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Bonnell V, Zhang Y, Brown A, Horton J, Josling G, Chiu TP, Rohs R, Mahony S, Gordân R, Llinás M. DNA sequence and chromatin differentiate sequence-specific transcription factor binding in the human malaria parasite Plasmodium falciparum. Nucleic Acids Res 2024; 52:10161-10179. [PMID: 38966997 PMCID: PMC11417369 DOI: 10.1093/nar/gkae585] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/30/2024] [Accepted: 06/27/2024] [Indexed: 07/06/2024] Open
Abstract
Development of the malaria parasite, Plasmodium falciparum, is regulated by a limited number of sequence-specific transcription factors (TFs). However, the mechanisms by which these TFs recognize genome-wide binding sites is largely unknown. To address TF specificity, we investigated the binding of two TF subsets that either bind CACACA or GTGCAC DNA sequence motifs and further characterized two additional ApiAP2 TFs, PfAP2-G and PfAP2-EXP, which bind unique DNA motifs (GTAC and TGCATGCA). We also interrogated the impact of DNA sequence and chromatin context on P. falciparum TF binding by integrating high-throughput in vitro and in vivo binding assays, DNA shape predictions, epigenetic post-translational modifications, and chromatin accessibility. We found that DNA sequence context minimally impacts binding site selection for paralogous CACACA-binding TFs, while chromatin accessibility, epigenetic patterns, co-factor recruitment, and dimerization correlate with differential binding. In contrast, GTGCAC-binding TFs prefer different DNA sequence context in addition to chromatin dynamics. Finally, we determined that TFs that preferentially bind divergent DNA motifs may bind overlapping genomic regions due to low-affinity binding to other sequence motifs. Our results demonstrate that TF binding site selection relies on a combination of DNA sequence and chromatin features, thereby contributing to the complexity of P. falciparum gene regulatory mechanisms.
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Affiliation(s)
- Victoria A Bonnell
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA
| | - Yuning Zhang
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
- Program in Computational Biology and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Alan S Brown
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA
| | - John Horton
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
| | - Gabrielle A Josling
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA
| | - Tsu-Pei Chiu
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
| | - Remo Rohs
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA
- Department of Chemistry, University of Southern California, Los Angeles, CA 90089, USA
- Department of Physics and Astronomy, University of Southern California, Los Angeles, CA 90089, USA
- Thomas Lord Department of Computer Science, University of Southern California, Los Angeles, CA 90089, USA
| | - Shaun Mahony
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
| | - Raluca Gordân
- Center for Genomic and Computational Biology, Duke University, Durham, NC 27708, USA
- Department of Biostatistics and Bioinformatics, Duke University, Durham, NC 27708, USA
- Department of Computer Science, Duke University, Durham, NC 27708, USA
- Department of Molecular Genetics and Microbiology, Duke University, Durham, NC 27708, USA
| | - Manuel Llinás
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Eukaryotic Gene Regulation, The Pennsylvania State University, University Park, PA 16802, USA
- Huck Institutes Center for Malaria Research, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Chemistry, The Pennsylvania State University, University Park, PA 16802, USA
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2
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Tetzlaff S, Hillebrand A, Drakoulis N, Gluhic Z, Maschmann S, Lyko P, Wicke S, Schmitz-Linneweber C. Small RNAs from mitochondrial genome recombination sites are incorporated into T. gondii mitoribosomes. eLife 2024; 13:e95407. [PMID: 38363119 PMCID: PMC10948144 DOI: 10.7554/elife.95407] [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: 12/29/2023] [Accepted: 01/23/2024] [Indexed: 02/17/2024] Open
Abstract
The mitochondrial genomes of apicomplexans comprise merely three protein-coding genes, alongside a set of thirty to forty genes encoding small RNAs (sRNAs), many of which exhibit homologies to rRNA from E. coli. The expression status and integration of these short RNAs into ribosomes remains unclear and direct evidence for active ribosomes within apicomplexan mitochondria is still lacking. In this study, we conducted small RNA sequencing on the apicomplexan Toxoplasma gondii to investigate the occurrence and function of mitochondrial sRNAs. To enhance the analysis of sRNA sequencing outcomes, we also re-sequenced the T. gondii mitochondrial genome using an improved organelle enrichment protocol and Nanopore sequencing. It has been established previously that the T. gondii genome comprises 21 sequence blocks that undergo recombination among themselves but that their order is not entirely random. The enhanced coverage of the mitochondrial genome allowed us to characterize block combinations at increased resolution. Employing this refined genome for sRNA mapping, we find that many small RNAs originated from the junction sites between protein-coding blocks and rRNA sequence blocks. Surprisingly, such block border sRNAs were incorporated into polysomes together with canonical rRNA fragments and mRNAs. In conclusion, apicomplexan ribosomes are active within polysomes and are indeed assembled through the integration of sRNAs, including previously undetected sRNAs with merged mRNA-rRNA sequences. Our findings lead to the hypothesis that T. gondii's block-based genome organization enables the dual utilization of mitochondrial sequences as both messenger RNAs and ribosomal RNAs, potentially establishing a link between the regulation of rRNA and mRNA expression.
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Affiliation(s)
| | | | | | - Zala Gluhic
- Molecular Genetics, Humboldt University BerlinBerlinGermany
| | | | - Peter Lyko
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
| | - Susann Wicke
- Biodiversity and Evolution, Humboldt University BerlinBerlinGermany
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3
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Butenko A, Lukeš J, Speijer D, Wideman JG. Mitochondrial genomes revisited: why do different lineages retain different genes? BMC Biol 2024; 22:15. [PMID: 38273274 PMCID: PMC10809612 DOI: 10.1186/s12915-024-01824-1] [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: 05/05/2023] [Accepted: 01/11/2024] [Indexed: 01/27/2024] Open
Abstract
The mitochondria contain their own genome derived from an alphaproteobacterial endosymbiont. From thousands of protein-coding genes originally encoded by their ancestor, only between 1 and about 70 are encoded on extant mitochondrial genomes (mitogenomes). Thanks to a dramatically increasing number of sequenced and annotated mitogenomes a coherent picture of why some genes were lost, or relocated to the nucleus, is emerging. In this review, we describe the characteristics of mitochondria-to-nucleus gene transfer and the resulting varied content of mitogenomes across eukaryotes. We introduce a 'burst-upon-drift' model to best explain nuclear-mitochondrial population genetics with flares of transfer due to genetic drift.
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Affiliation(s)
- Anzhelika Butenko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Science, University of Ostrava, Ostrava, Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic
- Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic
| | - Dave Speijer
- Medical Biochemistry, Amsterdam UMC, University of Amsterdam, Amsterdam, The Netherlands
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA.
