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Tiwari A, Verma N, Shukla H, Mishra S, Kennedy K, Chatterjee T, Kuldeep J, Parwez S, Siddiqi MI, Ralph SA, Mishra S, Habib S. DNA N-glycosylases Ogg1 and EndoIII as components of base excision repair in Plasmodium falciparum organelles. Int J Parasitol 2024:S0020-7519(24)00137-1. [PMID: 38964640 DOI: 10.1016/j.ijpara.2024.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/31/2024] [Accepted: 06/28/2024] [Indexed: 07/06/2024]
Abstract
The integrity of genomes of the two crucial organelles of the malaria parasite - an apicoplast and mitochondrion in each cell - must be maintained by DNA repair mediated by proteins targeted to these compartments. We explored the localisation and function of Plasmodium falciparum base excision repair (BER) DNA N-glycosylase homologs PfEndoIII and PfOgg1. These N-glycosylases would putatively recognise DNA lesions prior to the action of apurinic/apyrimidinic (AP)-endonucleases. Both Ape1 and Apn1 endonucleases have earlier been shown to function solely in the parasite mitochondrion. Immunofluorescence localisation showed that PfEndoIII was exclusively mitochondrial. PfOgg1 was not seen clearly in mitochondria when expressed as a PfOgg1leader-GFP fusion, although chromatin immunoprecipitation assays showed that it could interact with both mitochondrial and apicoplast DNA. Recombinant PfEndoIII functioned as a DNA N-glycosylase as well as an AP-lyase on thymine glycol (Tg) lesions. We further studied the importance of Ogg1 in the malaria life cycle using reverse genetic approaches in Plasmodium berghei. Targeted disruption of PbOgg1 resulted in loss of 8-oxo-G specific DNA glycosylase/lyase activity. PbOgg1 knockout did not affect blood, mosquito or liver stage development but caused reduced blood stage infection after inoculation of sporozoites in mice. A significant reduction in erythrocyte infectivity by PbOgg1 knockout hepatic merozoites was also observed, thus showing that PbOgg1 ensures smooth transition from liver to blood stage infection. Our results strengthen the view that the Plasmodium mitochondrial genome is an important site for DNA repair by the BER pathway.
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Affiliation(s)
- Anupama Tiwari
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Neetu Verma
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Himadri Shukla
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Shivani Mishra
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Kit Kennedy
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Tribeni Chatterjee
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Jitendra Kuldeep
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India
| | - Shahid Parwez
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - M I Siddiqi
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | - Stuart A Ralph
- Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Victoria 3010, Australia
| | - Satish Mishra
- Division of Molecular Microbiology and Immunology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
| | - Saman Habib
- Division of Biochemistry and Structural Biology, CSIR-Central Drug Research Institute, Lucknow 226031, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India.
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2
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Mamudu CO, Tebamifor ME, Sule MO, Dokunmu TM, Ogunlana OO, Iheagwam FN. Apicoplast-Resident Processes: Exploiting the Chink in the Armour of Plasmodium falciparum Parasites. Adv Pharmacol Pharm Sci 2024; 2024:9940468. [PMID: 38765186 PMCID: PMC11101256 DOI: 10.1155/2024/9940468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 03/25/2024] [Accepted: 04/20/2024] [Indexed: 05/21/2024] Open
Abstract
The discovery of a relict plastid, also known as an apicoplast (apicomplexan plastid), that houses housekeeping processes and metabolic pathways critical to Plasmodium parasites' survival has prompted increased research on identifying potent inhibitors that can impinge on apicoplast-localised processes. The apicoplast is absent in humans, yet it is proposed to originate from the eukaryote's secondary endosymbiosis of a primary symbiont. This symbiotic relationship provides a favourable microenvironment for metabolic processes such as haem biosynthesis, Fe-S cluster synthesis, isoprenoid biosynthesis, fatty acid synthesis, and housekeeping processes such as DNA replication, transcription, and translation, distinct from analogous mammalian processes. Recent advancements in comprehending the biology of the apicoplast reveal it as a vulnerable organelle for malaria parasites, offering numerous potential targets for effective antimalarial therapies. We provide an overview of the metabolic processes occurring in the apicoplast and discuss the organelle as a viable antimalarial target in light of current advances in drug discovery. We further highlighted the relevance of these metabolic processes to Plasmodium falciparum during the different stages of the lifecycle.
