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Milanes JE, Yan VC, Pham CD, Muller F, Kwain S, Rees KC, Dominy BN, Whitehead DC, Millward SW, Bolejack M, Shek R, Tillery L, Phan IQ, Staker B, Moseman EA, Zhang X, Ma X, Jebet A, Yin X, Morris JC. Enolase inhibitors as therapeutic leads for Naegleria fowleri infection. PLoS Pathog 2024; 20:e1012412. [PMID: 39088549 DOI: 10.1371/journal.ppat.1012412] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Accepted: 07/11/2024] [Indexed: 08/03/2024] Open
Abstract
Infections with the pathogenic free-living amoebae Naegleria fowleri can lead to life-threatening illnesses including catastrophic primary amoebic meningoencephalitis (PAM). Efficacious treatment options for these infections are lacking and the mortality rate remains >95% in the US. Glycolysis is very important for the infectious trophozoite lifecycle stage and inhibitors of glucose metabolism have been found to be toxic to the pathogen. Recently, human enolase 2 (ENO2) phosphonate inhibitors have been developed as lead agents to treat glioblastoma multiforme (GBM). These compounds, which cure GBM in a rodent model, are well-tolerated in mammals because enolase 1 (ENO1) is the predominant isoform used systemically. Here, we describe findings that demonstrate these agents are potent inhibitors of N. fowleri ENO (NfENO) and are lethal to amoebae. In particular, (1-hydroxy-2-oxopiperidin-3-yl) phosphonic acid (HEX) was a potent enzyme inhibitor (IC50 = 0.14 ± 0.04 μM) that was toxic to trophozoites (EC50 = 0.21 ± 0.02 μM) while the reported CC50 was >300 μM. Molecular docking simulation revealed that HEX binds strongly to the active site of NfENO with a binding affinity of -8.6 kcal/mol. Metabolomic studies of parasites treated with HEX revealed a 4.5 to 78-fold accumulation of glycolytic intermediates upstream of NfENO. Last, nasal instillation of HEX increased longevity of amoebae-infected rodents. Two days after infection, animals were treated for 10 days with 3 mg/kg HEX, followed by one week of observation. At the end of the one-week observation, eight of 12 HEX-treated animals remained alive (resulting in an indeterminable median survival time) while one of 12 vehicle-treated rodents remained, yielding a median survival time of 10.9 days. However, intranasal HEX delivery was not curative as brains of six of the eight survivors were positive for amoebae. These findings suggest that HEX requires further evaluation to develop as a lead for treatment of PAM.
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Affiliation(s)
- Jillian E Milanes
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Victoria C Yan
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Cong-Dat Pham
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Florian Muller
- Sporos Bioventures, Houston, Texas, United States of America
| | - Samuel Kwain
- Department of Chemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Kerrick C Rees
- Department of Chemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Brian N Dominy
- Department of Chemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Daniel C Whitehead
- Department of Chemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
| | - Steven W Millward
- Department of Cancer Systems Imaging, UT MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Madison Bolejack
- UCB BioSciences, Bainbridge Island, Washington, United States of America
| | - Roger Shek
- Center for Emerging and Re-emerging Infectious Diseases and Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Logan Tillery
- Center for Emerging and Re-emerging Infectious Diseases and Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Isabelle Q Phan
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - Bart Staker
- Seattle Structural Genomics Center for Infectious Disease, Center for Global Infection Disease Research, Seattle Children's Research Institute, Seattle, Washington, United States of America
| | - E Ashley Moseman
- Department of Immunology, Duke University School of Medicine, Durham, North Carolina, United States of America
| | - Xiang Zhang
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States of America
| | - Xipeng Ma
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States of America
| | - Audriy Jebet
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States of America
| | - Xinmin Yin
- Department of Chemistry, University of Louisville, Louisville, Kentucky, United States of America
| | - James C Morris
- Department of Genetics and Biochemistry, Eukaryotic Pathogens Innovation Center, Clemson University, Clemson, South Carolina, United States of America
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Milanes JE, Yan VC, Pham CD, Muller F, Kwain S, Rees KC, Dominy BN, Whitehead DC, Millward SW, Bolejack M, Abendroth J, Phan IQ, Staker B, Moseman EA, Zhang X, Ma X, Jebet A, Yin X, Morris JC. Enolase inhibitors as therapeutic leads for Naegleria fowleri infection. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.16.575558. [PMID: 38293107 PMCID: PMC10827119 DOI: 10.1101/2024.01.16.575558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/01/2024]
Abstract
Infections with the pathogenic free-living amoebae Naegleria fowleri can lead to life-threatening illnesses including catastrophic primary amebic meningoencephalitis (PAM). Efficacious treatment options for these infections are lacking and the mortality rate remains >95% in the US. Glycolysis is very important for the infectious trophozoite lifecycle stage and inhibitors of glucose metabolism have been found to be toxic to the pathogen. Recently, human enolase 2 (ENO2) phosphonate inhibitors have been developed as lead agents to treat glioblastoma multiforme (GBM). These compounds, which cure GBM in a rodent model, are well-tolerated in mammals because enolase 1 (ENO1) is the predominant isoform used systemically. Here, we describe findings that demonstrate that these agents are potent inhibitors of N. fowleri ENO ( Nf ENO) and are lethal to amoebae. In particular, (1-hydroxy-2-oxopiperidin-3-yl) phosphonic acid (HEX) was a potent enzyme inhibitor (IC 50 value of 0.14 ± 0.04 µM) that was toxic to trophozoites (EC 50 value of 0.21 ± 0.02 µM) while the reported CC 50 was >300 µM. Molecular docking simulation revealed that HEX binds strongly to the active site of Nf ENO with a binding affinity of -8.6 kcal/mol. Metabolomic studies of parasites treated with HEX revealed a 4.5 to 78-fold accumulation of glycolytic intermediates upstream of Nf ENO. Last, nasal instillation of HEX increased longevity of amoebae-infected rodents. Two days after infection, animals were treated for 10 days with 3 mg/kg HEX, followed by one week of observation. At the conclusion of the experiment, eight of 12 HEX-treated animals remained alive (resulting in an indeterminable median survival time) while one of 12 vehicle-treated rodents remained, yielding a median survival time of 10.9 days. Brains of six of the eight survivors were positive for amoebae, suggesting the agent at the tested dose suppressed, but did not eliminate, infection. These findings suggest that HEX is a promising lead for the treatment of PAM.
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Dereeper A, Allouch N, Guerlais V, Garnier M, Ma L, De Jonckheere JF, Joseph SJ, Ali IKM, Talarmin A, Marcelino I. Naegleria genus pangenome reveals new structural and functional insights into the versatility of these free-living amoebae. Front Microbiol 2023; 13:1056418. [PMID: 36817109 PMCID: PMC9928731 DOI: 10.3389/fmicb.2022.1056418] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2022] [Accepted: 12/21/2022] [Indexed: 02/04/2023] Open
Abstract
Introduction Free-living amoebae of the Naegleria genus belong to the major protist clade Heterolobosea and are ubiquitously distributed in soil and freshwater habitats. Of the 47 Naegleria species described, N. fowleri is the only one being pathogenic to humans, causing a rare but fulminant primary amoebic meningoencephalitis. Some Naegleria genome sequences are publicly available, but the genetic basis for Naegleria diversity and ability to thrive in diverse environments (including human brain) remains unclear. Methods Herein, we constructed a high-quality Naegleria genus pangenome to obtain a comprehensive catalog of genes encoded by these amoebae. For this, we first sequenced, assembled, and annotated six new Naegleria genomes. Results and Discussion Genome architecture analyses revealed that Naegleria may use genome plasticity features such as ploidy/aneuploidy to modulate their behavior in different environments. When comparing 14 near-to-complete genome sequences, our results estimated the theoretical Naegleria pangenome as a closed genome, with 13,943 genes, including 3,563 core and 10,380 accessory genes. The functional annotations revealed that a large fraction of Naegleria genes show significant sequence similarity with those already described in other kingdoms, namely Animalia and Plantae. Comparative analyses highlighted a remarkable genomic heterogeneity, even for closely related strains and demonstrate that Naegleria harbors extensive genome variability, reflected in different metabolic repertoires. If Naegleria core genome was enriched in conserved genes essential for metabolic, regulatory and survival processes, the accessory genome revealed the presence of genes involved in stress response, macromolecule modifications, cell signaling and immune response. Commonly reported N. fowleri virulence-associated genes were present in both core and accessory genomes, suggesting that N. fowleri's ability to infect human brain could be related to its unique species-specific genes (mostly of unknown function) and/or to differential gene expression. The construction of Naegleria first pangenome allowed us to move away from a single reference genome (that does not necessarily represent each species as a whole) and to identify essential and dispensable genes in Naegleria evolution, diversity and biology, paving the way for further genomic and post-genomic studies.
