1
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Ovciarikova J, Shikha S, Lacombe A, Courjol F, McCrone R, Hussain W, Maclean A, Lemgruber L, Martins-Duarte ES, Gissot M, Sheiner L. Two ancient membrane pores mediate mitochondrial-nucleus membrane contact sites. J Cell Biol 2024; 223:e202304075. [PMID: 38456969 PMCID: PMC10923651 DOI: 10.1083/jcb.202304075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2023] [Revised: 11/28/2023] [Accepted: 01/29/2024] [Indexed: 03/09/2024] Open
Abstract
Coordination between nucleus and mitochondria is essential for cell survival, and thus numerous communication routes have been established between these two organelles over eukaryotic cell evolution. One route for organelle communication is via membrane contact sites, functional appositions formed by molecular tethers. We describe a novel nuclear-mitochondrial membrane contact site in the protozoan Toxoplasma gondii. We have identified specific contacts occurring at the nuclear pore and demonstrated an interaction between components of the nuclear pore and the mitochondrial protein translocon, highlighting them as molecular tethers. Genetic disruption of the nuclear pore or the TOM translocon components, TgNup503 or TgTom40, respectively, result in contact site reduction, supporting their potential involvement in this tether. TgNup503 depletion further leads to specific mitochondrial morphology and functional defects, supporting a role for nuclear-mitochondrial contacts in mediating their communication. The discovery of a contact formed through interaction between two ancient mitochondrial and nuclear complexes sets the ground for better understanding of mitochondrial-nuclear crosstalk in eukaryotes.
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Affiliation(s)
- Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Shikha Shikha
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Alice Lacombe
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Flavie Courjol
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Rosalind McCrone
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Wasim Hussain
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Andrew Maclean
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Leandro Lemgruber
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
| | - Erica S. Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Mathieu Gissot
- CNRS, Inserm, CHU Lille, Institut Pasteur de Lille, U1019—UMR 9017—CIIL—Center for Infection and Immunity of Lille, University of Lille, Lille, France
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow, UK
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2
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Asady B, Sampels V, Romano JD, Levitskaya J, Lige B, Khare P, Le A, Coppens I. Function and regulation of a steroidogenic CYP450 enzyme in the mitochondrion of Toxoplasma gondii. PLoS Pathog 2023; 19:e1011566. [PMID: 37651449 PMCID: PMC10499268 DOI: 10.1371/journal.ppat.1011566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 09/13/2023] [Accepted: 07/19/2023] [Indexed: 09/02/2023] Open
Abstract
As an obligate intracellular parasite, Toxoplasma gondii must import essential nutrients from the host cell into the parasitophorous vacuole. We previously reported that the parasite scavenges cholesterol from host endocytic organelles for incorporation into membranes and storage as cholesteryl esters in lipid droplets. In this study, we have investigated whether Toxoplasma utilizes cholesterol as a precursor for the synthesis of metabolites, such as steroids. In mammalian cells, steroidogenesis occurs in mitochondria and involves membrane-bound type I cytochrome P450 oxidases that are activated through interaction with heme-binding proteins containing a cytochrome b5 domain, such as members of the membrane-associated progesterone receptor (MAPR) family. Our LC-MS targeted lipidomics detect selective classes of hormone steroids in Toxoplasma, with a predominance for anti-inflammatory hydroxypregnenolone species, deoxycorticosterone and dehydroepiandrosterone. The genome of Toxoplasma contains homologs encoding a single type I CYP450 enzyme (we named TgCYP450mt) and a single MAPR (we named TgMAPR). We showed that TgMAPR is a hemoprotein with conserved residues in a heme-binding cytochrome b5 domain. Both TgCYP450 and TgMAPR localize to the mitochondrion and show interactions in in situ proximity ligation assays. Genetic ablation of cyp450mt is not tolerated by Toxoplasma; we therefore engineered a conditional knockout strain and showed that iΔTgCYP450mt parasites exhibit growth impairment in cultured cells. Parasite strains deficient for mapr could be generated; however, ΔTgMAPR parasites suffer from poor global fitness, loss of plasma membrane integrity, aberrant mitochondrial cristae, and an abnormally long S-phase in their cell cycle. Compared to wild-type parasites, iΔTgCYP450mt and ΔTgMAPR lost virulence in mice and metabolomics studies reveal that both mutants have reduced levels of steroids. These observations point to a steroidogenic pathway operational in the mitochondrion of a protozoan that involves an evolutionary conserved TgCYP450mt enzyme and its binding partner TgMAPR.
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Affiliation(s)
- Beejan Asady
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Vera Sampels
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Julia D. Romano
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Jelena Levitskaya
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Bao Lige
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
| | - Pratik Khare
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
| | - Anne Le
- Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, Maryland, United States of America
- Department of Pathology and Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, Maryland, United States of America
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3
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Yang Y, Lin M, Chen X, Zhao X, Chen L, Zhao M, Yao C, Sheng K, Yang Y, Ma G, Du A. The first apicoplast tRNA thiouridylase plays a vital role in the growth of Toxoplasma gondii. Front Cell Infect Microbiol 2022; 12:947039. [PMID: 36046743 PMCID: PMC9420914 DOI: 10.3389/fcimb.2022.947039] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 07/18/2022] [Indexed: 01/27/2023] Open
Abstract
Toxoplasmosis caused by the protozoan Toxoplasma gondii is one of the most common parasitic diseases in humans and almost all warm-blooded animals. Lys, Glu, and Gln-specific tRNAs contain a super-modified 2-thiourea (s2U) derivatives at the position 34, which is essential for all living organisms by maintaining the structural stability and aminoacylation of tRNA, and the precision and efficiency of codon recognition during protein translation. However, the enzyme(s) involved in this modification in T. gondii remains elusive. In this report, three putative tRNA-specific 2-thiolation enzymes were identified, of which two were involved in the s2U34 modification of tRNALys, tRNAGlu, and tRNAGln. One was named TgMnmA, an apicoplast-located tRNA-specific 2-thiolation enzyme in T. gondii. Knockout of TgMnmA showed that this enzyme is important for the lytic cycle of tachyzoites. Loss of TgMnmA also led to abnormities in apicoplast biogenesis and severely disturbed apicoplast genomic transcription. Notably, mice survived from the infection with 10 TgMnmA-KO RH tachyzoites. These findings provide new insights into s2U34 tRNA modification in Apicomplexa, and suggest TgMnmA, the first apicoplast tRNA thiouridylase identified in all apicomplexans, as a potential drug target.
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Affiliation(s)
- Yimin Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Mi Lin
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Xueqiu Chen
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - XianFeng Zhao
- Animals & Plant Inspection and Quarantine Technology Center of Shenzhen Customs, Shenzhen, China
| | - Lulu Chen
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Mingxiu Zhao
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Chaoqun Yao
- Department of Biomedical Sciences and One Health Center for Zoonoses and Tropical Veterinary Medicine, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Kaiyin Sheng
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Yi Yang
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Guangxu Ma
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Aifang Du
- Institute of Preventive Veterinary Medicine and Zhejiang Provincial Key Laboratory of Preventive Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
- *Correspondence: Aifang Du,
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4
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Lunghi M, Kloehn J, Krishnan A, Varesio E, Vadas O, Soldati-Favre D. Pantothenate biosynthesis is critical for chronic infection by the neurotropic parasite Toxoplasma gondii. Nat Commun 2022; 13:345. [PMID: 35039477 PMCID: PMC8764084 DOI: 10.1038/s41467-022-27996-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 01/03/2022] [Indexed: 11/16/2022] Open
Abstract
Coenzyme A (CoA) is an essential molecule acting in metabolism, post-translational modification, and regulation of gene expression. While all organisms synthesize CoA, many, including humans, are unable to produce its precursor, pantothenate. Intriguingly, like most plants, fungi and bacteria, parasites of the coccidian subgroup of Apicomplexa, including the human pathogen Toxoplasma gondii, possess all the enzymes required for de novo synthesis of pantothenate. Here, the importance of CoA and pantothenate biosynthesis for the acute and chronic stages of T. gondii infection is dissected through genetic, biochemical and metabolomic approaches, revealing that CoA synthesis is essential for T. gondii tachyzoites, due to the parasite's inability to salvage CoA or intermediates of the pathway. In contrast, pantothenate synthesis is only partially active in T. gondii tachyzoites, making the parasite reliant on its uptake. However, pantothenate synthesis is crucial for the establishment of chronic infection, offering a promising target for intervention against the persistent stage of T. gondii.
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Affiliation(s)
- Matteo Lunghi
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Emmanuel Varesio
- Institute of Pharmaceutical Sciences of Western Switzerland (ISPSO), University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
- Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, 1211, Geneva, Switzerland
| | - Oscar Vadas
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
- Protein and peptide purification platform, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211, Geneva, Switzerland.
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5
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Usey MM, Huet D. Parasite powerhouse: A review of the Toxoplasma gondii mitochondrion. J Eukaryot Microbiol 2022; 69:e12906. [PMID: 35315174 PMCID: PMC9490983 DOI: 10.1111/jeu.12906] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Toxoplasma gondii is a member of the apicomplexan phylum, a group of single-celled eukaryotic parasites that cause significant human morbidity and mortality around the world. T. gondii harbors two organelles of endosymbiotic origin: a non-photosynthetic plastid, known as the apicoplast, and a single mitochondrion derived from the ancient engulfment of an α-proteobacterium. Due to excitement surrounding the novelty of the apicoplast, the T. gondii mitochondrion was, to a certain extent, overlooked for about two decades. However, recent work has illustrated that the mitochondrion is an essential hub of apicomplexan-specific biology. Development of novel techniques, such as cryo-electron microscopy, complexome profiling, and next-generation sequencing have led to a renaissance in mitochondrial studies. This review will cover what is currently known about key features of the T. gondii mitochondrion, ranging from its genome to protein import machinery and biochemical pathways. Particular focus will be given to mitochondrial features that diverge significantly from the mammalian host, along with discussion of this important organelle as a drug target.
