1
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Gamboa-Suárez BA, Lotta-Arévalo IA, Sarmiento-Salazar F, Matta NE. Finding a needle in a haystack: DNA Haemoproteus columbae enrichment using percoll density gradient and flow cytometry. Vet Parasitol 2024; 328:110170. [PMID: 38513447 DOI: 10.1016/j.vetpar.2024.110170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 03/06/2024] [Accepted: 03/11/2024] [Indexed: 03/23/2024]
Abstract
Isolation of genomic DNA of blood parasites in birds, reptiles, amphibians, and fishes is a challenging task, given that their red blood cells are nucleated; for that reason, parasite genomic DNA is only a fraction of the total extracted DNA, and it is challenging to obtain concentrated high-quality genetic material. Percoll Density Gradient (PDG) and flow cytometry are tools for separating and analyzing cell populations or even a single cell, and both represent potent approaches for isolating avian haemosporidians parasites. Our experimental design included several steps seeking to concentrate the parasite´s DNA. We used blood samples from a Rock pigeon infected with Haemoproteus columbae. After inducing parasite exflagellation and gametogenesis in vitro, we subjected the samples to a Percoll Density Gradient to separate the parasites from the rest of the blood cells. Following centrifugation, the layer containing extracellular parasites underwent a flow cytometry and cell sorting process, during which we selected two different subpopulations of cells for analysis. Based on qPCR analyses, we demonstrate parasite DNA enrichment in Percoll Density Gradient and flow cytometry samples; simultaneously, these samples showed the lowest concentration of Columba livia DNA. However, the concentration of parasite DNA was higher in the PDG than in the cell sorting sample. This study reports the concentration of the Haemoproteus parasite by flow cytometry without DNA-intercalating dyes, and this methodology can serve as a technique for DNA enrichment of blood parasites infecting nucleated red blood cells to improve techniques that allow obtaining complete genomes.
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Affiliation(s)
- Brayan Andrés Gamboa-Suárez
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia; Departamento de Salud Animal, Facultad de Medicina Veterinaria y de Zootecnia, Universidad Nacional de Colombia, Sede Bogotá, Colombia.
| | | | - Felipe Sarmiento-Salazar
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
| | - Nubia E Matta
- Departamento de Biología, Facultad de Ciencias, Universidad Nacional de Colombia, Sede Bogotá, Colombia
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2
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Pastusiak A, Reddy MR, Chen X, Hoyer I, Dorman J, Gebhardt ME, Carpi G, Norris DE, Pipas JM, Jackson EK. A metagenomic analysis of the phase 2 Anopheles gambiae 1000 genomes dataset reveals a wide diversity of cobionts associated with field collected mosquitoes. Commun Biol 2024; 7:667. [PMID: 38816486 PMCID: PMC11139907 DOI: 10.1038/s42003-024-06337-9] [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: 03/07/2023] [Accepted: 05/15/2024] [Indexed: 06/01/2024] Open
Abstract
The Anopheles gambiae 1000 Genomes (Ag1000G) Consortium previously utilized deep sequencing methods to catalogue genetic diversity across African An. gambiae populations. We analyzed the complete datasets of 1142 individually sequenced mosquitoes through Microsoft Premonition's Bayesian mixture model based (BMM) metagenomics pipeline. All specimens were confirmed as either An. gambiae sensu stricto (s.s.) or An. coluzzii with a high degree of confidence ( > 98% identity to reference). Homo sapiens DNA was identified in all specimens indicating contamination may have occurred either at the time of specimen collection, preparation and/or sequencing. We found evidence of vertebrate hosts in 162 specimens. 59 specimens contained validated Plasmodium falciparum reads. Human hepatitis B and primate erythroparvovirus-1 viral sequences were identified in fifteen and three mosquito specimens, respectively. 478 of the 1,142 specimens were found to contain bacterial reads and bacteriophage-related contigs were detected in 27 specimens. This analysis demonstrates the capacity of metagenomic approaches to elucidate important vector-host-pathogen interactions of epidemiological significance.
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Affiliation(s)
| | - Michael R Reddy
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA.
| | - Xiaoji Chen
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Isaiah Hoyer
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
| | - Jack Dorman
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Mary E Gebhardt
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - Giovanna Carpi
- Department of Biological Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Douglas E Norris
- The W. Harry Feinstone Department of Molecular Microbiology and Immunology, Johns Hopkins Malaria Research Institute, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, 21205, USA
| | - James M Pipas
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Ethan K Jackson
- Microsoft Premonition, Microsoft Research, Redmond, WA, 98052, USA
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3
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Fragoso MSI, de Siqueira CM, Vitorino FNL, Vieira AZ, Martins-Duarte ÉS, Faoro H, da Cunha JPC, Ávila AR, Nardelli SC. TgKDAC4: A Unique Deacetylase of Toxoplasma' s Apicoplast. Microorganisms 2023; 11:1558. [PMID: 37375060 DOI: 10.3390/microorganisms11061558] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/04/2023] [Accepted: 05/09/2023] [Indexed: 06/29/2023] Open
Abstract
Toxoplasma gondii is an obligate intracellular parasite of the phylum Apicomplexa and causes toxoplasmosis infections, a disease that affects a quarter of the world's population and has no effective cure. Epigenetic regulation is one of the mechanisms controlling gene expression and plays an essential role in all organisms. Lysine deacetylases (KDACs) act as epigenetic regulators affecting gene silencing in many eukaryotes. Here, we focus on TgKDAC4, an enzyme unique to apicomplexan parasites, and a class IV KDAC, the least-studied class of deacetylases so far. This enzyme shares only a portion of the specific KDAC domain with other organisms. Phylogenetic analysis from the TgKDAC4 domain shows a putative prokaryotic origin. Surprisingly, TgKDAC4 is located in the apicoplast, making it the only KDAC found in this organelle to date. Transmission electron microscopy assays confirmed the presence of TgKDAC4 in the periphery of the apicoplast. We identified possible targets or/and partners of TgKDAC4 by immunoprecipitation assays followed by mass spectrometry analysis, including TgCPN60 and TgGAPDH2, both located at the apicoplast and containing acetylation sites. Understanding how the protein works could provide new insights into the metabolism of the apicoplast, an essential organelle for parasite survival.
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Affiliation(s)
| | | | - Francisca Nathália Luna Vitorino
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
| | | | - Érica Santos Martins-Duarte
- Department of Parasitology, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte 31270-901, Brazil
| | - Helisson Faoro
- Instituto Carlos Chagas, Fundação Oswaldo Cruz, Curitiba 81350-010, Brazil
| | - Júlia Pinheiro Chagas da Cunha
- Special Laboratory of Cell Cycle, Center of Toxins, Immune Response and Cell Signalling (CeTICS), Instituto Butantan, São Paulo 05503-900, Brazil
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4
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Sharma M, Nair DT. Pfprex from
Plasmodium falciparum
can bypass oxidative stress‐induced DNA lesions. FEBS J 2022; 289:5218-5240. [DOI: 10.1111/febs.16414] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/13/2022] [Accepted: 02/25/2022] [Indexed: 12/24/2022]
Affiliation(s)
- Minakshi Sharma
- Regional Centre for Biotechnology Faridabad India
- Kalinga Institute of Industrial Technology Bhubaneshwar India
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5
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Kuroiwa T, Yagisawa F, Fujiwara T, Misumi O, Nagata N, Imoto Y, Yoshida Y, Mogi Y, Miyagishima SY, Kuroiwa H. Smooth Loop-Like Mitochondrial Nucleus in the Primitive Red Alga <i>Cyanidioschyzon merolae</i> Revealed by Drying Treatment. CYTOLOGIA 2021. [DOI: 10.1508/cytologia.86.89] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Fumi Yagisawa
- Center for Research Advancement and Collaboration, University of the Ryukyus
| | - Takayuki Fujiwara
- Department of Gene Function and Phenomics, National Institute of Genetics
| | - Osami Misumi
- Department of Biological Science and Chemistry, Faculty of Science, Yamaguchi University
| | - Noriko Nagata
- Department of Chemical and Biological Science, Japan Women’s University
| | - Yuuta Imoto
- Department of Cell Biology, Johns Hopkins University School of Medicine
| | - Yamato Yoshida
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Yuko Mogi
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | | | - Haruko Kuroiwa
- Department of Chemical and Biological Science, Japan Women’s University
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6
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Martins-Duarte ÉS, Sheiner L, Reiff SB, de Souza W, Striepen B. Replication and partitioning of the apicoplast genome of Toxoplasma gondii is linked to the cell cycle and requires DNA polymerase and gyrase. Int J Parasitol 2021; 51:493-504. [PMID: 33581138 PMCID: PMC8113025 DOI: 10.1016/j.ijpara.2020.11.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Revised: 10/30/2020] [Accepted: 11/08/2020] [Indexed: 10/26/2022]
Abstract
Apicomplexans are the causative agents of numerous important infectious diseases including malaria and toxoplasmosis. Most of them harbour a chloroplast-like organelle called the apicoplast that is essential for the parasites' metabolism and survival. While most apicoplast proteins are nuclear encoded, the organelle also maintains its own genome, a 35 kb circle. In this study we used Toxoplasma gondii to identify and characterise essential proteins involved in apicoplast genome replication and to understand how apicoplast genome segregation unfolds over time. We demonstrated that the DNA replication enzymes Prex, DNA gyrase and DNA single stranded binding protein localise to the apicoplast. We show in knockdown experiments that apicoplast DNA Gyrase A and B, and Prex are required for apicoplast genome replication and growth of the parasite. Analysis of apicoplast genome replication by structured illumination microscopy in T. gondii tachyzoites showed that apicoplast nucleoid division and segregation initiate at the beginning of S phase and conclude during mitosis. Thus, the replication and division of the apicoplast nucleoid is highly coordinated with nuclear genome replication and mitosis. Our observations highlight essential components of apicoplast genome maintenance and shed light on the timing of this process in the context of the overall parasite cell cycle.