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Affiliation(s)
- Alexis Dereeper
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Nina Allouch
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Vincent Guerlais
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Maëlle Garnier
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Laurence Ma
- Institut Pasteur de Paris, Biomics, Paris, France
| | | | - Sandeep J. Joseph
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Ibne Karim M. Ali
- Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Antoine Talarmin
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France
| | - Isabel Marcelino
- Institut Pasteur de la Guadeloupe, Unité TReD-Path, Les Abymes, Guadeloupe, France,*Correspondence: Isabel Marcelino,
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Andrade-Alviárez D, Bonive-Boscan AD, Cáceres AJ, Quiñones W, Gualdrón-López M, Ginger ML, Michels PAM. Delineating transitions during the evolution of specialised peroxisomes: Glycosome formation in kinetoplastid and diplonemid protists. Front Cell Dev Biol 2022; 10:979269. [PMID: 36172271 PMCID: PMC9512073 DOI: 10.3389/fcell.2022.979269] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Accepted: 08/17/2022] [Indexed: 12/01/2022] Open
Abstract
One peculiarity of protists belonging to classes Kinetoplastea and Diplonemea within the phylum Euglenozoa is compartmentalisation of most glycolytic enzymes within peroxisomes that are hence called glycosomes. This pathway is not sequestered in peroxisomes of the third Euglenozoan class, Euglenida. Previous analysis of well-studied kinetoplastids, the ‘TriTryps’ parasites Trypanosoma brucei, Trypanosoma cruzi and Leishmania spp., identified within glycosomes other metabolic processes usually not present in peroxisomes. In addition, trypanosomatid peroxins, i.e. proteins involved in biogenesis of these organelles, are divergent from human and yeast orthologues. In recent years, genomes, transcriptomes and proteomes for a variety of euglenozoans have become available. Here, we track the possible evolution of glycosomes by querying these databases, as well as the genome of Naegleria gruberi, a non-euglenozoan, which belongs to the same protist supergroup Discoba. We searched for orthologues of TriTryps proteins involved in glycosomal metabolism and biogenesis. Predicted cellular location(s) of each metabolic enzyme identified was inferred from presence or absence of peroxisomal-targeting signals. Combined with a survey of relevant literature, we refine extensively our previously postulated hypothesis about glycosome evolution. The data agree glycolysis was compartmentalised in a common ancestor of the kinetoplastids and diplonemids, yet additionally indicates most other processes found in glycosomes of extant trypanosomatids, but not in peroxisomes of other eukaryotes were either sequestered in this ancestor or shortly after separation of the two lineages. In contrast, peroxin divergence is evident in all euglenozoans. Following their gain of pathway complexity, subsequent evolution of peroxisome/glycosome function is complex. We hypothesize compartmentalisation in glycosomes of glycolytic enzymes, their cofactors and subsequently other metabolic enzymes provided selective advantage to kinetoplastids and diplonemids during their evolution in changing marine environments. We contend two specific properties derived from the ancestral peroxisomes were key: existence of nonselective pores for small solutes and the possibility of high turnover by pexophagy. Critically, such pores and pexophagy are characterised in extant trypanosomatids. Increasing amenability of free-living kinetoplastids and recently isolated diplonemids to experimental study means our hypothesis and interpretation of bioinformatic data are suited to experimental interrogation.
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Affiliation(s)
- Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Alejandro D. Bonive-Boscan
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Ana J. Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida, Venezuela
| | | | - Michael L. Ginger
- School of Applied Sciences, University of Huddersfield, Huddersfield, United Kingdom
| | - Paul A. M. Michels
- Centre for Immunity, Infection and Evolution and Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, Edinburgh, United Kingdom
- *Correspondence: Paul A. M. Michels,
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5
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Herman EK, Greninger A, van der Giezen M, Ginger ML, Ramirez-Macias I, Miller HC, Morgan MJ, Tsaousis AD, Velle K, Vargová R, Záhonová K, Najle SR, MacIntyre G, Muller N, Wittwer M, Zysset-Burri DC, Eliáš M, Slamovits CH, Weirauch MT, Fritz-Laylin L, Marciano-Cabral F, Puzon GJ, Walsh T, Chiu C, Dacks JB. Genomics and transcriptomics yields a system-level view of the biology of the pathogen Naegleria fowleri. BMC Biol 2021; 19:142. [PMID: 34294116 PMCID: PMC8296547 DOI: 10.1186/s12915-021-01078-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 06/24/2021] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material causing direct tissue damage and massive inflammation. The cellular basis distinguishing N. fowleri from other Naegleria species, which are all non-pathogenic, is not known. Yet, with the geographic range of N. fowleri advancing, potentially due to climate change, understanding how this pathogen invades and kills is both important and timely. RESULTS Here, we report an -omics approach to understanding N. fowleri biology and infection at the system level. We sequenced two new strains of N. fowleri and performed a transcriptomic analysis of low- versus high-pathogenicity N. fowleri cultured in a mouse infection model. Comparative analysis provides an in-depth assessment of encoded protein complement between strains, finding high conservation. Molecular evolutionary analyses of multiple diverse cellular systems demonstrate that the N. fowleri genome encodes a similarly complete cellular repertoire to that found in free-living N. gruberi. From transcriptomics, neither stress responses nor traits conferred from lateral gene transfer are suggested as critical for pathogenicity. By contrast, cellular systems such as proteases, lysosomal machinery, and motility, together with metabolic reprogramming and novel N. fowleri proteins, are all implicated in facilitating pathogenicity within the host. Upregulation in mouse-passaged N. fowleri of genes associated with glutamate metabolism and ammonia transport suggests adaptation to available carbon sources in the central nervous system. CONCLUSIONS In-depth analysis of Naegleria genomes and transcriptomes provides a model of cellular systems involved in opportunistic pathogenicity, uncovering new angles to understanding the biology of a rare but highly fatal pathogen.