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Affiliation(s)
- Collins Ojonugwa Mamudu
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Mercy Eyitomi Tebamifor
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Mary Ohunene Sule
- Confluence University of Science and Technology, Osara, Kogi, Nigeria
| | - Titilope Modupe Dokunmu
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
| | - Olubanke Olujoke Ogunlana
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant Applied Informatics and Communication Africa Centre of Excellence, Ota, Nigeria
- Covenant University Public Health and Wellbeing Research Cluster, Covenant University, Ota, Nigeria
| | - Franklyn Nonso Iheagwam
- Department of Biochemistry, Covenant University, Ota, Nigeria
- Covenant University Public Health and Wellbeing Research Cluster, Covenant University, Ota, Nigeria
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3
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Abstract
Apicomplexan parasites constitute more than 6,000 species infecting a wide range of hosts. These include important pathogens such as those causing malaria and toxoplasmosis. Their evolutionary emergence coincided with the dawn of animals. Mitochondrial genomes of apicomplexan parasites have undergone dramatic reduction in their coding capacity, with genes for only three proteins and ribosomal RNA genes present in scrambled fragments originating from both strands. Different branches of the apicomplexans have undergone rearrangements of these genes, with Toxoplasma having massive variations in gene arrangements spread over multiple copies. The vast evolutionary distance between the parasite and the host mitochondria has been exploited for the development of antiparasitic drugs, especially those used to treat malaria, wherein inhibition of the parasite mitochondrial respiratory chain is selectively targeted with little toxicity to the host mitochondria. We describe additional unique characteristics of the parasite mitochondria that are being investigated and provide greater insights into these deep-branching eukaryotic pathogens.
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Affiliation(s)
- Ian M Lamb
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Ijeoma C Okoye
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Michael W Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
| | - Akhil B Vaidya
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania, USA;
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4
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Sun W, Wang B, Wang P, Liu B, Pan B. Microenvironment pH modified solid dispersion of Toltrazuril as a new strategy to improve the treatment of experimental Apicomplexan infection. Acta Trop 2023; 238:106797. [PMID: 36528088 DOI: 10.1016/j.actatropica.2022.106797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2022] [Revised: 11/27/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022]
Abstract
The phylum Apicomplexa contains some of the most serious human and veterinary parasites, including Eimeria magna, Toxoplasma gondii, and many others. Toltrazuril (TOL) has activity against multiple stages of Apicomplexan parasites, but its clinical use is limited by low bioavailability. In present study, we prepared one new formulation named the microenvironment pH modified solid dispersion (pHM-SD), which was composed of three components including Ca(OH)2, TOL, and PVPk30 with the weight ratio of 1:8:8. In vivo evaluation for bioavailability and efficacy of the pHM-SD was conducted following oral administration and hypodermic injection. The performance of the pHM-SD was also contrast to corresponding results of raw material drug and commercial Baycox® to evaluate the advantages for clinical application. The results showed that the bioavailability of prototype TOL and its active metabolites toltrazuril sulfoxide (TOLSO), toltrazuril sulfone (TOLSO2) in rabbits were improved remarkably after oral administration of the pHM-SD. The safety of the pHM-SD via oral administration was adequately verified via the histopathological examination. We subsequently evaluated effects of the pHM-SD on Eimeria magna oocysts and Toxoplasma gondii tachyzoites. In vivo anti-coccidia efficacy further confirmed that the pHM-SD could be used as a strategy to minimize the oocyst exposure. In vitro cytotoxicity and anti-Toxoplasma tests showed that the pHM-SD had little damage to host cells within the concentration of 100 μg/ mL, and the anti-Toxoplasma efficacy was significantly improved compared with TOL. Combined with the above-mentioned experimental results, we conclude that the pHM-SD maybe a promising candidate for providing better clinical outcomes.
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Affiliation(s)
- Weiwei Sun
- College of Veterinary Medicine, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Hai Dian District, Beijing 100193, China
| | - Bohan Wang
- College of Veterinary Medicine, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Hai Dian District, Beijing 100193, China
| | - Penglong Wang
- College of Veterinary Medicine, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Hai Dian District, Beijing 100193, China
| | - Boxing Liu
- College of Veterinary Medicine, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Hai Dian District, Beijing 100193, China
| | - Baoliang Pan
- College of Veterinary Medicine, China Agricultural University, No. 2 Yuan Ming Yuan West Road, Hai Dian District, Beijing 100193, China.
