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Yazaki E, Uehara T, Sakamoto H, Inagaki Y. Dinotoms possess two evolutionary distinct autophagy-related ubiquitin-like conjugation systems. Protist 2024; 175:126067. [PMID: 39341116 DOI: 10.1016/j.protis.2024.126067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2024] [Revised: 08/29/2024] [Accepted: 09/15/2024] [Indexed: 09/30/2024]
Abstract
Autophagy is an intracellular degradation mechanism by which cytoplasmic materials are delivered to and degraded in the lysosome-fused autophagosome (autolysosome) and proposed to have been established at an early stage of eukaryotic evolution. Dinoflagellates harboring endosymbiotic diatoms (so-called "dinotoms"), which retain their own nuclei and mitochondria in addition to plastids, have been investigated as an intermediate toward the full integration of a eukaryotic phototroph into the host-controlled organelle (i.e., plastid) through endosymbiosis. Pioneering studies systematically evaluated the degree of host governance on several metabolic pathways in the endosymbiotic diatoms (ESDs). However, little attention has been paid to the impact of the endosymbiotic lifestyle on the autophagy operated in the ESDs. In this study, we searched for ATG3, ATG4, ATG5, ATG7, ATG8, ATG10, and ATG12, which are required for autophagosome formation, in the RNA-seq data from dinotoms Durinskia baltica and Kryptoperidinium foliaceum. We detected two evolutionally distinct sets of the ATG proteins in the dinotom species, one affiliated with the dinoflagellate homologs and the other with the diatom homologs in phylogenetic analyses. The results suggest that the ATG proteins descended from the diatom taken up by the dinoflagellate host persist for autophagosome formation and, most likely, autophagy.
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Affiliation(s)
- Euki Yazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Ibaraki, Japan; RIKEN iTHEMS, Wako, Saitama, Japan.
| | - Tadaaki Uehara
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hirokazu Sakamoto
- Department of Infection and Host Defense, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan; Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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2
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Pietluch F, Mackiewicz P, Ludwig K, Gagat P. A New Model and Dating for the Evolution of Complex Plastids of Red Alga Origin. Genome Biol Evol 2024; 16:evae192. [PMID: 39240751 DOI: 10.1093/gbe/evae192] [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: 11/10/2023] [Revised: 08/14/2024] [Accepted: 08/31/2024] [Indexed: 09/08/2024] Open
Abstract
Complex plastids, characterized by more than two bounding membranes, still present an evolutionary puzzle for the traditional endosymbiotic theory. Unlike primary plastids that directly evolved from cyanobacteria, complex plastids originated from green or red algae. The Chromalveolata hypothesis proposes a single red alga endosymbiosis that involved the ancestor of all the Chromalveolata lineages: cryptophytes, haptophytes, stramenopiles, and alveolates. As extensive phylogenetic analyses contradict the monophyly of Chromalveolata, serial plastid endosymbiosis models were proposed, suggesting a single secondary red alga endosymbiosis within Cryptophyta, followed by subsequent plastid transfers to other chromalveolates. Our findings based on 97 plastid-encoded markers, 112 species, and robust phylogenetic methods challenge all the existing models. They reveal two independent secondary endosymbioses, one within Cryptophyta and one within stramenopiles, precisely the phylum Ochrophyta, with two different groups of red algae. Consequently, we propose a new model for the emergence of red alga plastid-containing lineages and, through molecular clock analyses, estimate their ages.
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Affiliation(s)
- Filip Pietluch
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Paweł Mackiewicz
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Kacper Ludwig
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
| | - Przemysław Gagat
- Department of Bioinformatics and Genomics, Faculty of Biotechnology, University of Wroclaw, 50-383 Wroclaw, Poland
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3
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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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4
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Miyagishima SY. Taming the perils of photosynthesis by eukaryotes: constraints on endosymbiotic evolution in aquatic ecosystems. Commun Biol 2023; 6:1150. [PMID: 37952050 PMCID: PMC10640588 DOI: 10.1038/s42003-023-05544-0] [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: 07/06/2023] [Accepted: 11/03/2023] [Indexed: 11/14/2023] Open
Abstract
An ancestral eukaryote acquired photosynthesis by genetically integrating a cyanobacterial endosymbiont as the chloroplast. The chloroplast was then further integrated into many other eukaryotic lineages through secondary endosymbiotic events of unicellular eukaryotic algae. While photosynthesis enables autotrophy, it also generates reactive oxygen species that can cause oxidative stress. To mitigate the stress, photosynthetic eukaryotes employ various mechanisms, including regulating chloroplast light absorption and repairing or removing damaged chloroplasts by sensing light and photosynthetic status. Recent studies have shown that, besides algae and plants with innate chloroplasts, several lineages of numerous unicellular eukaryotes engage in acquired phototrophy by hosting algal endosymbionts or by transiently utilizing chloroplasts sequestrated from algal prey in aquatic ecosystems. In addition, it has become evident that unicellular organisms engaged in acquired phototrophy, as well as those that feed on algae, have also developed mechanisms to cope with photosynthetic oxidative stress. These mechanisms are limited but similar to those employed by algae and plants. Thus, there appear to be constraints on the evolution of those mechanisms, which likely began by incorporating photosynthetic cells before the establishment of chloroplasts by extending preexisting mechanisms to cope with oxidative stress originating from mitochondrial respiration and acquiring new mechanisms.
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Affiliation(s)
- Shin-Ya Miyagishima
- Department of Gene Function and Phenomics, National Institute of Genetics, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
- The Graduate University for Advanced Studies, SOKENDAI, 1111 Yata, Mishima, Shizuoka, 411-8540, Japan.