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Affiliation(s)
- Emily K Herman
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, Alberta, Canada.
| | - Alex Greninger
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
- Department of Laboratory Medicine, University of Washington Medical Center, Montlake, USA
| | - Mark van der Giezen
- Centre for Organelle Research, Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, Stavanger, Norway
| | - Michael L Ginger
- School of Applied Sciences, Department of Biological and Geographical Sciences, University of Huddersfield, Huddersfield, UK
| | - Inmaculada Ramirez-Macias
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Department of Cardiology, Hospital Clinico Universitario Virgen de la Arrixaca. Instituto Murciano de Investigación Biosanitaria. Centro de Investigación Biomedica en Red-Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Haylea C Miller
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
- CSIRO, Indian Oceans Marine Research Centre, Environomics Future Science Platform, Crawley, WA, Australia
| | - Matthew J Morgan
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | | | - Katrina Velle
- Department of Biology, University of Massachusetts, Amherst, UK
| | - Romana Vargová
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Kristína Záhonová
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
- Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Sebastian Rodrigo Najle
- Institut de Biologia Evolutiva (UPF-CSIC), Barcelona, Spain
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), 08003, Barcelona, Catalonia, Spain
| | - Georgina MacIntyre
- Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada
| | - Norbert Muller
- Institute of Parasitology, Vetsuisse Faculty Bern, University of Bern, Bern, Switzerland
| | - Mattias Wittwer
- Spiez Laboratory, Federal Office for Civil Protection, Austrasse, Spiez, Switzerland
| | - Denise C Zysset-Burri
- Department of Ophthalmology, Inselspital, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - Matthew T Weirauch
- Center for Autoimmune Genomics and Etiology and Divisions of Biomedical Informatics and Developmental Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, USA
| | | | - Francine Marciano-Cabral
- Department of Microbiology and Immunology, Virginia Commonwealth University School of Medicine, Richmond, Virginia, USA
| | - Geoffrey J Puzon
- CSIRO Land and Water, Centre for Environment and Life Sciences, Private Bag No.5, Wembley, Western Australia 6913, Australia
| | - Tom Walsh
- CSIRO Land and Water, Black Mountain Laboratories, Canberra, Australia
| | - Charles Chiu
- Laboratory Medicine and Medicine / Infectious Diseases, UCSF-Abbott Viral Diagnostics and Discovery Center, UCSF Clinical Microbiology Laboratory UCSF School of Medicine, San Francisco, USA
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, Faculty of Medicine and Dentistry, University of Alberta, Edmonton, Canada.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
- Department of Life Sciences, The Natural History Museum, London, UK.
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Colpaert M, Kadouche D, Ducatez M, Pillonel T, Kebbi-Beghdadi C, Cenci U, Huang B, Chabi M, Maes E, Coddeville B, Couderc L, Touzet H, Bray F, Tirtiaux C, Ball S, Greub G, Colleoni C. Conservation of the glycogen metabolism pathway underlines a pivotal function of storage polysaccharides in Chlamydiae. Commun Biol 2021; 4:296. [PMID: 33674787 PMCID: PMC7935935 DOI: 10.1038/s42003-021-01794-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 02/03/2021] [Indexed: 01/31/2023] Open
Abstract
The order Chlamydiales includes obligate intracellular pathogens capable of infecting mammals, fishes and amoeba. Unlike other intracellular bacteria for which intracellular adaptation led to the loss of glycogen metabolism pathway, all chlamydial families maintained the nucleotide-sugar dependent glycogen metabolism pathway i.e. the GlgC-pathway with the notable exception of both Criblamydiaceae and Waddliaceae families. Through detailed genome analysis and biochemical investigations, we have shown that genome rearrangement events have resulted in a defective GlgC-pathway and more importantly we have evidenced a distinct trehalose-dependent GlgE-pathway in both Criblamydiaceae and Waddliaceae families. Altogether, this study strongly indicates that the glycogen metabolism is retained in all Chlamydiales without exception, highlighting the pivotal function of storage polysaccharides, which has been underestimated to date. We propose that glycogen degradation is a mandatory process for fueling essential metabolic pathways that ensure the survival and virulence of extracellular forms i.e. elementary bodies of Chlamydiales.
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Affiliation(s)
- Matthieu Colpaert
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Derifa Kadouche
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Mathieu Ducatez
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Trestan Pillonel
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Carole Kebbi-Beghdadi
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Ugo Cenci
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Binquan Huang
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
- State Key Laboratory for Conservation and Utilization of Bio-Resources in Yunnan/School of Agriculture, Yunnan University, Kunming, China
| | - Malika Chabi
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Emmanuel Maes
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Bernadette Coddeville
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Loïc Couderc
- University of Lille, CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, US 41 - UMS 2014 - PLBS, Lille, France
| | - Hélène Touzet
- University of Lille, CNRS, Centrale Lille, UMR 9189 - CRIStAL - Centre de Recherche en Informatique Signal et Automatique de Lille, Lille, France
| | - Fabrice Bray
- University of Lille, CNRS, USR 3290-MSAP-Miniaturisation pour la Synthèse, l'Analyse et la Protéomique, Lille, France
| | - Catherine Tirtiaux
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Steven Ball
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France
| | - Gilbert Greub
- Institute of Microbiology, University of Lausanne and University Hospital Center, Lausanne, Switzerland
| | - Christophe Colleoni
- University of Lille, CNRS, UMR8576-UGSF-Unité de Glycobiologie Structurale et Fonctionnelle, Lille, France.
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The extrachromosomal elements of the Naegleria genus: How little we know. Plasmid 2021; 115:102567. [PMID: 33617907 DOI: 10.1016/j.plasmid.2021.102567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 02/05/2021] [Accepted: 02/10/2021] [Indexed: 11/20/2022]
Abstract
There are currently 47 characterized species in the Naegleria genus of free-living amoebae. Each amoeba has thousands of extrachromosomal elements that are closed circular structures comprised of a single ribosomal DNA (rDNA) copy and a large non-rDNA sequence. Despite the presence of putative open reading frames and introns, ribosomal RNA is the only established transcript. A single origin of DNA replication (ori) has been mapped within the non-rDNA sequence for one species (N. gruberi), a finding that strongly indicates that these episomes replicate independently of the cell's chromosomal DNA component. This article reviews that which has been published about these interesting DNA elements and by analyzing available sequence data, discusses the possibility that different phylogenetically related clusters of Naegleria species individually conserve ori structures and suggests where the rRNA promoter and termination sites may be located.
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Maciver SK, McLaughlin PJ, Apps DK, Piñero JE, Lorenzo-Morales J. Opinion: Iron, Climate Change and the ‘Brain Eating Amoeba’ Naegleria fowleri. Protist 2021. [DOI: 10.1016/j.protis.2020.125791] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Rojas-Pirela M, Andrade-Alviárez D, Rojas V, Kemmerling U, Cáceres AJ, Michels PA, Concepción JL, Quiñones W. Phosphoglycerate kinase: structural aspects and functions, with special emphasis on the enzyme from Kinetoplastea. Open Biol 2020; 10:200302. [PMID: 33234025 PMCID: PMC7729029 DOI: 10.1098/rsob.200302] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Phosphoglycerate kinase (PGK) is a glycolytic enzyme that is well conserved among the three domains of life. PGK is usually a monomeric enzyme of about 45 kDa that catalyses one of the two ATP-producing reactions in the glycolytic pathway, through the conversion of 1,3-bisphosphoglycerate (1,3BPGA) to 3-phosphoglycerate (3PGA). It also participates in gluconeogenesis, catalysing the opposite reaction to produce 1,3BPGA and ADP. Like most other glycolytic enzymes, PGK has also been catalogued as a moonlighting protein, due to its involvement in different functions not associated with energy metabolism, which include pathogenesis, interaction with nucleic acids, tumorigenesis progression, cell death and viral replication. In this review, we have highlighted the overall aspects of this enzyme, such as its structure, reaction kinetics, activity regulation and possible moonlighting functions in different protistan organisms, especially both free-living and parasitic Kinetoplastea. Our analysis of the genomes of different kinetoplastids revealed the presence of open-reading frames (ORFs) for multiple PGK isoforms in several species. Some of these ORFs code for unusually large PGKs. The products appear to contain additional structural domains fused to the PGK domain. A striking aspect is that some of these PGK isoforms are predicted to be catalytically inactive enzymes or ‘dead’ enzymes. The roles of PGKs in kinetoplastid parasites are analysed, and the apparent significance of the PGK gene duplication that gave rise to the different isoforms and their expression in Trypanosoma cruzi is discussed.