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Elahi R, Prigge ST. New insights into apicoplast metabolism in blood-stage malaria parasites. Curr Opin Microbiol 2023; 71:102255. [PMID: 36563485 PMCID: PMC9852000 DOI: 10.1016/j.mib.2022.102255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Revised: 11/21/2022] [Accepted: 11/23/2022] [Indexed: 12/24/2022]
Abstract
The apicoplast of Plasmodium falciparum is the only source of essential isoprenoid precursors and Coenzyme A (CoA) in the parasite. Isoprenoid precursor synthesis relies on the iron-sulfur cluster (FeS) cofactors produced within the apicoplast, rendering FeS synthesis an essential function of this organelle. Recent reports provide important insights into the roles of FeS cofactors and the use of isoprenoid precursors and CoA both inside and outside the apicoplast. Here, we review the recent insights into the roles of these metabolites in blood-stage malaria parasites and discuss new questions that have been raised in light of these discoveries.
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Affiliation(s)
- Rubayet Elahi
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA; The Johns Hopkins Malaria Research Institute, Baltimore, MD, USA
| | - Sean T Prigge
- Department of Molecular Microbiology and Immunology, Johns Hopkins University, Baltimore, MD, USA; The Johns Hopkins Malaria Research Institute, Baltimore, MD, USA.
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6
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Buchanan HD, Goodman CD, McFadden GI. Roles of the apicoplast across the life cycles of rodent and human malaria parasites. J Eukaryot Microbiol 2022; 69:e12947. [PMID: 36070203 PMCID: PMC9828729 DOI: 10.1111/jeu.12947] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Malaria parasites are diheteroxenous, requiring two hosts-a vertebrate and a mosquito-to complete their life cycle. Mosquitoes are the definitive host where malaria parasite sex occurs, and vertebrates are the intermediate host, supporting asexual amplification and more significant geographic spread. In this review, we examine the roles of a single malaria parasite compartment, the relict plastid known as the apicoplast, at each life cycle stage. We focus mainly on two malaria parasite species-Plasmodium falciparum and P. berghei-comparing the changing, yet ever crucial, roles of their apicoplasts.
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Affiliation(s)
- Hayley D. Buchanan
- Department of Infectious Diseases, Faculty of Medicine, Dentistry and Health Sciences, Melbourne Medical SchoolThe University of MelbourneMelbourneVic.Australia,Faculty of Science, School of BioSciencesThe University of MelbourneMelbourneVic.Australia
| | - Christopher D. Goodman
- Faculty of Science, School of BioSciencesThe University of MelbourneMelbourneVic.Australia
| | - Geoffrey I. McFadden
- Faculty of Science, School of BioSciencesThe University of MelbourneMelbourneVic.Australia
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7
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Zhao N, Ming S, Sun L, Wang B, Li H, Zhang X, Zhao X. Identification and Characterization of Eimeria tenella Microneme Protein (EtMIC8). Microbiol Spectr 2021; 9:e0022821. [PMID: 34479414 PMCID: PMC8562341 DOI: 10.1128/spectrum.00228-21] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/22/2021] [Indexed: 11/20/2022] Open
Abstract
Microneme proteins (MICs) of Eimeria tenella play key roles in motility, migration, attachment, and invasion processes. More than 20 apicomplexan parasite's MICs have been identified, with nine Eimeria MICs being reported. In this study, a novel E. tenella MIC was identified, and its gene structural features, developmental expression levels, localization, role in adhesion and invasion, and immunogenicity were studied. The results showed that the open reading frame was 1,650 bp, encoding 550 amino acids. It contains a signal sequence, a transmembrane region, four low-complexity boxes, and five epidermal growth factor-like domains (EGF). Subcellular localization revealed its distribution on the membrane surface of the parasite. These characteristics are consistent with the common features of MICs and are named EtMIC8. Anti-EtMIC8 antibodies recognized a specific binding of about 100 kDa in E. tenella, which was twice as large as the prokaryotic expression (about 50 kDa), suggesting that MIC8 may exist naturally as a dimer. EtMIC8 was expressed at higher levels in sporozoites (3.08-fold) and merozoites (2.1-fold) than in sporulated oocysts. The attachment assays using a yeast surface display of MIC8 and its different domains showed that the adherence rates of EtMIC8 to host cells were significantly higher than those of the control (3.17-fold), which was the full contribution of EGF, but neither was alone. Anti-EtMIC8 antibodies significantly reduced the invasion rate of sporozoites into host cells compared to those of the control (P < 0.01). Recombinant EtMIC8-EGF peptides could provide moderate protective efficacy (anticoccidial index [ACI]: 169.7), induce humoral responses, and upregulate CD3+CD8+ lymphocyte cells.