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5
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Yamada N, Lepetit B, Mann DG, Sprecher BN, Buck JM, Bergmann P, Kroth PG, Bolton JJ, Dąbek P, Witkowski A, Kim SY, Trobajo R. Prey preference in a kleptoplastic dinoflagellate is linked to photosynthetic performance. THE ISME JOURNAL 2023; 17:1578-1588. [PMID: 37391621 PMCID: PMC10504301 DOI: 10.1038/s41396-023-01464-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Revised: 06/12/2023] [Accepted: 06/16/2023] [Indexed: 07/02/2023]
Abstract
Dinoflagellates of the family Kryptoperidiniaceae, known as "dinotoms", possess diatom-derived endosymbionts and contain individuals at three successive evolutionary stages: a transiently maintained kleptoplastic stage; a stage containing multiple permanently maintained diatom endosymbionts; and a further permanent stage containing a single diatom endosymbiont. Kleptoplastic dinotoms were discovered only recently, in Durinskia capensis; until now it has not been investigated kleptoplastic behavior and the metabolic and genetic integration of host and prey. Here, we show D. capensis is able to use various diatom species as kleptoplastids and exhibits different photosynthetic capacities depending on the diatom species. This is in contrast with the prey diatoms in their free-living stage, as there are no differences in their photosynthetic capacities. Complete photosynthesis including both the light reactions and the Calvin cycle remain active only when D. capensis feeds on its habitual associate, the "essential" diatom Nitzschia captiva. The organelles of another edible diatom, N. inconspicua, are preserved intact after ingestion by D. capensis and expresses the psbC gene of the photosynthetic light reaction, while RuBisCO gene expression is lost. Our results indicate that edible but non-essential, "supplemental" diatoms are used by D. capensis for producing ATP and NADPH, but not for carbon fixation. D. capensis has established a species-specifically designed metabolic system allowing carbon fixation to be performed only by its essential diatoms. The ability of D. capensis to ingest supplemental diatoms as kleptoplastids may be a flexible ecological strategy, to use these diatoms as "emergency supplies" while no essential diatoms are available.
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Affiliation(s)
- Norico Yamada
- Department of Biology, University of Konstanz, Konstanz, Germany.
| | - Bernard Lepetit
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - David G Mann
- Marine and Continental Waters Program, Institute for Food and Agricultural Research and Technology, La Ràpita, Spain
- Royal Botanic Garden Edinburgh, Edinburgh, UK
| | | | - Jochen M Buck
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Paavo Bergmann
- Electron Microscopy Centre, University of Konstanz, Konstanz, Germany
| | - Peter G Kroth
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - John J Bolton
- Department of Biological Sciences, University of Cape Town, Cape Town, South Africa
| | - Przemysław Dąbek
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Szczecin, Poland
| | - So-Yeon Kim
- Department of Oceanography, Kunsan National University, Gunsan, Republic of Korea
| | - Rosa Trobajo
- Marine and Continental Waters Program, Institute for Food and Agricultural Research and Technology, La Ràpita, Spain
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6
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Sørensen MES, Zlatogursky VV, Onuţ-Brännström I, Walraven A, Foster RA, Burki F. A novel kleptoplastidic symbiosis revealed in the marine centrohelid Meringosphaera with evidence of genetic integration. Curr Biol 2023; 33:3571-3584.e6. [PMID: 37536342 PMCID: PMC7615077 DOI: 10.1016/j.cub.2023.07.017] [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] [Revised: 06/01/2023] [Accepted: 07/11/2023] [Indexed: 08/05/2023]
Abstract
Plastid symbioses between heterotrophic hosts and algae are widespread and abundant in surface oceans. They are critically important both for extant ecological systems and for understanding the evolution of plastids. Kleptoplastidy, where the plastids of prey are temporarily retained and continuously re-acquired, provides opportunities to study the transitional states of plastid establishment. Here, we investigated the poorly studied marine centrohelid Meringosphaera and its previously unidentified symbionts using culture-independent methods from environmental samples. Investigations of the 18S rDNA from single-cell assembled genomes (SAGs) revealed uncharacterized genetic diversity within Meringosphaera that likely represents multiple species. We found that Meringosphaera harbors plastids of Dictyochophyceae origin (stramenopiles), for which we recovered six full plastid genomes and found evidence of two distinct subgroups that are congruent with host identity. Environmental monitoring by qPCR and catalyzed reporter deposition-fluorescence in situ hybridization (CARD-FISH) revealed seasonal dynamics of both host and plastid. In particular, we did not detect the plastids for 6 months of the year, which, combined with the lack of plastids in some SAGs, suggests that the plastids are temporary and the relationship is kleptoplastidic. Importantly, we found evidence of genetic integration of the kleptoplasts as we identified host-encoded plastid-associated genes, with evolutionary origins likely from the plastid source as well as from other alga sources. This is only the second case where host-encoded kleptoplast-targeted genes have been predicted in an ancestrally plastid-lacking group. Our results provide evidence for gene transfers and protein re-targeting as relatively early events in the evolution of plastid symbioses.
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Affiliation(s)
- Megan E S Sørensen
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden; Institute of Microbial Cell Biology, Heinrich Heine University, 40225 Düsseldorf, Germany.
| | - Vasily V Zlatogursky
- Department of Botany, University of British Columbia, V6T 1Z4 Vancouver, BC, Canada; Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Ioana Onuţ-Brännström
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden; Department of Ecology and Genetics, Uppsala University, 752 36 Uppsala, Sweden; Natural History Museum, University of Oslo, 0562 Oslo, Norway
| | - Anne Walraven
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden
| | - Rachel A Foster
- Department of Ecology, Environment and Plant Sciences, Stockholm University, 106 91 Stockholm, Sweden
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, 752 36 Uppsala, Sweden; Science for Life Laboratory, Uppsala University, 752 37 Uppsala, Sweden.