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Affiliation(s)
- Maura Rojas-Pirela
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Diego Andrade-Alviárez
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Verónica Rojas
- Instituto de Biología, Facultad de Ciencias, Pontificia Universidad Católica de Valparaiso, Valparaiso 2373223, Chile
| | - Ulrike Kemmerling
- Instituto de Ciencias Biomédicas, Universidad de Chile, Facultad de Medicina, Santiago de Chile 8380453, Santigo de Chile
| | - Ana J Cáceres
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Paul A Michels
- Centre for Immunity, Infection and Evolution, The King's Buildings, Edinburgh EH9 3FL, UK.,Centre for Translational and Chemical Biology, School of Biological Sciences, The University of Edinburgh, The King's Buildings, Edinburgh EH9 3FL, UK
| | - Juan Luis Concepción
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
| | - Wilfredo Quiñones
- Laboratorio de Enzimología de Parásitos, Departamento de Biología, Facultad de Ciencias, Universidad de Los Andes, Mérida 5101, Venezuela
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10
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González-Robles A, González-Lázaro M, Lagunes-Guillén AE, Omaña-Molina M, Lares-Jiménez LF, Lares-Villa F, Martínez-Palomo A. Ultrastructural, Cytochemical, and Comparative Genomic Evidence of Peroxisomes in Three Genera of Pathogenic Free-Living Amoebae, Including the First Morphological Data for the Presence of This Organelle in Heteroloboseans. Genome Biol Evol 2020; 12:1734-1750. [PMID: 32602891 PMCID: PMC7549135 DOI: 10.1093/gbe/evaa129] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Peroxisomes perform various metabolic processes that are primarily related to the elimination of reactive oxygen species and oxidative lipid metabolism. These organelles are present in all major eukaryotic lineages, nevertheless, information regarding the presence of peroxisomes in opportunistic parasitic protozoa is scarce and in many cases it is still unknown whether these organisms have peroxisomes at all. Here, we performed ultrastructural, cytochemical, and bioinformatic studies to investigate the presence of peroxisomes in three genera of free-living amoebae from two different taxonomic groups that are known to cause fatal infections in humans. By transmission electron microscopy, round structures with a granular content limited by a single membrane were observed in Acanthamoeba castellanii, Acanthamoeba griffini, Acanthamoeba polyphaga, Acanthamoeba royreba, Balamuthia mandrillaris (Amoebozoa), and Naegleria fowleri (Heterolobosea). Further confirmation for the presence of peroxisomes was obtained by treating trophozoites in situ with diaminobenzidine and hydrogen peroxide, which showed positive reaction products for the presence of catalase. We then performed comparative genomic analyses to identify predicted peroxin homologues in these organisms. Our results demonstrate that a complete set of peroxins-which are essential for peroxisome biogenesis, proliferation, and protein import-are present in all of these amoebae. Likewise, our in silico analyses allowed us to identify a complete set of peroxins in Naegleria lovaniensis and three novel peroxin homologues in Naegleria gruberi. Thus, our results indicate that peroxisomes are present in these three genera of free-living amoebae and that they have a similar peroxin complement despite belonging to different evolutionary lineages.
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Affiliation(s)
- Arturo González-Robles
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Mónica González-Lázaro
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Anel Edith Lagunes-Guillén
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
| | - Maritza Omaña-Molina
- Facultad de Estudios Superiores Iztacala, Universidad Nacional Autónoma de México, Tlanepantla, Estado de México, Mexico
| | - Luis Fernando Lares-Jiménez
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Fernando Lares-Villa
- Departamento de Ciencias Agronómicas y Veterinarias, Instituto Tecnológico de Sonora, Ciudad Obregón, Sonora, Mexico
| | - Adolfo Martínez-Palomo
- Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del IPN, Ciudad de México, Mexico
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11
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Hasni I, Decloquement P, Demanèche S, Mameri RM, Abbe O, Colson P, La Scola B. Insight into the Lifestyle of Amoeba Willaertia magna during Bioreactor Growth Using Transcriptomics and Proteomics. Microorganisms 2020; 8:microorganisms8050771. [PMID: 32455615 PMCID: PMC7285305 DOI: 10.3390/microorganisms8050771] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 05/18/2020] [Accepted: 05/18/2020] [Indexed: 12/20/2022] Open
Abstract
Willaertia magna C2c maky is a thermophilic free-living amoeba strain that showed ability to eliminate Legionella pneumophila, a pathogenic bacterium living in the aquatic environment. The amoeba industry has proposed the use of Willaertia magna as a natural biocide to control L. pneumophila proliferation in cooling towers. Here, transcriptomic and proteomic studies were carried out in order to expand knowledge on W. magna produced in a bioreactor. Illumina RNA-seq generated 217 million raw reads. A total of 8790 transcripts were identified, of which 6179 and 5341 were assigned a function through comparisons with National Center of Biotechnology Information (NCBI) reference sequence and the Clusters of Orthologous Groups of proteins (COG) databases, respectively. To corroborate these transcriptomic data, we analyzed the W. magna proteome using LC–MS/MS. A total of 3561 proteins were identified. The results of transcriptome and proteome analyses were highly congruent. Metabolism study showed that W. magna preferentially consumed carbohydrates and fatty acids to grow. Finally, an in-depth analysis has shown that W. magna produces several enzymes that are probably involved in the metabolism of secondary metabolites. Overall, our multi-omic study of W. magna opens the way to a better understanding of the genetics and biology of this amoeba.
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Affiliation(s)
- Issam Hasni
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
| | - Philippe Decloquement
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
| | - Sandrine Demanèche
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Rayane Mouh Mameri
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Olivier Abbe
- R&D Department, Amoéba, 69680 Chassieu, France; (S.D.); (R.M.M.); (O.A.)
| | - Philippe Colson
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
| | - Bernard La Scola
- Aix-Marseille University, Institut de Recherche pour le Développement IRD 198, Assistance Publique—Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), UM63, 13005 Marseille, France; (I.H.); (P.D.); (P.C.)
- Institut Hospitalo-Universitaire (IHU)—Méditerranée Infection, 13005 Marseille, France
- Correspondence: ; Tel.: +33-4-9132-4375; Fax: +33-4-9138-7772
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12
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Bellini NK, da Fonseca ALM, Reyes-Batlle M, Lorenzo-Morales J, Rocha O, Thiemann OH. Isolation of Naegleria spp . from a Brazilian Water Source. Pathogens 2020; 9:E90. [PMID: 32024031 PMCID: PMC7169387 DOI: 10.3390/pathogens9020090] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 01/23/2020] [Accepted: 01/28/2020] [Indexed: 12/13/2022] Open
Abstract
The genus Naegleria, of the free-living amoeba (FLA) group, has been investigated mainly due to its human health impact, resulting in deadly infections and their worldwide distribution on freshwater systems. Naegleria fowleri, colloquially known as the "brain-eating amoeba," is the most studied Naegleria species because it causes primary amoebic meningoencephalitis (PAM) of high lethality. The assessment of FLA biodiversity is fundamental to evaluate the presence of pathogenic species and the possibility of human contamination. However, the knowledge of FLA distribution in Brazil is unknown, and to rectify this situation, we present research on identifying Naegleria spp. in the Monjolinho River as a model study. The river is a public Brazilian freshwater source that crosses the city of São Carlos, in São Paulo state, Brazil. Five distinct sampling sites were examined through limnological features, trophozoites culturing, and PCR against internal transcribed spacer (ITS) regions and 5.8S rRNA sequences. The results identified N. philippinensis, N. canariensisi, N. australiensis, N. gruberi, N. dobsoni sequences, as well as a Hartmannella sequence. The methodology delineated here represents the first Brazilian Naegleria spp. study on a freshwater system. Our results stress the urgency of a large scale evaluation of the presence of free-living amoebas in Brazil.