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Affiliation(s)
- Érica S Martins-Duarte
- Laboratório de Quimioterapia de Protozoários Egler Chiari, Departamento de Parasitologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil; Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil.
| | - Lilach Sheiner
- Wellcome Centre for Integrative Parasitology, University of Glasgow, 120 University Place Glasgow, United Kingdom
| | - Sarah B Reiff
- Department of Cellular Biology, University of Georgia, Athens, GA, USA
| | - Wanderley de Souza
- Núcleo de Biologia Estrutural e Bioimagens (CENABIO) - Instituto Nacional de Ciência e Tecnologia em Biologia Estrutural e Biomagens (INBEB), Rio de Janeiro, RJ, Brazil; Laboratório de Ultraestrutura Celular Hertha Meyer, Instituto de Biofísica Carlos Chagas Filho, Universidade Federal do Rio de Janeiro, Rio de Janeiro, RJ, Brazil
| | - Boris Striepen
- Department of Cellular Biology, University of Georgia, Athens, GA, USA; Department of Pathobiology, School of Veterinary Medicine, University of Pennsylvania, Philadelphia, PA. USA
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7
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Kim S, Park KS. Highly specific nuclear labeling via in situ formation of fluorescent copper nanoparticles. NANOSCALE 2021; 13:81-84. [PMID: 33351013 DOI: 10.1039/d0nr06657e] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
When imaging cells, nuclear counterstaining is imperative; however, many commercial nuclear-staining dyes based on nucleic acid intercalation result in nonspecific signals in the cytoplasm. Here, we propose a new strategy that stains the nucleus with high specificity by in situ formation of DNA-templated copper nanoparticles (CuNPs). We demonstrated that genomic DNA in the nucleus enabled rapid formation of highly fluorescent CuNPs immediately following addition of a copper ion source and ascorbate as a reducing agent. Moreover, we found that RNA and mitochondrial DNA, largely responsible for nonspecific cytoplasmic signals from commercial nuclear-staining dyes, did not mediate the formation of the highly fluorescent CuNPs, resulting in highly specific nuclear staining at a reduced cost relative to commercially available methods. Furthermore, we verified the compatibility of the proposed method with other fluorescence-labeling techniques. These results demonstrated the efficacy of this method and its promise as a powerful tool for cell imaging.
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Affiliation(s)
- Seokjoon Kim
- Department of Biological Engineering, College of Engineering, Konkuk University, Seoul 05029, Republic of Korea.
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8
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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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9
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Abstract
The shape and number of mitochondria respond to the metabolic needs during the cell cycle of the eukaryotic cell. In the best-studied model systems of animals and fungi, the cells contain many mitochondria, each carrying its own nucleoid. The organelles, however, mostly exist as a dynamic network, which undergoes constant cycles of division and fusion. These mitochondrial dynamics are driven by intricate protein machineries centered around dynamin-related proteins (DRPs). Here, we review recent advances on the dynamics of mitochondria and mitochondrion-related organelles (MROs) of parasitic protists. In contrast to animals and fungi, many parasitic protists from groups of Apicomplexa or Kinetoplastida carry only a single mitochondrion with a single nucleoid. In these groups, mitochondrial division is strictly coupled to the cell cycle, and the morphology of the organelle responds to the cell differentiation during the parasite life cycle. On the other hand, anaerobic parasitic protists such as Giardia, Entamoeba, and Trichomonas contain multiple MROs that have lost their organellar genomes. We discuss the function of DRPs, the occurrence of mitochondrial fusion, and mitophagy in the parasitic protists from the perspective of eukaryote evolution.
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Affiliation(s)
- Luboš Voleman
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
| | - Pavel Doležal
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Prague, Czech Republic
- * E-mail:
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10
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Lamien-Meda A, Fuehrer HP, Noedl H. Novel high resolution melting (HRM) and snapback assays for simultaneous detection and differentiation of Plasmodium ovale spp. Acta Trop 2019; 192:75-81. [PMID: 30711423 DOI: 10.1016/j.actatropica.2019.01.018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Revised: 01/18/2019] [Accepted: 01/18/2019] [Indexed: 12/16/2022]
Abstract
Plasmodium ovale spp. are two of the six species of apicomplexan parasites belonging to the genus Plasmodium commonly causing disease in humans. A recent phylogeny study has identified both Plasmodium ovale species (P. ovale curtisi and P. ovale wallikeri) as two sympatric occurring species. The actual prevalence and clinical relevance of P. ovale spp. are likely underestimated due to low parasitemia and mixed infections, which pose a major challenge to microscopic diagnosis and are frequently undetectable using malaria Rapid Diagnostic Tests (RDTs). The aim of this work is to develop a HRM-based assay for simultaneous detection and differentiation of P. ovale wallikeri and P. ovale curtisi. Thirty three well-documented P. ovale spp. samples from previous studies were used for this study. The newly developed High Resolution Melting (HRM) assay targeting the apicoplast genome was highly specific to both P. ovale species. Adding a snapback tail at the 5' end of the forward primer for a nested HRM PCR, increased the melting temperature (Tm) difference between the two species. To our knowledge this study reports the first direct HRM assay developed on the apicoplast genome, specific for both P. ovale species. This method provides added value to the WHO open request of developing new practical malaria diagnostic methods for the malaria elimination program and could contribute to a quick and efficient diagnosis of low-level parasitemia, symptomatic or asymptomatic, as well as mixed or single P. ovale infections.
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Affiliation(s)
- Aline Lamien-Meda
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria.
| | - Hans-Peter Fuehrer
- Institute of Parasitology, University of Veterinary Medicine, Vienna, Austria
| | - Harald Noedl
- Institute of Specific Prophylaxis and Tropical Medicine, Medical University of Vienna, Austria
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11
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Ramakrishnan C, Maier S, Walker RA, Rehrauer H, Joekel DE, Winiger RR, Basso WU, Grigg ME, Hehl AB, Deplazes P, Smith NC. An experimental genetically attenuated live vaccine to prevent transmission of Toxoplasma gondii by cats. Sci Rep 2019; 9:1474. [PMID: 30728393 PMCID: PMC6365665 DOI: 10.1038/s41598-018-37671-8] [Citation(s) in RCA: 92] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 12/11/2018] [Indexed: 12/20/2022] Open
Abstract
Almost any warm-blooded creature can be an intermediate host for Toxoplasma gondii. However, sexual reproduction of T. gondii occurs only in felids, wherein fertilisation of haploid macrogametes by haploid microgametes, results in diploid zygotes, around which a protective wall develops, forming unsporulated oocysts. Unsporulated oocysts are shed in the faeces of cats and meiosis gives rise to haploid sporozoites within the oocysts. These, now infectious, sporulated oocysts contaminate the environment as a source of infection for people and their livestock. RNA-Seq analysis of cat enteric stages of T. gondii uncovered genes expressed uniquely in microgametes and macrogametes. A CRISPR/Cas9 strategy was used to create a T. gondii strain that exhibits defective fertilisation, decreased fecundity and generates oocysts that fail to produce sporozoites. Inoculation of cats with this engineered parasite strain totally prevented oocyst excretion following infection with wild-type T. gondii, demonstrating that this mutant is an attenuated, live, transmission-blocking vaccine.
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Affiliation(s)
- Chandra Ramakrishnan
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Simone Maier
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Robert A Walker
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Hubert Rehrauer
- Functional Genomics Center Zürich, Winterthurerstrasse 190, 8057, Zürich, Switzerland
| | - Deborah E Joekel
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Rahel R Winiger
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Walter U Basso
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland
| | - Michael E Grigg
- Molecular Parasitology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, Maryland, USA
| | - Adrian B Hehl
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland.
| | - Peter Deplazes
- Institute of Parasitology, University of Zürich, Winterthurerstrasse 266a, 8057, Zürich, Switzerland.
| | - Nicholas C Smith
- Research School of Biology, Australian National University, Canberra, ACT, 0200, Australia. .,School of Science and Health, Western Sydney University, Parramatta South Campus, Sydney, NSW, 2116, Australia.
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12
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Ikuta T, Igawa K, Tame A, Kuroiwa T, Kuroiwa H, Aoki Y, Takaki Y, Nagai Y, Ozawa G, Yamamoto M, Deguchi R, Fujikura K, Maruyama T, Yoshida T. Surfing the vegetal pole in a small population: extracellular vertical transmission of an 'intracellular' deep-sea clam symbiont. ROYAL SOCIETY OPEN SCIENCE 2016; 3:160130. [PMID: 27293794 PMCID: PMC4892456 DOI: 10.1098/rsos.160130] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 04/21/2016] [Indexed: 06/06/2023]
Abstract
Symbiont transmission is a key event for understanding the processes underlying symbiotic associations and their evolution. However, our understanding of the mechanisms of symbiont transmission remains still fragmentary. The deep-sea clam Calyptogena okutanii harbours obligate sulfur-oxidizing intracellular symbiotic bacteria in the gill epithelial cells. In this study, we determined the localization of their symbiont associating with the spawned eggs, and the population size of the symbiont transmitted via the eggs. We show that the symbionts are located on the outer surface of the egg plasma membrane at the vegetal pole, and that each egg carries approximately 400 symbiont cells, each of which contains close to 10 genomic copies. The very small population size of the symbiont transmitted via the eggs might narrow the bottleneck and increase genetic drift, while polyploidy and its transient extracellular lifestyle might slow the rate of genome reduction. Additionally, the extracellular localization of the symbiont on the egg surface may increase the chance of symbiont exchange. This new type of extracellular transovarial transmission provides insights into complex interactions between the host and symbiont, development of both host and symbiont, as well as the population dynamics underlying genetic drift and genome evolution in microorganisms.