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Affiliation(s)
- Madelaine M. Usey
- Department of Cellular BiologyUniversity of GeorgiaAthensGeorgiaUSA,Center for Tropical and Emerging Global DiseasesUniversity of GeorgiaAthensGeorgiaUSA
| | - Diego Huet
- Center for Tropical and Emerging Global DiseasesUniversity of GeorgiaAthensGeorgiaUSA,Department of Pharmaceutical and Biomedical SciencesUniversity of GeorgiaAthensGeorgiaUSA
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6
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Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
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Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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7
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Zhao YH, Zhou T, Wang JX, Li Y, Fang MF, Liu JN, Li ZH. Evolution and structural variations in chloroplast tRNAs in gymnosperms. BMC Genomics 2021; 22:750. [PMID: 34663228 PMCID: PMC8524817 DOI: 10.1186/s12864-021-08058-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2020] [Accepted: 10/06/2021] [Indexed: 11/22/2022] Open
Abstract
Background Chloroplast transfer RNAs (tRNAs) can participate in various vital processes. Gymnosperms have important ecological and economic value, and they are the dominant species in forest ecosystems in the Northern Hemisphere. However, the evolution and structural changes in chloroplast tRNAs in gymnosperms remain largely unclear. Results In this study, we determined the nucleotide evolution, phylogenetic relationships, and structural variations in 1779 chloroplast tRNAs in gymnosperms. The numbers and types of tRNA genes present in the chloroplast genomes of different gymnosperms did not differ greatly, where the average number of tRNAs was 33 and the frequencies of occurrence for various types of tRNAs were generally consistent. Nearly half of the anticodons were absent. Molecular sequence variation analysis identified the conserved secondary structures of tRNAs. About a quarter of the tRNA genes were found to contain precoded 3′ CCA tails. A few tRNAs have undergone novel structural changes that are closely related to their minimum free energy, and these structural changes affect the stability of the tRNAs. Phylogenetic analysis showed that tRNAs have evolved from multiple common ancestors. The transition rate was higher than the transversion rate in gymnosperm chloroplast tRNAs. More loss events than duplication events have occurred in gymnosperm chloroplast tRNAs during their evolutionary process. Conclusions These findings provide novel insights into the molecular evolution and biological characteristics of chloroplast tRNAs in gymnosperms. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-021-08058-3.
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Affiliation(s)
- Yu-He Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Tong Zhou
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jiu-Xia Wang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Yan Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Min-Feng Fang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China
| | - Jian-Ni Liu
- State Key Laboratory of Continental Dynamics, Department of Geology, Early Life Institute, Northwest University, Xi'an, 710069, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi'an, 710069, China.
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8
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Mallo N, Ovciarikova J, Martins-Duarte ES, Baehr SC, Biddau M, Wilde ML, Uboldi AD, Lemgruber L, Tonkin CJ, Wideman JG, Harding CR, Sheiner L. Depletion of a Toxoplasma porin leads to defects in mitochondrial morphology and contacts with the endoplasmic reticulum. J Cell Sci 2021; 134:272536. [PMID: 34523684 PMCID: PMC8572010 DOI: 10.1242/jcs.255299] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2020] [Accepted: 09/06/2021] [Indexed: 01/21/2023] Open
Abstract
The voltage-dependent anion channel (VDAC) is a ubiquitous channel in the outer membrane of the mitochondrion with multiple roles in protein, metabolite and small molecule transport. In mammalian cells, VDAC protein, as part of a larger complex including the inositol triphosphate receptor, has been shown to have a role in mediating contacts between the mitochondria and endoplasmic reticulum (ER). We identify VDAC of the pathogenic apicomplexan Toxoplasma gondii and demonstrate its importance for parasite growth. We show that VDAC is involved in protein import and metabolite transfer to mitochondria. Further, depletion of VDAC resulted in significant morphological changes in the mitochondrion and ER, suggesting a role in mediating contacts between these organelles in T. gondii. This article has an associated First Person interview with the first author of the paper. Summary: Depletion of the Toxoplasma voltage-dependent anion channel highlights the importance of endoplasmic reticulum–mitochondria membrane contact sites in maintaining organelle morphology.
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Affiliation(s)
- Natalia Mallo
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Erica S Martins-Duarte
- Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 486 31270-901, Brazil
| | - Stephan C Baehr
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Marco Biddau
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Mary-Louise Wilde
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3086, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Alessandro D Uboldi
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3086, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Leandro Lemgruber
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK.,Glasgow Imaging Facility, University of Glasgow, Glasgow G12 8TA, UK
| | - Christopher J Tonkin
- The Walter and Eliza Hall Institute of Medical Research, Melbourne, VIC 3086, Australia.,Department of Medical Biology, The University of Melbourne, Melbourne, VIC 3010, Australia
| | - Jeremy G Wideman
- Biodesign Center for Mechanisms of Evolution, School of Life Sciences, Arizona State University, Tempe, AZ 85287, USA
| | - Clare R Harding
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, Glasgow G12 8TA, UK
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9
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Kloehn J, Lunghi M, Varesio E, Dubois D, Soldati-Favre D. Untargeted Metabolomics Uncovers the Essential Lysine Transporter in Toxoplasma gondii. Metabolites 2021; 11:metabo11080476. [PMID: 34436417 PMCID: PMC8399914 DOI: 10.3390/metabo11080476] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 07/09/2021] [Accepted: 07/20/2021] [Indexed: 12/15/2022] Open
Abstract
Apicomplexan parasites are responsible for devastating diseases, including malaria, toxoplasmosis, and cryptosporidiosis. Current treatments are limited by emerging resistance to, as well as the high cost and toxicity of existing drugs. As obligate intracellular parasites, apicomplexans rely on the uptake of many essential metabolites from their host. Toxoplasma gondii, the causative agent of toxoplasmosis, is auxotrophic for several metabolites, including sugars (e.g., myo-inositol), amino acids (e.g., tyrosine), lipidic compounds and lipid precursors (cholesterol, choline), vitamins, cofactors (thiamine) and others. To date, only few apicomplexan metabolite transporters have been characterized and assigned a substrate. Here, we set out to investigate whether untargeted metabolomics can be used to identify the substrate of an uncharacterized transporter. Based on existing genome- and proteome-wide datasets, we have identified an essential plasma membrane transporter of the major facilitator superfamily in T. gondii-previously termed TgApiAT6-1. Using an inducible system based on RNA degradation, TgApiAT6-1 was depleted, and the mutant parasite's metabolome was compared to that of non-depleted parasites. The most significantly reduced metabolite in parasites depleted in TgApiAT6-1 was identified as the amino acid lysine, for which T. gondii is predicted to be auxotrophic. Using stable isotope-labeled amino acids, we confirmed that TgApiAT6-1 is required for efficient lysine uptake. Our findings highlight untargeted metabolomics as a powerful tool to identify the substrate of orphan transporters.
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Affiliation(s)
- Joachim Kloehn
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
- Correspondence: (J.K.); (D.S.-F.); Tel.: +41-22-379-57-16 (J.K.); +41-22-379-56-72 (D.S.-F.)
| | - Matteo Lunghi
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
| | - Emmanuel Varesio
- Institute of Pharmaceutical Sciences of Western Switzerland, School of Pharmaceutical Sciences, Mass Spectrometry Core Facility (MZ 2.0), University of Geneva, 1211 Geneva, Switzerland;
| | - David Dubois
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
| | - Dominique Soldati-Favre
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland; (M.L.); (D.D.)
- Correspondence: (J.K.); (D.S.-F.); Tel.: +41-22-379-57-16 (J.K.); +41-22-379-56-72 (D.S.-F.)
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10
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Cobbold SA, V Tutor M, Frasse P, McHugh E, Karnthaler M, Creek DJ, Odom John A, Tilley L, Ralph SA, McConville MJ. Non-canonical metabolic pathways in the malaria parasite detected by isotope-tracing metabolomics. Mol Syst Biol 2021; 17:e10023. [PMID: 33821563 PMCID: PMC8022201 DOI: 10.15252/msb.202010023] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 02/02/2021] [Accepted: 02/04/2021] [Indexed: 12/26/2022] Open
Abstract
The malaria parasite, Plasmodium falciparum, proliferates rapidly in human erythrocytes by actively scavenging multiple carbon sources and essential nutrients from its host cell. However, a global overview of the metabolic capacity of intraerythrocytic stages is missing. Using multiplex 13 C-labelling coupled with untargeted mass spectrometry and unsupervised isotopologue grouping, we have generated a draft metabolome of P. falciparum and its host erythrocyte consisting of 911 and 577 metabolites, respectively, corresponding to 41% of metabolites and over 70% of the metabolic reaction predicted from the parasite genome. An additional 89 metabolites and 92 reactions were identified that were not predicted from genomic reconstructions, with the largest group being associated with metabolite damage-repair systems. Validation of the draft metabolome revealed four previously uncharacterised enzymes which impact isoprenoid biosynthesis, lipid homeostasis and mitochondrial metabolism and are necessary for parasite development and proliferation. This study defines the metabolic fate of multiple carbon sources in P. falciparum, and highlights the activity of metabolite repair pathways in these rapidly growing parasite stages, opening new avenues for drug discovery.
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Affiliation(s)
- Simon A Cobbold
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Madel V Tutor
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Philip Frasse
- Department of MedicineWashington University School of MedicineSt. LouisMOUSA
| | - Emma McHugh
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Markus Karnthaler
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Darren J Creek
- Monash Institute of Pharmaceutical SciencesMonash UniversityParkvilleVic.Australia
| | - Audrey Odom John
- The Children’s Hospital of PhiladelphiaUniversity of PennsylvaniaPhiladelphiaPAUSA
| | - Leann Tilley
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
| | - Malcolm J McConville
- Department of Biochemistry and Molecular BiologyBio21 Institute of Molecular Science and BiotechnologyUniversity of MelbourneParkvilleVic.Australia
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11
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Krishnan A, Soldati-Favre D. Amino Acid Metabolism in Apicomplexan Parasites. Metabolites 2021; 11:61. [PMID: 33498308 PMCID: PMC7909243 DOI: 10.3390/metabo11020061] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/05/2021] [Accepted: 01/14/2021] [Indexed: 12/22/2022] Open
Abstract
Obligate intracellular pathogens have coevolved with their host, leading to clever strategies to access nutrients, to combat the host's immune response, and to establish a safe niche for intracellular replication. The host, on the other hand, has also developed ways to restrict the replication of invaders by limiting access to nutrients required for pathogen survival. In this review, we describe the recent advancements in both computational methods and high-throughput -omics techniques that have been used to study and interrogate metabolic functions in the context of intracellular parasitism. Specifically, we cover the current knowledge on the presence of amino acid biosynthesis and uptake within the Apicomplexa phylum, focusing on human-infecting pathogens: Toxoplasma gondii and Plasmodium falciparum. Given the complex multi-host lifecycle of these pathogens, we hypothesize that amino acids are made, rather than acquired, depending on the host niche. We summarize the stage specificities of enzymes revealed through transcriptomics data, the relevance of amino acids for parasite pathogenesis in vivo, and the role of their transporters. Targeting one or more of these pathways may lead to a deeper understanding of the specific contributions of biosynthesis versus acquisition of amino acids and to design better intervention strategies against the apicomplexan parasites.