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Affiliation(s)
- Natália Karla Bellini
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, SP 13560-590, Brazil; (N.K.B.); (A.L.M.d.F.)
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, S/N, 38203 La Laguna, Tenerife, Canary Islands, Spain; (M.R.-B.); (J.L.-M.)
| | - Ana Letícia Moreira da Fonseca
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, SP 13560-590, Brazil; (N.K.B.); (A.L.M.d.F.)
| | - María Reyes-Batlle
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, S/N, 38203 La Laguna, Tenerife, Canary Islands, Spain; (M.R.-B.); (J.L.-M.)
| | - Jacob Lorenzo-Morales
- Instituto Universitario de Enfermedades Tropicales y Salud Pública de Canarias, Universidad de La Laguna, Avda. Astrofísico Fco. Sánchez, S/N, 38203 La Laguna, Tenerife, Canary Islands, Spain; (M.R.-B.); (J.L.-M.)
| | - Odete Rocha
- Departamento de Ecologia e Biologia Evolutiva, Universidade Federal de São Carlos, Rodovia Washington Luis, km 235, São Carlos, SP 13565-905, Brazil;
| | - Otavio Henrique Thiemann
- Instituto de Física de São Carlos, Universidade de São Paulo, Caixa Postal 369, São Carlos, SP 13560-590, Brazil; (N.K.B.); (A.L.M.d.F.)
- Departamento de Genética e Evolução, Universidade Federal de São Carlos, São Carlos, SP 13565-905, Brazil
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13
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Lipids Are the Preferred Substrate of the Protist Naegleria gruberi, Relative of a Human Brain Pathogen. Cell Rep 2019; 25:537-543.e3. [PMID: 30332635 PMCID: PMC6205838 DOI: 10.1016/j.celrep.2018.09.055] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 08/22/2018] [Accepted: 09/16/2018] [Indexed: 11/24/2022] Open
Abstract
Naegleria gruberi is a free-living non-pathogenic amoeboflagellate and relative of Naegleria fowleri, a deadly pathogen causing primary amoebic meningoencephalitis (PAM). A genomic analysis of N. gruberi exists, but physiological evidence for its core energy metabolism or in vivo growth substrates is lacking. Here, we show that N. gruberi trophozoites need oxygen for normal functioning and growth and that they shun both glucose and amino acids as growth substrates. Trophozoite growth depends mainly upon lipid oxidation via a mitochondrial branched respiratory chain, both ends of which require oxygen as final electron acceptor. Growing N. gruberi trophozoites thus have a strictly aerobic energy metabolism with a marked substrate preference for the oxidation of fatty acids. Analyses of N. fowleri genome data and comparison with those of N. gruberi indicate that N. fowleri has the same type of metabolism. Specialization to oxygen-dependent lipid breakdown represents an additional metabolic strategy in protists. Naegleria gruberi is a strict aerobe and needs oxygen for normal functioning and growth Unique among protists, N. gruberi prefers lipids over glucose as an energy source Lipid breakdown proceeds via a branched respiratory chain, both ends using oxygen N. fowleri, the fatal human brain amoeba, is predicted to have the same food preference
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14
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Hasni I, Chelkha N, Baptiste E, Mameri MR, Lachuer J, Plasson F, Colson P, La Scola B. Investigation of potential pathogenicity of Willaertia magna by investigating the transfer of bacteria pathogenicity genes into its genome. Sci Rep 2019; 9:18318. [PMID: 31797948 PMCID: PMC6892926 DOI: 10.1038/s41598-019-54580-6] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 11/10/2019] [Indexed: 12/14/2022] Open
Abstract
Willaertia magna c2c maky is a thermophilic amoeba closely related to the genus Naegleria. This free-living amoeba has the ability to eliminate Legionella pneumophila, which is an amoeba-resisting bacterium living in an aquatic environment. To prevent the proliferation of L. pneumophila in cooling towers, the use of W. magna as natural biocide has been proposed. To provide a better understanding of the W. magna genome, whole-genome sequencing was performed through the study of virulence factors and lateral gene transfers. This amoeba harbors a genome of 36.5 megabases with 18,519 predicted genes. BLASTp analyses reported protein homology between 136 W. magna sequences and amoeba-resistant microorganisms. Horizontal gene transfers were observed based on the basis of the phylogenetic reconstruction hypothesis. We detected 15 homologs of N. fowleri genes related to virulence, although these latter were also found in the genome of N. gruberi, which is a non-pathogenic amoeba. Furthermore, the cytotoxicity test performed on human cells supports the hypothesis that the strain c2c maky is a non-pathogenic amoeba. This work explores the genomic repertory for the first draft genome of genus Willaertia and provides genomic data for further comparative studies on virulence of related pathogenic amoeba, N. fowleri.
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Affiliation(s)
- Issam Hasni
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.,Amoéba, Chassieu, France
| | - Nisrine Chelkha
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Emeline Baptiste
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | | | - Joel Lachuer
- ProfileXpert/Viroscan3D, UCBL UMS 3453 CNRS - US7 INSERM, Lyon, France.,Inserm U1052, CNRS UMR5286, Centre de Recherche en Cancérologie de Lyon, Lyon, France.,Université de Lyon, Lyon, France
| | | | - Philippe Colson
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France
| | - Bernard La Scola
- Aix-Marseille Université UM63, Institut de Recherche pour le Développement IRD 198, Assistance Publique - Hôpitaux de Marseille (AP-HM), Microbes, Evolution, Phylogeny and Infection (MEΦI), Institut Hospitalo-Universitaire (IHU) - Méditerranée Infection, Marseille, France.
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15
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Mullican JC, Chapman NM, Tracy S. Mapping the Single Origin of Replication in the Naegleria gruberi Extrachromosomal DNA Element. Protist 2019; 170:141-152. [DOI: 10.1016/j.protis.2019.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 01/28/2019] [Accepted: 02/06/2019] [Indexed: 10/27/2022]
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16
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Garner E, McLain J, Bowers J, Engelthaler DM, Edwards MA, Pruden A. Microbial Ecology and Water Chemistry Impact Regrowth of Opportunistic Pathogens in Full-Scale Reclaimed Water Distribution Systems. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2018; 52:9056-9068. [PMID: 30040385 DOI: 10.1021/acs.est.8b02818] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Need for global water security has spurred growing interest in wastewater reuse to offset demand for municipal water. While reclaimed (i.e., nonpotable) microbial water quality regulations target fecal indicator bacteria, opportunistic pathogens (OPs), which are subject to regrowth in distribution systems and spread via aerosol inhalation and other noningestion routes, may be more relevant. This study compares the occurrences of five OP gene markers ( Acanthamoeba spp., Legionella spp., Mycobacterium spp., Naegleria fowleri, Pseudomonas aeruginosa) in reclaimed versus potable water distribution systems and characterizes factors potentially contributing to their regrowth. Samples were collected over four sampling events at the point of compliance for water exiting treatment plants and at five points of use at four U.S. utilities bearing both reclaimed and potable water distribution systems. Reclaimed water systems harbored unique water chemistry (e.g., elevated nutrients), microbial community composition, and OP occurrence patterns compared to potable systems examined here and reported in the literature. Legionella spp. genes, Mycobacterium spp. genes, and total bacteria, represented by 16S rRNA genes, were more abundant in reclaimed than potable water distribution system samples ( p ≤ 0.0001). This work suggests that further consideration should be given to managing reclaimed water distribution systems with respect to nonpotable exposures to OPs.