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Affiliation(s)
- Tetsuro Ikuta
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Kanae Igawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
| | - Akihiro Tame
- Marine Works Japan, Ltd, 3-54-1 Oppamahigashi, Yokosuka, Kanagawa 237-0063, Japan
| | - Tsuneyoshi Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Haruko Kuroiwa
- Department of Chemical and Biological Sciences, Japan Women's University, 2-8-1 Mejirodai, Bunkyo-ku, Tokyo 112-8681, Japan
- Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency, Gobancho, Chiyoda-ku, Tokyo 102-0076, Japan
| | - Yui Aoki
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yoshihiro Takaki
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Yukiko Nagai
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Genki Ozawa
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
| | - Masahiro Yamamoto
- Department of Subsurface Geobiological Analysis and Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Ryusaku Deguchi
- Department of Biology, Miyagi University of Education, Aoba-ku, Sendai, Miyagi 980-0845, Japan
| | - Katsunori Fujikura
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Tadashi Maruyama
- Research and Development Center for Marine Biosciences, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
| | - Takao Yoshida
- Department of Marine Biodiversity Research, Japan Agency for Marine-Earth Science and Technology (JAMSTEC), 2-15 Natsushima, Yokosuka, Kanagawa 237-0061, Japan
- Graduate School of Marine Science and Technology, Tokyo University of Marine Science and Technology, 4-5-7 Konan, Minato-ku, Tokyo 108-8477, Japan
- Department of Marine Biosciences, School of Marine Biosciences, Kitasato University, 1-15-1 Kitasato, Minami-ku, Sagamihara, Kanagawa 252-0373, Japan
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13
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Tang Girdwood SC, Nenortas E, Shapiro TA. Targeting the gyrase of Plasmodium falciparum with topoisomerase poisons. Biochem Pharmacol 2015; 95:227-37. [PMID: 25881748 DOI: 10.1016/j.bcp.2015.03.018] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 03/31/2015] [Indexed: 11/17/2022]
Abstract
Drug-resistant malaria poses a major public health problem throughout the world and the need for new antimalarial drugs is growing. The apicoplast, a chloroplast-like organelle essential for malaria parasite survival and with no counterpart in humans, offers an attractive target for selectively toxic new therapies. The apicoplast genome (plDNA) is a 35 kb circular DNA that is served by gyrase, a prokaryotic type II topoisomerase. Gyrase is poisoned by fluoroquinolone antibacterials that stabilize a catalytically inert ternary complex of enzyme, its plDNA substrate, and inhibitor. We used fluoroquinolones to study the gyrase and plDNA of Plasmodium falciparum. New methods for isolating and separating plDNA reveal four topologically different forms and permit a quantitative exam of perturbations that result from gyrase poisoning. In keeping with its role in DNA replication, gyrase is most abundant in late stages of the parasite lifecycle, but several lines of evidence indicate that even in these cells the enzyme is present in relatively low abundance: about 1 enzyme for every two plDNAs or a ratio of 1 gyrase: 70 kb DNA. For a spectrum of quinolones, correlation was generally good between antimalarial activity and gyrase poisoning, the putative molecular mechanism of drug action. However, in P. falciparum there is evidence for off-target toxicity, particularly for ciprofloxacin. These studies highlight the utility of the new methods and of fluoroquinolones as a tool for studying the in situ workings of gyrase and its plDNA substrate.
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Affiliation(s)
- Sonya C Tang Girdwood
- Division of Clinical Pharmacology, Department of Medicine, The Johns Hopkins University, Baltimore, MD, United States; Malaria Research Institute, The Johns Hopkins University, Baltimore, MD, United States; Department of Pediatrics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, United States(1).
| | - Elizabeth Nenortas
- Division of Clinical Pharmacology, Department of Medicine, The Johns Hopkins University, Baltimore, MD, United States; Malaria Research Institute, The Johns Hopkins University, Baltimore, MD, United States.
| | - Theresa A Shapiro
- Division of Clinical Pharmacology, Department of Medicine, The Johns Hopkins University, Baltimore, MD, United States; Malaria Research Institute, The Johns Hopkins University, Baltimore, MD, United States.
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14
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Oriero CE, van Geertruyden JP, Jacobs J, D'Alessandro U, Nwakanma D. Validation of an apicoplast genome target for the detection of Plasmodium species using polymerase chain reaction and loop mediated isothermal amplification. Clin Microbiol Infect 2015; 21:686.e1-7. [PMID: 25747504 DOI: 10.1016/j.cmi.2015.02.025] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Revised: 02/18/2015] [Accepted: 02/24/2015] [Indexed: 11/30/2022]
Abstract
The genome of the Plasmodium apicoplast, which has a higher copy number compared with current targets for molecular diagnosis of malaria, appears to be a suitable target for detection of submicroscopic infections that are capable of sustaining transmission. Novel primers targeting a conserved segment of the apicoplast (PFC10_AP|0010:rRNA) were designed and used in a number of different high throughput platforms such as single-step PCR (ssPCR), nested PCR (nPCR) and loop-mediated isothermal amplification (LAMP) for parasite detection. Replicates of ten-fold serial dilutions of Plasmodium falciparum 3D7 DNA, with equivalent parasite density ranges of 200,000 to 0.2 parasites/μL, were used to determine the limit of detection and repeatability of each assay. A panel of 184 archived DNA samples extracted from either EDTA whole blood or dried blood spots, from across West Africa and South East Asia was used to determine the diagnostic performance of the assays. All assays amplified the 2 parasites/μL dilution except the ssPCR, which amplified two of the three replicates. Using an 18S rRNA PCR as reference, the sensitivity was 98% (95% CI 93-100%) for the LAMP assay, 87% (95% CI 79-93%) for ssPCR and 100% (95% CI 97-100%) for nPCR. Specificity was 91% (95% CI 83-96%) for LAMP, 82% (95% CI 72-90%) for ssPCR and 66% (95% CI 54-76%) for nPCR. The apicoplast genome-based nPCR detected more positive samples overall than the reference method. Discrepant samples were confirmed as true positives using a probe-based real-time quantitative PCR assay. The results show that the apicoplast genome is a suitable target for molecular diagnosis of malaria.
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Affiliation(s)
- C E Oriero
- Medical Research Council, Fajara, Gambia; International Health Unit, University of Antwerp, Belgium; Institute of Tropical Medicine, Antwerp, Belgium.
| | | | - J Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium; Department of Microbiology and Immunology, University of Leuven, Belgium
| | - U D'Alessandro
- Medical Research Council, Fajara, Gambia; Institute of Tropical Medicine, Antwerp, Belgium; London School of Tropical Medicine and Hygiene, London, UK
| | - D Nwakanma
- Medical Research Council, Fajara, Gambia
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15
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Farrell A, Coleman BI, Benenati B, Brown KM, Blader IJ, Marth GT, Gubbels MJ. Whole genome profiling of spontaneous and chemically induced mutations in Toxoplasma gondii. BMC Genomics 2014; 15:354. [PMID: 24885922 PMCID: PMC4035079 DOI: 10.1186/1471-2164-15-354] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2013] [Accepted: 05/02/2014] [Indexed: 12/18/2022] Open
Abstract
Background Next generation sequencing is helping to overcome limitations in organisms less accessible to classical or reverse genetic methods by facilitating whole genome mutational analysis studies. One traditionally intractable group, the Apicomplexa, contains several important pathogenic protozoan parasites, including the Plasmodium species that cause malaria. Here we apply whole genome analysis methods to the relatively accessible model apicomplexan, Toxoplasma gondii, to optimize forward genetic methods for chemical mutagenesis using N-ethyl-N-nitrosourea (ENU) and ethylmethane sulfonate (EMS) at varying dosages. Results By comparing three different lab-strains we show that spontaneously generated mutations reflect genome composition, without nucleotide bias. However, the single nucleotide variations (SNVs) are not distributed randomly over the genome; most of these mutations reside either in non-coding sequence or are silent with respect to protein coding. This is in contrast to the random genomic distribution of mutations induced by chemical mutagenesis. Additionally, we report a genome wide transition vs transversion ratio (ti/tv) of 0.91 for spontaneous mutations in Toxoplasma, with a slightly higher rate of 1.20 and 1.06 for variants induced by ENU and EMS respectively. We also show that in the Toxoplasma system, surprisingly, both ENU and EMS have a proclivity for inducing mutations at A/T base pairs (78.6% and 69.6%, respectively). Conclusions The number of SNVs between related laboratory strains is relatively low and managed by purifying selection away from changes to amino acid sequence. From an experimental mutagenesis point of view, both ENU (24.7%) and EMS (29.1%) are more likely to generate variation within exons than would naturally accumulate over time in culture (19.1%), demonstrating the utility of these approaches for yielding proportionally greater changes to the amino acid sequence. These results will not only direct the methods of future chemical mutagenesis in Toxoplasma, but also aid in designing forward genetic approaches in less accessible pathogenic protozoa as well. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-354) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | | | | | - Marc-Jan Gubbels
- Department of Biology, Boston College, Higgins Hall 355, 140 Commonwealth Avenue, Chestnut Hill, MA 02467, USA.
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16
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An FtsH protease is recruited to the mitochondrion of Plasmodium falciparum. PLoS One 2013; 8:e74408. [PMID: 24058559 PMCID: PMC3772908 DOI: 10.1371/journal.pone.0074408] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Accepted: 08/01/2013] [Indexed: 11/19/2022] Open
Abstract
The two organelles, apicoplast and mitochondrion, of the malaria parasite Plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. Little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. We report the identification of an AAA+/FtsH protease homolog (PfFtsH1) that exhibits ATP- and Zn(2+)-dependent protease activity. PfFtsH1 undergoes processing, forms oligomeric assemblies, and is associated with the membrane fraction of the parasite cell. Generation of a transfectant parasite line with hemagglutinin-tagged PfFtsH1, and immunofluorescence assay with anti-PfFtsH1 Ab demonstrated that the protein localises to P. falciparum mitochondria. Phylogenetic analysis and the single transmembrane region identifiable in PfFtsH1 suggest that it is an i-AAA like inner mitochondrial membrane protein. Expression of PfFtsH1 in Escherichia coli converted a fraction of bacterial cells into division-defective filamentous forms implying a sequestering effect of the Plasmodium factor on the bacterial homolog, indicative of functional conservation with EcFtsH. These results identify a membrane-associated mitochondrial AAA+/FtsH protease as a candidate regulatory protein for organelle biogenesis in P. falciparum.