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Affiliation(s)
- Aarti Krishnan
- Department of Microbiology and Molecular Medicine, University of Geneva, CMU, Rue Michel-Servet 1, 1211 Geneva, Switzerland;
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12
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Oberstaller J, Otto TD, Rayner JC, Adams JH. Essential Genes of the Parasitic Apicomplexa. Trends Parasitol 2021; 37:304-316. [PMID: 33419671 DOI: 10.1016/j.pt.2020.11.007] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/11/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
Genome-scale mutagenesis screens for genes essential for apicomplexan parasite survival have been completed in three species: Plasmodium falciparum, the major human malaria parasite, Plasmodium berghei, a model rodent malaria parasite, and the more distantly related Toxoplasma gondii, the causative agent of toxoplasmosis. These three species share 2606 single-copy orthologs, 1500 of which have essentiality data in all three screens. In this review, we explore the overlap between these datasets to define the core essential genes of the phylum Apicomplexa. We further discuss the implications of these groundbreaking studies for understanding apicomplexan parasite biology, and we identify promising areas of focus for developing new pan-apicomplexan parasite interventions.
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Affiliation(s)
- Jenna Oberstaller
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA
| | - Thomas D Otto
- Centre of Immunobiology, Institute of Infection, Immunity and Inflammation, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Julian C Rayner
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge Biomedical Campus, The Keith Peters Building, Hills Road, Cambridge, Cambridgeshire, CB2 0XY, UK
| | - John H Adams
- Center for Global Health and Infectious Diseases and USF Genomics Program, College of Public Health, University of South Florida, 3720 Spectrum Boulevard, Suite 404, Tampa, FL 33612, USA.
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13
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Shetty S, Varshney U. Regulation of translation by one-carbon metabolism in bacteria and eukaryotic organelles. J Biol Chem 2021; 296:100088. [PMID: 33199376 PMCID: PMC7949028 DOI: 10.1074/jbc.rev120.011985] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2020] [Revised: 11/15/2020] [Accepted: 11/16/2020] [Indexed: 12/20/2022] Open
Abstract
Protein synthesis is an energetically costly cellular activity. It is therefore important that the process of mRNA translation remains in excellent synchrony with cellular metabolism and its energy reserves. Unregulated translation could lead to the production of incomplete, mistranslated, or misfolded proteins, squandering the energy needed for cellular sustenance and causing cytotoxicity. One-carbon metabolism (OCM), an integral part of cellular intermediary metabolism, produces a number of one-carbon unit intermediates (formyl, methylene, methenyl, methyl). These OCM intermediates are required for the production of amino acids such as methionine and other biomolecules such as purines, thymidylate, and redox regulators. In this review, we discuss how OCM impacts the translation apparatus (composed of ribosome, tRNA, mRNA, and translation factors) and regulates crucial steps in protein synthesis. More specifically, we address how the OCM metabolites regulate the fidelity and rate of translation initiation in bacteria and eukaryotic organelles such as mitochondria. Modulation of the fidelity of translation initiation by OCM opens new avenues to understand alternative translation mechanisms involved in stress tolerance and drug resistance.
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Affiliation(s)
- Sunil Shetty
- Biozentrum, University of Basel, Basel, Switzerland
| | - Umesh Varshney
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore, India; Jawaharlal Nehru Centre for Advanced Scientific Studies, Jakkur, Bangalore, India.
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14
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Sah S, Shah RA, Govindan A, Varada R, Rex K, Varshney U. Utilisation of 10-formyldihydrofolate as substrate by dihydrofolate reductase (DHFR) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) tranformylase/IMP cyclohydrolase (PurH) in Escherichia coli. MICROBIOLOGY-SGM 2019; 164:982-991. [PMID: 29799386 DOI: 10.1099/mic.0.000671] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Dihydrofolate reductase (DHFR) and 5-aminoimidazole-4-carboxamide ribonucleotide (AICAR) transformylase/IMP cyclohydrolase (PurH) play key roles in maintaining folate pools in cells, and are targets of antimicrobial and anticancer drugs. While the activities of bacterial DHFR and PurH on their classical substrates (DHF and 10-CHO-THF, respectively) are known, their activities and kinetic properties of utilisation of 10-CHO-DHF are unknown. We have determined the kinetic properties (k cat/K m) of conversion of 10-CHO-DHF to 10-CHO-THF by DHFR, and to DHF by PurH. We show that DHFR utilises 10-CHO-DHF about one third as efficiently as it utilises DHF. The 10-CHO-DHF is also utilised (as a formyl group donor) by PurH albeit slightly less efficiently than 10-CHO-THF. The utilisation of 10-CHO-DHF by DHFR is ~50 fold more efficient than its utilisation by PurH. A folate deficient Escherichia coli (∆pabA) grows well when supplemented with adenine, glycine, thymine and methionine, the metabolites that arise from the one-carbon metabolic pathway. Notably, when the ∆pabA strain harboured a folate transporter, it grew in the presence of 10-CHO-DHF alone, suggesting that it (10-CHO-DHF) can enter one-carbon metabolic pathway to provide the required metabolites. Thus, our studies reveal that both DHFR and PurH could utilise 10-CHO-DHF for folate homeostasis in E. coli.
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Affiliation(s)
- Shivjee Sah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Riyaz Ahmad Shah
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Ashwin Govindan
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Rajagopal Varada
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Kervin Rex
- Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
| | - Umesh Varshney
- Jawaharlal Nehru Centre for Advanced Scientific Research, Bangalore 560064, India.,Department of Microbiology and Cell Biology, Indian Institute of Science, Bangalore 560012, India
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15
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Lacombe A, Maclean AE, Ovciarikova J, Tottey J, Mühleip A, Fernandes P, Sheiner L. Identification of the
Toxoplasma gondii
mitochondrial ribosome, and characterisation of a protein essential for mitochondrial translation. Mol Microbiol 2019; 112:1235-1252. [PMID: 31339607 PMCID: PMC6851545 DOI: 10.1111/mmi.14357] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2019] [Indexed: 01/20/2023]
Abstract
Apicomplexan parasites cause diseases such as malaria and toxoplasmosis. The apicomplexan mitochondrion shows striking differences from common model organisms, including fundamental processes such as mitochondrial translation. Despite evidence that mitochondrial translation is essential for parasite survival, it is largely understudied. Progress has been restricted by the absence of functional assays to detect apicomplexan mitochondrial translation, a lack of knowledge of proteins involved in the process and the inability to identify and detect mitoribosomes. We report the localization of 12 new mitochondrial proteins, including 6 putative mitoribosomal proteins. We demonstrate the integration of three mitoribosomal proteins in macromolecular complexes, and provide evidence suggesting these are apicomplexan mitoribosomal subunits, detected here for the first time. Finally, a new analytical pipeline detected defects in mitochondrial translation upon depletion of the small subunit protein 35 (TgmS35), while other mitochondrial functions remain unaffected. Our work lays a foundation for the study of apicomplexan mitochondrial translation.
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Affiliation(s)
- Alice Lacombe
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Andrew E. Maclean
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Jana Ovciarikova
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Julie Tottey
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
- UMR 1282 ISP INRA‐Université François Rabelais de Tours Nouzilly France
| | - Alexander Mühleip
- Department of Biochemistry and Biophysics Stockholm University Stockholm Sweden
| | - Paula Fernandes
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology University of Glasgow 120 University Place GlasgowG12 8TAUK
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16
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Hillebrand A, Matz JM, Almendinger M, Müller K, Matuschewski K, Schmitz-Linneweber C. Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite. Nucleic Acids Res 2019; 46:10417-10431. [PMID: 30102371 PMCID: PMC6212722 DOI: 10.1093/nar/gky710] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
Gene expression in mitochondria of Plasmodium falciparum is essential for parasite survival. The molecular mechanisms of Plasmodium organellar gene expression remain poorly understood. This includes the enigmatic assembly of the mitochondrial ribosome from highly fragmented rRNAs. Here, we present the identification of clustered organellar short RNA fragments (cosRNAs) that are possible footprints of RNA-binding proteins (RBPs) in Plasmodium organelles. In plants, RBPs of the pentatricopeptide repeat (PPR) class produce footprints as a consequence of their function in processing organellar RNAs. Intriguingly, many of the Plasmodium cosRNAs overlap with 5'-ends of rRNA fragments. We hypothesize that these are footprints of RBPs involved in assembling the rRNA fragments into a functioning ribosome. A bioinformatics search of the Plasmodium nuclear genome identified a hitherto unrecognized organellar helical-hairpin-repeat protein family that we term heptatricopeptide repeat (HPR) proteins. We demonstrate that selected HPR proteins are targeted to mitochondria in P. berghei and that one of them, PbHPR1, associates with RNA, but not DNA in vitro. A phylogenetic search identified HPR proteins in a wide variety of eukaryotes. We hypothesize that HPR proteins are required for processing and stabilizing RNAs in Apicomplexa and other taxa.