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4
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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Serial Endosymbiotic Events. Methods Mol Biol 2024; 2776:21-41. [PMID: 38502496 DOI: 10.1007/978-1-0716-3726-5_2] [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] [Indexed: 03/21/2024]
Abstract
A considerable part of the diversity of eukaryotic phototrophs consists of algae with plastids that evolved from endosymbioses between two eukaryotes. These complex plastids are characterized by a high number of envelope membranes (more than two) and some of them contain a residual nucleus of the endosymbiotic alga called a nucleomorph. Complex plastid-bearing algae are thus chimeric cell assemblies, eukaryotic symbionts living in a eukaryotic host. In contrast, the primary plastids of the Archaeplastida (plants, green algae, red algae, and glaucophytes) possibly evolved from a single endosymbiosis with a cyanobacterium and are surrounded by two membranes. Complex plastids have been acquired several times by unrelated groups of eukaryotic heterotrophic hosts, suggesting that complex plastids are somewhat easier to obtain than primary plastids. Evidence suggests that complex plastids arose twice independently in the green lineage (euglenophytes and chlorarachniophytes) through secondary endosymbiosis, and four times in the red lineage, first through secondary endosymbiosis in cryptophytes, then by higher-order events in stramenopiles, alveolates, and haptophytes. Engulfment of primary and complex plastid-containing algae by eukaryotic hosts (secondary, tertiary, and higher-order endosymbioses) is also responsible for numerous plastid replacements in dinoflagellates. Plastid endosymbiosis is accompanied by massive gene transfer from the endosymbiont to the host nucleus and cell adaptation of both endosymbiotic partners, which is related to the trophic switch to phototrophy and loss of autonomy of the endosymbiont. Such a process is essential for the metabolic integration and division control of the endosymbiont in the host. Although photosynthesis is the main advantage of acquiring plastids, loss of photosynthesis often occurs in algae with complex plastids. This chapter summarizes the essential knowledge of the acquisition, evolution, and function of complex plastids.
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Affiliation(s)
- Zoltán Füssy
- Scripps Institution of Oceanography, University of California San Diego, La Jolla, CA, USA
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic.
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic.
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5
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Maciszewski K, Fells A, Karnkowska A. Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes. Mol Biol Evol 2022; 39:6834297. [PMID: 36403966 PMCID: PMC9728796 DOI: 10.1093/molbev/msac255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.
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Affiliation(s)
| | - Alicja Fells
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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6
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Oborník M. Organellar Evolution: A Path from Benefit to Dependence. Microorganisms 2022; 10:microorganisms10010122. [PMID: 35056571 PMCID: PMC8781833 DOI: 10.3390/microorganisms10010122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 12/10/2022] Open
Abstract
Eukaryotic organelles supposedly evolved from their bacterial ancestors because of their benefits to host cells. However, organelles are quite often retained, even when the beneficial metabolic pathway is lost, due to something other than the original beneficial function. The organellar function essential for cell survival is, in the end, the result of organellar evolution, particularly losses of redundant metabolic pathways present in both the host and endosymbiont, followed by a gradual distribution of metabolic functions between the organelle and host. Such biological division of metabolic labor leads to mutual dependence of the endosymbiont and host. Changing environmental conditions, such as the gradual shift of an organism from aerobic to anaerobic conditions or light to dark, can make the original benefit useless. Therefore, it can be challenging to deduce the original beneficial function, if there is any, underlying organellar acquisition. However, it is also possible that the organelle is retained because it simply resists being eliminated or digested untill it becomes indispensable.
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Affiliation(s)
- Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 37005 České Budějovice, Czech Republic;
- Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
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7
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Berná L, Rego N, Francia ME. The Elusive Mitochondrial Genomes of Apicomplexa: Where Are We Now? Front Microbiol 2021; 12:751775. [PMID: 34721355 PMCID: PMC8554336 DOI: 10.3389/fmicb.2021.751775] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022] Open
Abstract
Mitochondria are vital organelles of eukaryotic cells, participating in key metabolic pathways such as cellular respiration, thermogenesis, maintenance of cellular redox potential, calcium homeostasis, cell signaling, and cell death. The phylum Apicomplexa is entirely composed of obligate intracellular parasites, causing a plethora of severe diseases in humans, wild and domestic animals. These pathogens include the causative agents of malaria, cryptosporidiosis, neosporosis, East Coast fever and toxoplasmosis, among others. The mitochondria in Apicomplexa has been put forward as a promising source of undiscovered drug targets, and it has been validated as the target of atovaquone, a drug currently used in the clinic to counter malaria. Apicomplexans present a single tubular mitochondria that varies widely both in structure and in genomic content across the phylum. The organelle is characterized by massive gene migrations to the nucleus, sequence rearrangements and drastic functional reductions in some species. Recent third generation sequencing studies have reignited an interest for elucidating the extensive diversity displayed by the mitochondrial genomes of apicomplexans and their intriguing genomic features. The underlying mechanisms of gene transcription and translation are also ill-understood. In this review, we present the state of the art on mitochondrial genome structure, composition and organization in the apicomplexan phylum revisiting topological and biochemical information gathered through classical techniques. We contextualize this in light of the genomic insight gained by second and, more recently, third generation sequencing technologies. We discuss the mitochondrial genomic and mechanistic features found in evolutionarily related alveolates, and discuss the common and distinct origins of the apicomplexan mitochondria peculiarities.
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Affiliation(s)
- Luisa Berná
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Molecular Biology Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Sección Biomatemática-Laboratorio de Genómica Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Natalia Rego
- Bioinformatics Unit, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - María E Francia
- Laboratory of Apicomplexan Biology, Institut Pasteur de Montevideo, Montevideo, Uruguay.,Departamento de Parasitología y Micología, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
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8
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Namasivayam S, Baptista RP, Xiao W, Hall EM, Doggett JS, Troell K, Kissinger JC. A novel fragmented mitochondrial genome in the protist pathogen Toxoplasma gondii and related tissue coccidia. Genome Res 2021; 31:852-865. [PMID: 33906963 PMCID: PMC8092004 DOI: 10.1101/gr.266403.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 03/09/2021] [Indexed: 12/19/2022]
Abstract
Mitochondrial genome content and structure vary widely across the eukaryotic tree of life, with protists displaying extreme examples. Apicomplexan and dinoflagellate protists have evolved highly reduced mitochondrial genome sequences, mtDNA, consisting of only three cytochrome genes and fragmented rRNA genes. Here, we report the independent evolution of fragmented cytochrome genes in Toxoplasma and related tissue coccidia and evolution of a novel genome architecture consisting minimally of 21 sequence blocks (SBs) totaling 5.9 kb that exist as nonrandom concatemers. Single-molecule Nanopore reads consisting entirely of SBs ranging from 0.1 to 23.6 kb reveal both whole and fragmented cytochrome genes. Full-length cytochrome transcripts including a divergent coxIII are detected. The topology of the mitochondrial genome remains an enigma. Analysis of a cob point mutation reveals that homoplasmy of SBs is maintained. Tissue coccidia are important pathogens of man and animals, and the mitochondrion represents an important therapeutic target. The mtDNA sequence has been elucidated, but a definitive genome architecture remains elusive.