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Affiliation(s)
- Ningning Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Shuzhen Ming
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Lingyu Sun
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Bingxiang Wang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Hongmei Li
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Xiao Zhang
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
| | - Xiaomin Zhao
- Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Shandong Agricultural University, Taian City, Shandong Province, China
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
- Shandong Provincial Engineering Technology Research Center of Animal Disease Control and Prevention, Shandong Agricultural University, Taian City, Shandong Province, China
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8
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Mohammad Sadik, Mohammad Afsar, Ramachandran R, Habib S. [Fe-S] biogenesis and unusual assembly of the ISC scaffold complex in the Plasmodium falciparum mitochondrion. Mol Microbiol 2021; 116:606-623. [PMID: 34032321 DOI: 10.1111/mmi.14735] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 05/06/2021] [Accepted: 05/06/2021] [Indexed: 12/16/2022]
Abstract
The malaria parasite harbors two [Fe-S] biogenesis pathways of prokaryotic origin-the SUF and ISC systems in the apicoplast and mitochondrion, respectively. While the SUF machinery has been delineated, there is little experimental evidence on the ISC pathway. We confirmed mitochondrial targeting of Plasmodium falciparum ISC proteins followed by analyses of cysteine desulfurase, scaffold, and [Fe-S]-carrier components. PfIscU functioned as the scaffold in complex with the PfIscS-PfIsd11 cysteine desulfurase and could directly assemble [4Fe-4S] without prior [2Fe-2S] formation seen in other homologs. Small angle X-ray scattering and spectral studies showed that PfIscU, a trimer, bound one [4Fe-4S]. In a deviation from reported complexes from other organisms, the P. falciparum desulfurase-scaffold complex assembled around a PfIscS tetramer instead of a dimer, resulting in a symmetric hetero-hexamer [2× (2PfIscS-2PfIsd11-2PfIscU)]. PfIscU directly transferred [4Fe-4S] to the apo-protein aconitase B thus abrogating the requirement of intermediary proteins for conversion of [2Fe-2S] to [4Fe-4S] before transfer to [4Fe-4S]-recipients. Among the putative cluster-carriers, PfIscA2 was more efficient than PfNifU-like protein; PfIscA1 primarily bound iron, suggesting its potential role as a Fe2+ carrier/donor. Our results identify the core P. falciparum ISC machinery and reveal unique features compared with those in bacteria or yeast and human mitochondria.
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Affiliation(s)
- Mohammad Sadik
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Mohammad Afsar
- Division of Molecular and Structural Biology, CSIR-Central Drug Research Institute, Lucknow, India
| | - Ravishankar Ramachandran
- 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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9
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Zhang Y, Wang C, Jia H. Biogenesis and maintenance of the apicoplast in model apicomplexan parasites. Parasitol Int 2020; 81:102270. [PMID: 33321224 DOI: 10.1016/j.parint.2020.102270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2020] [Revised: 12/08/2020] [Accepted: 12/09/2020] [Indexed: 11/27/2022]
Abstract
The apicoplast is a non-photosynthetic relict plastid of Apicomplexa that evolved from a secondary symbiotic system. During its evolution, most of the genes derived from its alga ancestor were lost. Only genes involved in several valuable metabolic pathways, such as the synthesis of isoprenoid precursors, heme, and fatty acids, have been transferred to the host genome and retained to help these parasites adapt to a complex life cycle and various living environments. The biological function of an apicoplast is essential for most apicomplexan parasites. Considering their potential as drug targets, the metabolic functions of this symbiotic organelle have been intensively investigated through computational and biological means. Moreover, we know that not only organellar metabolic functions are linked with other organelles, but also their biogenesis processes have developed and evolved to tailor their biological functions and proper inheritance. Several distinct features have been found in the biogenesis process of apicoplasts. For example, the apicoplast borrows a dynamin-related protein (DrpA) from its host to implement organelle division. The autophagy system has also been repurposed for linking the apicoplast and centrosome during replication and the division process. However, many vital questions remain to be answered about how these parasites maintain and properly inherit this symbiotic organelle. Here we review our current knowledge about its biogenesis process and discuss several critical questions remaining to be answered in this field.