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17
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Janouskovec J, Sobotka R, Lai DH, Flegontov P, Koník P, Komenda J, Ali S, Prásil O, Pain A, Oborník M, Lukes J, Keeling PJ. Split photosystem protein, linear-mapping topology, and growth of structural complexity in the plastid genome of Chromera velia. Mol Biol Evol 2013; 30:2447-62. [PMID: 23974208 DOI: 10.1093/molbev/mst144] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
The canonical photosynthetic plastid genomes consist of a single circular-mapping chromosome that encodes a highly conserved protein core, involved in photosynthesis and ATP generation. Here, we demonstrate that the plastid genome of the photosynthetic relative of apicomplexans, Chromera velia, departs from this view in several unique ways. Core photosynthesis proteins PsaA and AtpB have been broken into two fragments, which we show are independently transcribed, oligoU-tailed, translated, and assembled into functional photosystem I and ATP synthase complexes. Genome-wide transcription profiles support expression of many other highly modified proteins, including several that contain extensions amounting to hundreds of amino acids in length. Canonical gene clusters and operons have been fragmented and reshuffled into novel putative transcriptional units. Massive genomic coverage by paired-end reads, coupled with pulsed-field gel electrophoresis and polymerase chain reaction, consistently indicate that the C. velia plastid genome is linear-mapping, a unique state among all plastids. Abundant intragenomic duplication probably mediated by recombination can explain protein splits, extensions, and genome linearization and is perhaps the key driving force behind the many features that defy the conventional ways of plastid genome architecture and function.
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Affiliation(s)
- Jan Janouskovec
- Department of Botany, University of British Columbia, Vancouver, British Columbia, Canada
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18
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Jacot D, Daher W, Soldati-Favre D. Toxoplasma gondii myosin F, an essential motor for centrosomes positioning and apicoplast inheritance. EMBO J 2013; 32:1702-16. [PMID: 23695356 DOI: 10.1038/emboj.2013.113] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2012] [Accepted: 04/22/2013] [Indexed: 11/09/2022] Open
Abstract
Members of the Apicomplexa phylum possess an organelle surrounded by four membranes, originating from the secondary endosymbiosis of a red alga. This so-called apicoplast hosts essential metabolic pathways. We report here that apicoplast inheritance is an actin-based process. Concordantly, parasites depleted in either profilin or actin depolymerizing factor, or parasites overexpressing the FH2 domain of formin 2, result in loss of the apicoplast. The class XXII myosin F (MyoF) is conserved across the phylum and localizes in the vicinity of the Toxoplasma gondii apicoplast during division. Conditional knockdown of TgMyoF severely affects apicoplast turnover, leading to parasite death. This recapitulates the phenotype observed upon perturbation of actin dynamics that led to the accumulation of the apicoplast and secretory organelles in enlarged residual bodies. To further dissect the mode of action of this motor, we conditionally stabilized the tail of MyoF, which forms an inactive heterodimer with endogenous TgMyoF. This dominant negative mutant reveals a central role of this motor in the positioning of the two centrosomes prior to daughter cell formation and in apicoplast segregation.
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Affiliation(s)
- Damien Jacot
- Department of Microbiology and Molecular Medicine, CMU, University of Geneva, Geneva, Switzerland
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19
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The HU protein is important for apicoplast genome maintenance and inheritance in Toxoplasma gondii. EUKARYOTIC CELL 2012; 11:905-15. [PMID: 22611021 DOI: 10.1128/ec.00029-12] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The apicoplast, a chloroplast-like organelle, is an essential cellular component of most apicomplexan parasites, including Plasmodium and Toxoplasma. The apicoplast maintains its own genome, a 35-kb DNA molecule that largely encodes proteins required for organellar transcription and translation. Interference with apicoplast genome maintenance and function is a validated target for drug therapy for malaria and toxoplasmosis. However, the many proteins required for genome maintenance and inheritance remain largely unstudied. Here we genetically characterize a nucleus-encoded homolog to the bacterial HU protein in Toxoplasma gondii. In bacteria, HU is a DNA-binding structural protein with fundamental roles in transcription, replication initiation, and DNA repair. Immunofluorescence assays reveal that in T. gondii this protein localizes to the apicoplast. We have found that the HU protein from Toxoplasma can successfully complement bacterial ΔhupA mutants, supporting a similar function. We were able to construct a genetic knockout of HU in Toxoplasma. This Δhu mutant is barely viable and exhibits significant growth retardation. Upon further analysis of the mutant phenotype, we find that this mutant has a dramatically reduced apicoplast genome copy number and, furthermore, suffers defects in the segregation of the apicoplast organelle. Our findings not only show that the HU protein is important for Toxoplasma cell biology but also demonstrate the importance of the apicoplast genome in the biogenesis of the organelle.
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20
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GFP-targeting allows visualization of the apicoplast throughout the life cycle of live malaria parasites. Biol Cell 2012; 101:415-30, 5 p following 430. [DOI: 10.1042/bc20080202] [Citation(s) in RCA: 64] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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21
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Payne TM, Payne AJ, Knoll LJ. A Toxoplasma gondii mutant highlights the importance of translational regulation in the apicoplast during animal infection. Mol Microbiol 2011; 82:1204-16. [PMID: 22059956 DOI: 10.1111/j.1365-2958.2011.07879.x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Toxoplasma gondii is an obligate intracellular parasite of all warm-blooded animals. We previously described a forward genetic screen to identify T. gondii mutants defective in the establishment of a chronic infection. One of the mutants isolated was disrupted in the 3' untranslated region (3'UTR) of an orthologue of bacterial translation elongation factor G (EFG). The mutant does not have a growth defect in tissue culture. Genetic complementation of this mutant with the genomic locus of TgEFG restores virulence in an acute infection mouse model. Epitope tagged TgEFG localized to the apicoplast, via a non-canonical targeting signal, where it functions as an elongation factor for translation in the apicoplast. Comparisons of TgEFG expression constructs with wild-type or mutant 3'UTRs showed that a wild-type 3'UTR is necessary for translation of TgEFG. In tissue culture, the TgEFG transcript is equally abundant in wild-type and mutant parasites; however, during an animal infection, the TgEFG transcript is increased more than threefold in the mutant. These results highlight that in tissue culture, translation in the apicoplast can be diminished, but during an animal infection, translation in the apicoplast must be fully functional.
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Affiliation(s)
- T Matthew Payne
- Department of Medical Microbiology and Immunology, University of Wisconsin-Madison, Madison, WI 53706, USA
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22
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Sato S. The apicomplexan plastid and its evolution. Cell Mol Life Sci 2011; 68:1285-96. [PMID: 21380560 PMCID: PMC3064897 DOI: 10.1007/s00018-011-0646-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2011] [Revised: 02/15/2011] [Accepted: 02/15/2011] [Indexed: 11/24/2022]
Abstract
Protistan species belonging to the phylum Apicomplexa have a non-photosynthetic secondary plastid-the apicoplast. Although its tiny genome and even the entire nuclear genome has been sequenced for several organisms bearing the organelle, the reason for its existence remains largely obscure. Some of the functions of the apicoplast, including housekeeping ones, are significantly different from those of other plastids, possibly due to the organelle's unique symbiotic origin.
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Affiliation(s)
- Shigeharu Sato
- Division of Parasitology, MRC National Institute for Medical Research, Mill Hill, London, UK.
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23
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Zhao Q, Zhang M, Hong L, Zhou K, Lin Y. Evaluation of drug effects on Toxoplasma gondii nuclear and plastid DNA replication using real-time PCR. Parasitol Res 2010; 106:1257-62. [PMID: 20186551 DOI: 10.1007/s00436-010-1792-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2009] [Accepted: 02/03/2010] [Indexed: 01/07/2023]
Abstract
Toxoplasma gondii Nicolle and Manceaux, 1908 is a unicellular protozoan that can infect a broad spectrum of organisms including humans. In addition to a nuclear genome, it also carries a circular DNA within a plastid-like organelle (apicoplast) and a linear genome within its mitochondria. The plastid organelle has been shown to be the target of various anti-parasitic drugs or antibiotics. To evaluate the effects of agents on the DNA replication of T. gondii, we tested six drugs (ciprofloxacin, acetylspiramycin, clindamycin, azithromycin, artemether, and sulfadiazine) on the parasite cultured in Hela cells. After drug treatment for 48 h, the parasite growth and DNA replication were evaluated and quantitated using TaqMan real-time quantitative PCR with oligonucleotide primers synthesized based on a gene from the apicoplast genome (ycf24, Genbank accession no. U87145) and a gene from the nuclear genome (uprt, Genbank accession no. U10246). Our results showed that ciprofloxacin was the most effective in inhibiting the replication of the plastid DNA after 48 h drug treatment, with a reduction of 22% in the copy number of the plastid DNA. Artemether was the most effective drug in suppressing the proliferation of tachyzoites. This study also demonstrates that real-time quantitative PCR is a simple and useful technique for monitoring parasite growth and DNA replication.
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Affiliation(s)
- Qing Zhao
- School of Life Sciences, Xiamen University, Xiamen, Fujian, China.
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24
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Seeber F, Soldati-Favre D. Metabolic Pathways in the Apicoplast of Apicomplexa. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2010; 281:161-228. [DOI: 10.1016/s1937-6448(10)81005-6] [Citation(s) in RCA: 121] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
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25
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Bontell IL, Hall N, Ashelford KE, Dubey JP, Boyle JP, Lindh J, Smith JE. Whole genome sequencing of a natural recombinant Toxoplasma gondii strain reveals chromosome sorting and local allelic variants. Genome Biol 2009; 10:R53. [PMID: 19457243 PMCID: PMC2718519 DOI: 10.1186/gb-2009-10-5-r53] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2009] [Revised: 05/01/2009] [Accepted: 05/20/2009] [Indexed: 11/29/2022] Open
Abstract
Extensive sequence analysis of eight Toxoplasma gondii isolates from Uganda has revealed chromosome sorting and local allelic variants. Background Toxoplasma gondii is a zoonotic parasite of global importance. In common with many protozoan parasites it has the capacity for sexual recombination, but current evidence suggests this is rarely employed. The global population structure is dominated by a small number of clonal genotypes, which exhibit biallelic variation and limited intralineage divergence. Little is known of the genotypes present in Africa despite the importance of AIDS-associated toxoplasmosis. Results We here present extensive sequence analysis of eight isolates from Uganda, including the whole genome sequencing of a type II/III recombinant isolate, TgCkUg2. 454 sequencing gave 84% coverage across the approximate 61 Mb genome and over 70,000 single nucleotide polymorphisms (SNPs) were mapped against reference strains. TgCkUg2 was shown to contain entire chromosomes of either type II or type III origin, demonstrating chromosome sorting rather than intrachromosomal recombination. We mapped 1,252 novel polymorphisms and clusters of new SNPs within coding sequence implied selective pressure on a number of genes, including surface antigens and rhoptry proteins. Further sequencing of the remaining isolates, six type II and one type III strain, confirmed the presence of novel SNPs, suggesting these are local allelic variants within Ugandan type II strains. In mice, the type III isolate had parasite burdens at least 30-fold higher than type II isolates, while the recombinant strain had an intermediate burden. Conclusions Our data demonstrate that recombination between clonal lineages does occur in nature but there is nevertheless close homology between African and North American isolates. The quantity of high confidence SNP data generated in this study and the availability of the putative parental strains to this natural recombinant provide an excellent basis for future studies of the genetic divergence and of genotype-phenotype relationships.