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Affiliation(s)
- Sivaranjani Namasivayam
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Rodrigo P Baptista
- Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
| | - Wenyuan Xiao
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA
| | - Erica M Hall
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA
| | - Joseph S Doggett
- Division of Infectious Diseases, Oregon Health Sciences University, Portland, Oregon 97239, USA.,Division of Infectious Diseases, Veterans Affairs Portland Health Care System, Portland, Oregon 97239, USA
| | - Karin Troell
- Department of Microbiology, National Veterinary Institute, SE-751 89 Uppsala, Sweden
| | - Jessica C Kissinger
- Department of Genetics, University of Georgia, Athens, Georgia 30602, USA.,Center for Tropical and Emerging Global Diseases, University of Georgia, Athens, Georgia 30602, USA.,Institute of Bioinformatics, University of Georgia, Athens, Georgia 30602, USA
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9
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Smith D, Kannan G, Coppens I, Wang F, Nguyen HM, Cerutti A, Olafsson EB, Rimple PA, Schultz TL, Mercado Soto NM, Di Cristina M, Besteiro S, Carruthers VB. Toxoplasma TgATG9 is critical for autophagy and long-term persistence in tissue cysts. eLife 2021; 10:e59384. [PMID: 33904393 PMCID: PMC8128441 DOI: 10.7554/elife.59384] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 04/27/2021] [Indexed: 12/29/2022] Open
Abstract
Many of the world's warm-blooded species are chronically infected with Toxoplasma gondii tissue cysts, including an estimated one-third of the global human population. The cellular processes that permit long-term persistence within the cyst are largely unknown for T. gondii and related coccidian parasites that impact human and animal health. Herein, we show that genetic ablation of TgATG9 substantially reduces canonical autophagy and compromises bradyzoite viability. Transmission electron microscopy revealed numerous structural abnormalities occurring in ∆atg9 bradyzoites. Intriguingly, abnormal mitochondrial networks were observed in TgATG9-deficient bradyzoites, some of which contained numerous different cytoplasmic components and organelles. ∆atg9 bradyzoite fitness was drastically compromised in vitro and in mice, with very few brain cysts identified in mice 5 weeks post-infection. Taken together, our data suggests that TgATG9, and by extension autophagy, is critical for cellular homeostasis in bradyzoites and is necessary for long-term persistence within the cyst of this coccidian parasite.
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Affiliation(s)
- David Smith
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Geetha Kannan
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Isabelle Coppens
- Department of Molecular Microbiology and Immunology, Johns Hopkins University Bloomberg School of Public HealthBaltimoreUnited States
| | - Fengrong Wang
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Hoa Mai Nguyen
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Aude Cerutti
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Einar B Olafsson
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Patrick A Rimple
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Tracey L Schultz
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Nayanna M Mercado Soto
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
| | - Manlio Di Cristina
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di PerugiaPerugiaItaly
| | - Sébastien Besteiro
- Laboratory of PathogenHost Interactions, UMR 5235, CNRS, Université de MontpellierMontpellierFrance
| | - Vern B Carruthers
- Department of Microbiology and Immunology, University of Michigan Medical SchoolAnn ArborUnited States
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10
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Peng SE, Moret A, Chang C, Mayfield AB, Ren YT, Chen WNU, Giordano M, Chen CS. A shift away from mutualism under food-deprived conditions in an anemone-dinoflagellate association. PeerJ 2020; 8:e9745. [PMID: 33194344 PMCID: PMC7602683 DOI: 10.7717/peerj.9745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2019] [Accepted: 07/27/2020] [Indexed: 11/20/2022] Open
Abstract
The mutualistic symbiosis between anthozoans and intra-gastrodermal dinoflagellates of the family Symbiodiniaceae is the functional basis of all coral reef ecosystems, with the latter providing up to 95% of their fixed photosynthate to their hosts in exchange for nutrients. However, recent studies of sponges, jellyfish, and anemones have revealed the potential for this mutualistic relationship to shift to parasitism under stressful conditions. Over a period of eight weeks, we compared the physiological conditions of both inoculated and aposymbiotic anemones (Exaiptasia pallida) that were either fed or starved. By the sixth week, both fed groups of anemones were significantly larger than their starved counterparts. Moreover, inoculated and starved anemones tended to disintegrate into “tissue balls” within eight weeks, and 25% of the samples died; in contrast, starved aposymbiotic anemones required six months to form tissue balls, and no anemones from this group died. Our results show that the dinoflagellates within inoculated anemones may have posed a fatal metabolic burden on their hosts during starvation; this may be because of the need to prioritize their own metabolism and nourishment at the expense of their hosts. Collectively, our study reveals the potential of this dynamic symbiotic association to shift away from mutualism during food-deprived conditions.