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Affiliation(s)
- Emily Garner
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Jean McLain
- Water Resources Research Center , University of Arizona , Tucson , Arizona 85719 , United States
| | - Jolene Bowers
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - David M Engelthaler
- Translational Genomics Research Institute , Flagstaff , Arizona 86005 , United States
| | - Marc A Edwards
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
| | - Amy Pruden
- Via Department of Civil and Environmental Engineering , Virginia Tech , Blacksburg , Virginia 24061 , United States
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17
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Iron economy in Naegleria gruberi reflects its metabolic flexibility. Int J Parasitol 2018; 48:719-727. [PMID: 29738737 DOI: 10.1016/j.ijpara.2018.03.005] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Revised: 03/07/2018] [Accepted: 03/08/2018] [Indexed: 11/24/2022]
Abstract
Naegleria gruberi is a free-living amoeba, closely related to the human pathogen Naegleria fowleri, the causative agent of the deadly human disease primary amoebic meningoencephalitis. Herein, we investigated the effect of iron limitation on different aspects of N. gruberi metabolism. Iron metabolism is among the most conserved pathways found in all eukaryotes. It includes the delivery, storage and utilisation of iron in many cell processes. Nevertheless, most of the iron metabolism pathways of N. gruberi are still not characterised, even though iron balance within the cell is crucial. We found a single homolog of ferritin in the N. gruberi genome and showed its localisation in the mitochondrion. Using comparative mass spectrometry, we identified 229 upregulated and 184 down-regulated proteins under iron-limited conditions. The most down-regulated protein under iron-limited conditions was hemerythrin, and a similar effect on the expression of hemerythrin was found in N. fowleri. Among the other down-regulated proteins were [FeFe]-hydrogenase and its maturase HydG and several heme-containing proteins. The activities of [FeFe]-hydrogenase, as well as alcohol dehydrogenase, were also decreased by iron deficiency. Our results indicate that N. gruberi is able to rearrange its metabolism according to iron availability, prioritising mitochondrial pathways. We hypothesise that the mitochondrion is the center for iron homeostasis in N. gruberi, with mitochondrially localised ferritin as a potential key component of this process.
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18
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Cárdenas-Zúñiga R, Silva-Olivares A, Villalba-Magdaleno JDA, Sánchez-Monroy V, Serrano-Luna J, Shibayama M. Amphotericin B induces apoptosis-like programmed cell death in Naegleria fowleri and Naegleria gruberi. MICROBIOLOGY-SGM 2017; 163:940-949. [PMID: 28721850 DOI: 10.1099/mic.0.000500] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Naegleria fowleri and Naegleria gruberi belong to the free-living amoebae group. It is widely known that the non-pathogenic species N. gruberi is usually employed as a model to describe molecular pathways in this genus, mainly because its genome has been recently described. However, N. fowleri is an aetiological agent of primary amoebic meningoencephalitis, an acute and fatal disease. Currently, the most widely used drug for its treatment is amphotericin B (AmB). It was previously reported that AmB has an amoebicidal effect in both N. fowleri and N. gruberi trophozoites by inducing morphological changes that resemble programmed cell death (PCD). PCD is a mechanism that activates morphological, biochemical and genetic changes. However, PCD has not yet been characterized in the genus Naegleria. The aim of the present work was to evaluate the typical markers to describe PCD in both amoebae. These results showed that treated trophozoites displayed several parameters of apoptosis-like PCD in both species. We observed ultrastructural changes, an increase in reactive oxygen species, phosphatidylserine externalization and a decrease in intracellular potassium, while DNA degradation was evaluated using the TUNEL assay and agarose gels, and all of these parameters are related to PCD. Finally, we analysed the expression of apoptosis-related genes, such as sir2 and atg8, in N. gruberi. Taken together, our results showed that AmB induces the morphological, biochemical and genetic changes of apoptosis-like PCD in the genus Naegleria.
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Affiliation(s)
- Roberto Cárdenas-Zúñiga
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Angélica Silva-Olivares
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, San Pedro Zacatenco, 07360, Mexico City, Mexico
| | | | - Virginia Sánchez-Monroy
- Laboratorio de Biomedicina Molecular, Escuela Nacional de Medicina y Homeopatía, Instituto Politénico Nacional, Calle Guillermo Massieu H. 239, Col. La Escalera, 07320, Mexico City, Mexico
| | - Jesús Serrano-Luna
- Department of Cell Biology, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, San Pedro Zacatenco, 07360, Mexico City, Mexico
| | - Mineko Shibayama
- Department of Infectomics and Molecular Pathogenesis, Center for Research and Advanced Studies of the National Polytechnic Institute, Av. IPN 2508, San Pedro Zacatenco, 07360, Mexico City, Mexico
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Yu Z, Miller HC, Puzon GJ, Clowers BH. Development of Untargeted Metabolomics Methods for the Rapid Detection of Pathogenic Naegleria fowleri. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2017; 51:4210-4219. [PMID: 28290675 DOI: 10.1021/acs.est.6b05969] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by Naegleria fowleri is extremely lethal, with mortality rates above 95%. As a thermophile, this organism is often found in moderate-to-warm climates and has the potential to colonize drinking water distribution systems (DWDSs). Current detection approaches require days to obtain results, whereas swift corrective action can maximize the benefit of public health. Presently, there is little information regarding the underlying in situ metabolism for this amoeba but the potential exists to exploit differentially expressed metabolic signatures as a rapid detection technique. This research outlines the biochemical profiles of selected pathogenic and nonpathogenic Naegleria in vitro using an untargeted metabolomics approach to identify a panel of diagnostically meaningful compounds that may enable rapid detection of viable pathogenic N. fowleri and augment results from traditional monitoring approaches.
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Affiliation(s)
- Zhihao Yu
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164, United States
| | - Haylea C Miller
- CSIRO Land and Water, Centre for Environment and Life Sciences , Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Geoffrey J Puzon
- CSIRO Land and Water, Centre for Environment and Life Sciences , Private Bag No. 5, Wembley, Western Australia 6913, Australia
| | - Brian H Clowers
- Department of Chemistry, Washington State University , P.O. Box 644630, Pullman, Washington 99164, United States
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20
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Ahmed Khan N, Baqir H, Siddiqui R. The immortal amoeba: a useful model to study cellular differentiation processes? Pathog Glob Health 2016; 109:305-6. [PMID: 26878933 DOI: 10.1080/20477724.2015.1103504] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Affiliation(s)
- Naveed Ahmed Khan
- 1 Department of Biological Sciences, Faculty of Science and Technology, Sunway University , Bandar Sunway, Malaysia
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21
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Machado ATP, Silva M, Iulek J. Expression, purification, enzymatic characterization and crystallization of glyceraldehyde-3-phosphate dehydrogenase from Naegleria gruberi, the first one from phylum Percolozoa. Protein Expr Purif 2016; 127:125-130. [PMID: 27426132 DOI: 10.1016/j.pep.2016.07.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2016] [Revised: 06/28/2016] [Accepted: 07/12/2016] [Indexed: 11/28/2022]
Abstract
Naegleria gruberi had its genome sequenced by Fritz-Laylin and collaborators in 2010. It is not pathogenic, but has characteristics similar to those of Naegleria fowleri, opportunistic pathogen that can cause fatal encephalitis in humans. N. gruberi genome has contributed to a better understanding of the primitive eukaryotic metabolism and revealed the complexity of several metabolic pathways. In this paper we describe the expression, purification, enzyme characterization and crystallization of N. gruberi GAPDH, the first one for an organism belonging to phylum Percolozoa. The results indicated that 10 mM, 8.0 and 25 °C are the optimum arsenate concentration, pH and temperature, respectively. The enzyme presents allosteric positive cooperativity for substrates NAD(+) and G3P as indicated by the Hill coefficients. The phylogenetic proximity between N. fowleri and N. gruberi suggests that contributions from the study of the latter might provide information to assist the search for treatments of Primary Amebic Meningoencephalitis, especially, in this work, taking into account that GAPDH is identified as a therapeutic target.