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Affiliation(s)
- Arne Hillebrand
- Humboldt University Berlin, Molecular Genetics, Berlin, Germany
| | - Joachim M Matz
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
| | | | - Katja Müller
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
| | - Kai Matuschewski
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
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17
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Abstract
Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Alternative splicing is a widespread, essential, and complex component of gene regulation. Apicomplexan parasites have long been recognized to produce alternatively spliced transcripts for some genes and can produce multiple protein products that are essential for parasite growth. Recent approaches are now providing more wide-ranging surveys of the extent of alternative splicing; some indicate that alternative splicing is less widespread than in other model eukaryotes, whereas others suggest levels comparable to those of previously studied groups. In many cases, apicomplexan alternative splicing events appear not to generate multiple alternative proteins but instead produce aberrant or noncoding transcripts. Nonetheless, appropriate regulation of alternative splicing is clearly essential in Plasmodium and Toxoplasma parasites, suggesting a biological role for at least some of the alternative splicing observed. Several studies have now disrupted conserved regulators of alternative splicing and demonstrated lethal effects in apicomplexans. This minireview discusses methods to accurately determine the extent of alternative splicing in Apicomplexa and discuss potential biological roles for this conserved process in a phylum of parasites with compact genomes.
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18
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Tosetti N, Dos Santos Pacheco N, Soldati-Favre D, Jacot D. Three F-actin assembly centers regulate organelle inheritance, cell-cell communication and motility in Toxoplasma gondii. eLife 2019; 8:e42669. [PMID: 30753127 PMCID: PMC6372287 DOI: 10.7554/elife.42669] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Accepted: 01/29/2019] [Indexed: 01/06/2023] Open
Abstract
Toxoplasma gondii possesses a limited set of actin-regulatory proteins and relies on only three formins (FRMs) to nucleate and polymerize actin. We combined filamentous actin (F-actin) chromobodies with gene disruption to assign specific populations of actin filaments to individual formins. FRM2 localizes to the apical juxtanuclear region and participates in apicoplast inheritance. Restricted to the residual body, FRM3 maintains the intravacuolar cell-cell communication. Conoidal FRM1 initiates a flux of F-actin crucial for motility, invasion and egress. This flux depends on myosins A and H and is controlled by phosphorylation via PKG (protein kinase G) and CDPK1 (calcium-dependent protein kinase 1) and by methylation via AKMT (apical lysine methyltransferase). This flux is independent of microneme secretion and persists in the absence of the glideosome-associated connector (GAC). This study offers a coherent model of the key players controlling actin polymerization, stressing the importance of well-timed post-translational modifications to power parasite motility.
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Affiliation(s)
- Nicolò Tosetti
- Department of Microbiology and Molecular Medicine, CMUUniversity of GenevaGenevaSwitzerland
| | | | | | - Damien Jacot
- Department of Microbiology and Molecular Medicine, CMUUniversity of GenevaGenevaSwitzerland
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19
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Nyamai DW, Tastan Bishop Ö. Aminoacyl tRNA synthetases as malarial drug targets: a comparative bioinformatics study. Malar J 2019; 18:34. [PMID: 30728021 PMCID: PMC6366043 DOI: 10.1186/s12936-019-2665-6] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2018] [Accepted: 01/27/2019] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Treatment of parasitic diseases has been challenging due to evolution of drug resistant parasites, and thus there is need to identify new class of drugs and drug targets. Protein translation is important for survival of malarial parasite, Plasmodium, and the pathway is present in all of its life cycle stages. Aminoacyl tRNA synthetases are primary enzymes in protein translation as they catalyse amino acid addition to the cognate tRNA. This study sought to understand differences between Plasmodium and human aminoacyl tRNA synthetases through bioinformatics analysis. METHODS Plasmodium berghei, Plasmodium falciparum, Plasmodium fragile, Plasmodium knowlesi, Plasmodium malariae, Plasmodium ovale, Plasmodium vivax, Plasmodium yoelii and human aminoacyl tRNA synthetase sequences were retrieved from UniProt database and grouped into 20 families based on amino acid specificity. These families were further divided into two classes. Both families and classes were analysed. Motif discovery was carried out using the MEME software, sequence identity calculation was done using an in-house Python script, multiple sequence alignments were performed using PROMALS3D and TCOFFEE tools, and phylogenetic tree calculations were performed using MEGA vs 7.0 tool. Possible alternative binding sites were predicted using FTMap webserver and SiteMap tool. RESULTS Motif discovery revealed Plasmodium-specific motifs while phylogenetic tree calculations showed that Plasmodium proteins have different evolutionary history to the human homologues. Human aaRSs sequences showed low sequence identity (below 40%) compared to Plasmodium sequences. Prediction of alternative binding sites revealed potential druggable sites in PfArgRS, PfMetRS and PfProRS at regions that are weakly conserved when compared to the human homologues. Multiple sequence analysis, motif discovery, pairwise sequence identity calculations and phylogenetic tree analysis showed significant differences between parasite and human aaRSs proteins despite functional and structural conservation. These differences may provide a basis for further exploration of Plasmodium aminoacyl tRNA synthetases as potential drug targets. CONCLUSION This study showed that, despite, functional and structural conservation, Plasmodium aaRSs have key differences from the human homologues. These differences in Plasmodium aaRSs can be targeted to develop anti-malarial drugs with less toxicity to the host.
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Affiliation(s)
- Dorothy Wavinya Nyamai
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (RUBi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown, 6140, South Africa.
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20
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Huet D, Rajendran E, van Dooren GG, Lourido S. Identification of cryptic subunits from an apicomplexan ATP synthase. eLife 2018; 7:e38097. [PMID: 30204085 PMCID: PMC6133553 DOI: 10.7554/elife.38097] [Citation(s) in RCA: 34] [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: 05/04/2018] [Accepted: 08/17/2018] [Indexed: 01/22/2023] Open
Abstract
The mitochondrial ATP synthase is a macromolecular motor that uses the proton gradient to generate ATP. Proper ATP synthase function requires a stator linking the catalytic and rotary portions of the complex. However, sequence-based searches fail to identify genes encoding stator subunits in apicomplexan parasites like Toxoplasma gondii or the related organisms that cause malaria. Here, we identify 11 previously unknown subunits from the Toxoplasma ATP synthase, which lack homologs outside the phylum. Modeling suggests that two of them, ICAP2 and ICAP18, are distantly related to mammalian stator subunits. Our analysis shows that both proteins form part of the ATP synthase complex. Depletion of ICAP2 leads to aberrant mitochondrial morphology, decreased oxygen consumption, and disassembly of the complex, consistent with its role as an essential component of the Toxoplasma ATP synthase. Our findings highlight divergent features of the central metabolic machinery in apicomplexans, which may reveal new therapeutic opportunities.
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Affiliation(s)
- Diego Huet
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
| | - Esther Rajendran
- Research School of BiologyAustralian National UniversityCanberraAustralia
| | - Giel G van Dooren
- Research School of BiologyAustralian National UniversityCanberraAustralia
| | - Sebastian Lourido
- Whitehead Institute for Biomedical ResearchCambridgeUnited States
- Department of BiologyMassachusetts Institute of TechnologyCambridgeMassachusetts, United States
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21
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Mallo N, Fellows J, Johnson C, Sheiner L. Protein Import into the Endosymbiotic Organelles of Apicomplexan Parasites. Genes (Basel) 2018; 9:E412. [PMID: 30110980 PMCID: PMC6115763 DOI: 10.3390/genes9080412] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2018] [Revised: 07/31/2018] [Accepted: 08/07/2018] [Indexed: 01/26/2023] Open
Abstract
: The organelles of endosymbiotic origin, plastids, and mitochondria, evolved through the serial acquisition of endosymbionts by a host cell. These events were accompanied by gene transfer from the symbionts to the host, resulting in most of the organellar proteins being encoded in the cell nuclear genome and trafficked into the organelle via a series of translocation complexes. Much of what is known about organelle protein translocation mechanisms is based on studies performed in common model organisms; e.g., yeast and humans or Arabidopsis. However, studies performed in divergent organisms are gradually accumulating. These studies provide insights into universally conserved traits, while discovering traits that are specific to organisms or clades. Apicomplexan parasites feature two organelles of endosymbiotic origin: a secondary plastid named the apicoplast and a mitochondrion. In the context of the diseases caused by apicomplexan parasites, the essential roles and divergent features of both organelles make them prime targets for drug discovery. This potential and the amenability of the apicomplexan Toxoplasma gondii to genetic manipulation motivated research about the mechanisms controlling both organelles' biogenesis. Here we provide an overview of what is known about apicomplexan organelle protein import. We focus on work done mainly in T. gondii and provide a comparison to model organisms.
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Affiliation(s)
- Natalia Mallo
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place Glasgow, Glasgow G12 8QQ, UK.
| | - Justin Fellows
- Genetics and Biochemistry Branch, National Institute for Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, MD 20892, USA.
| | - Carla Johnson
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place Glasgow, Glasgow G12 8QQ, UK.
| | - Lilach Sheiner
- Wellcome Centre for Molecular Parasitology, University of Glasgow, 120 University Place Glasgow, Glasgow G12 8QQ, UK.
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22
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Verechshagina NA, Konstantinov YM, Kamenski PA, Mazunin IO. Import of Proteins and Nucleic Acids into Mitochondria. BIOCHEMISTRY (MOSCOW) 2018; 83:643-661. [DOI: 10.1134/s0006297918060032] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Rono MK, Nyonda MA, Simam JJ, Ngoi JM, Mok S, Kortok MM, Abdullah AS, Elfaki MM, Waitumbi JN, El-Hassan IM, Marsh K, Bozdech Z, Mackinnon MJ. Adaptation of Plasmodium falciparum to its transmission environment. Nat Ecol Evol 2017; 2:377-387. [PMID: 29255304 DOI: 10.1038/s41559-017-0419-9] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 11/20/2017] [Indexed: 12/19/2022]
Abstract
Success in eliminating malaria will depend on whether parasite evolution outpaces control efforts. Here, we show that Plasmodium falciparum parasites (the deadliest of the species causing human malaria) found in low-transmission-intensity areas have evolved to invest more in transmission to new hosts (reproduction) and less in within-host replication (growth) than parasites found in high-transmission areas. At the cellular level, this adaptation manifests as increased production of reproductive forms (gametocytes) early in the infection at the expense of processes associated with multiplication inside red blood cells, especially membrane transport and protein trafficking. At the molecular level, this manifests as changes in the expression levels of genes encoding epigenetic and translational machinery. Specifically, expression levels of the gene encoding AP2-G-the transcription factor that initiates reproduction-increase as transmission intensity decreases. This is accompanied by downregulation and upregulation of genes encoding HDAC1 and HDA1-two histone deacetylases that epigenetically regulate the parasite's replicative and reproductive life-stage programmes, respectively. Parasites in reproductive mode show increased reliance on the prokaryotic translation machinery found inside the plastid-derived organelles. Thus, our dissection of the parasite's adaptive regulatory architecture has identified new potential molecular targets for malaria control.