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Affiliation(s)
- Shao-En Peng
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Alessandro Moret
- Dipatimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
| | - Cherilyn Chang
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
| | - Anderson B. Mayfield
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Cooperative Institute for Marine and Atmospheric Sciences Studies, University of Miami, Miami, FL, United States of America
- Atlantic Oceanographic and Meteorological Laboratory, National Oceanic and Atmospheric Administration, Miami, FL, United States of America
| | - Yu-Ting Ren
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
| | - Wan-Nan U. Chen
- Department of Biological Science and Technology, I-Shou University, Kaohsiung, Taiwan
| | - Mario Giordano
- Dipatimento di Scienze della Vita e dell’Ambiente, Università Politecnica delle Marche, Ancona, Italy
- Institute of Microbiology ASCR, Algatech, Trebon, Czech Republic
| | - Chii-Shiarng Chen
- National Museum of Marine Biology and Aquarium, Pingtung, Taiwan
- Graduate Institute of Marine Biology, National Dong Hwa University, Pingtung, Taiwan
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11
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Kayama M, Maciszewski K, Yabuki A, Miyashita H, Karnkowska A, Kamikawa R. Highly Reduced Plastid Genomes of the Non-photosynthetic Dictyochophyceans Pteridomonas spp. (Ochrophyta, SAR) Are Retained for tRNA-Glu-Based Organellar Heme Biosynthesis. FRONTIERS IN PLANT SCIENCE 2020; 11:602455. [PMID: 33329672 PMCID: PMC7728698 DOI: 10.3389/fpls.2020.602455] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 11/03/2020] [Indexed: 05/05/2023]
Abstract
Organisms that have lost their photosynthetic capabilities are present in a variety of eukaryotic lineages, such as plants and disparate algal groups. Most of such non-photosynthetic eukaryotes still carry plastids, as these organelles retain essential biological functions. Most non-photosynthetic plastids possess genomes with varied protein-coding contents. Such remnant plastids are known to be present in the non-photosynthetic, bacteriovorous alga Pteridomonas danica (Dictyochophyceae, Ochrophyta), which, regardless of its obligatory heterotrophic lifestyle, has been reported to retain the typically plastid-encoded gene for ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) large subunit (rbcL). The presence of rbcL without photosynthetic activity suggests that investigating the function of plastids in Pteridomonas spp. would likely bring unique insights into understanding the reductive evolution of plastids, their genomes, and plastid functions retained after the loss of photosynthesis. In this study, we demonstrate that two newly established strains of the non-photosynthetic genus Pteridomonas possess highly reduced plastid genomes lacking rbcL gene, in contrast to the previous report. Interestingly, we discovered that all plastid-encoded proteins in Pteridomonas spp. are involved only in housekeeping processes (e.g., transcription, translation and protein degradation), indicating that all metabolite synthesis pathways in their plastids are supported fully by nuclear genome-encoded proteins. Moreover, through an in-depth survey of the available transcriptomic data of another strain of the genus, we detected no candidate sequences for nuclear-encoded, plastid-directed Fe-S cluster assembly pathway proteins, suggesting complete loss of this pathway in the organelle, despite its widespread conservation in non-photosynthetic plastids. Instead, the transcriptome contains plastid-targeted components of heme biosynthesis, glycolysis, and pentose phosphate pathways. The retention of the plastid genomes in Pteridomonas spp. is not explained by the Suf-mediated constraint against loss of plastid genomes, previously proposed for Alveolates, as they lack Suf genes. Bearing all these findings in mind, we propose the hypothesis that plastid DNA is retained in Pteridomonas spp. for the purpose of providing glutamyl-tRNA, encoded by trnE gene, as a substrate for the heme biosynthesis pathway.
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Affiliation(s)
- Motoki Kayama
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Kacper Maciszewski
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
| | - Akinori Yabuki
- Japan Agency for Marine-Earth Science and Technology, Yokosuka, Japan
| | - Hideaki Miyashita
- Graduate School of Human and Environmental Studies, Kyoto University, Kyoto, Japan
| | - Anna Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland
- *Correspondence: Anna Karnkowska,
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
- Ryoma Kamikawa,
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12
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Sharaf A, Füssy Z, Tomčala A, Richtová J, Oborník M. Isolation of plastids and mitochondria from Chromera velia. PLANTA 2019; 250:1731-1741. [PMID: 31422509 DOI: 10.1007/s00425-019-03259-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Accepted: 08/08/2019] [Indexed: 06/10/2023]
Abstract
We present an easy and effective procedure to purify plastids and mitochondria from Chromera velia. Our method enables downstream analyses of protein and metabolite content of the organelles. Chromerids are alveolate algae that are the closest known phototrophic relatives to apicomplexan parasites such as Plasmodium or Toxoplasma. While genomic and transcriptomic resources for chromerids are in place, tools and experimental conditions for proteomic studies have not been developed yet. Here we describe a rapid and efficient protocol for simultaneous isolation of plastids and mitochondria from the chromerid alga Chromera velia. This procedure involves enzymatic treatment and breakage of cells, followed by differential centrifugation. While plastids sediment in the first centrifugation step, mitochondria remain in the supernatant. Subsequently, plastids can be purified from the crude pellet by centrifugation on a discontinuous 60%/70% sucrose density gradient, while mitochondria can be obtained by centrifugation on a discontinuous 33%/80% Percoll density gradient. Isolated plastids are autofluorescent, and their multi-membrane structure was confirmed by transmission electron microscopy. Fluorescent optical microscopy was used to identify isolated mitochondria stained with MitoTrackerTM green, while their intactness and membrane potential were confirmed by staining with MitoTrackerTM orange CMTMRos. Total proteins were extracted from isolated organellar fractions, and the purity of isolated organelles was confirmed using immunoblotting. Antibodies against the beta subunit of the mitochondrial ATP synthase and the plastid protochlorophyllide oxidoreductase did not cross-react on immunoblots, suggesting that each organellar fraction is free of the residues of the other. The presented protocol represents an essential step for further proteomic, organellar, and cell biological studies of C. velia and can be employed, with minor optimizations, in other thick-walled unicellular algae.
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Affiliation(s)
- Abdoallah Sharaf
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic.
- Genetic Department, Faculty of Agriculture, Ain Shams University, Cairo, 11241, Egypt.
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Aleš Tomčala
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Jitka Richtová
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre CAS, Branišovská 31, 37005, České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, 37005, České Budějovice, Czech Republic.
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13
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Muñoz-Gómez SA, Durnin K, Eme L, Paight C, Lane CE, Saffo MB, Slamovits CH. Nephromyces Represents a Diverse and Novel Lineage of the Apicomplexa That Has Retained Apicoplasts. Genome Biol Evol 2019; 11:2727-2740. [PMID: 31328784 PMCID: PMC6777426 DOI: 10.1093/gbe/evz155] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/16/2019] [Indexed: 12/13/2022] Open
Abstract
A most interesting exception within the parasitic Apicomplexa is Nephromyces, an extracellular, probably mutualistic, endosymbiont found living inside molgulid ascidian tunicates (i.e., sea squirts). Even though Nephromyces is now known to be an apicomplexan, many other questions about its nature remain unanswered. To gain further insights into the biology and evolutionary history of this unusual apicomplexan, we aimed to 1) find the precise phylogenetic position of Nephromyces within the Apicomplexa, 2) search for the apicoplast genome of Nephromyces, and 3) infer the major metabolic pathways in the apicoplast of Nephromyces. To do this, we sequenced a metagenome and a metatranscriptome from the molgulid renal sac, the specialized habitat where Nephromyces thrives. Our phylogenetic analyses of conserved nucleus-encoded genes robustly suggest that Nephromyces is a novel lineage sister to the Hematozoa, which comprises both the Haemosporidia (e.g., Plasmodium) and the Piroplasmida (e.g., Babesia and Theileria). Furthermore, a survey of the renal sac metagenome revealed 13 small contigs that closely resemble the genomes of the nonphotosynthetic reduced plastids, or apicoplasts, of other apicomplexans. We show that these apicoplast genomes correspond to a diverse set of most closely related but genetically divergent Nephromyces lineages that co-inhabit a single tunicate host. In addition, the apicoplast of Nephromyces appears to have retained all biosynthetic pathways inferred to have been ancestral to parasitic apicomplexans. Our results shed light on the evolutionary history of the only probably mutualistic apicomplexan known, Nephromyces, and provide context for a better understanding of its life style and intricate symbiosis.