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Affiliation(s)
| | - Marcio Silva
- Department of Education, Federal Technological University of Paraná, 84016-210, Ponta Grossa, PR, Brazil
| | - Jorge Iulek
- Department of Chemistry, State University of Ponta Grossa, 84030-900, Ponta Grossa, PR, Brazil.
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22
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Opperdoes FR, Butenko A, Flegontov P, Yurchenko V, Lukeš J. Comparative Metabolism of Free-living Bodo saltans
and Parasitic Trypanosomatids. J Eukaryot Microbiol 2016; 63:657-78. [DOI: 10.1111/jeu.12315] [Citation(s) in RCA: 64] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Revised: 03/10/2016] [Accepted: 03/20/2016] [Indexed: 12/20/2022]
Affiliation(s)
- Fred R. Opperdoes
- de Duve Institute; Université Catholique de Louvain; Brussels B-1200 Belgium
| | - Anzhelika Butenko
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
| | - Pavel Flegontov
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- A.A. Kharkevich Institute for Information Transmission Problems; Russian Academy of Sciences; Moscow 127 051 Russia
| | - Vyacheslav Yurchenko
- Life Science Research Centre; Faculty of Science; University of Ostrava; Ostrava 710 00 Czech Republic
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- Faculty of Science; Institute of Environmental Technologies; University of Ostrava; Ostrava 710 00 Czech Republic
| | - Julius Lukeš
- Biology Centre; Institute of Parasitology; Czech Academy of Sciences; České Budějovice (Budweis) 370 05 Czech Republic
- Faculty of Science; University of South Bohemia; České Budějovice (Budweis) 370 05 Czech Republic
- Canadian Institute for Advanced Research; Toronto ON M5G 1Z8 Canada
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23
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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] [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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Gabaldón T, Ginger ML, Michels PAM. Peroxisomes in parasitic protists. Mol Biochem Parasitol 2016; 209:35-45. [PMID: 26896770 DOI: 10.1016/j.molbiopara.2016.02.005] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2015] [Revised: 02/12/2016] [Accepted: 02/13/2016] [Indexed: 01/24/2023]
Abstract
Representatives of all major lineages of eukaryotes contain peroxisomes with similar morphology and mode of biogenesis, indicating a monophyletic origin of the organelles within the common ancestor of all eukaryotes. Peroxisomes originated from the endoplasmic reticulum, but despite a common origin and shared morphological features, peroxisomes from different organisms show a remarkable diversity of enzyme content and the metabolic processes present can vary dependent on nutritional or developmental conditions. A common characteristic and probable evolutionary driver for the origin of the organelle is an involvement in lipid metabolism, notably H2O2-dependent fatty-acid oxidation. Subsequent evolution of the organelle in different lineages involved multiple acquisitions of metabolic processes-often involving retargeting enzymes from other cell compartments-and losses. Information about peroxisomes in protists is still scarce, but available evidence, including new bioinformatics data reported here, indicate striking diversity amongst free-living and parasitic protists from different phylogenetic supergroups. Peroxisomes in only some protists show major involvement in H2O2-dependent metabolism, as in peroxisomes of mammalian, plant and fungal cells. Compartmentalization of glycolytic and gluconeogenic enzymes inside peroxisomes is characteristic of kinetoplastids and diplonemids, where the organelles are hence called glycosomes, whereas several other excavate parasites (Giardia, Trichomonas) have lost peroxisomes. Amongst alveolates and amoebozoans patterns of peroxisome loss are more complicated. Often, a link is apparent between the niches occupied by the parasitic protists, nutrient availability, and the absence of the organelles or their presence with a specific enzymatic content. In trypanosomatids, essentiality of peroxisomes may be considered for use in anti-parasite drug discovery.
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Affiliation(s)
- Toni Gabaldón
- Bioinformatics and Genomics Programme, Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Barcelona, Spain; Universitat Pompeu Fabra (UPF), Barcelona, Spain; Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain.
| | - Michael L Ginger
- Division of Biomedical and Life Sciences, Faculty of Health and Medicine, Lancaster University, Lancaster, UK; Department of Biological Sciences, University of Huddersfield, Queensgate, Huddersfield HD1 3DH, UK.
| | - Paul A M Michels
- Centre for Immunity, Infection and Evolution, School of Biological Sciences, University of Edinburgh, UK; Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, UK; Laboratorio de Enzimología de Parásitos, Departamento de Biología, Universidad de Los Andes, Mérida, Venezuela.
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25
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Munyampundu JP, Xu YP, Cai XZ. Phi Class of Glutathione S-transferase Gene Superfamily Widely Exists in Nonplant Taxonomic Groups. Evol Bioinform Online 2016; 12:59-71. [PMID: 26884677 PMCID: PMC4750895 DOI: 10.4137/ebo.s35909] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2015] [Revised: 12/13/2015] [Accepted: 12/13/2015] [Indexed: 01/13/2023] Open
Abstract
Glutathione S-transferases (GSTs) constitute a superfamily of enzymes involved in detoxification of noxious compounds and protection against oxidative damage. GST class Phi (GSTF), one of the important classes of plant GSTs, has long been considered as plant specific but was recently found in basidiomycete fungi. However, the range of nonplant taxonomic groups containing GSTFs remains unknown. In this study, the distribution and phylogenetic relationships of nonplant GSTFs were investigated. We identified GSTFs in ascomycete fungi, myxobacteria, and protists Naegleria gruberi and Aureococcus anophagefferens. GSTF occurrence in these bacteria and protists correlated with their genome sizes and habitats. While this link was missing across ascomycetes, the distribution and abundance of GSTFs among ascomycete genomes could be associated with their lifestyles to some extent. Sequence comparison, gene structure, and phylogenetic analyses indicated divergence among nonplant GSTFs, suggesting polyphyletic origins during evolution. Furthermore, in silico prediction of functional partners suggested functional diversification among nonplant GSTFs.
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Affiliation(s)
- Jean-Pierre Munyampundu
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
| | - You-Ping Xu
- Center of Analysis and Measurement, Zhejiang University, Hangzhou, China
| | - Xin-Zhong Cai
- Institute of Biotechnology, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou, China
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26
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Tsaousis AD, Nyvltová E, Sutak R, Hrdy I, Tachezy J. A nonmitochondrial hydrogen production in Naegleria gruberi. Genome Biol Evol 2015; 6:792-9. [PMID: 24682152 PMCID: PMC4007538 DOI: 10.1093/gbe/evu065] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Naegleria gruberi is a free-living heterotrophic aerobic amoeba well known for its ability to transform from an amoeba to a flagellate form. The genome of N. gruberi has been recently published, and in silico predictions demonstrated that Naegleria has the capacity for both aerobic respiration and anaerobic biochemistry to produce molecular hydrogen in its mitochondria. This finding was considered to have fundamental implications on the evolution of mitochondrial metabolism and of the last eukaryotic common ancestor. However, no actual experimental data have been shown to support this hypothesis. For this reason, we have decided to investigate the anaerobic metabolism of the mitochondrion of N. gruberi. Using in vivo biochemical assays, we have demonstrated that N. gruberi has indeed a functional [FeFe]-hydrogenase, an enzyme that is attributed to anaerobic organisms. Surprisingly, in contrast to the published predictions, we have demonstrated that hydrogenase is localized exclusively in the cytosol, while no hydrogenase activity was associated with mitochondria of the organism. In addition, cytosolic localization displayed for HydE, a marker component of hydrogenase maturases. Naegleria gruberi, an obligate aerobic organism and one of the earliest eukaryotes, is producing hydrogen, a function that raises questions on the purpose of this pathway for the lifestyle of the organism and potentially on the evolution of eukaryotes.