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7
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Johnson MD, Moeller HV, Paight C, Kellogg RM, McIlvin MR, Saito MA, Lasek-Nesselquist E. Functional control and metabolic integration of stolen organelles in a photosynthetic ciliate. Curr Biol 2023; 33:973-980.e5. [PMID: 36773606 DOI: 10.1016/j.cub.2023.01.027] [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: 09/27/2022] [Revised: 11/15/2022] [Accepted: 01/16/2023] [Indexed: 02/12/2023]
Abstract
Stealing prey plastids for metabolic gain is a common phenomenon among protists within aquatic ecosystems.1 Ciliates of the Mesodinium rubrum species complex are unique in that they also steal a transcriptionally active but non-dividing prey nucleus, the kleptokaryon, from certain cryptophytes.2 The kleptokaryon enables full control and replication of kleptoplastids but has a half-life of about 10 days.2 Once the kleptokaryon is lost, the ciliate experiences a slow loss of photosynthetic metabolism and eventually death.2,3,4 This transient ability to function phototrophically allows M. rubrum to form productive blooms in coastal waters.5,6,7,8 Here, we show, using multi-omics approaches, that an Antarctic strain of the ciliate not only depends on stolen Geminigera cryophila organelles for photosynthesis but also for anabolic synthesis of fatty acids, amino acids, and other essential macromolecules. Transcription of diverse pathways was higher in the kleptokaryon than that in G. cryophila, and many increased in higher light. Proteins of major biosynthetic pathways were found in greater numbers in the kleptokaryon relative to M. rubrum, implying anabolic dependency on foreign metabolism. We show that despite losing transcriptional control of the kleptokaryon, M. rubrum regulates kleptoplastid pigments with changing light, implying an important role for post-transcriptional control. These findings demonstrate that the integration of foreign organelles and their gene and protein expression, energy metabolism, and anabolism occur in the absence of a stable endosymbiotic association. Our results shed light on potential events early in the process of complex plastid acquisition and broaden our understanding of symbiogenesis.
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Affiliation(s)
- Matthew D Johnson
- Biology Department, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA.
| | - Holly V Moeller
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Christopher Paight
- Department of Ecology, Evolution, and Marine Biology, University of California, Santa Barbara, Santa Barbara, CA 93106, USA
| | - Riss M Kellogg
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Matthew R McIlvin
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
| | - Mak A Saito
- Department of Marine Chemistry and Geochemistry, Woods Hole Oceanographic Institution, Woods Hole, MA 02543, USA
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8
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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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9
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Van Vlierberghe M, Di Franco A, Philippe H, Baurain D. Decontamination, pooling and dereplication of the 678 samples of the Marine Microbial Eukaryote Transcriptome Sequencing Project. BMC Res Notes 2021; 14:306. [PMID: 34372933 PMCID: PMC8353744 DOI: 10.1186/s13104-021-05717-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2021] [Accepted: 07/27/2021] [Indexed: 11/10/2022] Open
Abstract
OBJECTIVES Complex algae are photosynthetic organisms resulting from eukaryote-to-eukaryote endosymbiotic-like interactions. Yet the specific lineages and mechanisms are still under debate. That is why large scale phylogenomic studies are needed. Whereas available proteomes provide a limited diversity of complex algae, MMETSP (Marine Microbial Eukaryote Transcriptome Sequencing Project) transcriptomes represent a valuable resource for phylogenomic analyses, owing to their broad and rich taxonomic sampling, especially of photosynthetic species. Unfortunately, this sampling is unbalanced and sometimes highly redundant. Moreover, we observed contaminated sequences in some samples. In such a context, tree inference and readability are impaired. Consequently, the aim of the data processing reported here is to release a unique set of clean and non-redundant transcriptomes produced through an original protocol featuring decontamination, pooling and dereplication steps. DATA DESCRIPTION We submitted 678 MMETSP re-assembly samples to our parallel consolidation pipeline. Hence, we combined 423 samples into 110 consolidated transcriptomes, after the systematic removal of the most contaminated samples (186). This approach resulted in a total of 224 high-quality transcriptomes, easy to use and suitable to compute less contaminated, less redundant and more balanced phylogenies.