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Affiliation(s)
- Sergio A Muñoz-Gómez
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Keira Durnin
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - Laura Eme
- Unité d'Ecologie, Sistématique et Evolution, CNRS, Université Paris-Sud, France
| | | | | | - Mary B Saffo
- Smithsonian National Museum of Natural History, Washington, District of Columbia
| | - Claudio H Slamovits
- Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada
- Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
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14
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Sharaf A, Gruber A, Jiroutová K, Oborník M. Characterization of Aminoacyl-tRNA Synthetases in Chromerids. Genes (Basel) 2019; 10:E582. [PMID: 31370303 PMCID: PMC6723311 DOI: 10.3390/genes10080582] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2019] [Revised: 07/23/2019] [Accepted: 07/28/2019] [Indexed: 01/24/2023] Open
Abstract
Aminoacyl-tRNA synthetases (AaRSs) are enzymes that catalyze the ligation of tRNAs to amino acids. There are AaRSs specific for each amino acid in the cell. Each cellular compartment in which translation takes place (the cytosol, mitochondria, and plastids in most cases), needs the full set of AaRSs; however, individual AaRSs can function in multiple compartments due to dual (or even multiple) targeting of nuclear-encoded proteins to various destinations in the cell. We searched the genomes of the chromerids, Chromera velia and Vitrella brassicaformis, for AaRS genes: 48 genes encoding AaRSs were identified in C. velia, while only 39 AaRS genes were found in V. brassicaformis. In the latter alga, ArgRS and GluRS were each encoded by a single gene occurring in a single copy; only PheRS was found in three genes, while the remaining AaRSs were encoded by two genes. In contrast, there were nine cases for which C. velia contained three genes of a given AaRS (45% of the AaRSs), all of them representing duplicated genes, except AsnRS and PheRS, which are more likely pseudoparalogs (acquired via horizontal or endosymbiotic gene transfer). Targeting predictions indicated that AaRSs are not (or not exclusively), in most cases, used in the cellular compartment from which their gene originates. The molecular phylogenies of the AaRSs are variable between the specific types, and similar between the two investigated chromerids. While genes with eukaryotic origin are more frequently retained, there is no clear pattern of orthologous pairs between C. velia and V. brassicaformis.
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Affiliation(s)
- Abdoallah Sharaf
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
- Genetics Department, Faculty of Agriculture, Ain Shams University, Cairo 11241, Egypt
| | - Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Kateřina Jiroutová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, 370 05 České Budějovice, Czech Republic.
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15
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Füssy Z, Faitová T, Oborník M. Subcellular Compartments Interplay for Carbon and Nitrogen Allocation in Chromera velia and Vitrella brassicaformis. Genome Biol Evol 2019; 11:1765-1779. [PMID: 31192348 PMCID: PMC6668581 DOI: 10.1093/gbe/evz123] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2019] [Indexed: 12/20/2022] Open
Abstract
Endosymbioses necessitate functional cooperation of cellular compartments to avoid pathway redundancy and streamline the control of biological processes. To gain insight into the metabolic compartmentation in chromerids, phototrophic relatives to apicomplexan parasites, we prepared a reference set of proteins probably localized to mitochondria, cytosol, and the plastid, taking advantage of available genomic and transcriptomic data. Training of prediction algorithms with the reference set now allows a genome-wide analysis of protein localization in Chromera velia and Vitrella brassicaformis. We confirm that the chromerid plastids house enzymatic pathways needed for their maintenance and photosynthetic activity, but for carbon and nitrogen allocation, metabolite exchange is necessary with the cytosol and mitochondria. This indeed suggests that the regulatory mechanisms operate in the cytosol to control carbon metabolism based on the availability of both light and nutrients. We discuss that this arrangement is largely shared with apicomplexans and dinoflagellates, possibly stemming from a common ancestral metabolic architecture, and supports the mixotrophy of the chromerid algae.
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Affiliation(s)
- Zoltán Füssy
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
| | - Tereza Faitová
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
- Faculty of Engineering and Natural Sciences, Department of Computer Science, Johannes Kepler University, Linz, Austria
| | - Miroslav Oborník
- Faculty of Science, Department of Molecular Biology and Genetics, University of South Bohemia, České Budějovice, Czech Republic
- Department of Evolutionary Protistology, Institute of Parasitology, Biology Centre CAS, České Budějovice, Czech Republic
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16
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Hillebrand A, Matz JM, Almendinger M, Müller K, Matuschewski K, Schmitz-Linneweber C. Identification of clustered organellar short (cos) RNAs and of a conserved family of organellar RNA-binding proteins, the heptatricopeptide repeat proteins, in the malaria parasite. Nucleic Acids Res 2019; 46:10417-10431. [PMID: 30102371 PMCID: PMC6212722 DOI: 10.1093/nar/gky710] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 07/24/2018] [Indexed: 11/13/2022] Open
Abstract
Gene expression in mitochondria of Plasmodium falciparum is essential for parasite survival. The molecular mechanisms of Plasmodium organellar gene expression remain poorly understood. This includes the enigmatic assembly of the mitochondrial ribosome from highly fragmented rRNAs. Here, we present the identification of clustered organellar short RNA fragments (cosRNAs) that are possible footprints of RNA-binding proteins (RBPs) in Plasmodium organelles. In plants, RBPs of the pentatricopeptide repeat (PPR) class produce footprints as a consequence of their function in processing organellar RNAs. Intriguingly, many of the Plasmodium cosRNAs overlap with 5'-ends of rRNA fragments. We hypothesize that these are footprints of RBPs involved in assembling the rRNA fragments into a functioning ribosome. A bioinformatics search of the Plasmodium nuclear genome identified a hitherto unrecognized organellar helical-hairpin-repeat protein family that we term heptatricopeptide repeat (HPR) proteins. We demonstrate that selected HPR proteins are targeted to mitochondria in P. berghei and that one of them, PbHPR1, associates with RNA, but not DNA in vitro. A phylogenetic search identified HPR proteins in a wide variety of eukaryotes. We hypothesize that HPR proteins are required for processing and stabilizing RNAs in Apicomplexa and other taxa.