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Affiliation(s)
- Irene Lindström Bontell
- Institute of Integrative and Comparative Biology, Clarendon Way, University of Leeds, Leeds LS2 9JT, UK.
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26
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van Dooren GG, Reiff SB, Tomova C, Meissner M, Humbel BM, Striepen B. A novel dynamin-related protein has been recruited for apicoplast fission in Toxoplasma gondii. Curr Biol 2009; 19:267-76. [PMID: 19217294 DOI: 10.1016/j.cub.2008.12.048] [Citation(s) in RCA: 91] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2008] [Revised: 11/18/2008] [Accepted: 12/22/2008] [Indexed: 01/06/2023]
Abstract
BACKGROUND Apicomplexan parasites cause numerous important human diseases, including malaria and toxoplasmosis. Apicomplexa belong to the Alveolata, a group that also includes ciliates and dinoflagellates. Apicomplexa retain a plastid organelle (the apicoplast) that was derived from an endosymbiotic relationship between the alveolate ancestor and a red alga. Apicoplasts are essential for parasite growth and must correctly divide and segregate into daughter cells upon cytokinesis. Apicoplast division depends on association with the mitotic spindle, although little is known about the molecular machinery involved in this process. Apicoplasts lack the conserved machinery that divides chloroplasts in plants and red algae, suggesting that these mechanisms are unique. RESULTS Here, we demonstrate that a dynamin-related protein in Toxoplasma gondii (TgDrpA) localizes to punctate regions on the apicoplast surface. We generate a conditional dominant-negative TgDrpA cell line to disrupt TgDrpA functions and demonstrate that TgDrpA is essential for parasite growth and apicoplast biogenesis. Fluorescence recovery after photobleaching and time-lapse imaging studies provide evidence for a direct role for TgDrpA in apicoplast fission. CONCLUSIONS Our data suggest that DrpA was likely recruited from the alveolate ancestor to function in fission of the symbiont and ultimately replaced the conserved division machinery of that symbiont.
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Affiliation(s)
- Giel G van Dooren
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, 30602, USA
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27
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Maeda-Sano K, Sato S, Ueda T, Yui R, Ito K, Hata M, Nakano A, Kita K, Murakami-Murofushi K, Sasaki N. Visualization of Mitochondrial and Apicoplast Nucleoids in the Human Malaria Parasite Plasmodium falciparum by SYBR Green I and PicoGreen Staining. CYTOLOGIA 2009. [DOI: 10.1508/cytologia.74.449] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Affiliation(s)
| | - Shigeharu Sato
- Division of Parasitology, MRC National Institute for Medical Research
| | - Takashi Ueda
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
| | - Ryoko Yui
- Division of Biological Science, Graduate School of Science, Nagoya University
| | - Kie Ito
- Division of Biology, Faculty of Science, Ochanomizu University
- Division of Biological Science, Graduate School of Science, Nagoya University
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo
| | - Masayuki Hata
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | - Akihiko Nakano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo
- RIKEN Advanced Science Institute
| | - Kiyoshi Kita
- Department of Biomedical Chemistry, Graduate School of Medicine, The University of Tokyo
| | | | - Narie Sasaki
- Division of Biological Science, Graduate School of Science, Nagoya University
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28
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Ram EVSR, Naik R, Ganguli M, Habib S. DNA organization by the apicoplast-targeted bacterial histone-like protein of Plasmodium falciparum. Nucleic Acids Res 2008; 36:5061-73. [PMID: 18663012 PMCID: PMC2528193 DOI: 10.1093/nar/gkn483] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Apicomplexans, including the pathogens Plasmodium and Toxoplasma, carry a nonphotosynthetic plastid of secondary endosymbiotic origin called the apicoplast. The P. falciparum apicoplast contains a 35 kb, circular DNA genome with limited coding capacity that lacks genes encoding proteins for DNA organization and replication. We report identification of a nuclear-encoded bacterial histone-like protein (PfHU) involved in DNA compaction in the apicoplast. PfHU is associated with apicoplast DNA and is expressed throughout the parasite's intra-erythocytic cycle. The protein binds DNA in a sequence nonspecific manner with a minimum binding site length of ∼27 bp and a Kd of ∼63 nM and displays a preference for supercoiled DNA. PfHU is capable of condensing Escherichia coli nucleoids in vivo indicating its role in DNA compaction. The unique 42 aa C-terminal extension of PfHU influences its DNA condensation properties. In contrast to bacterial HUs that bend DNA, PfHU promotes concatenation of linear DNA and inhibits DNA circularization. Atomic Force Microscopic study of PfHU–DNA complexes shows protein concentration-dependent DNA stiffening, intermolecular bundling and formation of DNA bridges followed by assembly of condensed DNA networks. Our results provide the first functional characterization of an apicomplexan HU protein and provide additional evidence for red algal ancestry of the apicoplast.
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Affiliation(s)
- E V S Raghu Ram
- Division of Molecular and Structural Biology, Central Drug Research Institute, Lucknow-226 001, India
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29
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Abstract
The protozoan phylum Apicomplexa encompasses approximately 5000 species of obligate intracellular parasites, including those responsible for malaria and toxoplasmosis. Rather than dividing by binary fission, apicomplexans use a remarkable mechanism for replication, assembling daughters de novo within the cytoplasm. Here, we exploit time-lapse microscopy of fluorescent markers targeted to various subcellular structures in Toxoplasma gondii tachyzoites to determine how these unicellular eukaryotes efficiently package a complete set of organelles, maintaining the highly polarized organization necessary for host cell invasion and pathogenesis. Golgi division and elongation of the apicoplast are among the first morphologically observable events, associated with an unusual pattern of centriolar migration. Daughter parasites are assembled on cytoskeletal scaffolding, whose growth proceeds from the apical end, first encapsulating the divided Golgi. Further extension of the cytoskeletal scaffold results in partitioning of the apicoplast, nucleus, endoplasmic reticulum, and finally the mitochondrion, which enters the developing daughters rapidly, but only very late during the division cycle. The specialized secretory organelles (micronemes and rhoptries) form de novo. This distinctive pattern of replication -- in which organellar segregation spans approximately 75% of the cell cycle, completely encompassing S phase -- suggests an unusual mechanism of cell cycle regulation.
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Affiliation(s)
- Manami Nishi
- Departments of Biology, and Cell and Developmental Biology, University of Pennsylvania, Philadelphia PA 19104, USA
| | | | - John M. Murray
- Departments of Biology, and Cell and Developmental Biology, University of Pennsylvania, Philadelphia PA 19104, USA
| | - David S. Roos
- Departments of Biology, and Cell and Developmental Biology, University of Pennsylvania, Philadelphia PA 19104, USA
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Matsuzaki M, Kuroiwa H, Kuroiwa T, Kita K, Nozaki H. A cryptic algal group unveiled: a plastid biosynthesis pathway in the oyster parasite Perkinsus marinus. Mol Biol Evol 2008; 25:1167-79. [PMID: 18359776 DOI: 10.1093/molbev/msn064] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Plastids are widespread in plant and algal lineages. They are also exploited by some nonphotosynthetic protists, including malarial parasites, to support their diverse modes of life. However, cryptic plastids may exist in other nonphotosynthetic protists, which could be important in studies on the diversity and evolution of plastids. The parasite Perkinsus marinus, which causes mass mortality in oyster farms, is a nonphotosynthetic protist that is phylogenetically related to plastid-bearing dinoflagellates and apicomplexans. In this study, we searched for P. marinus methylerythritol phosphate (MEP) pathway genes, responsible for de novo isoprenoid synthesis in plastids, and determined the full-length gene sequences for 6 of 7 of these genes. Phylogenetic analyses revealed that each P. marinus gene clusters with orthologs from plastid-bearing eukaryotes, which have MEP pathway genes with essentially the same mosaic pattern of evolutionary origin. A new analytical method called sliding-window iteration of TargetP was developed to examine the distribution of targeting preferences. This analysis revealed that the sequenced genes encode bipartite targeting peptides that are characteristic of proteins targeted to secondary plastids originating from endosymbiosis of eukaryotic algae. These results support our idea that Perkinsus is a cryptic algal group containing nonphotosynthetic secondary plastids. In fact, immunofluorescent microscopy indicated that 1 of the MEP pathway enzymes, 1-deoxy-D-xylulose 5-phosphate reductoisomerase, was localized to small compartments near mitochondrion, which are possibly plastids. This tiny organelle seems to contain very low quantities of DNA or may even lack DNA entirely. The MEP pathway genes are a useful tool for investigating plastid evolution in both of the photosynthetic and nonphotosynthetic eukaryotes and led us to propose the hypothesis that ancestral "chromalveolates" harbored plastids before a secondary endosymbiotic event.
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Affiliation(s)
- Motomichi Matsuzaki
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Tokyo, Japan.