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Affiliation(s)
- Mick Van Vlierberghe
- InBioS – PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
| | - Arnaud Di Franco
- Station D’Ecologie Théorique Et Expérimentale de Moulis, UMR CNRS 5321, Moulis, France
| | - Hervé Philippe
- Station D’Ecologie Théorique Et Expérimentale de Moulis, UMR CNRS 5321, Moulis, France
| | - Denis Baurain
- InBioS – PhytoSYSTEMS, Eukaryotic Phylogenomics, University of Liège, Liège, Belgium
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Abstract
The origin of plastids (chloroplasts) by endosymbiosis stands as one of the most important events in the history of eukaryotic life. The genetic, biochemical, and cell biological integration of a cyanobacterial endosymbiont into a heterotrophic host eukaryote approximately a billion years ago paved the way for the evolution of diverse algal groups in a wide range of aquatic and, eventually, terrestrial environments. Plastids have on multiple occasions also moved horizontally from eukaryote to eukaryote by secondary and tertiary endosymbiotic events. The overall picture of extant photosynthetic diversity can best be described as “patchy”: Plastid-bearing lineages are spread far and wide across the eukaryotic tree of life, nested within heterotrophic groups. The algae do not constitute a monophyletic entity, and understanding how, and how often, plastids have moved from branch to branch on the eukaryotic tree remains one of the most fundamental unsolved problems in the field of cell evolution. In this review, we provide an overview of recent advances in our understanding of the origin and spread of plastids from the perspective of comparative genomics. Recent years have seen significant improvements in genomic sampling from photosynthetic and nonphotosynthetic lineages, both of which have added important pieces to the puzzle of plastid evolution. Comparative genomics has also allowed us to better understand how endosymbionts become organelles.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, Nova Scotia, Canada.,Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Nova Scotia, Canada
| | - John M Archibald
- Department of Biochemistry & 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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11
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Cordoba J, Perez E, Van Vlierberghe M, Bertrand AR, Lupo V, Cardol P, Baurain D. De Novo Transcriptome Meta-Assembly of the Mixotrophic Freshwater Microalga Euglena gracilis. Genes (Basel) 2021; 12:842. [PMID: 34072576 PMCID: PMC8227486 DOI: 10.3390/genes12060842] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/24/2021] [Accepted: 05/27/2021] [Indexed: 01/01/2023] Open
Abstract
Euglena gracilis is a well-known photosynthetic microeukaryote considered as the product of a secondary endosymbiosis between a green alga and a phagotrophic unicellular belonging to the same eukaryotic phylum as the parasitic trypanosomatids. As its nuclear genome has proven difficult to sequence, reliable transcriptomes are important for functional studies. In this work, we assembled a new consensus transcriptome by combining sequencing reads from five independent studies. Based on a detailed comparison with two previously released transcriptomes, our consensus transcriptome appears to be the most complete so far. Remapping the reads on it allowed us to compare the expression of the transcripts across multiple culture conditions at once and to infer a functionally annotated network of co-expressed genes. Although the emergence of meaningful gene clusters indicates that some biological signal lies in gene expression levels, our analyses confirm that gene regulation in euglenozoans is not primarily controlled at the transcriptional level. Regarding the origin of E. gracilis, we observe a heavily mixed gene ancestry, as previously reported, and rule out sequence contamination as a possible explanation for these observations. Instead, they indicate that this complex alga has evolved through a convoluted process involving much more than two partners.
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Affiliation(s)
- Javier Cordoba
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Emilie Perez
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Mick Van Vlierberghe
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Amandine R. Bertrand
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Valérian Lupo
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
| | - Pierre Cardol
- InBioS—PhytoSYSTEMS, Laboratoire de Génétique et Physiologie des Microalgues, ULiège, B-4000 Liège, Belgium; (J.C.); (E.P.); (P.C.)
| | - Denis Baurain
- InBioS—PhytoSYSTEMS, Unit of Eukaryotic Phylogenomics, ULiège, B-4000 Liège, Belgium; (M.V.V.); (A.R.B.); (V.L.)
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12
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Goodson HV, Kelley JB, Brawley SH. Cytoskeletal diversification across 1 billion years: What red algae can teach us about the cytoskeleton, and vice versa. Bioessays 2021; 43:e2000278. [PMID: 33797088 DOI: 10.1002/bies.202000278] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Revised: 01/22/2021] [Accepted: 01/28/2021] [Indexed: 11/05/2022]
Abstract
The cytoskeleton has a central role in eukaryotic biology, enabling cells to organize internally, polarize, and translocate. Studying cytoskeletal machinery across the tree of life can identify common elements, illuminate fundamental mechanisms, and provide insight into processes specific to less-characterized organisms. Red algae represent an ancient lineage that is diverse, ecologically significant, and biomedically relevant. Recent genomic analysis shows that red algae have a surprising paucity of cytoskeletal elements, particularly molecular motors. Here, we review the genomic and cell biological evidence and propose testable models of how red algal cells might perform processes including cell motility, cytokinesis, intracellular transport, and secretion, given their reduced cytoskeletons. In addition to enhancing understanding of red algae and lineages that evolved from red algal endosymbioses (e.g., apicomplexan parasites), these ideas may also provide insight into cytoskeletal processes in animal cells.
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Affiliation(s)
- Holly V Goodson
- Department of Chemistry and Biochemistry and Department of Biological Sciences, University of Notre Dame, Notre Dame, Indiana, USA
| | - Joshua B Kelley
- Department of Molecular and Biomedical Sciences, University of Maine, Orono, Maine, USA
| | - Susan H Brawley
- School of Marine Sciences, University of Maine, Orono, Maine, USA
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13
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Strassert JFH, Irisarri I, Williams TA, Burki F. A molecular timescale for eukaryote evolution with implications for the origin of red algal-derived plastids. Nat Commun 2021; 12:1879. [PMID: 33767194 PMCID: PMC7994803 DOI: 10.1038/s41467-021-22044-z] [Citation(s) in RCA: 88] [Impact Index Per Article: 29.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 02/25/2021] [Indexed: 01/31/2023] Open
Abstract
In modern oceans, eukaryotic phytoplankton is dominated by lineages with red algal-derived plastids such as diatoms, dinoflagellates, and coccolithophores. Despite the ecological importance of these groups and many others representing a huge diversity of forms and lifestyles, we still lack a comprehensive understanding of their evolution and how they obtained their plastids. New hypotheses have emerged to explain the acquisition of red algal-derived plastids by serial endosymbiosis, but the chronology of these putative independent plastid acquisitions remains untested. Here, we establish a timeframe for the origin of red algal-derived plastids under scenarios of serial endosymbiosis, using Bayesian molecular clock analyses applied on a phylogenomic dataset with broad sampling of eukaryote diversity. We find that the hypotheses of serial endosymbiosis are chronologically possible, as the stem lineages of all red plastid-containing groups overlap in time. This period in the Meso- and Neoproterozoic Eras set the stage for the later expansion to dominance of red algal-derived primary production in the contemporary oceans, which profoundly altered the global geochemical and ecological conditions of the Earth.