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Affiliation(s)
- Arne Hillebrand
- Humboldt University Berlin, Molecular Genetics, Berlin, Germany
| | - Joachim M Matz
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
| | | | - Katja Müller
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
| | - Kai Matuschewski
- Humboldt University, Department of Molecular Parasitology, Berlin, Germany
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17
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Ludewig-Klingner AK, Michael V, Jarek M, Brinkmann H, Petersen J. Distribution and Evolution of Peroxisomes in Alveolates (Apicomplexa, Dinoflagellates, Ciliates). Genome Biol Evol 2018; 10:1-13. [PMID: 29202176 PMCID: PMC5755239 DOI: 10.1093/gbe/evx250] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/28/2017] [Indexed: 12/13/2022] Open
Abstract
The peroxisome was the last organelle to be discovered and five decades later it is still the Cinderella of eukaryotic compartments. Peroxisomes have a crucial role in the detoxification of reactive oxygen species, the beta-oxidation of fatty acids, and the biosynthesis of etherphospholipids, and they are assumed to be present in virtually all aerobic eukaryotes. Apicomplexan parasites including the malaria and toxoplasmosis agents were described as the first group of mitochondriate protists devoid of peroxisomes. This study was initiated to reassess the distribution and evolution of peroxisomes in the superensemble Alveolata (apicomplexans, dinoflagellates, ciliates). We established transcriptome data from two chromerid algae (Chromera velia, Vitrella brassicaformis), and two dinoflagellates (Prorocentrum minimum, Perkinsus olseni) and identified the complete set of essential peroxins in all four reference species. Our comparative genome analysis provides unequivocal evidence for the presence of peroxisomes in Toxoplasma gondii and related genera. Our working hypothesis of a common peroxisomal origin of all alveolates is supported by phylogenetic analyses of essential markers such as the import receptor Pex5. Vitrella harbors the most comprehensive set of peroxisomal proteins including the catalase and the glyoxylate cycle and it is thus a promising model organism to investigate the functional role of this organelle in Apicomplexa.
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Affiliation(s)
- Ann-Kathrin Ludewig-Klingner
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Victoria Michael
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Michael Jarek
- Helmholtz-Centre for Infection Research (HZI), Group of Genome Analytics, Braunschweig, Germany
| | - Henner Brinkmann
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
| | - Jörn Petersen
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Department of Protists and Cyanobacteria (PuC), Braunschweig, Germany
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18
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Salunke R, Mourier T, Banerjee M, Pain A, Shanmugam D. Highly diverged novel subunit composition of apicomplexan F-type ATP synthase identified from Toxoplasma gondii. PLoS Biol 2018; 16:e2006128. [PMID: 30005062 PMCID: PMC6059495 DOI: 10.1371/journal.pbio.2006128] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Revised: 07/25/2018] [Accepted: 06/22/2018] [Indexed: 12/18/2022] Open
Abstract
The mitochondrial F-type ATP synthase, a multisubunit nanomotor, is critical for maintaining cellular ATP levels. In T. gondii and other apicomplexan parasites, many subunit components necessary for proper assembly and functioning of this enzyme appear to be missing. Here, we report the identification of 20 novel subunits of T. gondii F-type ATP synthase from mass spectrometry analysis of partially purified monomeric (approximately 600 kDa) and dimeric (>1 MDa) forms of the enzyme. Despite extreme sequence diversification, key FO subunits a, b, and d can be identified from conserved structural features. Orthologs for these proteins are restricted to apicomplexan, chromerid, and dinoflagellate species. Interestingly, their absence in ciliates indicates a major diversion, with respect to subunit composition of this enzyme, within the alveolate clade. Discovery of these highly diversified novel components of the apicomplexan F-type ATP synthase complex could facilitate the development of novel antiparasitic agents. Structural and functional characterization of this unusual enzyme complex will advance our fundamental understanding of energy metabolism in apicomplexan species.
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Affiliation(s)
- Rahul Salunke
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
| | - Tobias Mourier
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Manidipa Banerjee
- Kusuma School of Biological Sciences, Indian Institute of Technology-Delhi, Hauz Khas, New Delhi, India
| | - Arnab Pain
- Pathogen Genomics Laboratory, BESE Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Dhanasekaran Shanmugam
- Biochemical Sciences Division, CSIR-National Chemical Laboratory, Pune, Maharashtra, India
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19
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Grattepanche J, Walker LM, Ott BM, Paim Pinto DL, Delwiche CF, Lane CE, Katz LA. Microbial Diversity in the Eukaryotic SAR Clade: Illuminating the Darkness Between Morphology and Molecular Data. Bioessays 2018; 40:e1700198. [DOI: 10.1002/bies.201700198] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2017] [Revised: 01/16/2018] [Indexed: 01/09/2023]
Affiliation(s)
| | - Laura M. Walker
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
| | - Brittany M. Ott
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | | | - Charles F. Delwiche
- Department of Cell Biology and Molecular Genetics, University of MarylandCollege ParkMD 20742USA
| | - Christopher E. Lane
- Department of Biological SciencesUniversity of Rhode IslandKingstonRI 02881USA
| | - Laura A. Katz
- Department of Biological Sciences, Smith CollegeNorthamptonMA 01063USA
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20
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Füssy Z, Oborník M. Complex Endosymbioses I: From Primary to Complex Plastids, Multiple Independent Events. Methods Mol Biol 2018; 1829:17-35. [PMID: 29987712 DOI: 10.1007/978-1-4939-8654-5_2] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
A substantial portion of eukaryote diversity consists of algae with complex plastids, i.e., plastids originating from eukaryote-to-eukaryote endosymbioses. These plastids are characteristic by a deviating number of envelope membranes (higher than two), and sometimes a remnant nucleus of the endosymbiont alga, termed the nucleomorph, is present. Complex plastid-bearing algae are therefore much like living matryoshka dolls, eukaryotes within eukaryotes. In comparison, primary plastids of Archaeplastida (plants, green algae, red algae, and glaucophytes) arose upon a single endosymbiosis event with a cyanobacterium and are surrounded by two membranes. Complex plastids were acquired several times by unrelated groups nested within eukaryotic heterotrophs, suggesting complex plastids are somewhat easier to obtain than primary plastids. This is consistent with the existence of higher-order and serial endosymbioses, i.e., engulfment of complex plastid-bearing algae by (tertiary) eukaryotic hosts and functional plastid replacements, respectively. Plastid endosymbiosis is typical by a massive transfer of genetic material from the endosymbiont to the host nucleus and metabolic rearrangements related to the trophic switch to phototrophy; this is necessary to establish metabolic integration of the plastid and control over its division. Although photosynthesis is the main advantage of plastid acquisition, algae that lost photosynthesis often maintain complex plastids, suggesting their roles beyond photosynthesis. This chapter summarizes basic knowledge on acquisition and functions of complex plastid.
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Affiliation(s)
- Zoltán Füssy
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005, České Budějovice, Czech Republic
| | - Miroslav Oborník
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, České Budějovice, 37005, Czech Republic.
- University of South Bohemia, Faculty of Science, Branišovská 31, 37005, České Budějovice, Czech Republic.