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Kuroiwa T, Misumi O, Nishida K, Yagisawa F, Yoshida Y, Fujiwara T, Kuroiwa H. Vesicle, mitochondrial, and plastid division machineries with emphasis on dynamin and electron-dense rings. INTERNATIONAL REVIEW OF CELL AND MOLECULAR BIOLOGY 2008; 271:97-152. [PMID: 19081542 DOI: 10.1016/s1937-6448(08)01203-3] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The original eukaryotic cells contained at least one set of double-membrane-bounded organelles (cell nucleus and mitochondria) and single-membrane-bounded organelles [endoplasmic reticulum, Golgi apparatus, lysosomes (vacuoles), and microbodies (peroxisomes)]. An increase in the number of organelles accompanied the evolution of these cells into Amoebozoa and Opisthokonta. Furthermore, the basic cells, containing mitochondria, engulfed photosynthetic Cyanobacteria, which were converted to plastids, and the cells thereby evolved into cells characteristic of the Bikonta. How did basic single- and double-membrane-bounded organelles originate from bacteria-like cells during early eukaryotic evolution? To answer this question, the important roles of the GTPase dynamin- and electron-dense rings in the promotion of diverse cellular activities in eukaryotes, including endocytosis, vesicular transport, mitochondrial division, and plastid division, must be considered. In this review, vesicle division, mitochondrial division, and plastid division machineries, including the dynamin- and electron-dense rings, and their roles in the origin and biogenesis of organelles in eukaryote cells are summarized.
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Affiliation(s)
- T Kuroiwa
- Research Information Center of Extremophile, Rikkyo (St Paul's) University, Tokyo, Japan
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32
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Raghu Ram EVS, Kumar A, Biswas S, Kumar A, Chaubey S, Siddiqi MI, Habib S. Nuclear gyrB encodes a functional subunit of the Plasmodium falciparum gyrase that is involved in apicoplast DNA replication. Mol Biochem Parasitol 2007; 154:30-9. [PMID: 17499371 DOI: 10.1016/j.molbiopara.2007.04.001] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2006] [Revised: 04/02/2007] [Accepted: 04/03/2007] [Indexed: 11/30/2022]
Abstract
The DNA replication machinery of the Plasmodium falciparum apicoplast is a validated drug target. Nuclear-encoded gyrase subunits are predicted to play a critical role in maintaining DNA topology during the D-loop/bi-directional ori replication process of the parasite. We show the presence of P. falciparum gyrase subunits in parasite lysates by using antibodies generated against recombinant gyrase A and B. The ATPase activity of PfGyrB was inhibited by novobiocin that also caused parasite death in culture. Reduction of apicoplast/nuclear DNA ratio in the presence of novobiocin indicated that the drug targets apicoplast DNA replication. Molecular modeling of gyrase A and B subunits revealed extensive fold conservation with the Escherichia coli counterparts as well as the presence of a long disordered loop adjacent to the ATPase domain of PfGyrB. Our results have implications for development of PfGyrB as a drug target against malaria.
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Affiliation(s)
- E V S Raghu Ram
- Division of Molecular and Structural Biology, Central Drug Research Institute, Post Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
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Vaishnava S, Striepen B. The cell biology of secondary endosymbiosis--how parasites build, divide and segregate the apicoplast. Mol Microbiol 2006; 61:1380-7. [PMID: 16968220 DOI: 10.1111/j.1365-2958.2006.05343.x] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protozoan parasites of the phylum Apicomplexa harbour a chloroplast-like organelle, the apicoplast. The biosynthetic pathways localized to this organelle are of cyanobacterial origin and therefore offer attractive targets for the development of new drugs for the treatment of malaria and toxoplasmosis. The apicoplast also provides a unique system to study the cell biology of endosymbiosis. This organelle is the product of secondary endosymbiosis, the marriage of an alga and an auxotrophic eukaryote. This origin has led to a fascinating set of novel cellular mechanisms that are clearly distinct from those employed by the plant chloroplast. Here we explore how the apicoplast interacts with its 'host' to secure building blocks for its biogenesis and how the organelle is divided and segregated during mitosis. Considerable advances in parasite genetics and genomics have transformed apicomplexans, long considered hard to study, into highly tractable model organisms. We discuss how these resources might be marshalled to develop a detailed mechanistic picture of apicoplast cell biology.
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Affiliation(s)
- Shipra Vaishnava
- Department of Cellular Biology, University of Georgia, Paul D. Coverdell Center, 500 D.W. Brooks Drive, Athens, GA 30602, USA
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Ferguson DJP, Campbell SA, Henriquez FL, Phan L, Mui E, Richards TA, Muench SP, Allary M, Lu JZ, Prigge ST, Tomley F, Shirley MW, Rice DW, McLeod R, Roberts CW. Enzymes of type II fatty acid synthesis and apicoplast differentiation and division in Eimeria tenella. Int J Parasitol 2006; 37:33-51. [PMID: 17112527 PMCID: PMC2803676 DOI: 10.1016/j.ijpara.2006.10.003] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2006] [Revised: 09/26/2006] [Accepted: 10/03/2006] [Indexed: 11/16/2022]
Abstract
Apicomplexan parasites, Eimeria tenella, Plasmodium spp. and Toxoplasma gondii, possess a homologous plastid-like organelle termed the apicoplast, derived from the endosymbiotic enslavement of a photosynthetic alga. However, currently no eimerian nuclear encoded apicoplast targeted proteins have been identified, unlike in Plasmodium spp. and T. gondii. In this study, we demonstrate that nuclear encoded enoyl reductase of E. tenella (EtENR) has a predicted N-terminal bipartite transit sequence, typical of apicoplast-targeted proteins. Using a combination of immunocytochemistry and EM we demonstrate that this fatty acid biosynthesis protein is located in the apicoplast of E. tenella. Using the EtENR as a tool to mark apicoplast development during the Eimeria lifecycle, we demonstrate that nuclear and apicoplast division appear to be independent events, both organelles dividing prior to daughter cell formation, with each daughter cell possessing one to four apicoplasts. We believe this is the first report of multiple apicoplasts present in the infectious stage of an apicomplexan parasite. Furthermore, the microgametes lacked an identifiable apicoplast consistent with maternal inheritance via the macrogamete. It was found that the size of the organelle and the abundance of EtENR varied with developmental stage of the E. tenella lifecycle. The high levels of EtENR protein observed during asexual development and macrogametogony is potentially associated with the increased synthesis of fatty acids required for the rapid formation of numerous merozoites and for the extracellular development and survival of the oocyst. Taken together the data demonstrate that the E. tenella apicoplast participates in type II fatty acid biosynthesis with increased expression of ENR during parasite growth. Apicoplast division results in the simultaneous formation of multiple fragments. The division mechanism is unknown, but is independent of nuclear division and occurs prior to daughter formation.
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Affiliation(s)
- D J P Ferguson
- Nuffield Department of Pathology, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DU, UK.
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35
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Kuroiwa T, Nishida K, Yoshida Y, Fujiwara T, Mori T, Kuroiwa H, Misumi O. Structure, function and evolution of the mitochondrial division apparatus. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1763:510-21. [PMID: 16690143 DOI: 10.1016/j.bbamcr.2006.03.007] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2005] [Revised: 03/18/2006] [Accepted: 03/27/2006] [Indexed: 10/24/2022]
Abstract
Mitochondria are derived from free-living alpha-proteobacteria that were engulfed by eukaryotic host cells through the process of endosymbiosis, and therefore have their own DNA which is organized using basic proteins to form organelle nuclei (nucleoids). Mitochondria divide and are split amongst the daughter cells during cell proliferation. Their division can be separated into two main events: division of the mitochondrial nuclei and division of the matrix (the so-called mitochondrial division, or mitochondriokinesis). In this review, we first focus on the cytogenetical relationships between mitochondrial nuclear division and mitochondriokinesis. Mitochondriokinesis occurs after mitochondrial nuclear division, similar to bacterial cytokinesis. We then describe the fine structure and dynamics of the mitochondrial division ring (MD ring) as a basic morphological background for mitochondriokinesis. Electron microscopy studies first identified a small electron-dense MD ring in the cytoplasm at the constriction sites of dividing mitochondria in the slime mold Physarum polycephalum, and then two large MD rings (with outer cytoplasmic and inner matrix sides) in the red alga Cyanidioschyzon merolae. Now MD rings have been found in all eukaryotes. In the third section, we describe the relationships between the MD ring and the FtsZ ring descended from ancestral bacteria. Other than the GTPase, FtsZ, mitochondria have lost most of the proteins required for bacterial cytokinesis as a consequence of endosymbiosis. The FtsZ protein forms an electron transparent ring (FtsZ or Z ring) in the matrix inside the inner MD ring. For the fourth section, we describe the dynamic association between the outer MD ring with a ring composed of the eukaryote-specific GTPase dynamin. Recent studies have revealed that eukaryote-specific GTPase dynamins form an electron transparent ring between the outer membrane and the MD ring. Thus, mitochondriokinesis is thought to be controlled by a mitochondrial division (MD) apparatus including a dynamic trio, namely the FtsZ, MD and dynamin rings, which consist of a chimera of rings from bacteria and eukaryotes in primitive organisms. Since the genes for the MD ring and dynamin rings are not found in the prokaryotic genome, the host genomes may make these rings to actively control mitochondrial division. In the fifth part, we focus on the dynamic changes in the formation and disassembly of the FtsZ, MD and dynamin rings. FtsZ rings are digested during a later period of mitochondrial division and then finally the MD and dynamin ring apparatuses pinched off the daughter mitochondria, supporting the idea that the host genomes are responsible for the ultimate control of mitochondrial division. We discuss the evolution, from the original vesicle division (VD) apparatuses to VD apparatuses including classical dynamin rings and MD apparatuses. It is likely that the MD apparatuses involving the dynamic trio evolved into the plastid division (PD) apparatus in Bikonta, while in Opisthokonta, the MD apparatus was simplified during evolution and may have branched into the mitochondrial fusion apparatus. Finally, we describe the possibility of intact isolation of large MD/PD apparatuses, the identification of all their proteins and their related genes using C. merolae genome information and TOF-MS analyses. These results will assist in elucidating the universal mechanism and evolution of MD, PD and VD apparatuses.
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Affiliation(s)
- Tsuneyoshi Kuroiwa
- Laboratory of Cell Biology and Frontier Project Life's Adaptation Strategies of Environmental Change, Department of Life Sciences, College of Science, Rikkyo University, 3-34-1 Nishiikebukuro, Toshima-ku, Tokyo 171-8501, Japan.
