotrophic, and its members bear green secondary plastids. In this paper we present the plastid genome of the euglenid Eutreptiella, which we assembled from 454 sequencing of Eutreptiella gDNA. Comparison of this genome and the only other available plastid genomes of photosynthetic euglenid, Euglena gracilis, revealed that they contain a virtually identical set of 57 protein coding genes, 24 genes fewer than the genome of Pyramimonas parkeae, the closest extant algal relative of the euglenid plastid. Searching within the transcriptomes of Euglena and Eutreptiella showed that 6 of the missing genes were transferred to the nucleus of the euglenid host while 18 have been probably lost completely. Euglena and Eutreptiella represent the deepest bifurcation in the photosynthetic clade, and therefore all these gene transfers and losses must have happened before the last common ancestor of all known photosynthetic euglenids. After the split of Euglena and Eutreptiella only one additional gene loss took place. The conservation of gene content in the two lineages of euglenids is in contrast to the variability of gene order and intron counts, which diversified dramatically. Our results show that the early secondary plastid of euglenids was much more susceptible to gene losses and endosymbiotic gene transfers than the established plastid, which is surprisingly resistant to changes in gene content.
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Affiliation(s)
- Štěpánka Hrdá
- Charles University in Prague, Faculty of Science, Department of Parasitology, Prague, Czech Republic
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Muehlich S, Hampl V, Khalid S, Singer S, Frank N, Breuhahn K, Gudermann T, Prywes R. The transcriptional coactivators megakaryoblastic leukemia 1/2 mediate the effects of loss of the tumor suppressor deleted in liver cancer 1. Oncogene 2011; 31:3913-23. [DOI: 10.1038/onc.2011.560] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
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Szabová J, Růžička P, Verner Z, Hampl V, Lukeš J. Experimental Examination of EFL and MATX Eukaryotic Horizontal Gene Transfers: Coexistence of Mutually Exclusive Transcripts Predates Functional Rescue. Mol Biol Evol 2011; 28:2371-8. [DOI: 10.1093/molbev/msr060] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Stairs CW, Roger AJ, Hampl V. Eukaryotic Pyruvate Formate Lyase and Its Activating Enzyme Were Acquired Laterally from a Firmicute. Mol Biol Evol 2011; 28:2087-99. [DOI: 10.1093/molbev/msr032] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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Abstract
Important fetal and perinatal pathologies, especially intrauterine growth restriction (IUGR), are thought to stem from placental hypoxia-induced vasoconstriction of the fetoplacental vessels, leading to placental hypoperfusion and thus fetal undernutrition. However, the effects of hypoxia on the fetoplacental vessels have been surprisingly little studied. We review here available experimental data on acute hypoxic fetoplacental vasoconstriction (HFPV) and on chronic hypoxic elevation of fetoplacental vascular resistance. The mechanism of HFPV includes hypoxic inhibition of potassium channels in the plasma membrane of fetoplacental vascular smooth muscle and consequent membrane depolarization that activates voltage gated calcium channels. This in turn causes calcium influx and contractile apparatus activation. The mechanism of chronic hypoxic elevation of fetoplacental vascular resistance is virtually unknown except of signs of the involvement of morphological remodeling.
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Affiliation(s)
- V Hampl
- Center for Cardiovascular Research, Prague, Czech Republic.
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Chovanec M, Novotná J, Wilhelm J, Hampl V, Vízek M, Herget J. Hypercapnia attenuates hypoxic pulmonary hypertension by inhibiting lung radical injury. Physiol Res 2010; 58 Suppl 2:S79-S86. [PMID: 20131939 DOI: 10.33549/physiolres.931923] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Chronic lung hypoxia results in hypoxic pulmonary hypertension. Concomitant chronic hypercapnia partly inhibits the effect of hypoxia on pulmonary vasculature. Adult male rats exposed to 3 weeks hypoxia (Fi(02)=0.1) combined with hypercapnia (Fi(C02)=0.04-0.05) had lower pulmonary arterial blood pressure, increased weight of the right heart ventricle, and less pronounced structural remodeling of the peripheral pulmonary arteries compared with rats exposed only to chronic hypoxia (Fi(02)=0.1). According to our hypothesis, hypoxic pulmonary hypertension is triggered by hypoxic injury to the walls of the peripheral pulmonary arteries. Hypercapnia inhibits release of both oxygen radicals and nitric oxide at the beginning of exposure to the hypoxic environment. The plasma concentration of nitrotyrosine, the marker of peroxynitrite activity, is lower in hypoxic rats exposed to hypercapnia than in those exposed to hypoxia alone. Hypercapnia blunts hypoxia-induced collagenolysis in the walls of prealveolar pulmonary arteries. We conclude that hypercapnia inhibits the development of hypoxic pulmonary hypertension by the inhibition of radical injury to the walls of peripheral pulmonary arteries.