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Affiliation(s)
- Jürgen F H Strassert
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Berlin, Germany
| | - Iker Irisarri
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden
- Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales (MNCN-CSIC), Madrid, Spain
- Department of Applied Bioinformatics, Institute for Microbiology and Genetics, University of Göttingen, and Campus Institute Data Science (CIDAS), Göttingen, Germany
| | - Tom A Williams
- School of Biological Sciences, University of Bristol, Life Sciences Building, Bristol, UK
| | - Fabien Burki
- Department of Organismal Biology, Program in Systematic Biology, Uppsala University, Uppsala, Sweden.
- Science for Life Laboratory, Uppsala University, Uppsala, Sweden.
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14
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Farhat S, Le P, Kayal E, Noel B, Bigeard E, Corre E, Maumus F, Florent I, Alberti A, Aury JM, Barbeyron T, Cai R, Da Silva C, Istace B, Labadie K, Marie D, Mercier J, Rukwavu T, Szymczak J, Tonon T, Alves-de-Souza C, Rouzé P, Van de Peer Y, Wincker P, Rombauts S, Porcel BM, Guillou L. Rapid protein evolution, organellar reductions, and invasive intronic elements in the marine aerobic parasite dinoflagellate Amoebophrya spp. BMC Biol 2021; 19:1. [PMID: 33407428 PMCID: PMC7789003 DOI: 10.1186/s12915-020-00927-9] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Accepted: 11/12/2020] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Dinoflagellates are aquatic protists particularly widespread in the oceans worldwide. Some are responsible for toxic blooms while others live in symbiotic relationships, either as mutualistic symbionts in corals or as parasites infecting other protists and animals. Dinoflagellates harbor atypically large genomes (~ 3 to 250 Gb), with gene organization and gene expression patterns very different from closely related apicomplexan parasites. Here we sequenced and analyzed the genomes of two early-diverging and co-occurring parasitic dinoflagellate Amoebophrya strains, to shed light on the emergence of such atypical genomic features, dinoflagellate evolution, and host specialization. RESULTS We sequenced, assembled, and annotated high-quality genomes for two Amoebophrya strains (A25 and A120), using a combination of Illumina paired-end short-read and Oxford Nanopore Technology (ONT) MinION long-read sequencing approaches. We found a small number of transposable elements, along with short introns and intergenic regions, and a limited number of gene families, together contribute to the compactness of the Amoebophrya genomes, a feature potentially linked with parasitism. While the majority of Amoebophrya proteins (63.7% of A25 and 59.3% of A120) had no functional assignment, we found many orthologs shared with Dinophyceae. Our analyses revealed a strong tendency for genes encoded by unidirectional clusters and high levels of synteny conservation between the two genomes despite low interspecific protein sequence similarity, suggesting rapid protein evolution. Most strikingly, we identified a large portion of non-canonical introns, including repeated introns, displaying a broad variability of associated splicing motifs never observed among eukaryotes. Those introner elements appear to have the capacity to spread over their respective genomes in a manner similar to transposable elements. Finally, we confirmed the reduction of organelles observed in Amoebophrya spp., i.e., loss of the plastid, potential loss of a mitochondrial genome and functions. CONCLUSION These results expand the range of atypical genome features found in basal dinoflagellates and raise questions regarding speciation and the evolutionary mechanisms at play while parastitism was selected for in this particular unicellular lineage.
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Affiliation(s)
- Sarah Farhat
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
- School of Marine and Atmospheric Sciences, Stony Brook University, Stony Brook, New York, 11794, USA
| | - Phuong Le
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Ehsan Kayal
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Benjamin Noel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Estelle Bigeard
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Erwan Corre
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Florian Maumus
- URGI, INRA, Université Paris-Saclay, 78026, Versailles, France
| | - Isabelle Florent
- Unité Molécules de Communication et Adaptation des Microorganismes (MCAM, UMR7245), Muséum national d'Histoire naturelle, CNRS, CP 52, 57 rue Cuvier, 75005, Paris, France
| | - Adriana Alberti
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jean-Marc Aury
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tristan Barbeyron
- Sorbonne Université, CNRS, UMR 8227, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
| | - Ruibo Cai
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Corinne Da Silva
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Benjamin Istace
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Karine Labadie
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Dominique Marie
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Jonathan Mercier
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Tsinda Rukwavu
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Jeremy Szymczak
- Sorbonne Université, CNRS, FR2424, Station Biologique de Roscoff, Place Georges Teissier, 29680, Roscoff, France
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France
| | - Thierry Tonon
- Centre for Novel Agricultural Products, Department of Biology, University of York, Heslington, York, YO10 5DD, UK
| | - Catharina Alves-de-Souza
- Algal Resources Collection, MARBIONC, Center for Marine Sciences, University of North Carolina Wilmington, 5600 Marvin K. Moss Lane, Wilmington, NC, 28409, USA
| | - Pierre Rouzé
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Yves Van de Peer
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
- Department of Biochemistry, Genetics and Microbiology, University of Pretoria, Pretoria, South Africa
| | - Patrick Wincker
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France
| | - Stephane Rombauts
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB Center for Plant Systems Biology, Ghent, Belgium
| | - Betina M Porcel
- Génomique Métabolique, Genoscope, Institut François Jacob, CEA, CNRS, Univ. Evry, Université Paris-Saclay, 91057, Evry, France.
| | - Laure Guillou
- Sorbonne Université, CNRS, UMR7144 Adaptation et Diversité en Milieu Marin, Ecology of Marine Plankton (ECOMAP), Station Biologique de Roscoff SBR, 29680, Roscoff, France.