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36
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Köhler S. Multi-membrane-bound structures of Apicomplexa: II. the ovoid mitochondrial cytoplasmic (OMC) complex of Toxoplasma gondii tachyzoites. Parasitol Res 2006; 98:355-69. [PMID: 16470415 DOI: 10.1007/s00436-005-0066-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2005] [Accepted: 10/07/2005] [Indexed: 10/25/2022]
Abstract
Apicomplexa including the causative agents of toxoplasmosis and malaria reportedly possess one or few tubular-shaped mitochondria that permeate, more or less branched, throughout these unicellular parasites. Electron micrographs generated herein from serial-sectioned Toxoplasma gondii tachyzoites demonstrated, however, a greater diversity regarding both the shape of the cultured parasite's single mitochondrion and its sub-structural organization. Moreover, a unique subcellular construction was detected that basically comprised a pouch-shaped subdivision of the tachyzoite mitochondrion plus a fraction of parasitic cytoplasm enclosed therein. This composite assembling, termed ovoid mitochondrial cytoplasmic (OMC) complex, characteristically displayed a highly reduced matrix lumen of its mitochondrial border construction, which furthermore often failed to possess any cristae or contained tightly pleated cristae, thus creating a pouch-shaped multi-laminar wall of four or more membranous layers, respectively. Given this architecture, cross-sectioned OMC complexes of T. gondii tachyzoites frequently mimicked in size and shape the parasites' plastid-like organelle (apicoplast). Moreover, like the apicoplast, the OMC complex was often found adjacent to the tachyzoite's single Golgi complex and constantly located in close proximity to the outer membrane of the parasite's nuclear envelope. The T. gondii OMC complex differed, however, from the apicoplast in its exact fine structural organization and a stage-restricted presence that was apparently linked to mitochondrial growth and/or division. Any special function(s) possibly performed by the T. gondii OMC complex remains, nevertheless, to be elucidated.
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Affiliation(s)
- Sabine Köhler
- Institute for Zoomorphology, Cell Biology and Parasitology, Heinrich Heine Universität Düsseldorf, Universitätsstrasse 1, Düsseldorf, Germany.
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37
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Vaishnava S, Morrison DP, Gaji RY, Murray JM, Entzeroth R, Howe DK, Striepen B. Plastid segregation and cell division in the apicomplexan parasite Sarcocystis neurona. J Cell Sci 2005; 118:3397-407. [PMID: 16079283 DOI: 10.1242/jcs.02458] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Apicomplexan parasites harbor a secondary plastid that is essential to their survival. Several metabolic pathways confined to this organelle have emerged as promising parasite-specific drug targets. The maintenance of the organelle and its genome is an equally valuable target. We have studied the replication and segregation of this important organelle using the parasite Sarcocystis neurona as a cell biological model. This model system makes it possible to differentiate and dissect organellar growth, fission and segregation over time, because of the parasite's peculiar mode of cell division. S. neurona undergoes five cycles of chromosomal replication without nuclear division, thus yielding a cell with a 32N nucleus. This nucleus undergoes a sixth replication cycle concurrent with nuclear division and cell budding to give rise to 64 haploid daughter cells. Interestingly, intranuclear spindles persist throughout the cell cycle, thereby providing a potential mechanism to organize chromosomes and organelles in an organism that undergoes dramatic changes in ploidy. The development of the plastid mirrors that of the nucleus, a continuous organelle, which grows throughout the parasite's development and shows association with all centrosomes. Pharmacological ablation of the parasite's multiple spindles demonstrates their essential role in the organization and faithful segregation of the plastid. By using several molecular markers we have timed organelle fission to the last replication cycle and tied it to daughter cell budding. Finally, plastids were labeled by fluorescent protein expression using a newly developed S. neurona transfection system. With these transgenic parasites we have tested our model in living cells employing laser bleaching experiments.
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Affiliation(s)
- Shipra Vaishnava
- Department of Cellular Biology, University of Georgia, Athens, GA 30602, USA
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38
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Miyagishima SY. Origin and evolution of the chloroplast division machinery. JOURNAL OF PLANT RESEARCH 2005; 118:295-306. [PMID: 16143878 DOI: 10.1007/s10265-005-0226-2] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2005] [Accepted: 07/13/2005] [Indexed: 05/04/2023]
Abstract
Chloroplasts were originally established in eukaryotes by the endosymbiosis of a cyanobacterium; they then spread through diversification of the eukaryotic hosts and subsequent engulfment of eukaryotic algae by previously nonphotosynthetic eukaryotes. The continuity of chloroplasts is maintained by division of preexisting chloroplasts. Like their ancestors, chloroplasts use a bacterial division system based on the FtsZ ring and some associated factors, all of which are now encoded in the host nuclear genome. The majority of bacterial division factors are absent from chloroplasts and several new factors have been added by the eukaryotic host. For example, the ftsZ gene has been duplicated and modified, plastid-dividing (PD) rings were most likely added by the eukaryotic host, and a member of the dynamin family of proteins evolved to regulate chloroplast division. The identification of several additional proteins involved in the division process, along with data from diverse lineages of organisms, our current knowledge of mitochondrial division, and the mining of genomic sequence data have enabled us to begin to understand the universality and evolution of the division system. The principal features of the chloroplast division system thus far identified are conserved across several lineages, including those with secondary chloroplasts, and may reflect primeval features of mitochondrial division.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Plant Biology, Michigan State University, East Lansing, 48824, USA.
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39
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Ferguson DJP, Henriquez FL, Kirisits MJ, Muench SP, Prigge ST, Rice DW, Roberts CW, McLeod RL. Maternal inheritance and stage-specific variation of the apicoplast in Toxoplasma gondii during development in the intermediate and definitive host. EUKARYOTIC CELL 2005; 4:814-26. [PMID: 15821140 PMCID: PMC1087807 DOI: 10.1128/ec.4.4.814-826.2005] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The structure and location of Toxoplasma gondii apicoplasts were examined in intermediate and definitive hosts and shown to vary in a stage-specific manner. Immunocytochemistry and electron microscopy studies were used to identify changes in the morphology of apicoplasts and in their enoyl reductase (ENR) content during asexual and sexual development. Apicoplasts in tachyzoites were small, multimembraned organelles anterior to nuclei that divided and segregated with the nuclei during endodyogeny. In nonproliferating bradyzoites within mature tissue cysts (1 to 24 months), apicoplasts had high levels of ENR. During coccidian development, asexual multiplication (endopolygeny), resulting in simultaneous formation of up to 30 daughters (merozoites), involved an initial growth phase associated with repeated nuclear divisions during which apicoplasts appeared as single, elongated, branched structures with increased levels of ENR. At initiation of merozoite formation, enlarged apicoplasts divided simultaneously, with constrictions, into portions that segregated to developing daughters. In sexual stages, apicoplast division did not occur during microgametogony, and apicoplasts were absent from the microgametes that were formed. In contrast, during macrogametogony, the apicoplast appeared as a large, branched, perinuclear structure that had very high levels of ENR in the absence of nuclear division. Marked increases in the size of apicoplasts and levels of ENR may be related to requirements of the macrogametocytes to synthesize and store all components necessary for oocyst formation and subsequent extracellular sporulation. Thus, it is shown that apicoplasts are present and contain ENR in all T. gondii life cycle stages except microgametes, which will result in maternal inheritance of the organelle.
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Affiliation(s)
- David J P Ferguson
- Department of Pathology, University of Oxford, John Radcliffe Hospital, United Kingdom
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40
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Abstract
Considerable work still needs to be done to understand more fully the basic processes going on inside the non-photosynthetic plastid organelle of Plasmodium spp., the causative agent of malaria. Following an explosion of genomic and transcriptional information in recent years, research workers are still analysing these data looking for new material relevant to the plastid. Several metabolic and housekeeping functions based on bacterial biochemistry have been elucidated and this has given impetus to finding lead inhibitors based on established anti-microbials. Structural investigations of plastid-associated enzymes identified as potential targets have begun. This review gives a perspective on the research to date and hopes to emphasize that a practical outcome for the clinic should be an important focus of future efforts. Malaria parasites have become resistant to front-line anti-malarials that are widely used and were formerly dependable. This has become a worrying problem in many regions where malaria is endemic. The time lag between hunting for new inhibitors and their application as pharmaceuticals is so long and costly that a steady stream of new ventures has to be undertaken to give a reasonable chance of finding affordable and appropriate anti-malarials for the future. Attempts to find inhibitors of the plastid organelle of the malaria parasite should be intensified in such programmes.
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Affiliation(s)
- R J M Iain Wilson
- National Institute for Medical Research, Mill Hill, London, NW7 1AA, UK.
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41
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Singh D, Kumar A, Raghu Ram EVS, Habib S. Multiple replication origins within the inverted repeat region of the Plasmodium falciparum apicoplast genome are differentially activated. Mol Biochem Parasitol 2005; 139:99-106. [PMID: 15610824 DOI: 10.1016/j.molbiopara.2004.09.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2004] [Revised: 08/07/2004] [Accepted: 09/13/2004] [Indexed: 10/26/2022]
Abstract
The 35 kb circular genome (plDNA) of the Plasmodium falciparum apicoplast replicates by the bidirectional ori/D-loop mechanism. PlDNA replication was previously shown to initiate within the inverted repeat (IR) region of the apicoplast genome [Williamson DH, Preiser PR, Moore PW, McCready S, Strath M, Wilson RJM (Iain). The plastid DNA of the malaria parasite Plasmodium falciparum is replicated by two mechanisms. Mol Microbiol 2002;45:533-42; Singh D, Chaubey S, Habib S. Replication of the Plasmodium falciparum apicoplast DNA initiates within the inverted repeat region. Mol Biochem Parasitol 2003;126:9-14.] and the presence of at least two ori within each segment of the IR was postulated. Using 5' end-labelled nascent DNA as probe, we now demonstrate the utilization of several putative ori located within the IR for plDNA replication. Quantitation of signals obtained for different segments of the IR as well as determination of the number of molecules emanating from two ori regions by competitive PCR analysis indicated differential strengths of ori during plDNA replication prior to schizogony.