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Affiliation(s)
- Martin K Rono
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Pwani University Bioscience Research Centre, Pwani University, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Mary A Nyonda
- Department of Microbiology and Molecular Medicine, Medical Faculty, University of Geneva, Geneva, Switzerland
| | | | - Joyce M Ngoi
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | - Sachel Mok
- Columbia University Medical Center, New York, NY, USA
| | - Moses M Kortok
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya
| | | | - Mohammed M Elfaki
- Department of Microbiology and Parasitology, Faculty of Medicine, Jazan University, Gizan, Jazan, Saudi Arabia
| | - John N Waitumbi
- Walter Reed Army Institute of Research/Kenya Medical Research Institute, Kisumu, Kenya
| | - Ibrahim M El-Hassan
- Faculty of Public Health and Tropical Medicine, Jazan University, Gizan, Jazan, Saudi Arabia
| | - Kevin Marsh
- Kenya Medical Research Institute-Wellcome Trust Research Programme, Kilifi, Kenya.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
| | - Zbynek Bozdech
- School of Biological Sciences, Nanyang Technological University, Singapore
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+Targeting Mitochondrial Functions as Antimalarial Regime, What Is Next? CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0075-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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25
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Habib S, Vaishya S, Gupta K. Translation in Organelles of Apicomplexan Parasites. Trends Parasitol 2016; 32:939-952. [DOI: 10.1016/j.pt.2016.07.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2016] [Revised: 07/19/2016] [Accepted: 07/25/2016] [Indexed: 01/27/2023]
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26
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Targeting Protein Translation in Organelles of the Apicomplexa. Trends Parasitol 2016; 32:953-965. [DOI: 10.1016/j.pt.2016.09.011] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2016] [Revised: 09/21/2016] [Accepted: 09/23/2016] [Indexed: 12/15/2022]
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27
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Pasaje CFA, Cheung V, Kennedy K, Lim EE, Baell JB, Griffin MDW, Ralph SA. Selective inhibition of apicoplast tryptophanyl-tRNA synthetase causes delayed death in Plasmodium falciparum. Sci Rep 2016; 6:27531. [PMID: 27277538 PMCID: PMC4899734 DOI: 10.1038/srep27531] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2016] [Accepted: 05/19/2016] [Indexed: 11/11/2022] Open
Abstract
The malaria parasite Plasmodium falciparum relies on efficient protein translation. An essential component of translation is the tryptophanyl-tRNA synthetase (TrpRS) that charges tRNAtrp. Here we characterise two isoforms of TrpRS in Plasmodium; one eukaryotic type localises to the cytosol and a bacterial type localises to the remnant plastid (apicoplast). We show that the apicoplast TrpRS aminoacylates bacterial tRNAtrp while the cytosolic TrpRS charges eukaryotic tRNAtrp. An inhibitor of bacterial TrpRSs, indolmycin, specifically inhibits aminoacylation by the apicoplast TrpRS in vitro, and inhibits ex vivo Plasmodium parasite growth, killing parasites with a delayed death effect characteristic of apicoplast inhibitors. Indolmycin treatment ablates apicoplast inheritance and is rescuable by addition of the apicoplast metabolite isopentenyl pyrophosphate (IPP). These data establish that inhibition of an apicoplast housekeeping enzyme leads to loss of the apicoplast and this is sufficient for delayed death. Apicoplast TrpRS is essential for protein translation and is a promising, specific antimalarial target.
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Affiliation(s)
- Charisse Flerida A Pasaje
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Vanessa Cheung
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Kit Kennedy
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Erin E Lim
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Jonathan B Baell
- Medicinal Chemistry, Monash Institute of Pharmaceutical Sciences, Monash University, 399 Royal Parade, Parkville, 3052 Victoria, Australia
| | - Michael D W Griffin
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
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Khan S. Recent advances in the biology and drug targeting of malaria parasite aminoacyl-tRNA synthetases. Malar J 2016; 15:203. [PMID: 27068331 PMCID: PMC4828885 DOI: 10.1186/s12936-016-1247-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 03/30/2016] [Indexed: 11/22/2022] Open
Abstract
Escalating drug resistance in malaria parasites and lack of vaccine entails the discovery of novel drug targets and inhibitor molecules. The multi-component protein translation machinery is a rich source of such drug targets. Malaria parasites contain three translational compartments: the cytoplasm, apicoplast and mitochondrion, of which the latter two are of the prokaryotic type. Recent explorations by many groups into the malaria parasite protein translation enzymes, aminoacyl-tRNA synthetases (aaRSs), have yielded many promising inhibitors. The understanding of the biology of this unique set of 36 enzymes has become much clearer in recent times. Current review discusses the advances made in understanding of crucial aaRSs from Plasmodium and also the specific inhibitors found against malaria aaRSs.
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Affiliation(s)
- Sameena Khan
- Drug Discovery Research Centre, Translational Health Science and Technology Institute (THSTI), NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurgaon Expressway, PO box #04, Faridabad, 121001, India.
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29
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Vaishya S, Kumar V, Gupta A, Siddiqi MI, Habib S. Polypeptide release factors and stop codon recognition in the apicoplast and mitochondrion of Plasmodium falciparum. Mol Microbiol 2016; 100:1080-95. [PMID: 26946524 DOI: 10.1111/mmi.13369] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/02/2016] [Indexed: 11/30/2022]
Abstract
Correct termination of protein synthesis would be a critical step in translation of organellar open reading frames (ORFs) of the apicoplast and mitochondrion of the malaria parasite. We identify release factors (RFs) responsible for recognition of the UAA and UGA stop-codons of apicoplast ORFs and the sole UAA stop-codon that terminates translation from the three mitochondrial ORFs. A single nuclear-encoded canonical RF2, PfRF2Api , localizes to the apicoplast. It has a conserved tripeptide motif (SPF) for stop-codon recognition and is sufficient for peptidyl-tRNA hydrolysis (PTH) from both UAA and UGA. Two RF family proteins are targeted to the parasite mitochondrion; a canonical RF1, PfRF1Mit , with a variant codon-recognition motif (PxN instead of the conserved RF1 PxT) is the major peptidyl-hydrolase with specific recognition of the UAA codon relevant to mitochondrial ORFs. Mutation of the N residue of the PfRF1Mit PxN motif and two other conserved residues of the codon recognition domain lowers PTH activity from pre-termination ribosomes indicating their role in codon-recognition. The second RF imported by the mitochondrion is the non-canonical PfICT1 that functions as a dimer and mediates codon nonspecific peptide release. Our results help delineate a critical step in organellar translation in Plasmodium, which is an important target for anti-malarials.
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Affiliation(s)
- Suniti Vaishya
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Vikash Kumar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ankit Gupta
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Imran Siddiqi
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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30
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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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31
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Mailu BM, Li L, Arthur J, Nelson TM, Ramasamy G, Fritz-Wolf K, Becker K, Gardner MJ. Plasmodium Apicoplast Gln-tRNAGln Biosynthesis Utilizes a Unique GatAB Amidotransferase Essential for Erythrocytic Stage Parasites. J Biol Chem 2015; 290:29629-41. [PMID: 26318454 DOI: 10.1074/jbc.m115.655100] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Indexed: 01/25/2023] Open
Abstract
The malaria parasite Plasmodium falciparum apicoplast indirect aminoacylation pathway utilizes a non-discriminating glutamyl-tRNA synthetase to synthesize Glu-tRNA(Gln) and a glutaminyl-tRNA amidotransferase to convert Glu-tRNA(Gln) to Gln-tRNA(Gln). Here, we show that Plasmodium falciparum and other apicomplexans possess a unique heterodimeric glutamyl-tRNA amidotransferase consisting of GatA and GatB subunits (GatAB). We localized the P. falciparum GatA and GatB subunits to the apicoplast in blood stage parasites and demonstrated that recombinant GatAB converts Glu-tRNA(Gln) to Gln-tRNA(Gln) in vitro. We demonstrate that the apicoplast GatAB-catalyzed reaction is essential to the parasite blood stages because we could not delete the Plasmodium berghei gene encoding GatA in blood stage parasites in vivo. A phylogenetic analysis placed the split between Plasmodium GatB, archaeal GatE, and bacterial GatB prior to the phylogenetic divide between bacteria and archaea. Moreover, Plasmodium GatA also appears to have emerged prior to the bacterial-archaeal phylogenetic divide. Thus, although GatAB is found in Plasmodium, it emerged prior to the phylogenetic separation of archaea and bacteria.