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Affiliation(s)
- M Chovanec
- Department of Physiology, Second Medical School, Charles University, Prague, Czech Republic.
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Kašný M, Mikeš L, Hampl V, Dvořák J, Caffrey CR, Dalton JP, Horák P. Chapter 4 Peptidases of Trematodes. ADVANCES IN PARASITOLOGY 2009; 69:205-97. [DOI: 10.1016/s0065-308x(09)69004-7] [Citation(s) in RCA: 61] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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Hampl V, Cepicka I, Flegr J, Tachezy J, Kulda J. Morphological and molecular diversity of the monocercomonadid genera Monocercomonas, Hexamastix, and Honigbergiella gen. nov. Protist 2007; 158:365-83. [PMID: 17499022 DOI: 10.1016/j.protis.2007.02.003] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2007] [Accepted: 02/24/2007] [Indexed: 10/23/2022]
Abstract
The family Monocercomonadidae (Parabasala, Trichomonadida) is characterized by the absence of a costa and in most species also of an undulating membrane; both of which are typical structures of trichomonadids. We have examined 25 isolates of Monocercomonadidae species by sequencing of the SSU rDNA and the ITS region and by light and transmission electron microscopy. The isolates formed three distinct phylogenetically unrelated clades: (1) Monocercomonas colubrorum, (2) Monocercomonas ruminantium together with a strain ATCC 50321 designated as Pseudotrichomonas keilini, and (3) Hexamastix. Twenty isolates of Monocercomonas colubrorum split into three clades with no host-specificity. The morphological differences among clades were insufficient to classify them as a separate species. Non-monophyly of the cattle commensal Monocercomonas ruminantium with the type species Monocercomonas colubrorum and absence of Pseudotrichomonas characters in the free-living strain ATCC 50321 led to their reclassification into a new genus (Honigbergiella gen. nov.). The close relationship of these strains indicates a recent switch between a free-living habit and endobiosis. Two strains of Hexamastix represented different species -Hexamastix kirbyi Honigberg 1955 and Hexamastix mitis sp. nov. Polyphyly of the Monocercomonadidae confirmed that the absence of a costa and an undulating membrane are not taxonomically significant characters and were probably secondarily lost in some or all clades. Our observations, however, indicated that other characters - infrakinetosomal body, comb-like structure, marginal lamella, and the type of axostyle - are fully consistent with the position of Monocercomonadidae species in the parabasalian tree and are, therefore, reasonable taxonomic characters.
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MESH Headings
- Animals
- DNA, Protozoan/chemistry
- DNA, Protozoan/genetics
- DNA, Ribosomal/chemistry
- DNA, Ribosomal/genetics
- DNA, Ribosomal Spacer/genetics
- Genes, rRNA
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Organelles/ultrastructure
- Phylogeny
- RNA, Protozoan/genetics
- RNA, Ribosomal, 18S/genetics
- Sequence Analysis, DNA
- Sequence Homology, Nucleic Acid
- Trichomonadida/classification
- Trichomonadida/cytology
- Trichomonadida/genetics
- Trichomonadida/ultrastructure
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Affiliation(s)
- Vladimír Hampl
- Department of Parasitology, Charles University in Prague, Prague, Czech Republic.
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Ošťádalová I, Vobecký J, Chvojková Z, Miková D, Hampl V, Ošťádal B. Selenium increases tolerance of the neonatal rat heart to ischemia/reperfusion injury. J Mol Cell Cardiol 2006. [DOI: 10.1016/j.yjmcc.2006.03.112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Kolárová L, Rudolfová J, Hampl V, Skírnisson K. Allobilharzia visceralis gen. nov., sp. nov. (Schistosomatidae-Trematoda) from Cygnus cygnus (L.) (Anatidae). Parasitol Int 2006; 55:179-86. [PMID: 16627001 DOI: 10.1016/j.parint.2005.10.009] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2005] [Revised: 09/06/2005] [Accepted: 10/18/2005] [Indexed: 10/24/2022]
Abstract
In Iceland, the examination of whooper swans (Cygnus cygnus L.) viscera resulted in the detection of adult digenean flukes of the family Schistosomatidae. The mature worms occurring in the blood vessels of the large intestine and mesenterium caused vascular lesions, around the eggs deposited in the intestinal mucosa and liver granulomatous reactions developed. The morphology of the isolated schistosomes shows certain similarity with the flukes of the genus Trichobilharzia; in males reduced gynecophoral canal, and on both sexes both suckers and spatulate ends are present. However, the Icelandic flukes possess other morphological features which are distinct from the genus: the point of caecal reunion in males takes place posterior to gynecophoral canal and the genital pore is behind acetabulum and anterior to caecal reunion. In order to evaluate the identity of Icelandic schistosomes, sequencing of ITS region of DNA was performed, and the obtained sequence was deposited in GenBank under the accession no. DQ067561. Following phylogenetic analysis of relationship between the sequence of Icelandic flukes and database sequences of other bird schistosome genera (Trichobilharzia, Gigantobilharzia and Dendritobilharzia) showed different position of Icelandic worms in the phylogenetic tree. In conclusion, our study revealed new genus and species of schistosome flukes--Allobilharzia visceralis gen. et sp. n.