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21
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Ganley JG, Toro-Moreno M, Derbyshire ER. Exploring the Untapped Biosynthetic Potential of Apicomplexan Parasites. Biochemistry 2017; 57:365-375. [DOI: 10.1021/acs.biochem.7b00877] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Jack G. Ganley
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Maria Toro-Moreno
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
| | - Emily R. Derbyshire
- Department
of Chemistry, Duke University, 124 Science Drive, Durham, North Carolina 27708, United States
- Department
of Molecular Genetics and Microbiology, Duke University Medical Center, 213 Research Drive, Durham, North Carolina 27710, United States
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22
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Reñé A, Alacid E, Ferrera I, Garcés E. Evolutionary Trends of Perkinsozoa (Alveolata) Characters Based on Observations of Two New Genera of Parasitoids of dinoflagellates, Dinovorax gen. nov. and Snorkelia gen. nov. Front Microbiol 2017; 8:1594. [PMID: 28970818 PMCID: PMC5609580 DOI: 10.3389/fmicb.2017.01594] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 08/04/2017] [Indexed: 11/13/2022] Open
Abstract
Parasites are one of the ecologically most relevant groups of marine food webs, but their taxonomic and biological complexity hampers the assessment of their diversity and evolutionary trends. Moreover, the within-host processes that govern parasitoid infection, development and reproduction are often unknown. In this study, we describe a new species of a perkinsozoan endoparasitoid that infects the toxic dinoflagellate Dinophysis sacculus, by including observations of its morphology, ultrastructure, life-cycle development and phylogeny. The SSU rDNA sequence and main morphological features were also obtained for a second parasitoid species infecting the bloom-forming dinoflagellate Levanderina fissa. Phylogenetic analyses including the sequences obtained show that all known Perkinsozoa species infecting dinoflagellates cluster together. However, sequences of Parvilucifera prorocentri and those obtained in this study cluster at the base of the clade, while the rest of Parvilucifera representatives form a separated highly-supported cluster. These results, together with differing morphological characters like the formation of a germ-tube, the presence of trichocysts, or the heterochromatin presence in zoospores nucleus justify the erection of Dinovorax pyriformis gen. nov. et sp. nov., and Snorkelia prorocentri gen. nov. et comb. nov. (=Parvilucifera prorocentri). The morphological features and phylogenetic position of these parasitoids represent ancestral characters for the Perkinsozoa phylum, and also for Dinozoa clade, allowing the inference of the evolutionary framework of these Alveolata members.
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Affiliation(s)
- Albert Reñé
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Elisabet Alacid
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Isabel Ferrera
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
| | - Esther Garcés
- Departament de Biologia Marina i Oceanografia, Institut de Ciències del Mar (CSIC)Barcelona, Spain
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Ainsworth TD, Fordyce AJ, Camp EF. The Other Microeukaryotes of the Coral Reef Microbiome. Trends Microbiol 2017; 25:980-991. [PMID: 28720387 DOI: 10.1016/j.tim.2017.06.007] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2017] [Revised: 06/08/2017] [Accepted: 06/16/2017] [Indexed: 12/21/2022]
Abstract
In marine ecosystems microbial communities are critical to ocean function, global primary productivity, and biogeochemical cycles. Both prokaryotic and eukaryotic microbes are essential symbionts and mutualists, nonpathogenic invaders, primary pathogens, have been linked to disease emergence, and can underpin broader ecosystem changes. However, in the effort to determine coral-microbial interactions, the structure and function of the eukaryotic microbes of the microbiome have been studied less. Eukaryotic microbes are important members of the microbiome, constitute entire kingdoms of life, and make important contributions to ecosystem function. Here, we outline the roles of eukaryotic microbes in marine systems and their contribution to ecosystem change, and discuss the microeukaryotic microbiome of corals and coral reefs.
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Affiliation(s)
- T D Ainsworth
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4810, QLD, Australia.
| | - A J Fordyce
- Australian Research Council Centre of Excellence for Coral Reef Studies, James Cook University, Townsville 4810, QLD, Australia
| | - E F Camp
- Climate Change Cluster, University of Technology Sydney, PO Box 123, Broadway, NSW, 2007, Australia
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Gagat P, Mackiewicz D, Mackiewicz P. Peculiarities within peculiarities - dinoflagellates and their mitochondrial genomes. MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:191-195. [PMID: 33473765 PMCID: PMC7800619 DOI: 10.1080/23802359.2017.1307699] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
After the establishment of an endosymbiotic relationship between a proto-mitochondrion and its probable archaeal host, mitochondrial genomes underwent a spectacular reductive evolution. An interesting pathway was chosen by mitogenomes of unicellular protists called dinoflagellates, which experienced an additional wave of reduction followed by amplification and rearrangement leading to their secondary complexity. The former resulted in a mitogenome consisting of only three protein-coding genes, the latter in their multiple copies being scattered across numerous chromosomes and the evolution of complex processes for their expression. These stunning features raise a question about the future of the dinoflagellate mitochondrial genome.
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Affiliation(s)
- Przemysław Gagat
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Dorota Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
| | - Paweł Mackiewicz
- Department of Genomics, Faculty of Biotechnology, University of Wrocław, Wrocław, Poland
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25
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High photochemical trapping efficiency in Photosystem I from the red clade algae Chromera velia and Phaeodactylum tricornutum. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2017; 1858:56-63. [DOI: 10.1016/j.bbabio.2016.10.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Revised: 10/06/2016] [Accepted: 10/07/2016] [Indexed: 11/23/2022]
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Klug D, Mair GR, Frischknecht F, Douglas RG. A small mitochondrial protein present in myzozoans is essential for malaria transmission. Open Biol 2016; 6:160034. [PMID: 27053680 PMCID: PMC4852462 DOI: 10.1098/rsob.160034] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Myzozoans (which include dinoflagellates, chromerids and apicomplexans) display notable divergence from their ciliate sister group, including a reduced mitochondrial genome and divergent metabolic processes. The factors contributing to these divergent processes are still poorly understood and could serve as potential drug targets in disease-causing protists. Here, we report the identification and characterization of a small mitochondrial protein from the rodent-infecting apicomplexan parasite Plasmodium berghei that is essential for development in its mosquito host. Parasites lacking the gene mitochondrial protein ookinete developmental defect (mpodd) showed malformed parasites that were unable to transmit to mosquitoes. Knockout parasites displayed reduced mitochondrial mass without affecting organelle integrity, indicating no role of the protein in mitochondrial biogenesis or morphology maintenance but a likely role in mitochondrial import or metabolism. Using genetic complementation experiments, we identified a previously unrecognized Plasmodium falciparum homologue that can rescue the mpodd(−) phenotype, thereby showing that the gene is functionally conserved. As far as can be detected, mpodd is found in myzozoans, has homologues in the phylum Apicomplexa and appears to have arisen in free-living dinoflagellates. This suggests that the MPODD protein has a conserved mitochondrial role that is important for myzozoans. While previous studies identified a number of essential proteins which are generally highly conserved evolutionarily, our study identifies, for the first time, a non-canonical protein fulfilling a crucial function in the mitochondrion during parasite transmission.