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Affiliation(s)
- Ying Zhang
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China; State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Haping Street 678, Nangang District, Harbin 150069, PR China
| | - Chunren Wang
- Heilongjiang Provincial Key Laboratory of Prevention and Control of Bovine Diseases, College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, Daqing, Heilongjiang Province 163319, PR China
| | - Honglin Jia
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Haping Street 678, Nangang District, Harbin 150069, PR China.
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10
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Ling L, Mulaka M, Munro J, Dass S, Mather MW, Riscoe MK, Llinás M, Zhou J, Ke H. Genetic ablation of the mitoribosome in the malaria parasite Plasmodium falciparum sensitizes it to antimalarials that target mitochondrial functions. J Biol Chem 2020; 295:7235-7248. [PMID: 32273345 PMCID: PMC7247301 DOI: 10.1074/jbc.ra120.012646] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Revised: 04/04/2020] [Indexed: 02/05/2023] Open
Abstract
The mitochondrion of malaria parasites contains several clinically validated drug targets. Within Plasmodium spp., the causative agents of malaria, the mitochondrial DNA (mtDNA) is only 6 kb long, being the smallest mitochondrial genome among all eukaryotes. The mtDNA encodes only three proteins of the mitochondrial electron transport chain and ∼27 small, fragmented rRNA genes having lengths of 22-195 nucleotides. The rRNA fragments are thought to form a mitochondrial ribosome (mitoribosome), together with ribosomal proteins imported from the cytosol. The mitoribosome of Plasmodium falciparum is essential for maintenance of the mitochondrial membrane potential and parasite viability. However, the role of the mitoribosome in sustaining the metabolic status of the parasite mitochondrion remains unclear. The small ribosomal subunit in P. falciparum has 14 annotated mitoribosomal proteins, and employing a CRISPR/Cas9-based conditional knockdown tool, here we verified the location and tested the essentiality of three candidates (PfmtRPS12, PfmtRPS17, and PfmtRPS18). Using immuno-EM, we provide evidence that the P. falciparum mitoribosome is closely associated with the mitochondrial inner membrane. Upon knockdown of the mitoribosome, parasites became hypersensitive to inhibitors targeting mitochondrial Complex III (bc1), dihydroorotate dehydrogenase (DHOD), and the F1F0-ATP synthase complex. Furthermore, the mitoribosome knockdown blocked the pyrimidine biosynthesis pathway and reduced the cellular pool of pyrimidine nucleotides. These results suggest that disruption of the P. falciparum mitoribosome compromises the metabolic capacity of the mitochondrion, rendering the parasite hypersensitive to a panel of inhibitors that target mitochondrial functions.
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Affiliation(s)
- Liqin Ling
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129; Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Maruthi Mulaka
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129
| | - Justin Munro
- Department of Chemistry and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Swati Dass
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129
| | - Michael W Mather
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129
| | - Michael K Riscoe
- Portland Veterans Affairs Medical Center, Portland, Oregon 97239
| | - Manuel Llinás
- Department of Chemistry and Huck Center for Malaria Research, Pennsylvania State University, University Park, Pennsylvania 16802; Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Jing Zhou
- Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Hangjun Ke
- Center for Molecular Parasitology, Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania 19129.
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11
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Pacheco MA, Matta NE, Valkiunas G, Parker PG, Mello B, Stanley CE, Lentino M, Garcia-Amado MA, Cranfield M, Kosakovsky Pond SL, Escalante AA. Mode and Rate of Evolution of Haemosporidian Mitochondrial Genomes: Timing the Radiation of Avian Parasites. Mol Biol Evol 2019; 35:383-403. [PMID: 29126122 PMCID: PMC5850713 DOI: 10.1093/molbev/msx285] [Citation(s) in RCA: 101] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Haemosporidians are a diverse group of vector-borne parasitic protozoa that includes the agents of human malaria; however, most of the described species are found in birds and reptiles. Although our understanding of these parasites’ diversity has expanded by analyses of their mitochondrial genes, there is limited information on these genes’ evolutionary rates. Here, 114 mitochondrial genomes (mtDNA) were studied from species belonging to four genera: Leucocytozoon, Haemoproteus, Hepatocystis, and Plasmodium. Contrary to previous assertions, the mtDNA is phylogenetically informative. The inferred phylogeny showed that, like the genus Plasmodium, the Leucocytozoon and Haemoproteus genera are not monophyletic groups. Although sensitive to the assumptions of the molecular dating method used, the estimated times indicate that the diversification of the avian haemosporidian subgenera/genera took place after the Cretaceous–Paleogene boundary following the radiation of modern birds. Furthermore, parasite clade differences in mtDNA substitution rates and strength of negative selection were detected. These differences may affect the biological interpretation of mtDNA gene lineages used as a proxy to species in ecological and parasitological investigations. Given that the mitochondria are critically important in the parasite life cycle stages that take place in the vector and that the transmission of parasites belonging to particular clades has been linked to specific insect families/subfamilies, this study suggests that differences in vectors have affected the mode of evolution of haemosporidian mtDNA genes. The observed patterns also suggest that the radiation of haemosporidian parasites may be the result of community-level evolutionary processes between their vertebrate and invertebrate hosts.