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Affiliation(s)
- Divya Singh
- Division of Molecular and Structural Biology, Central Drug Research Institute, P.O. Box 173, Chattar Manzil, Mahatma Gandhi Marg, Lucknow 226001, India
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42
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Foth BJ, McFadden GI. The apicoplast: a plastid in Plasmodium falciparum and other Apicomplexan parasites. INTERNATIONAL REVIEW OF CYTOLOGY 2003; 224:57-110. [PMID: 12722949 DOI: 10.1016/s0074-7696(05)24003-2] [Citation(s) in RCA: 138] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Apicomplexan parasites cause severe diseases such as malaria, toxoplasmosis, and coccidiosis (caused by Plasmodium spp., Toxoplasma, and Eimeria, respectively). These parasites contain a relict plastid-termed "apicoplast"--that originated from the engulfment of an organism of the red algal lineage. The apicoplast is indispensable but its exact role in parasites is unknown. The apicoplast has its own genome and expresses a small number of genes, but the vast majority of the apicoplast proteome is encoded in the nuclear genome. The products of these nuclear genes are posttranslationally targeted to the organelle via the secretory pathway courtesy of a bipartite N-terminal leader sequence. Apicoplasts are nonphotosynthetic but retain other typical plastid functions such as fatty acid, isoprenoid and heme synthesis, and products of these pathways might be exported from the apicoplast for use by the parasite. Apicoplast pathways are essentially prokaryotic and therefore excellent drug targets. Some antibiotics inhibiting these molecular processes are already in chemotherapeutic use, whereas many new drugs will hopefully spring from our growing understanding of this intriguing organelle.
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Affiliation(s)
- Bernardo J Foth
- Plant Cell Biology Research Centre, School of Botany, University of Melbourne, Parkville, Victoria 3010, Australia
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43
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Abstract
Photosynthetic eukaryotes have evolved plastid division mechanisms since acquisition of plastids through endosymbiosis. The emerging evolutionary origin of the plastid division mechanism is remarkably complex. The constituents of the division apparatus of plastids may have complex origins. The one constituent is the plastid FtsZ ring taken over from the cyanobacteria-like ancestral endosymbionts. The second is the doublet of concentric plastid dividing rings (or triplet in red algae), possibly acquired by ancestral host eukaryotes following the primary endosymbiotic event. Placement of the division apparatus at the correct division site may involve a system analogous to the bacterial Min system. Plastid nucleoid partitioning may be mediated by binding to envelope or thylakoid membranes. Multiple copies of plastid DNA and symmetrical distribution of the nucleoids in the plastids may permit faithful transmission to daughter plastids via equal binary plastid divisions. Cyanelles retain peptidoglycan wall and cyanelle division occurs through septum formation such as bacterial cell division. Cyanelle division involves the cyanelle ring analogous to the inner stromal plastid-dividing (PD) ring. According to the prevailing hypothesis that primary endosymbiosis occurred only once, cyanelle division may represent an intermediate stage between cyanobacterial division and the well-known plastid division among extant plants. With the secondary plastids, which are surrounded by three or four membranes, the PD ring also participates in division of the inner two "true" plastid envelope membranes, and the third and the outermost membranes divide by unknown mechanisms.
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Affiliation(s)
- Haruki Hashimoto
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
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Nishida K, Takahara M, Miyagishima SY, Kuroiwa H, Matsuzaki M, Kuroiwa T. Dynamic recruitment of dynamin for final mitochondrial severance in a primitive red alga. Proc Natl Acad Sci U S A 2003; 100:2146-51. [PMID: 12566569 PMCID: PMC149973 DOI: 10.1073/pnas.0436886100] [Citation(s) in RCA: 124] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2002] [Indexed: 11/18/2022] Open
Abstract
Dynamins are a eukaryote-specific family of GTPases. Some family members are involved in diverse and varied cellular activities. Here, we report that the primitive red alga Cyanidioschyzon merolae retains only one dynamin homolog, CmDnm1, belonging to the mitochondrial division subfamily. Previously, the bacterial cell division protein, FtsZ, was shown to localize at the mitochondrial division site in the alga. We showed that FtsZ and dynamin coexist as mitochondrial division-associated proteins that act during different phases of division. CmDnm1 was recruited from 10-20 cytoplasmic patches (dynamin patches) to the midpoint of the constricted mitochondrion-dividing ring (MD ring), which was observed as an electron-dense structure on the cytoplasmic side. CmDnm1 is probably not required for early constriction; it forms a ring or spiral when the outer mitochondrial membrane is finally severed, whereas the FtsZ and MD rings are formed before constriction. It is thought that the FtsZ, MD, and dynamin rings are involved in scaffolding, constriction, and final separation, respectively. In eukaryotes, mitochondrial severance is probably the most conserved role for the dynamin family.
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Affiliation(s)
- Keiji Nishida
- Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Tokyo 113-0033, Japan.
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Cavalier-Smith T. Genomic reduction and evolution of novel genetic membranes and protein-targeting machinery in eukaryote-eukaryote chimaeras (meta-algae). Philos Trans R Soc Lond B Biol Sci 2003; 358:109-33; discussion 133-4. [PMID: 12594921 PMCID: PMC1693104 DOI: 10.1098/rstb.2002.1194] [Citation(s) in RCA: 130] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Chloroplasts originated just once, from cyanobacteria enslaved by a biciliate protozoan to form the plant kingdom (green plants, red and glaucophyte algae), but subsequently, were laterally transferred to other lineages to form eukaryote-eukaryote chimaeras or meta-algae. This process of secondary symbiogenesis (permanent merger of two phylogenetically distinct eukaryote cells) has left remarkable traces of its evolutionary role in the more complex topology of the membranes surrounding all non-plant (meta-algal) chloroplasts. It took place twice, soon after green and red algae diverged over 550 Myr ago to form two independent major branches of the eukaryotic tree (chromalveolates and cabozoa), comprising both meta-algae and numerous secondarily non-photosynthetic lineages. In both cases, enslavement probably began by evolving a novel targeting of endomembrane vesicles to the perialgal vacuole to implant host porter proteins for extracting photosynthate. Chromalveolates arose by such enslavement of a unicellular red alga and evolution of chlorophyll c to form the kingdom Chromista and protozoan infrakingdom Alveolata, which diverged from the ancestral chromalveolate chimaera. Cabozoa arose when the common ancestor of euglenoids and cercozoan chlorarachnean algae enslaved a tetraphyte green alga with chlorophyll a and b. I suggest that in cabozoa the endomembrane vesicles originally budded from the Golgi, whereas in chromalveolates they budded from the endoplasmic reticulum (ER) independently of Golgi-targeted vesicles, presenting a potentially novel target for drugs against alveolate Sporozoa such as malaria parasites and Toxoplasma. These hypothetical ER-derived vesicles mediated fusion of the perialgal vacuole and rough ER (RER) in the ancestral chromist, placing the former red alga within the RER lumen. Subsequently, this chimaera diverged to form cryptomonads, which retained the red algal nucleus as a nucleomorph (NM) with approximately 464 protein-coding genes (30 encoding plastid proteins) and a red or blue phycobiliprotein antenna pigment, and the chromobiotes (heterokonts and haptophytes), which lost phycobilins and evolved the brown carotenoid fucoxanthin that colours brown seaweeds, diatoms and haptophytes. Chromobiotes transferred the 30 genes to the nucleus and lost the NM genome and nuclear-pore complexes, but retained its membrane as the periplastid reticulum (PPR), putatively the phospholipid factory of the periplastid space (former algal cytoplasm), as did the ancestral alveolate independently. The chlorarachnean NM has three minute chromosomes bearing approximately 300 genes riddled with pygmy introns. I propose that the periplastid membrane (PPM, the former algal plasma membrane) of chromalveolates, and possibly chlorarachneans, grows by fusion of vesicles emanating from the NM envelope or PPR. Dinoflagellates and euglenoids independently lost the PPM and PPR (after diverging from Sporozoa and chlorarachneans, respectively) and evolved triple chloroplast envelopes comprising the original plant double envelope and an extra outermost membrane, the EM, derived from the perialgal vacuole. In all metaalgae most chloroplast proteins are coded by nuclear genes and enter the chloroplast by using bipartite targeting sequences--an upstream signal sequence for entering the ER and a downstream chloroplast transit sequence. I present a new theory for the four-fold diversification of the chloroplast OM protein translocon following its insertion into the PPM to facilitate protein translocation across it (of both periplastid and plastid proteins). I discuss evidence from genome sequencing and other sources on the contrasting modes of protein targeting, cellular integration, and evolution of these two major lineages of eukaryote "cells within cells". They also provide powerful evidence for natural selection's effectiveness in eliminating most functionless DNA and therefore of a universally useful non-genic function for nuclear non-coding DNA, i.e. most DNA in the biosphere, and dramatic examples of genomic reduction. I briefly argue that chloroplast replacement in dinoflagellates, which happened at least twice, may have been evolutionarily easier than secondary symbiogenesis because parts of the chromalveolate protein-targeting machinery could have helped enslave the foreign plastids.
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Affiliation(s)
- T Cavalier-Smith
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
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Abstract
This review offers a snapshot of our current understanding of the origin, biology, and metabolic significance of the non-photosynthetic plastid organelle found in apicomplexan parasites. These protists are of considerable medical and veterinary importance world-wide, Plasmodium spp., the causative agent of malaria being foremost in terms of human disease. It has been estimated that approximately 8% of the genes currently recognized by the malarial genome sequencing project (now nearing completion) are of bacterial/plastid origin. The bipartite presequences directing the products of these genes back to the plastid have provided fresh evidence that secondary endosymbiosis accounts for this organelle's presence in these parasites. Mounting phylogenetic evidence has strengthened the likelihood that the plastid originated from a red algal cell. Most importantly, we now have a broad understanding of several bacterial metabolic systems confined within the boundaries of the parasite plastid. The primary ones are type II fatty acid biosynthesis and isoprenoid biosynthesis. Some aspects of heme biosynthesis also might take place there. Retention of the plastid's relict genome and its still ill-defined capacity to participate in protein synthesis might be linked to an important house-keeping process, i.e. guarding the type II fatty acid biosynthetic pathway from oxidative damage. Fascinating observations have shown the parasite plastid does not divide by constriction as in typical plants, and that plastid-less parasites fail to thrive after invading a new cell. The modes of plastid DNA replication within the phylum also have provided surprises. Besides indicating the potential of the parasite plastid for therapeutic intervention, this review exposes many gaps remaining in our knowledge of this intriguing organelle. The rapid progress being made shows no sign of slackening.
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Affiliation(s)
- R J M Iain Wilson
- National Institute for Medical Research, Mill Hill, London NW7 1AA, UK.
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