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Affiliation(s)
- Boniface M Mailu
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Ling Li
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Jen Arthur
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Todd M Nelson
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Gowthaman Ramasamy
- From the Center for Infectious Disease Research, Seattle, Washington 98109
| | - Karin Fritz-Wolf
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and the Max-Planck Institute for Medical Research, Jahnstrasse 29, D-69120 Heidelberg, Germany
| | - Katja Becker
- the Department of Biochemistry and Molecular Biology, Interdisciplinary Research Center, Justus Liebig University, Giessen 35392 Germany, and
| | - Malcolm J Gardner
- From the Center for Infectious Disease Research, Seattle, Washington 98109, the Department of Global Health, University of Washington, Seattle, Washington 98195,
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32
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Gile GH, Moog D, Slamovits CH, Maier UG, Archibald JM. Dual Organellar Targeting of Aminoacyl-tRNA Synthetases in Diatoms and Cryptophytes. Genome Biol Evol 2015; 7:1728-42. [PMID: 25994931 PMCID: PMC4494062 DOI: 10.1093/gbe/evv095] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
The internal compartmentation of eukaryotic cells not only allows separation of biochemical processes but it also creates the requirement for systems that can selectively transport proteins across the membrane boundaries. Although most proteins function in a single subcellular compartment, many are able to enter two or more compartments, a phenomenon known as dual or multiple targeting. The aminoacyl-tRNA synthetases (aaRSs), which catalyze the ligation of tRNAs to their cognate amino acids, are particularly prone to functioning in multiple subcellular compartments. They are essential for translation, so they are required in every compartment where translation takes place. In diatoms, there are three such compartments, the plastid, the mitochondrion, and the cytosol. In cryptophytes, translation also takes place in the periplastid compartment (PPC), which is the reduced cytoplasm of the plastid’s red algal ancestor and which retains a reduced red algal nucleus. We searched the organelle and nuclear genomes of the cryptophyte Guillardia theta and the diatoms Phaeodactylum tricornutum and Thalassiosira pseudonana for aaRS genes and found an insufficient number of genes to provide each compartment with a complete set of aaRSs. We therefore inferred, with support from localization predictions, that many aaRSs are dual targeted. We tested four of the predicted dual targeted aaRSs with green fluorescent protein fusion localizations in P. tricornutum and found evidence for dual targeting to the mitochondrion and plastid in P. tricornutum and G. theta, and indications for dual targeting to the PPC and cytosol in G. theta. This is the first report of dual targeting in diatoms or cryptophytes.
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Affiliation(s)
- Gillian H Gile
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Daniel Moog
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Present address: Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
| | - Uwe-G Maier
- LOEWE Centre for Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, Germany Laboratory for Cell Biology, Philipps University Marburg, Germany
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada Program in Integrated Microbial Biodiversity, Canadian Institute for Advanced Research, Toronto, Ontario, Canada
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33
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Yeoh LM, Goodman CD, Hall NE, van Dooren GG, McFadden GI, Ralph SA. A serine-arginine-rich (SR) splicing factor modulates alternative splicing of over a thousand genes in Toxoplasma gondii. Nucleic Acids Res 2015; 43:4661-75. [PMID: 25870410 PMCID: PMC4482073 DOI: 10.1093/nar/gkv311] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2014] [Accepted: 03/27/2015] [Indexed: 11/12/2022] Open
Abstract
Single genes are often subject to alternative splicing, which generates alternative mature mRNAs. This phenomenon is widespread in animals, and observed in over 90% of human genes. Recent data suggest it may also be common in Apicomplexa. These parasites have small genomes, and economy of DNA is evolutionarily favoured in this phylum. We investigated the mechanism of alternative splicing in Toxoplasma gondii, and have identified and localized TgSR3, a homologue of ASF/SF2 (alternative-splicing factor/splicing factor 2, a serine-arginine–rich, or SR protein) to a subnuclear compartment. In addition, we conditionally overexpressed this protein, which was deleterious to growth. qRT-PCR was used to confirm perturbation of splicing in a known alternatively-spliced gene. We performed high-throughput RNA-seq to determine the extent of splicing modulated by this protein. Current RNA-seq algorithms are poorly suited to compact parasite genomes, and hence we complemented existing tools by writing a new program, GeneGuillotine, that addresses this deficiency by segregating overlapping reads into distinct genes. In order to identify the extent of alternative splicing, we released another program, JunctionJuror, that detects changes in intron junctions. Using this program, we identified about 2000 genes that were constitutively alternatively spliced in T. gondii. Overexpressing the splice regulator TgSR3 perturbed alternative splicing in over 1000 genes.
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Affiliation(s)
- Lee M Yeoh
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Christopher D Goodman
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Nathan E Hall
- Department of Genetics, La Trobe Institute for Molecular Science, La Trobe University, Bundoora, Victoria 3086, Australia Life Sciences Computation Centre, Victorian Life Sciences Computation Initiative, Carlton, Victoria 3010, Australia
| | - Giel G van Dooren
- Research School of Biology, The Australian National University, Acton, ACT 2601, Australia
| | - Geoffrey I McFadden
- School of BioSciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, Victoria 3010, Australia
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34
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Haider A, Allen SM, Jackson KE, Ralph SA, Habib S. Targeting and function of proteins mediating translation initiation in organelles of Plasmodium falciparum. Mol Microbiol 2015; 96:796-814. [PMID: 25689481 DOI: 10.1111/mmi.12972] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/14/2015] [Indexed: 01/13/2023]
Abstract
The malaria parasite Plasmodium falciparum has two translationally active organelles - the apicoplast and mitochondrion, which import nuclear-encoded translation factors to mediate protein synthesis. Initiation of translation is a complex step wherein initiation factors (IFs) act in a regulated manner to form an initiation complex. We identified putative organellar IFs and investigated the targeting, structure and function of IF1, IF2 and IF3 homologues encoded by the parasite nuclear genome. A single PfIF1 is targeted to the apicoplast. Apart from its critical ribosomal interactions, PfIF1 also exhibited nucleic-acid binding and melting activities and mediated transcription anti-termination. This suggests a prominent ancillary function for PfIF1 in destabilisation of DNA and RNA hairpin loops encountered during transcription and translation of the A+T rich apicoplast genome. Of the three putative IF2 homologues, only one (PfIF2a) was an organellar protein with mitochondrial localisation. We additionally identified an IF3 (PfIF3a) that localised exclusively to the mitochondrion and another protein, PfIF3b, that was apicoplast targeted. PfIF3a exhibited ribosome anti-association activity, and monosome splitting by PfIF3a was enhanced by ribosome recycling factor (PfRRF2) and PfEF-G(Mit). These results fill a gap in our understanding of organellar translation in Plasmodium, which is the site of action of several anti-malarial compounds.
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Affiliation(s)
- Afreen Haider
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Stacey M Allen
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Katherine E Jackson
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Stuart A Ralph
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Melbourne, Vic., 3010, Australia
| | - Saman Habib
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
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35
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Factors mediating plastid dependency and the origins of parasitism in apicomplexans and their close relatives. Proc Natl Acad Sci U S A 2015; 112:10200-7. [PMID: 25717057 DOI: 10.1073/pnas.1423790112] [Citation(s) in RCA: 136] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Apicomplexans are a major lineage of parasites, including causative agents of malaria and toxoplasmosis. How such highly adapted parasites evolved from free-living ancestors is poorly understood, particularly because they contain nonphotosynthetic plastids with which they have a complex metabolic dependency. Here, we examine the origin of apicomplexan parasitism by resolving the evolutionary distribution of several key characteristics in their closest free-living relatives, photosynthetic chromerids and predatory colpodellids. Using environmental sequence data, we describe the diversity of these apicomplexan-related lineages and select five species that represent this diversity for transcriptome sequencing. Phylogenomic analysis recovered a monophyletic lineage of chromerids and colpodellids as the sister group to apicomplexans, and a complex distribution of retention versus loss for photosynthesis, plastid genomes, and plastid organelles. Reconstructing the evolution of all plastid and cytosolic metabolic pathways related to apicomplexan plastid function revealed an ancient dependency on plastid isoprenoid biosynthesis, predating the divergence of apicomplexan and dinoflagellates. Similarly, plastid genome retention is strongly linked to the retention of two genes in the plastid genome, sufB and clpC, altogether suggesting a relatively simple model for plastid retention and loss. Lastly, we examine the broader distribution of a suite of molecular characteristics previously linked to the origins of apicomplexan parasitism and find that virtually all are present in their free-living relatives. The emergence of parasitism may not be driven by acquisition of novel components, but rather by loss and modification of the existing, conserved traits.
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Inhibition of protein synthesis and malaria parasite development by drug targeting of methionyl-tRNA synthetases. Antimicrob Agents Chemother 2015; 59:1856-67. [PMID: 25583729 DOI: 10.1128/aac.02220-13] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Aminoacyl-tRNA synthetases (aaRSs) are housekeeping enzymes that couple cognate tRNAs with amino acids to transmit genomic information for protein translation. The Plasmodium falciparum nuclear genome encodes two P. falciparum methionyl-tRNA synthetases (PfMRS), termed PfMRS(cyt) and PfMRS(api). Phylogenetic analyses revealed that the two proteins are of primitive origin and are related to heterokonts (PfMRS(cyt)) or proteobacteria/primitive bacteria (PfMRS(api)). We show that PfMRS(cyt) localizes in parasite cytoplasm, while PfMRS(api) localizes to apicoplasts in asexual stages of malaria parasites. Two known bacterial MRS inhibitors, REP3123 and REP8839, hampered Plasmodium growth very effectively in the early and late stages of parasite development. Small-molecule drug-like libraries were screened against modeled PfMRS structures, and several "hit" compounds showed significant effects on parasite growth. We then tested the effects of the hit compounds on protein translation by labeling nascent proteins with (35)S-labeled cysteine and methionine. Three of the tested compounds reduced protein synthesis and also blocked parasite growth progression from the ring stage to the trophozoite stage. Drug docking studies suggested distinct modes of binding for the three compounds, compared with the enzyme product methionyl adenylate. Therefore, this study provides new targets (PfMRSs) and hit compounds that can be explored for development as antimalarial drugs.
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37
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One-carbon metabolic pathway rewiring in Escherichia coli reveals an evolutionary advantage of 10-formyltetrahydrofolate synthetase (Fhs) in survival under hypoxia. J Bacteriol 2014; 197:717-26. [PMID: 25448816 DOI: 10.1128/jb.02365-14] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
In cells, N(10)-formyltetrahydrofolate (N(10)-fTHF) is required for formylation of eubacterial/organellar initiator tRNA and purine nucleotide biosynthesis. Biosynthesis of N(10)-fTHF is catalyzed by 5,10-methylene-tetrahydrofolate dehydrogenase/cyclohydrolase (FolD) and/or 10-formyltetrahydrofolate synthetase (Fhs). All eubacteria possess FolD, but some possess both FolD and Fhs. However, the reasons for possessing Fhs in addition to FolD have remained unclear. We used Escherichia coli, which naturally lacks fhs, as our model. We show that in E. coli, the essential function of folD could be replaced by Clostridium perfringens fhs when it was provided on a medium-copy-number plasmid or integrated as a single-copy gene in the chromosome. The fhs-supported folD deletion (ΔfolD) strains grow well in a complex medium. However, these strains require purines and glycine as supplements for growth in M9 minimal medium. The in vivo levels of N(10)-fTHF in the ΔfolD strain (supported by plasmid-borne fhs) were limiting despite the high capacity of the available Fhs to synthesize N(10)-fTHF in vitro. Auxotrophy for purines could be alleviated by supplementing formate to the medium, and that for glycine was alleviated by engineering THF import into the cells. The ΔfolD strain (harboring fhs on the chromosome) showed a high NADP(+)-to-NADPH ratio and hypersensitivity to trimethoprim. The presence of fhs in E. coli was disadvantageous for its aerobic growth. However, under hypoxia, E. coli strains harboring fhs outcompeted those lacking it. The computational analysis revealed a predominant natural occurrence of fhs in anaerobic and facultative anaerobic bacteria.