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Affiliation(s)
- M Andreína Pacheco
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Nubia E Matta
- Departamento de Biología, Grupo de Investigación Caracterización Genética e Inmunología, Sede Bogotá-Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | | | - Patricia G Parker
- Department of Biology, Whitney R. Harris World Ecology Center, University of Missouri-St. Louis, St. Louis, MO
| | - Beatriz Mello
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Craig E Stanley
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | | | - Maria Alexandra Garcia-Amado
- Laboratorio de Fisiología Gastrointestinal, Centro de Biofísica y Bioquímica, Instituto Venezolano de Investigaciones Científicas (IVIC), Miranda, Venezuela
| | - Michael Cranfield
- Gorilla Doctors, the Wildlife Health Center School of Veterinary Medicine, University of California, Davis, CA
| | - Sergei L Kosakovsky Pond
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
| | - Ananias A Escalante
- Department of Biology, Institute for Genomics and Evolutionary Medicine (igem), Temple University, Philadelphia, PA
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12
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Virji AZ, Thekkiniath J, Ma W, Lawres L, Knight J, Swei A, Roch KL, Mamoun CB. Insights into the evolution and drug susceptibility of Babesia duncani from the sequence of its mitochondrial and apicoplast genomes. Int J Parasitol 2019; 49:105-113. [PMID: 30176236 PMCID: PMC6395566 DOI: 10.1016/j.ijpara.2018.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2018] [Revised: 04/04/2018] [Accepted: 05/03/2018] [Indexed: 11/22/2022]
Abstract
Babesia microti and Babesia duncani are the main causative agents of human babesiosis in the United States. While significant knowledge about B. microti has been gained over the past few years, nothing is known about B. duncani biology, pathogenesis, mode of transmission or sensitivity to currently recommended therapies. Studies in immunocompetent wild type mice and hamsters have shown that unlike B. microti, infection with B. duncani results in severe pathology and ultimately death. The parasite factors involved in B. duncani virulence remain unknown. Here we report the first known completed sequence and annotation of the apicoplast and mitochondrial genomes of B. duncani. We found that the apicoplast genome of this parasite consists of a 34 kb monocistronic circular molecule encoding functions that are important for apicoplast gene transcription as well as translation and maturation of the organelle's proteins. The mitochondrial genome of B. duncani consists of a 5.9 kb monocistronic linear molecule with two inverted repeats of 48 bp at both ends. Using the conserved cytochrome b (Cytb) and cytochrome c oxidase subunit I (coxI) proteins encoded by the mitochondrial genome, phylogenetic analysis revealed that B. duncani defines a new lineage among apicomplexan parasites distinct from B. microti, Babesia bovis, Theileria spp. and Plasmodium spp. Annotation of the apicoplast and mitochondrial genomes of B. duncani identified targets for development of effective therapies. Our studies set the stage for evaluation of the efficacy of these drugs alone or in combination against B. duncani in culture as well as in animal models.
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Affiliation(s)
- Azan Z Virji
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Jose Thekkiniath
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - Wenxiu Ma
- Department of Statistics, University of California, 900 University Avenue, Riverside, CA 92521, USA
| | - Lauren Lawres
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA
| | - James Knight
- Department of Genetics, Yale School of Medicine, New Haven, CT 06520, USA
| | - Andrea Swei
- Department of Biology, San Francisco State University, 1600 Holloway Ave, San Francisco, CA 94132, USA
| | - Karine Le Roch
- Department of Cell Biology & Neuroscience, 900 University Avenue, University of California, Riverside, CA 92521, USA
| | - Choukri Ben Mamoun
- Department of Internal Medicine, Section of Infectious Diseases, Yale School of Medicine, New Haven, CT 06520, USA.