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Affiliation(s)
- Libuse Kolárová
- National Reference Laboratory for Tissue Helminthoses, Department of Microbiology, Institute for Postgradual Medical Education and 3rd Faculty of Medicine, Charles University, Ruská 85, 100 05 Prague 10, Czech Republic.
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Hampl V, Vrlík M, Cepicka I, Pecka Z, Kulda J, Tachezy J. Affiliation of Cochlosoma to trichomonads confirmed by phylogenetic analysis of the small-subunit rRNA gene and a new family concept of the order Trichomonadida. Int J Syst Evol Microbiol 2006; 56:305-12. [PMID: 16403903 DOI: 10.1099/ijs.0.63754-0] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The protozoan genus Cochlosoma includes parasitic intestinal flagellates of birds and mammals of uncertain taxonomic classification. The presence of an adhesive disc, superficially similar to that of Giardia, led to a proposal that Cochlosoma should be classified as diplomonads. Careful morphological and ultrastructural observations, however, revealed conspicuous homologies to trichomonads. We addressed the question of classification and phylogenetic affiliation of Cochlosoma using the methods of molecular phylogenetics. Analyses based on the 16S rRNA gene sequence of the species Cochlosoma anatis very robustly placed Cochlosoma in the clade of the parabasalid subfamilies Trichomonadinae, Trichomitopsiinae and Pentatrichomonoidinae of the order Trichomonadida (bootstraps >94 %). The data did not provide robust support for any particular position of Cochlosoma within this clade because the sequence suffered from mutational saturation and produced a long branch. The most probable sister taxon of Cochlosoma is the genus Pentatrichomonas, because their relationship was supported specifically by the slowest-mutating, least-saturated positions as determined using the method slow-fast. Classification of the order Trichomonadida was revised to accommodate knowledge about its phylogeny - the family Cochlosomatidae and subfamilies Trichomitopsiinae and Pentatrichomonoidinae were abandoned, Trichomonadidae was amended and new families Tritrichomonadidae (formerly a subfamily) and Trichomitidae were proposed.
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Affiliation(s)
- Vladimír Hampl
- Department of Parasitology, Faculty of Science, Charles University, Vinicna 7, 128 44, Prague, Czech Republic.
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Cepicka I, Hampl V, Kulda J, Flegr J. New evolutionary lineages, unexpected diversity, and host specificity in the parabasalid genus Tetratrichomonas. Mol Phylogenet Evol 2006; 39:542-51. [PMID: 16473027 DOI: 10.1016/j.ympev.2006.01.005] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2005] [Revised: 12/12/2005] [Accepted: 01/05/2006] [Indexed: 11/27/2022]
Abstract
We studied morphological and molecular polymorphism of 53 Tetratrichomonas isolates obtained from amphibian, reptilian, mammalian hosts, and from a slug with the aid of protargol staining and analyses of ITS1-5.8S rRNA-ITS2, SSU rRNA, and alpha-tubulin gene sequences. The phylogenetic tree based on the concatenate of all sequences showed the monophyly of the genus Tetratrichomonas with respect to the genus Trichomonas. Our data suggest that two parabasalid genera, Pentatrichomonoides and Trichomonoides, may belong to the genus Tetratrichomonas. Tetratrichomonas isolates were divided into 16 robust host-specific and monophyletic groups that probably represent separate, mostly new, species. As only five Tetratrichomonas species were described from the examined host taxa so far, our study uncovered considerable species diversity within the genus. The wide host range, high level of species-specific host specificity, and newly revealed biodiversity make the genus Tetratrichomonas a valuable model for studying evolution of parasites.
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Affiliation(s)
- Ivan Cepicka
- Department of Parasitology, Faculty of Science, Charles University, Prague, Czech Republic.
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