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15
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Yamada N, Sakai H, Onuma R, Kroth PG, Horiguchi T. Five Non-motile Dinotom Dinoflagellates of the Genus Dinothrix. FRONTIERS IN PLANT SCIENCE 2020; 11:591050. [PMID: 33329655 PMCID: PMC7710806 DOI: 10.3389/fpls.2020.591050] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 10/21/2020] [Indexed: 06/12/2023]
Abstract
Dinothrix paradoxa and Gymnodinium quadrilobatum are benthic dinoflagellates possessing diatom-derived tertiary plastids, so-called dinotoms. Due to the lack of available genetic information, their phylogenetic relationship remains unknown. In this study, sequencing of 18S ribosomal DNA (rDNA) and the rbcL gene from temporary cultures isolated from natural samples revealed that they are close relatives of another dinotom, Galeidinium rugatum. The morphologies of these three dinotoms differ significantly from each other; however, they share a distinctive life cycle, in which the non-motile cells without flagella are their dominant phase. Cell division occurs in this non-motile phase, while swimming cells only appear for several hours after being released from each daughter cell. Furthermore, we succeeded in isolating and establishing two novel dinotom strains, HG180 and HG204, which show a similar life cycle and are phylogenetically closely related to the aforementioned three species. The non-motile cells of strain HG180 are characterized by the possession of a hemispheroidal cell covered with numerous nodes, while those of the strain HG204 form aggregations consisting of spherical smooth-surface cells. Based on the similarity in life cycles and phylogenetic closeness, we conclude that all five species should belong to a single genus, Dinothrix, the oldest genus within this clade. We transferred Ga. rugatum and Gy. quadrilobatum to Dinothrix, and described strains HG180 and HG204 as Dinothrix phymatodea sp. nov. and Dinothrix pseudoparadoxa sp. nov.
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Affiliation(s)
- Norico Yamada
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Hiroto Sakai
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Ryo Onuma
- Department of Natural History Sciences, Graduate School of Science, Hokkaido University, Sapporo, Japan
| | - Peter G. Kroth
- Department of Biology, University of Konstanz, Konstanz, Germany
| | - Takeo Horiguchi
- Department of Biological Sciences, Faculty of Science, Hokkaido University, Sapporo, Japan
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16
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Nomura M, Kamikawa R, Ishida KI. Fine Structure Observation of Feeding Behavior, Nephroselmis spp.-derived Chloroplast Enlargement, and Mitotic Processes in the Katablepharid Hatena arenicola. Protist 2020; 171:125714. [PMID: 32088560 DOI: 10.1016/j.protis.2020.125714] [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: 08/05/2019] [Revised: 01/19/2020] [Accepted: 01/21/2020] [Indexed: 11/17/2022]
Abstract
The difficult-to-cultivate katablepharid Hatena arenicola ingests green algae, Nephroselmis spp., and temporarily retains a Nephroselmis-derived cell compartment (kleptochloroplast), including a chloroplast within a phagocytotic vacuole. H. arenicola has a unique life history; during cell division, the Nephroselmis-derived cell compartment is only inherited by one of two daughter cells. However, the detailed morphological transition of the Nephroselmis cell to a kleptochloroplast and the mitotic process of the host cell remain unclear. Herein, we observed feeding behavior, enlargement of the Nephroselmis-derived chloroplast, and mitotic processes in H. arenicola using light and electron microscopy. During feeding behavior, H. arenicola peeled off the cell coverings and flagella of the Nephroselmis cell, which selectively accumulated in a vacuole separate to one containing a Nephroselmis cell body. An obvious nucleolus, but no heterochromatin was observed in the Nephroselmis-derived nucleus during the chloroplast-enlarging process, while compressed heterochromatin was explicitly observed in the nuclei of free-living Nephroselmis cells. The cell membrane of an ingested Nephroselmis cell disintegrated during enlargement of the Nephroselmis-derived chloroplast. The process of mitosis in H. arenicola was very similar to that of other katablepharids and cryptophytes.
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Affiliation(s)
- Mami Nomura
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan.
| | - Ryoma Kamikawa
- Graduate School of Human and Environmental Studies, Kyoto University, Yoshida, Nihonmatsu-cho, Sakyo-ku, Kyoto 606-8501, Japan
| | - Ken-Ichiro Ishida
- Faculty of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki 305-8572, Japan
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17
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Gavelis GS, Gile GH. How did cyanobacteria first embark on the path to becoming plastids?: lessons from protist symbioses. FEMS Microbiol Lett 2019; 365:5079637. [PMID: 30165400 DOI: 10.1093/femsle/fny209] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/23/2018] [Indexed: 12/13/2022] Open
Abstract
Symbioses between phototrophs and heterotrophs (a.k.a 'photosymbioses') are extremely common, and range from loose and temporary associations to obligate and highly specialized forms. In the history of life, the most transformative was the 'primary endosymbiosis,' wherein a cyanobacterium was engulfed by a eukaryote and became genetically integrated as a heritable photosynthetic organelle, or plastid. By allowing the rise of algae and plants, this event dramatically altered the biosphere, but its remote origin over one billion years ago has obscured the sequence of events leading to its establishment. Here, we review the genetic, physiological and developmental hurdles involved in early primary endosymbiosis. Since we cannot travel back in time to witness these evolutionary junctures, we will draw on examples of unicellular eukaryotes (protists) spanning diverse modes of photosymbiosis. We also review experimental approaches that could be used to recreate aspects of early primary endosymbiosis on a human timescale.