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13
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Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses. Sci Rep 2018; 8:17012. [PMID: 30451959 PMCID: PMC6242988 DOI: 10.1038/s41598-018-35389-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022] Open
Abstract
Euglenophytes are a familiar algal group with green alga-derived secondary plastids, but the knowledge of euglenophyte plastid function and evolution is still highly incomplete. With this in mind we sequenced and analysed the transcriptome of the non-photosynthetic species Euglena longa. The transcriptomic data confirmed the absence of genes for the photosynthetic machinery, but provided candidate plastid-localised proteins bearing N-terminal bipartite topogenic signals (BTSs) of the characteristic euglenophyte type. Further comparative analyses including transcriptome assemblies available for photosynthetic euglenophytes enabled us to unveil salient aspects of the basic euglenophyte plastid infrastructure, such as plastidial targeting of several proteins as C-terminal translational fusions with other BTS-bearing proteins or replacement of the conventional eubacteria-derived plastidial ribosomal protein L24 by homologs of archaeo-eukaryotic origin. Strikingly, no homologs of any key component of the TOC/TIC system and the plastid division apparatus are discernible in euglenophytes, and the machinery for intraplastidial protein targeting has been simplified by the loss of the cpSRP/cpFtsY system and the SEC2 translocon. Lastly, euglenophytes proved to encode a plastid-targeted homolog of the termination factor Rho horizontally acquired from a Lambdaproteobacteria-related donor. Our study thus further documents a substantial remodelling of the euglenophyte plastid compared to its green algal progenitor.
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Gupta K, Gupta A, Habib S. Characterization of a Plasmodium falciparum rRNA methyltransferase. Mol Biochem Parasitol 2018; 223:13-18. [DOI: 10.1016/j.molbiopara.2018.06.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2018] [Revised: 06/12/2018] [Accepted: 06/12/2018] [Indexed: 12/29/2022]
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Abstract
AbstractRibosome assembly is critical for translation and regulating the response to cellular events and requires a complex interplay of ribosomal RNA and proteins with assembly factors. We investigated putative participants in the biogenesis of the reduced organellar ribosomes of Plasmodium falciparum and identified homologues of two assembly GTPases – EngA and Obg that were found in mitochondria. Both are indispensable in bacteria and P. berghei EngA is among the ‘essential’ parasite blood stage proteins identified recently. PfEngA and PfObg1 interacted with parasite mitoribosomes in vivo. GTP stimulated PfEngA interaction with the 50S subunit of Escherichia coli surrogate ribosomes. Although PfObg1–ribosome interaction was independent of nucleotide binding, GTP hydrolysis by PfObg1 was enhanced upon ribosomal association. An additional function for PfObg1 in mitochondrial DNA transactions was suggested by its specific interaction with the parasite mitochondrial genome in vivo. Deletion analysis revealed that the positively-charged OBG (spoOB-associated GTP-binding protein) domain mediates DNA-binding. A role for PfEngA in mitochondrial genotoxic stress response was indicated by its over-expression upon methyl methanesulfonate-induced DNA damage. PfEngA had lower sensitivity to an E. coli EngA inhibitor suggesting differences with bacterial counterparts. Our results show the involvement of two important GTPases in P. falciparum mitochondrial function, with the first confirmed localization of an EngA homologue in eukaryotic mitochondria.
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García-Mauriño SM, Díaz-Quintana A, Rivero-Rodríguez F, Cruz-Gallardo I, Grüttner C, Hernández-Vellisca M, Díaz-Moreno I. A putative RNA binding protein from Plasmodium vivax apicoplast. FEBS Open Bio 2017; 8:177-188. [PMID: 29435408 PMCID: PMC5794462 DOI: 10.1002/2211-5463.12351] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/03/2017] [Accepted: 11/14/2017] [Indexed: 01/30/2023] Open
Abstract
Malaria is caused by Apicomplexa protozoans from the Plasmodium genus entering the bloodstream of humans and animals through the bite of the female mosquitoes. The annotation of the Plasmodium vivax genome revealed a putative RNA binding protein (apiRBP) that was predicted to be trafficked into the apicoplast, a plastid organelle unique to Apicomplexa protozoans. Although a 3D structural model of the apiRBP corresponds to a noncanonical RNA recognition motif with an additional C‐terminal α‐helix (α3), preliminary protein production trials were nevertheless unsuccessful. Theoretical solvation analysis of the apiRBP model highlighted an exposed hydrophobic region clustering α3. Hence, we used a C‐terminal GFP‐fused chimera to stabilize the highly insoluble apiRBP and determined its ability to bind U‐rich stretches of RNA. The affinity of apiRBP toward such RNAs is highly dependent on ionic strength, suggesting that the apiRBP–RNA complex is driven by electrostatic interactions. Altogether, apiRBP represents an attractive tool for apicoplast transcriptional studies and for antimalarial drug design.