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A dual-targeted aminoacyl-tRNA synthetase in Plasmodium falciparum charges cytosolic and apicoplast tRNACys. Biochem J 2014; 458:513-23. [PMID: 24428730 DOI: 10.1042/bj20131451] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Plasmodium parasites possess two endosymbiotic organelles: a mitochondrion and a relict plastid called the apicoplast. To accommodate the translational requirements of these organelles in addition to its cytosolic translation apparatus, the parasite must maintain a supply of charged tRNA molecules in each of these compartments. In the present study we investigate how the parasite manages these translational requirements for charged tRNACys with only a single gene for CysRS (cysteinyl-tRNA synthetase). We demonstrate that the single PfCysRS (Plasmodium falciparum CysRS) transcript is alternatively spliced, and, using a combination of endogenous and heterologous tagging experiments in both P. falciparum and Toxoplasma gondii, we show that CysRS isoforms traffic to the cytosol and apicoplast. PfCysRS can recognize and charge the eukaryotic tRNACys encoded by the Plasmodium nucleus as well as the bacterial-type tRNA encoded by the apicoplast genome, albeit with a preference for the eukaryotic type cytosolic tRNA. The results of the present study indicate that apicomplexan parasites have lost their original plastidic cysteinyl-tRNA synthetase, and have replaced it with a dual-targeted eukaryotic type CysRS that recognizes plastid and nuclear tRNACys. Inhibitors of the Plasmodium dual-targeted CysRS would potentially offer a therapy capable of the desirable immediate effects on parasite growth as well as the irreversibility of inhibitors that disrupt apicoplast inheritance.
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39
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Idiosyncrasies in decoding mitochondrial genomes. Biochimie 2014; 100:95-106. [PMID: 24440477 DOI: 10.1016/j.biochi.2014.01.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2013] [Accepted: 01/06/2014] [Indexed: 11/24/2022]
Abstract
Mitochondria originate from the α-proteobacterial domain of life. Since this unique event occurred, mitochondrial genomes of protozoans, fungi, plants and metazoans have highly derived and diverged away from the common ancestral DNA. These resulting genomes highly differ from one another, but all present-day mitochondrial DNAs have a very reduced coding capacity. Strikingly however, ATP production coupled to electron transport and translation of mitochondrial proteins are the two common functions retained in all mitochondrial DNAs. Paradoxically, most components essential for these two functions are now expressed from nuclear genes. Understanding how mitochondrial translation evolved in various eukaryotic models is essential to acquire new knowledge of mitochondrial genome expression. In this review, we provide a thorough analysis of the idiosyncrasies of mitochondrial translation as they occur between organisms. We address this by looking at mitochondrial codon usage and tRNA content. Then, we look at the aminoacyl-tRNA-forming enzymes in terms of peculiarities, dual origin, and alternate function(s). Finally we give examples of the atypical structural properties of mitochondrial tRNAs found in some organisms and the resulting adaptive tRNA-protein partnership.
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40
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Mailu BM, Ramasamay G, Mudeppa DG, Li L, Lindner SE, Peterson MJ, DeRocher AE, Kappe SHI, Rathod PK, Gardner MJ. A nondiscriminating glutamyl-tRNA synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. J Biol Chem 2013; 288:32539-32552. [PMID: 24072705 PMCID: PMC3820887 DOI: 10.1074/jbc.m113.507467] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 09/23/2013] [Indexed: 11/06/2022] Open
Abstract
The malaria parasite Plasmodium falciparum and related organisms possess a relict plastid known as the apicoplast. Apicoplast protein synthesis is a validated drug target in malaria because antibiotics that inhibit translation in prokaryotes also inhibit apicoplast protein synthesis and are sometimes used for malaria prophylaxis or treatment. We identified components of an indirect aminoacylation pathway for Gln-tRNA(Gln) biosynthesis in Plasmodium that we hypothesized would be essential for apicoplast protein synthesis. Here, we report our characterization of the first enzyme in this pathway, the apicoplast glutamyl-tRNA synthetase (GluRS). We expressed the recombinant P. falciparum enzyme in Escherichia coli, showed that it is nondiscriminating because it glutamylates both apicoplast tRNA(Glu) and tRNA(Gln), determined its kinetic parameters, and demonstrated its inhibition by a known bacterial GluRS inhibitor. We also localized the Plasmodium berghei ortholog to the apicoplast in blood stage parasites but could not delete the PbGluRS gene. These data show that Gln-tRNA(Gln) biosynthesis in the Plasmodium apicoplast proceeds via an essential indirect aminoacylation pathway that is reminiscent of bacteria and plastids.
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Affiliation(s)
- Boniface M Mailu
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | | | - Devaraja G Mudeppa
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700
| | - Ling Li
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Scott E Lindner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Megan J Peterson
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Amy E DeRocher
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109
| | - Stefan H I Kappe
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Pradipsinh K Rathod
- the Department of Chemistry, University of Washington, Seattle, Washington 98195-1700; the Department of Global Health, University of Washington, Seattle, Washington 98195
| | - Malcolm J Gardner
- From the Seattle Biomedical Research Institute, Seattle, Washington 98109,; the Department of Global Health, University of Washington, Seattle, Washington 98195.
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41
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Pon CL, Fabbretti A, Brandi L. Antibiotics Targeting Translation Initiation in Prokaryotes. Antibiotics (Basel) 2013. [DOI: 10.1002/9783527659685.ch17] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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42
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Cristodero M, Mani J, Oeljeklaus S, Aeberhard L, Hashimi H, Ramrath DJF, Lukeš J, Warscheid B, Schneider A. Mitochondrial translation factors of Trypanosoma brucei: elongation factor-Tu has a unique subdomain that is essential for its function. Mol Microbiol 2013; 90:744-55. [PMID: 24033548 DOI: 10.1111/mmi.12397] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/07/2013] [Indexed: 11/28/2022]
Abstract
Mitochondrial translation in the parasitic protozoan Trypanosoma brucei relies on imported eukaryotic-type tRNAs as well as on bacterial-type ribosomes that have the shortest known rRNAs. Here we have identified the mitochondrial translation elongation factors EF-Tu, EF-Ts, EF-G1 and release factor RF1 of trypanosomatids and show that their ablation impairs growth and oxidative phosphorylation. In vivo labelling experiments and a SILAC-based analysis of the global proteomic changes induced by EF-Tu RNAi directly link EF-Tu to mitochondrial translation. Moreover, EF-Tu RNAi reveals downregulation of many nuclear encoded subunits of cytochrome oxidase as well as of components of the bc1-complex, whereas most cytosolic ribosomal proteins were upregulated. Interestingly, T. brucei EF-Tu has a 30-amino-acid-long, highly charged subdomain, which is unique to trypanosomatids. A combination of RNAi and complementation experiments shows that this subdomain is essential for EF-Tu function, but that it can be replaced by a similar sequence found in eukaryotic EF-1a, the cytosolic counterpart of EF-Tu. A recent cryo-electron microscopy study revealed that trypanosomatid mitochondrial ribosomes have a unique intersubunit space that likely harbours the EF-Tu binding site. These findings suggest that the trypanosomatid-specific EF-Tu subdomain serves as an adaption for binding to these unusual mitochondrial ribosomes.
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Affiliation(s)
- Marina Cristodero
- Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012, Bern, Switzerland
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Kuzmenko A, Atkinson GC, Levitskii S, Zenkin N, Tenson T, Hauryliuk V, Kamenski P. Mitochondrial translation initiation machinery: conservation and diversification. Biochimie 2013; 100:132-40. [PMID: 23954798 PMCID: PMC3978653 DOI: 10.1016/j.biochi.2013.07.024] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2013] [Accepted: 07/29/2013] [Indexed: 11/29/2022]
Abstract
The highly streamlined mitochondrial genome encodes almost exclusively a handful of transmembrane components of the respiratory chain complex. In order to ensure the correct assembly of the respiratory chain, the products of these genes must be produced in the correct stoichiometry and inserted into the membrane, posing a unique challenge to the mitochondrial translational system. In this review we describe the proteins orchestrating mitochondrial translation initiation: bacterial-like general initiation factors mIF2 and mIF3, as well as mitochondria-specific components – mRNA-specific translational activators and mRNA-nonspecific accessory initiation factors. We consider how the fast rate of evolution in these organelles has not only created a system that is divergent from that of its bacterial ancestors, but has led to a huge diversity in lineage specific mechanistic features of mitochondrial translation initiation among eukaryotes. Mitochondrially-encoded proteins are mostly respiratory chain components. The mitochondrial translation system is thus organized in a very specific way. Initiation involves mRNA-specific activators and bacteria-like initiation factors. We show that Saccharomyces cerevisiae Aim23p is a functional ortholog of bacterial IF3. We review the lineage specific features of mitochondrial translation initiation.
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Affiliation(s)
- Anton Kuzmenko
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Gemma C Atkinson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Sergey Levitskii
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia
| | - Nikolay Zenkin
- Centre for Bacterial Cell Biology, Institute for Cell and Molecular Biosciences, Newcastle University, Newcastle upon Tyne NE2 4AX, United Kingdom
| | - Tanel Tenson
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia
| | - Vasili Hauryliuk
- University of Tartu, Institute of Technology, Nooruse 1, Tartu, Estonia; Department of Molecular Biology, Umeå University, Umeå, Sweden; Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, Umeå, Sweden.
| | - Piotr Kamenski
- Molecular Biology Department, Faculty of Biology, M.V. Lomonosov Moscow State University, 1/12 Leninskie Gory, 119991 Moscow, Russia.