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Affiliation(s)
- Dennis Klug
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Gunnar R Mair
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Friedrich Frischknecht
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
| | - Ross G Douglas
- Integrative Parasitology, Center for Infectious Diseases, Heidelberg University Medical School, Im Neuenheimer Feld 324, 69120 Heidelberg, Germany
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Füssy Z, Masařová P, Kručinská J, Esson HJ, Oborník M. Budding of the Alveolate Alga Vitrella brassicaformis Resembles Sexual and Asexual Processes in Apicomplexan Parasites. Protist 2016; 168:80-91. [PMID: 28061382 DOI: 10.1016/j.protis.2016.12.001] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Revised: 11/30/2016] [Accepted: 12/01/2016] [Indexed: 11/29/2022]
Abstract
Ease of cultivation and availability of genomic data promoted intensive research of free-living phototrophic relatives of apicomplexans, i.e. Chromera velia and Vitrella brassicaformis. Chromera and Vitrella differ significantly in their physiology, morphology, phylogenetic position and genomic features, but Vitrella has not gained as much attention. Here we describe two types of Vitrella zoosporangia. One contains zoospores surrounded by roughly structured matter, with an intracytoplasmic axoneme predicted to develop into a mature flagellum upon spore release, similarly to Plasmodium microgametes; in the second type, cells concurrently bud off the center of the sporangium, surrounded by smooth matter, and flagella develop extracellularly. This process of budding is reminiscent of microsporogenesis as seen in Toxoplasma. We suggest one (or both) of these processes generates gamete-like flagellate progeny. Based on live staining, fusion of zoospores does occur in cultures of V. brassicaformis. We failed to find an apical structure similar to the pseudoconoid in any life stage. V. brassicaformis may therefore either represent an ancestral state lacking an apical complex or has lost the apical complex secondarily. We propose that the common ancestor of Apicomplexa and "chrompodellids" exhibited a complex life cycle, which was reduced in chromerids and colpodellids as dictated by their environment.
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Affiliation(s)
- Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Petra Masařová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Jitka Kručinská
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia; Faculty of Science, University of South Bohemia, České Budějovice, Czechia
| | - Heather J Esson
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czechia; Faculty of Science, University of South Bohemia, České Budějovice, Czechia; Centre Algatech, Institute of Microbiology, Czech Academy of Sciences, Třeboň, Czechia.
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28
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Rubanov LI, Seliverstov AV, Zverkov OA, Lyubetsky VA. A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata. BMC Bioinformatics 2016; 17:385. [PMID: 27645252 PMCID: PMC5028923 DOI: 10.1186/s12859-016-1257-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Accepted: 09/13/2016] [Indexed: 01/24/2023] Open
Abstract
Background Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between apicomplexans can be very high, in particular, due to the positive selection pressure on them. This complicates the identification of highly conserved elements in alveolates, which is overcome by the proposed algorithm. Results A novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed. Conclusion We proposed an algorithm for the identification of highly conserved elements. The multitude of identified elements was used to infer the phylogeny of Alveolata. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1257-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Lev I Rubanov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia.
| | - Alexandr V Seliverstov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
| | - Oleg A Zverkov
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
| | - Vassily A Lyubetsky
- Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia
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Zíková A, Hampl V, Paris Z, Týč J, Lukeš J. Aerobic mitochondria of parasitic protists: Diverse genomes and complex functions. Mol Biochem Parasitol 2016; 209:46-57. [PMID: 26906976 DOI: 10.1016/j.molbiopara.2016.02.007] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 02/16/2016] [Accepted: 02/17/2016] [Indexed: 02/08/2023]
Abstract
In this review the main features of the mitochondria of aerobic parasitic protists are discussed. While the best characterized organelles are by far those of kinetoplastid flagellates and Plasmodium, we also consider amoebae Naegleria and Acanthamoeba, a ciliate Ichthyophthirius and related lineages. The simplistic view of the mitochondrion as just a power house of the cell has already been abandoned in multicellular organisms and available data indicate that this also does not apply for protists. We discuss in more details the following mitochondrial features: genomes, post-transcriptional processing, translation, biogenesis of iron-sulfur complexes, heme metabolism and the electron transport chain. Substantial differences in all these core mitochondrial features between lineages are compatible with the view that aerobic protists harbor organelles that are more complex and flexible than previously appreciated.
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Affiliation(s)
- Alena Zíková
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic.
| | - Vladimír Hampl
- Charles University in Prague, Faculty of Science, Prague, Czech Republic
| | - Zdeněk Paris
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Jiří Týč
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, České Budějovice (Budweis), Czech Republic; University of South Bohemia, Faculty of Science, České Budějovice (Budweis), Czech Republic; Canadian Institute for Advanced Research, Toronto, Canada.
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Zverkov OA, Seliverstov AV, Lyubetsky VA. Regulation of Expression and Evolution of Genes in Plastids of Rhodophytic Branch. Life (Basel) 2016; 6:E7. [PMID: 26840333 PMCID: PMC4810238 DOI: 10.3390/life6010007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2015] [Revised: 01/20/2016] [Accepted: 01/25/2016] [Indexed: 12/13/2022] Open
Abstract
A novel algorithm and original software were used to cluster all proteins encoded in plastids of 72 species of the rhodophytic branch. The results are publicly available at http://lab6.iitp.ru/ppc/redline72/ in a database that allows fast identification of clusters (protein families) both by a fragment of an amino acid sequence and by a phylogenetic profile of a protein. No such integral clustering with the corresponding functions can be found in the public domain. The putative regulons of the transcription factors Ycf28 and Ycf29 encoded in the plastids were identified using the clustering and the database. A regulation of translation initiation was proposed for the ycf24 gene in plastids of certain red algae and apicomplexans as well as a regulation of a putative gene in apicoplasts of Babesia spp. and Theileria parva. The conserved regulation of the ycf24 gene expression and specificity alternation of the transcription factor Ycf28 were shown in the plastids. A phylogenetic tree of plastids was generated for the rhodophytic branch. The hypothesis of the origin of apicoplasts from the common ancestor of all apicomplexans from plastids of red algae was confirmed.
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Affiliation(s)
- Oleg Anatolyevich Zverkov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
| | - Alexandr Vladislavovich Seliverstov
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
| | - Vassily Alexandrovich Lyubetsky
- Institute for Information Transmission Problems of the Russian Academy of Sciences (Kharkevich Institute), Bolshoy Karetny per. 19, Build. 1, Moscow 127051, Russia.
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