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Affiliation(s)
- Sofía M García-Mauriño
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Antonio Díaz-Quintana
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Francisco Rivero-Rodríguez
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | | | - Christian Grüttner
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Marian Hernández-Vellisca
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
| | - Irene Díaz-Moreno
- Instituto de Investigaciones Químicas (IIQ) Centro de Investigaciones Científicas Isla de la Cartuja (cicCartuja) Universidad de Sevilla Consejo Superior de Investigaciones Científicas (CSIC) Sevilla Spain
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Yakobov N, Debard S, Fischer F, Senger B, Becker HD. Cytosolic aminoacyl-tRNA synthetases: Unanticipated relocations for unexpected functions. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2017; 1861:387-400. [PMID: 29155070 DOI: 10.1016/j.bbagrm.2017.11.004] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Revised: 11/13/2017] [Accepted: 11/14/2017] [Indexed: 12/13/2022]
Abstract
Prokaryotic and eukaryotic cytosolic aminoacyl-tRNA synthetases (aaRSs) are essentially known for their conventional function of generating the full set of aminoacyl-tRNA species that are needed to incorporate each organism's repertoire of genetically-encoded amino acids during ribosomal translation of messenger RNAs. However, bacterial and eukaryotic cytosolic aaRSs have been shown to exhibit other essential nonconventional functions. Here we review all the subcellular compartments that prokaryotic and eukaryotic cytosolic aaRSs can reach to exert either a conventional or nontranslational role. We describe the physiological and stress conditions, the mechanisms and the signaling pathways that trigger their relocation and the new functions associated with these relocating cytosolic aaRS. Finally, given that these relocating pools of cytosolic aaRSs participate to a wide range of cellular pathways beyond translation, but equally important for cellular homeostasis, we mention some of the pathologies and diseases associated with the dis-regulation or malfunctioning of these nontranslational functions.
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Affiliation(s)
- Nathaniel Yakobov
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Sylvain Debard
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Frédéric Fischer
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Bruno Senger
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France
| | - Hubert Dominique Becker
- Génétique Moléculaire, Génomique, Microbiologie, UMR 7156, CNRS, Université de Strasbourg, Institut de Botanique, 28 rue Goethe, 67083 Strasbourg Cedex, France.
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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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19
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Bieri P, Leibundgut M, Saurer M, Boehringer D, Ban N. The complete structure of the chloroplast 70S ribosome in complex with translation factor pY. EMBO J 2016; 36:475-486. [PMID: 28007896 PMCID: PMC5694952 DOI: 10.15252/embj.201695959] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Revised: 11/24/2016] [Accepted: 11/28/2016] [Indexed: 01/21/2023] Open
Abstract
Chloroplasts are cellular organelles of plants and algae that are responsible for energy conversion and carbon fixation by the photosynthetic reaction. As a consequence of their endosymbiotic origin, they still contain their own genome and the machinery for protein biosynthesis. Here, we present the atomic structure of the chloroplast 70S ribosome prepared from spinach leaves and resolved by cryo‐EM at 3.4 Å resolution. The complete structure reveals the features of the 4.5S rRNA, which probably evolved by the fragmentation of the 23S rRNA, and all five plastid‐specific ribosomal proteins. These proteins, required for proper assembly and function of the chloroplast translation machinery, bind and stabilize rRNA including regions that only exist in the chloroplast ribosome. Furthermore, the structure reveals plastid‐specific extensions of ribosomal proteins that extensively remodel the mRNA entry and exit site on the small subunit as well as the polypeptide tunnel exit and the putative binding site of the signal recognition particle on the large subunit. The translation factor pY, involved in light‐ and temperature‐dependent control of protein synthesis, is bound to the mRNA channel of the small subunit and interacts with 16S rRNA nucleotides at the A‐site and P‐site, where it protects the decoding centre and inhibits translation by preventing tRNA binding. The small subunit is locked by pY in a non‐rotated state, in which the intersubunit bridges to the large subunit are stabilized.
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Affiliation(s)
- Philipp Bieri
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Marc Leibundgut
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Martin Saurer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Daniel Boehringer
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
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20
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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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