1
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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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2
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Single cell genomics reveals plastid-lacking Picozoa are close relatives of red algae. Nat Commun 2021; 12:6651. [PMID: 34789758 PMCID: PMC8599508 DOI: 10.1038/s41467-021-26918-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2021] [Accepted: 10/29/2021] [Indexed: 12/27/2022] Open
Abstract
The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we use single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.
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3
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Sato N. Are Cyanobacteria an Ancestor of Chloroplasts or Just One of the Gene Donors for Plants and Algae? Genes (Basel) 2021; 12:genes12060823. [PMID: 34071987 PMCID: PMC8227023 DOI: 10.3390/genes12060823] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/08/2021] [Accepted: 05/25/2021] [Indexed: 12/04/2022] Open
Abstract
Chloroplasts of plants and algae are currently believed to originate from a cyanobacterial endosymbiont, mainly based on the shared proteins involved in the oxygenic photosynthesis and gene expression system. The phylogenetic relationship between the chloroplast and cyanobacterial genomes was important evidence for the notion that chloroplasts originated from cyanobacterial endosymbiosis. However, studies in the post-genomic era revealed that various substances (glycolipids, peptidoglycan, etc.) shared by cyanobacteria and chloroplasts are synthesized by different pathways or phylogenetically unrelated enzymes. Membranes and genomes are essential components of a cell (or an organelle), but the origins of these turned out to be different. Besides, phylogenetic trees of chloroplast-encoded genes suggest an alternative possibility that chloroplast genes could be acquired from at least three different lineages of cyanobacteria. We have to seriously examine that the chloroplast genome might be chimeric due to various independent gene flows from cyanobacteria. Chloroplast formation could be more complex than a single event of cyanobacterial endosymbiosis. I present the “host-directed chloroplast formation” hypothesis, in which the eukaryotic host cell that had acquired glycolipid synthesis genes as an adaptation to phosphate limitation facilitated chloroplast formation by providing glycolipid-based membranes (pre-adaptation). The origins of the membranes and the genome could be different, and the origin of the genome could be complex.
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Affiliation(s)
- Naoki Sato
- Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo 153-8902, Japan
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4
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Irisarri I, Strassert JFH, Burki F. Phylogenomic Insights into the Origin of Primary Plastids. Syst Biol 2021; 71:105-120. [PMID: 33988690 DOI: 10.1093/sysbio/syab036] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Revised: 05/07/2021] [Accepted: 05/10/2021] [Indexed: 11/13/2022] Open
Abstract
The origin of plastids was a major evolutionary event that paved the way for an astonishing diversification of photosynthetic eukaryotes. Plastids originated by endosymbiosis between a heterotrophic eukaryotic host and cyanobacteria, presumably in a common ancestor of the primary photosynthetic eukaryotes (Archaeplastida). A single origin of primary plastids is well supported by plastid evidence but not by nuclear phylogenomic analyses, which have consistently failed to recover the monophyly of Archaeplastida hosts. Importantly, plastid monophyly and non-monophyletic hosts could be explained under scenarios of independent or serial eukaryote-to-eukaryote endosymbioses. Here, we assessed the strength of the signal for the monophyly of Archaeplastida hosts in four available phylogenomic datasets. The effect of phylogenetic methodology, data quality, alignment trimming strategy, gene and taxon sampling, and the presence of outlier genes were investigated. Our analyses revealed a lack of support for host monophyly in the shorter individual datasets. However, when analyzed together under rigorous data curation and complex mixture models, the combined nuclear datasets supported the monophyly of primary photosynthetic eukaryotes (Archaeplastida) and revealed a putative association with plastid-lacking Picozoa. This study represents an important step towards better understanding deep eukaryotic evolution and the origin of plastids.