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Affiliation(s)
- Anastasios D Tsaousis
- Department of Parasitology, Faculty of Science, Charles University in Prague, Czech Republic
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27
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De Jonckheere JF. What do we know by now about the genus Naegleria? Exp Parasitol 2014; 145 Suppl:S2-9. [DOI: 10.1016/j.exppara.2014.07.011] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2013] [Revised: 07/07/2014] [Accepted: 07/22/2014] [Indexed: 10/24/2022]
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da Silva MTA, Caldas VEA, Costa FC, Silvestre DAMM, Thiemann OH. Selenocysteine biosynthesis and insertion machinery in Naegleria gruberi. Mol Biochem Parasitol 2013; 188:87-90. [PMID: 23603359 DOI: 10.1016/j.molbiopara.2013.04.002] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2013] [Revised: 04/07/2013] [Accepted: 04/10/2013] [Indexed: 10/26/2022]
Abstract
Selenium (Se) is an essential trace element primarily found in selenoproteins as the 21st amino acid (selenocysteine, Sec, or U). Selenoproteins play an important role in growth and proliferation and are typically involved in cellular redox balance. Selenocysteine is encoded by an in-frame UGA codon specified by a stem-loop structure, the Sec insertion sequence element (SECIS), which, in eukaryotes, is located in the 3'-untranslated region (UTR). The availability of the Naegleria gruberi (ATCC 30224) genome sequence and the use of this organism as a model system for the pathogenic amoeba N. fowleri allowed us to investigate the Sec incorporation pathway in this primitive eukaryote. Using bioinformatics tools, we identified gene sequences encoding PSTK (O-phosphoseryl-tRNA(Sec) kinase), SepSecS (O-phosphoseryl-tRNA:selenocysteinyl-tRNA synthase), SelD/SPS2 (selenophosphate synthetase), EFSec (selenocysteine-specific elongation factor) and SBP (SECIS binding protein). These findings were confirmed by RT-PCR and by sequencing. A potential tRNA(Ser)Sec (SelC) gene and a putative selenoprotein with sequence similarity to a mitochondrial thioredoxin reductase (TR3) were also identified. Our results show that the selenocysteine incorporation machinery is indeed present in N. gruberi. Interestingly, the SelD/SPS2 gene is 2214 bp in length and contains two distinct domains. The N-terminal region shows sequence similarity to predicted methyltransferase proteins, and the C-terminal region is homologous to prokaryotic SelD/SPS2. Our results suggest the possibility of novel selenoproteins.
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Affiliation(s)
- M T A da Silva
- Laboratory of Protein Crystallography and Structural Biology, IFSC-USP, Av. Trabalhador São Carlense 400, P.O. Box 369, CEP 13560-970 São Carlos, SP, Brazil
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Auger C, Appanna V, Castonguay Z, Han S, Appanna VD. A facile electrophoretic technique to monitor phosphoenolpyruvate-dependent kinases. Electrophoresis 2012; 33:1095-101. [PMID: 22539312 DOI: 10.1002/elps.201100517] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Phosphoenolpyruvate (PEP)-dependent kinases are central to numerous metabolic processes and mediate the production of adenosine triphosphate (ATP) by substrate-level phosphorylation (SLP). While pyruvate kinase (PK, EC: 2.7.1.40), the final enzyme of the glycolytic pathway is critical in the anaerobic synthesis of ATP from ADP, pyruvate phosphate dikinase (PPDK, EC: 2.7.9.1), and phosphoenolpyruvate synthase (PEPS, EC: 2.7.9.2) help generate ATP from AMP coupled to PEP as a substrate. Here we demonstrate an inexpensive and effective electrophoretic technology to determine the activities of these enzymes by blue-native polyacrylamide gel electrophoresis (BN-PAGE). The generation of pyruvate is linked to exogenous lactate dehydrogenase (LDH), and the oxidation of reduced nicotinamide adenine dinucleotide (NADH) coupled to 2,6-dichloroindophenol (DCIP) and iodonitrotetrazolium chloride (INT) results in a formazan precipitate which is easily quantifiable. The selectivity of the enzymes is ensured by including either AMP or ADP and pyrophosphate (PP(i) ) or inorganic phosphate (P(i) ). Activity bands were readily obtained after incubation in the respective reaction mixtures for 20-30 min. Cell-free extract concentrations as low as 20 μg protein equivalent yielded activity bands and substrate levels were manipulated to optimize sensitivity of this analytical technique. High-pressure liquid chromatography (HPLC), two-dimensional (2-D) SDS-PAGE (where SDS is sodium dodecyl sulfate), and immunoblot studies of the excised activity band help further characterize these PEP-dependent kinases. Furthermore, these enzymes were readily identified on the same gel by incubating it sequentially in the respective reaction mixtures. This technique provides a facile method to elucidate these kinases in biological systems.
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Affiliation(s)
- Christopher Auger
- Department of Chemistry and Biochemistry, Laurentian University, Sudbury, Ontario, Canada
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Müller M, Mentel M, van Hellemond JJ, Henze K, Woehle C, Gould SB, Yu RY, van der Giezen M, Tielens AGM, Martin WF. Biochemistry and evolution of anaerobic energy metabolism in eukaryotes. Microbiol Mol Biol Rev 2012; 76:444-95. [PMID: 22688819 PMCID: PMC3372258 DOI: 10.1128/mmbr.05024-11] [Citation(s) in RCA: 502] [Impact Index Per Article: 41.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Major insights into the phylogenetic distribution, biochemistry, and evolutionary significance of organelles involved in ATP synthesis (energy metabolism) in eukaryotes that thrive in anaerobic environments for all or part of their life cycles have accrued in recent years. All known eukaryotic groups possess an organelle of mitochondrial origin, mapping the origin of mitochondria to the eukaryotic common ancestor, and genome sequence data are rapidly accumulating for eukaryotes that possess anaerobic mitochondria, hydrogenosomes, or mitosomes. Here we review the available biochemical data on the enzymes and pathways that eukaryotes use in anaerobic energy metabolism and summarize the metabolic end products that they generate in their anaerobic habitats, focusing on the biochemical roles that their mitochondria play in anaerobic ATP synthesis. We present metabolic maps of compartmentalized energy metabolism for 16 well-studied species. There are currently no enzymes of core anaerobic energy metabolism that are specific to any of the six eukaryotic supergroup lineages; genes present in one supergroup are also found in at least one other supergroup. The gene distribution across lineages thus reflects the presence of anaerobic energy metabolism in the eukaryote common ancestor and differential loss during the specialization of some lineages to oxic niches, just as oxphos capabilities have been differentially lost in specialization to anoxic niches and the parasitic life-style. Some facultative anaerobes have retained both aerobic and anaerobic pathways. Diversified eukaryotic lineages have retained the same enzymes of anaerobic ATP synthesis, in line with geochemical data indicating low environmental oxygen levels while eukaryotes arose and diversified.
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Affiliation(s)
| | - Marek Mentel
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Jaap J. van Hellemond
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - Katrin Henze
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Christian Woehle
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Sven B. Gould
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Re-Young Yu
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
| | - Mark van der Giezen
- Biosciences, College of Life and Environmental Sciences, University of Exeter, Exeter, United Kingdom
| | - Aloysius G. M. Tielens
- Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Center, Rotterdam, Netherlands
| | - William F. Martin
- Institute of Molecular Evolution, University of Düsseldorf, Düsseldorf, Germany
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