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Sheiner L, Vaidya AB, McFadden GI. The metabolic roles of the endosymbiotic organelles of Toxoplasma and Plasmodium spp. Curr Opin Microbiol 2013; 16:452-8. [PMID: 23927894 DOI: 10.1016/j.mib.2013.07.003] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2013] [Revised: 07/02/2013] [Accepted: 07/04/2013] [Indexed: 11/29/2022]
Abstract
The apicoplast and the mitochondrion of Apicomplexa cooperate in providing essential metabolites. Their co-evolution during the ancestral acquisition of a plastid and subsequent loss of photosynthesis resulted in divergent metabolic pathways compared with mammals and plants. This is most evident in their chimerical haem synthesis pathway. Toxoplasma and Plasmodium mitochondria operate canonical tricarboxylic acid (TCA) cycles and electron transport chains, although the roles differ between Toxoplasma tachyzoites and Plasmodium erythrocytic stages. Glutamine catabolism provides TCA intermediates in both parasites. Isoprenoid precursor synthesis is the only essential role of the apicoplast in Plasmodium erythrocytic stages. An apicoplast-located fatty acid synthesis is dispensable in these stages, which instead predominantly salvage fatty acids, while in Plasmodium liver stages and in Toxoplasma tachyzoites fatty acid synthesis is an essential role of the plastid.
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Affiliation(s)
- Lilach Sheiner
- Center for Tropical and Emerging Global Diseases & Department of Cellular Biology, University of Georgia, 500 D.W. Brooks Drive, Athens, GA 30602, USA.
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Gupta A, Mir SS, Jackson KE, Lim EE, Shah P, Sinha A, Siddiqi MI, Ralph SA, Habib S. Recycling factors for ribosome disassembly in the apicoplast and mitochondrion ofPlasmodium falciparum. Mol Microbiol 2013; 88:891-905. [DOI: 10.1111/mmi.12230] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/07/2013] [Indexed: 11/28/2022]
Affiliation(s)
- Ankit Gupta
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
| | - Snober S. Mir
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
| | - Katherine E. Jackson
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Erin E. Lim
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Priyanka Shah
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
| | - Ashima Sinha
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
| | - Mohammad Imran Siddiqi
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
| | - Stuart A. Ralph
- Department of Biochemistry and Molecular Biology; Bio21 Molecular Science and Biotechnology Institute; The University of Melbourne; Melbourne Vic. 3010 Australia
| | - Saman Habib
- Division of Molecular and Structural Biology; CSIR-Central Drug Research Institute; Lucknow India
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Hikosaka K, Kita K, Tanabe K. Diversity of mitochondrial genome structure in the phylum Apicomplexa. Mol Biochem Parasitol 2013; 188:26-33. [PMID: 23466751 DOI: 10.1016/j.molbiopara.2013.02.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Revised: 02/20/2013] [Accepted: 02/21/2013] [Indexed: 10/27/2022]
Abstract
Mitochondria are ubiquitous organelles in all eukaryotes that are essential for a range of cellular processes and cellular signaling. Nearly all mitochondria have their own DNA or mitochondrial (mt) genome, which varies considerably in size, structure and organization. The phylum Apicomplexa includes a variety of unicellular eukaryotes, some of which are parasites of clinical or economic importance. Recent studies have demonstrated that apicomplexan mt genomes, which include the smallest 6 kb genome of the malaria parasites, exhibit remarkably diverse structures. Apicomplexan parasites are interesting model organisms in order to understand the evolution of mt genomes. This review summarizes the structure of apicomplexan mt genomes and highlights the unique features and the evolution of the mt genome.
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Affiliation(s)
- Kenji Hikosaka
- Laboratory of Malariology, Research Institute for Microbial Diseases, Osaka University, Suita, Osaka, Japan
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The Plasmodium berghei Ca(2+)/H(+) exchanger, PbCAX, is essential for tolerance to environmental Ca(2+) during sexual development. PLoS Pathog 2013; 9:e1003191. [PMID: 23468629 PMCID: PMC3585132 DOI: 10.1371/journal.ppat.1003191] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2012] [Accepted: 12/28/2012] [Indexed: 12/15/2022] Open
Abstract
Ca(2+) contributes to a myriad of important cellular processes in all organisms, including the apicomplexans, Plasmodium and Toxoplasma. Due to its varied and essential roles, free Ca(2+) is tightly regulated by complex mechanisms. These mechanisms are therefore of interest as putative drug targets. One pathway in Ca(2+) homeostatic control in apicomplexans uses a Ca(2+)/H(+) exchanger (a member of the cation exchanger family, CAX). The P. falciparum CAX (PfCAX) has recently been characterised in asexual blood stage parasites. To determine the physiological importance of apicomplexan CAXs, tagging and knock-out strategies were undertaken in the genetically tractable T. gondii and P. berghei parasites. In addition, a yeast heterologous expression system was used to study the function of apicomplexan CAXs. Tagging of T. gondii and P. berghei CAXs (TgCAX and PbCAX) under control of their endogenous promoters could not demonstrate measureable expression of either CAX in tachyzoites and asexual blood stages, respectively. These results were consistent with the ability of parasites to tolerate knock-outs of the genes for TgCAX and PbCAX at these developmental stages. In contrast, PbCAX expression was detectable during sexual stages of development in female gametocytes/gametes, zygotes and ookinetes, where it was dispersed in membranous networks within the cytosol (with minimal mitochondrial localisation). Furthermore, genetically disrupted parasites failed to develop further from "round" form zygotes, suggesting that PbCAX is essential for ookinete development and differentiation. This impeded phenotype could be rescued by removal of extracellular Ca(2+). Therefore, PbCAX provides a mechanism for free living parasites to multiply within the ionic microenvironment of the mosquito midgut. Ca(2+) homeostasis mediated by PbCAX is critical and suggests plasmodial CAXs may be targeted in approaches designed to block parasite transmission.
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Eickel N, Kaiser G, Prado M, Burda PC, Roelli M, Stanway RR, Heussler VT. Features of autophagic cell death in Plasmodium liver-stage parasites. Autophagy 2013; 9:568-80. [PMID: 23388496 DOI: 10.4161/auto.23689] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Analyzing molecular determinants of Plasmodium parasite cell death is a promising approach for exploring new avenues in the fight against malaria. Three major forms of cell death (apoptosis, necrosis and autophagic cell death) have been described in multicellular organisms but which cell death processes exist in protozoa is still a matter of debate. Here we suggest that all three types of cell death occur in Plasmodium liver-stage parasites. Whereas typical molecular markers for apoptosis and necrosis have not been found in the genome of Plasmodium parasites, we identified genes coding for putative autophagy-marker proteins and thus concentrated on autophagic cell death. We characterized the Plasmodium berghei homolog of the prominent autophagy marker protein Atg8/LC3 and found that it localized to the apicoplast. A relocalization of PbAtg8 to autophagosome-like vesicles or vacuoles that appear in dying parasites was not, however, observed. This strongly suggests that the function of this protein in liver-stage parasites is restricted to apicoplast biology.
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Affiliation(s)
- Nina Eickel
- Institute of Cell Biology, University of Bern, Bern, Switzerland
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49
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Limenitakis J, Oppenheim RD, Creek DJ, Foth BJ, Barrett MP, Soldati-Favre D. The 2-methylcitrate cycle is implicated in the detoxification of propionate in Toxoplasma gondii. Mol Microbiol 2013; 87:894-908. [PMID: 23279335 PMCID: PMC3593168 DOI: 10.1111/mmi.12139] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2012] [Indexed: 12/22/2022]
Abstract
Toxoplasma gondii belongs to the coccidian subgroup of the Apicomplexa phylum. The Coccidia are obligate intracellular pathogens that establish infection in their mammalian host via the enteric route. These parasites lack a mitochondrial pyruvate dehydrogenase complex but have preserved the degradation of branched-chain amino acids (BCAA) as a possible pathway to generate acetyl-CoA. Importantly, degradation of leucine, isoleucine and valine could lead to concomitant accumulation of propionyl-CoA, a toxic metabolite that inhibits cell growth. Like fungi and bacteria, the Coccidia possess the complete set of enzymes necessary to metabolize and detoxify propionate by oxidation to pyruvate via the 2-methylcitrate cycle (2-MCC). Phylogenetic analysis provides evidence that the 2-MCC was acquired via horizontal gene transfer. In T. gondii tachyzoites, this pathway is split between the cytosol and the mitochondrion. Although the rate-limiting enzyme 2-methylisocitrate lyase is dispensable for parasite survival, its substrates accumulate in parasites deficient in the enzyme and its absence confers increased sensitivity to propionic acid. BCAA is also dispensable in tachyzoites, leaving unresolved the source of mitochondrial acetyl-CoA.
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Affiliation(s)
- Julien Limenitakis
- Department of Microbiology and Molecular Medicine, Faculty of Medicine, University of Geneva, CMU 1 Rue Michel Servet, 1211 Geneva, Switzerland
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Abstract
The life cycles of apicomplexan parasites such as Plasmodium spp. and Toxoplasma gondii are complex, consisting of proliferative and latent stages within multiple hosts. Dramatic transformations take place during the cycles, and they demand precise control of gene expression at all levels, including translation. This review focuses on the mechanisms that regulate translational control in Plasmodium and Toxoplasma, with a particular emphasis on the phosphorylation of the α subunit of eukaryotic translation initiation factor 2 (eIF2α). Phosphorylation of eIF2α (eIF2α∼P) is a conserved mechanism that eukaryotic cells use to repress global protein synthesis while enhancing gene-specific translation of a subset of mRNAs. Elevated levels of eIF2α∼P have been observed during latent stages in both Toxoplasma and Plasmodium, indicating that translational control plays a role in maintaining dormancy. Parasite-specific eIF2α kinases and phosphatases are also required for proper developmental transitions and adaptation to cellular stresses encountered during the life cycle. Identification of small-molecule inhibitors of apicomplexan eIF2α kinases may selectively interfere with parasite translational control and lead to the development of new therapies to treat malaria and toxoplasmosis.
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