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Affiliation(s)
- Iker Irisarri
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Biodiversity and Evolutionary Biology, Museo Nacional de Ciencias Naturales, José Gutiérrez Abascal 2, 28006 Madrid, Spain
| | - Jürgen F H Strassert
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Department of Ecosystem Research, Leibniz Institute of Freshwater Ecology and Inland Fisheries, Müggelseedamm 301, 12587 Berlin, Germany
| | - Fabien Burki
- Department of Organismal Biology (Systematic Biology), Uppsala University, Norbyv. 18D, 75236 Uppsala, Sweden.,Science For Life Laboratory, Uppsala University, 75236 Sweden
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5
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Palmgren M, Sørensen DM, Hallström BM, Säll T, Broberg K. Evolution of P2A and P5A ATPases: ancient gene duplications and the red algal connection to green plants revisited. PHYSIOLOGIA PLANTARUM 2020; 168:630-647. [PMID: 31268560 PMCID: PMC7065118 DOI: 10.1111/ppl.13008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/20/2019] [Accepted: 06/27/2019] [Indexed: 05/14/2023]
Abstract
In a search for slowly evolving nuclear genes that may cast light on the deep evolution of plants, we carried out phylogenetic analyses of two well-characterized subfamilies of P-type pumps (P2A and P5A ATPases) from representative branches of the eukaryotic tree of life. Both P-type ATPase genes were duplicated very early in eukaryotic evolution and before the divergence of the present eukaryotic supergroups. Synapomorphies identified in the sequences provide evidence that green plants and red algae are more distantly related than are green plants and eukaryotic supergroups in which secondary or tertiary plastids are common, such as several groups belonging to the clade that includes Stramenopiles, Alveolata, Rhizaria, Cryptophyta and Haptophyta (SAR). We propose that red algae branched off soon after the first photosynthesizing eukaryote had acquired a primary plastid, while in another lineage that led to SAR, the primary plastid was lost but, in some cases, regained as a secondary or tertiary plastid.
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Affiliation(s)
- Michael Palmgren
- Department of Plant and Environmental SciencesUniversity of CopenhagenCopenhagenDenmark
- Institute of Environmental MedicineKarolinska InstitutetStockholmSweden
| | | | - Björn M. Hallström
- Science for Life LaboratoryKTH – Royal Institute of TechnologyStockholmSweden
| | | | - Karin Broberg
- Institute of Environmental MedicineKarolinska InstitutetStockholmSweden
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6
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Morozov A, Galachyants YP. Diatom genes originating from red and green algae: Implications for the secondary endosymbiosis models. Mar Genomics 2019; 45:72-78. [DOI: 10.1016/j.margen.2019.02.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 02/13/2019] [Accepted: 02/13/2019] [Indexed: 11/27/2022]
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7
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Vesteg M, Hadariová L, Horváth A, Estraño CE, Schwartzbach SD, Krajčovič J. Comparative molecular cell biology of phototrophic euglenids and parasitic trypanosomatids sheds light on the ancestor of Euglenozoa. Biol Rev Camb Philos Soc 2019; 94:1701-1721. [PMID: 31095885 DOI: 10.1111/brv.12523] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 04/30/2019] [Accepted: 05/02/2019] [Indexed: 01/23/2023]
Abstract
Parasitic trypanosomatids and phototrophic euglenids are among the most extensively studied euglenozoans. The phototrophic euglenid lineage arose relatively recently through secondary endosymbiosis between a phagotrophic euglenid and a prasinophyte green alga that evolved into the euglenid secondary chloroplast. The parasitic trypanosomatids (i.e. Trypanosoma spp. and Leishmania spp.) and the freshwater phototrophic euglenids (i.e. Euglena gracilis) are the most evolutionary distant lineages in the Euglenozoa phylogenetic tree. The molecular and cell biological traits they share can thus be considered as ancestral traits originating in the common euglenozoan ancestor. These euglenozoan ancestral traits include common mitochondrial presequence motifs, respiratory chain complexes containing various unique subunits, a unique ATP synthase structure, the absence of mitochondria-encoded transfer RNAs (tRNAs), a nucleus with a centrally positioned nucleolus, closed mitosis without dissolution of the nuclear membrane and nucleoli, a nuclear genome containing the unusual 'J' base (β-D-glucosyl-hydroxymethyluracil), processing of nucleus-encoded precursor messenger RNAs (pre-mRNAs) via spliced-leader RNA (SL-RNA) trans-splicing, post-transcriptional gene silencing by the RNA interference (RNAi) pathway and the absence of transcriptional regulation of nuclear gene expression. Mitochondrial uridine insertion/deletion RNA editing directed by guide RNAs (gRNAs) evolved in the ancestor of the kinetoplastid lineage. The evolutionary origin of other molecular features known to be present only in either kinetoplastids (i.e. polycistronic transcripts, compaction of nuclear genomes) or euglenids (i.e. monocistronic transcripts, huge genomes, many nuclear cis-spliced introns, polyproteins) is unclear.