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Affiliation(s)
- Gregory S Gavelis
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
| | - Gillian H Gile
- School of Life Sciences, Arizona State University, Room 611, Life Science Tower E, 427 E, Tyler Mall, Tempe, AZ 85287, USA
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18
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Jirsová D, Füssy Z, Richtová J, Gruber A, Oborník M. Morphology, Ultrastructure, and Mitochondrial Genome of the Marine Non-Photosynthetic Bicosoecid Cafileria marina Gen. et sp. nov. Microorganisms 2019; 7:microorganisms7080240. [PMID: 31387253 PMCID: PMC6723347 DOI: 10.3390/microorganisms7080240] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 07/25/2019] [Accepted: 08/01/2019] [Indexed: 12/16/2022] Open
Abstract
In this paper, we describe a novel bacteriophagous biflagellate, Cafileria marina with two smooth flagellae, isolated from material collected from a rock surface in the Kvernesfjorden (Norway). This flagellate was characterized by scanning and transmission electron microscopy, fluorescence, and light microscopy. The sequence of the small subunit ribosomal RNA gene (18S) was used as a molecular marker for determining the phylogenetic position of this organism. Apart from the nuclear ribosomal gene, the whole mitochondrial genome was sequenced, assembled, and annotated. Morphological observations show that the newly described flagellate shares key ultrastructural characters with representatives of the family Bicosoecida (Heterokonta). Intriguingly, mitochondria of C. marina frequently associate with its nucleus through an electron-dense disc at the boundary of the two compartments. The function of this association remains unclear. Phylogenetic analyses corroborate the morphological data and place C. marina with other sequence data of representatives from the family Bicosoecida. We describe C. marina as a new species from a new genus in this family.
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Affiliation(s)
- Dagmar Jirsová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Jitka Richtová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Ansgar Gruber
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.
- Faculty of Science, University of South Bohemia, Branišovská 31, 370 05 České Budějovice, Czech Republic.
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19
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Yamada N, Bolton JJ, Trobajo R, Mann DG, Dąbek P, Witkowski A, Onuma R, Horiguchi T, Kroth PG. Discovery of a kleptoplastic 'dinotom' dinoflagellate and the unique nuclear dynamics of converting kleptoplastids to permanent plastids. Sci Rep 2019; 9:10474. [PMID: 31324824 PMCID: PMC6642167 DOI: 10.1038/s41598-019-46852-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 07/05/2019] [Indexed: 12/25/2022] Open
Abstract
A monophyletic group of dinoflagellates, called ‘dinotoms’, are known to possess evolutionarily intermediate plastids derived from diatoms. The diatoms maintain their nuclei, mitochondria, and the endoplasmic reticulum in addition with their plastids, while it has been observed that the host dinoflagellates retain the diatoms permanently by controlling diatom karyokinesis. Previously, we showed that dinotoms have repeatedly replaced their diatoms. Here, we show the process of replacements is at two different evolutionary stages in two closely related dinotoms, Durinskia capensis and D. kwazulunatalensis. We clarify that D. capensis is a kleptoplastic protist keeping its diatoms temporarily, only for two months. On the other hand, D. kwazulunatalensis is able to keep several diatoms permanently and exhibits unique dynamics to maintain the diatom nuclei: the nuclei change their morphologies into a complex string-shape alongside the plastids during interphase and these string-shaped nuclei then condense into multiple round nuclei when the host divides. These dynamics have been observed in other dinotoms that possess permanent diatoms, while they have never been observed in any other eukaryotes. We suggest that the establishment of this unique mechanism might be a critical step for dinotoms to be able to convert kleptoplastids into permanent plastids.
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Affiliation(s)
- Norico Yamada
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, 78457, Germany.
| | - John J Bolton
- Department of Biological Sciences, University of Cape Town, Cape Town, Western Cape, 7701, South Africa
| | - Rosa Trobajo
- Marine and Continental Waters Program, Institute for Food and Agricultural Research and Technology, Sant Carles de la Ràpita, Catalonia, 43540, Spain
| | - David G Mann
- Marine and Continental Waters Program, Institute for Food and Agricultural Research and Technology, Sant Carles de la Ràpita, Catalonia, 43540, Spain.,Royal Botanic Garden Edinburgh, Edinburgh, Scotland, EH5 3LR, United Kingdom
| | - Przemysław Dąbek
- Institute of Marine and Coastal Sciences, University of Szczecin, Szczecin, West Pomerania, 70383, Poland
| | - Andrzej Witkowski
- Institute of Marine and Coastal Sciences, University of Szczecin, Szczecin, West Pomerania, 70383, Poland
| | - Ryo Onuma
- Department of Gene Function and Phenomics, National Institute of Genetics, Mishima, Sizuoka, 4118540, Japan
| | - Takeo Horiguchi
- Department of Biological Sciences, Hokkaido University, Sapporo, Hokkaido, 0600810, Japan
| | - Peter G Kroth
- Department of Biology, University of Konstanz, Konstanz, Baden-Württemberg, 78457, Germany
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20
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Genes functioned in kleptoplastids of Dinophysis are derived from haptophytes rather than from cryptophytes. Sci Rep 2019; 9:9009. [PMID: 31227737 PMCID: PMC6588620 DOI: 10.1038/s41598-019-45326-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 06/05/2019] [Indexed: 11/29/2022] Open
Abstract
Toxic dinoflagellates belonging to the genus Dinophysis acquire plastids indirectly from cryptophytes through the consumption of the ciliate Mesodinium rubrum. Dinophysis acuminata harbours three genes encoding plastid-related proteins, which are thought to have originated from fucoxanthin dinoflagellates, haptophytes and cryptophytes via lateral gene transfer (LGT). Here, we investigate the origin of these plastid proteins via RNA sequencing of species related to D. fortii. We identified 58 gene products involved in porphyrin, chlorophyll, isoprenoid and carotenoid biosyntheses as well as in photosynthesis. Phylogenetic analysis revealed that the genes associated with chlorophyll and carotenoid biosyntheses and photosynthesis originated from fucoxanthin dinoflagellates, haptophytes, chlorarachniophytes, cyanobacteria and cryptophytes. Furthermore, nine genes were laterally transferred from fucoxanthin dinoflagellates, whose plastids were derived from haptophytes. Notably, transcription levels of different plastid protein isoforms varied significantly. Based on these findings, we put forth a novel hypothesis regarding the evolution of Dinophysis plastids that ancestral Dinophysis species acquired plastids from haptophytes or fucoxanthin dinoflagellates, whereas LGT from cryptophytes occurred more recently. Therefore, the evolutionary convergence of genes following LGT may be unlikely in most cases.
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21
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Crowell RM, Nienow JA, Cahoon AB. The complete chloroplast and mitochondrial genomes of the diatom Nitzschia palea (Bacillariophyceae) demonstrate high sequence similarity to the endosymbiont organelles of the dinotom Durinskia baltica. JOURNAL OF PHYCOLOGY 2019; 55:352-364. [PMID: 30536677 DOI: 10.1111/jpy.12824] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 11/07/2018] [Indexed: 06/09/2023]
Abstract
Nitzschia palea is a common freshwater diatom used as a bioindicator because of its tolerance of polluted waterways. There is also evidence it may be the tertiary endosymbiont within the "dinotom" dinoflagellate Durinskia baltica. A putative strain of N. palea was collected from a pond on the University of Virginia's College at Wise campus and cultured. For initial identification, three markers were sequenced-nuclear 18S rDNA, the chloroplast 23S rDNA, and rbcL. Morphological characteristics were determined using light and scanning electron microscopy; based on these observations the cells were identified as N. palea and named strain "Wise." DNA from N. palea was deep sequenced and the chloroplast and mitochondrial genomes assembled. Single gene phylogenies grouped N. palea-Wise within a clearly defined N. palea clade and showed it was most closely related to the strain "SpainA3." The chloroplast genome of N. palea is 119,447 bp with a quadripartite structure, 135 protein-coding, 28 tRNA, and 3 rRNA genes. The mitochondrial genome is 37,754 bp with a single repeat region as found in other diatom chondriomes, 37 protein-coding, 23 tRNA, and 2 rRNA genes. The chloroplast genomes of N. palea and D. baltica have identical gene content, synteny, and a 92.7% pair-wise sequence similarity with most differences occurring in intergenic regions. The N. palea mitochondrial genome and D. baltica's endosymbiont mitochondrial genome also have identical gene content and order with a sequence similarity of 90.7%. Genome-based phylogenies demonstrated that D. baltica is more similar to N. palea than any other diatom sequence currently available. These data provide the genome sequences of two organelles for a widespread diatom and show they are very similar to those of Durinskia baltica's endosymbiont.
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Affiliation(s)
- Roseanna M Crowell
- Department of Natural Sciences, University of Virginia's College at Wise, Wise, Virginia, 24293, USA
| | - James A Nienow
- Department of Biology, Valdosta State University, Valdosta, Georgia, 31698, USA
| | - Aubrey Bruce Cahoon
- Department of Natural Sciences, University of Virginia's College at Wise, Wise, Virginia, 24293, USA
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Sibbald SJ, Hopkins JF, Filloramo GV, Archibald JM. Ubiquitin fusion proteins in algae: implications for cell biology and the spread of photosynthesis. BMC Genomics 2019; 20:38. [PMID: 30642248 PMCID: PMC6332867 DOI: 10.1186/s12864-018-5412-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 12/26/2018] [Indexed: 11/12/2022] Open
Abstract
Background The process of gene fusion involves the formation of a single chimeric gene from multiple complete or partial gene sequences. Gene fusion is recognized as an important mechanism by which genes and their protein products can evolve new functions. The presence-absence of gene fusions can also be useful characters for inferring evolutionary relationships between organisms. Results Here we show that the nuclear genomes of two unrelated single-celled algae, the cryptophyte Guillardia theta and the chlorarachniophyte Bigelowiella natans, possess an unexpected diversity of genes for ubiquitin fusion proteins, including novel arrangements in which ubiquitin occupies amino-terminal, carboxyl-terminal, and internal positions relative to its fusion partners. We explore the evolution of the ubiquitin multigene family in both genomes, and show that both algae possess a gene encoding an ubiquitin-nickel superoxide dismutase fusion protein (Ubiq-NiSOD) that is widely but patchily distributed across the eukaryotic tree of life – almost exclusively in phototrophs. Conclusion Our results suggest that ubiquitin fusion proteins are more common than currently appreciated; because of its small size, the ubiquitin coding region can go undetected when gene predictions are carried out in an automated fashion. The punctate distribution of the Ubiq-NiSOD fusion across the eukaryotic tree could serve as a beacon for the spread of plastids from eukaryote to eukaryote by secondary and/or tertiary endosymbiosis. Electronic supplementary material The online version of this article (10.1186/s12864-018-5412-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Shannon J Sibbald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - Julia F Hopkins
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada.,Present Address: Informatics Program, Ontario Institute for Cancer Research, 661 University Avenue, Suite 510, Toronto, ON, M5G 0A3, Canada
| | - Gina V Filloramo
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada
| | - John M Archibald
- Department of Biochemistry and Molecular Biology, Dalhousie University, Sir Charles Tupper Medical Building, 5850 College Street, PO Box 15000, Halifax, Nova Scotia, B3H 4R2, Canada.
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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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