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Affiliation(s)
- Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Lucia Hadariová
- Biotechnology and Biomedicine Center of the Academy of Sciences and Charles University in Vestec (BIOCEV), 252 50, Vestec, Czech Republic.,Department of Parasitology, Faculty of Science, Charles University in Prague, 128 44, Prague, Czech Republic
| | - Anton Horváth
- Department of Biochemistry, Faculty of Natural Sciences, Comenius University, 842 15, Bratislava, Slovakia
| | - Carlos E Estraño
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Steven D Schwartzbach
- Department of Biological Sciences, University of Memphis, Memphis, TN, 38152-3560, USA
| | - Juraj Krajčovič
- Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia
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8
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Figueroa-Martinez F, Jackson C, Reyes-Prieto A. Plastid Genomes from Diverse Glaucophyte Genera Reveal a Largely Conserved Gene Content and Limited Architectural Diversity. Genome Biol Evol 2019; 11:174-188. [PMID: 30534986 PMCID: PMC6330054 DOI: 10.1093/gbe/evy268] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/10/2018] [Indexed: 12/30/2022] Open
Abstract
Plastid genome (ptDNA) data of Glaucophyta have been limited for many years to the genus Cyanophora. Here, we sequenced the ptDNAs of Gloeochaete wittrockiana, Cyanoptyche gloeocystis, Glaucocystis incrassata, and Glaucocystis sp. BBH. The reported sequences are the first genome-scale plastid data available for these three poorly studied glaucophyte genera. Although the Glaucophyta plastids appear morphologically “ancestral,” they actually bear derived genomes not radically different from those of red algae or viridiplants. The glaucophyte plastid coding capacity is highly conserved (112 genes shared) and the architecture of the plastid chromosomes is relatively simple. Phylogenomic analyses recovered Glaucophyta as the earliest diverging Archaeplastida lineage, but the position of viridiplants as the first branching group was not rejected by the approximately unbiased test. Pairwise distances estimated from 19 different plastid genes revealed that the highest sequence divergence between glaucophyte genera is frequently higher than distances between species of different classes within red algae or viridiplants. Gene synteny and sequence similarity in the ptDNAs of the two Glaucocystis species analyzed is conserved. However, the ptDNA of Gla. incrassata contains a 7.9-kb insertion not detected in Glaucocystis sp. BBH. The insertion contains ten open reading frames that include four coding regions similar to bacterial serine recombinases (two open reading frames), DNA primases, and peptidoglycan aminohydrolases. These three enzymes, often encoded in bacterial plasmids and bacteriophage genomes, are known to participate in the mobilization and replication of DNA mobile elements. It is therefore plausible that the insertion in Gla. incrassata ptDNA is derived from a DNA mobile element.
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Affiliation(s)
- Francisco Figueroa-Martinez
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,CONACyT-Universidad Autónoma Metropolitana Iztapalapa, Biotechnology Department, Mexico City, Mexico
| | - Christopher Jackson
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada.,School of Biosciences, University of Melbourne, Melbourne, Australia
| | - Adrian Reyes-Prieto
- Department of Biology, University of New Brunswick, Fredericton, New Brunswick, Canada
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9
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Nowack ECM, Weber APM. Genomics-Informed Insights into Endosymbiotic Organelle Evolution in Photosynthetic Eukaryotes. ANNUAL REVIEW OF PLANT BIOLOGY 2018; 69:51-84. [PMID: 29489396 DOI: 10.1146/annurev-arplant-042817-040209] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
The conversion of free-living cyanobacteria to photosynthetic organelles of eukaryotic cells through endosymbiosis transformed the biosphere and eventually provided the basis for life on land. Despite the presumable advantage conferred by the acquisition of photoautotrophy through endosymbiosis, only two independent cases of primary endosymbiosis have been documented: one that gave rise to the Archaeplastida, and the other to photosynthetic species of the thecate, filose amoeba Paulinella. Here, we review recent genomics-informed insights into the primary endosymbiotic origins of cyanobacteria-derived organelles. Furthermore, we discuss the preconditions for the evolution of nitrogen-fixing organelles. Recent genomic data on previously undersampled cyanobacterial and protist taxa provide new clues to the origins of the host cell and endosymbiont, and proteomic approaches allow insights into the rearrangement of the endosymbiont proteome during organellogenesis. We conclude that in addition to endosymbiotic gene transfers, horizontal gene acquisitions from a broad variety of prokaryotic taxa were crucial to organelle evolution.
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Affiliation(s)
- Eva C M Nowack
- Microbial Symbiosis and Organelle Evolution Group, Biology Department, Heinrich Heine University, 40225 Düsseldorf, Germany;
| | - Andreas P M Weber
- Institute of Plant Biochemistry, Cluster of Excellence on Plant Science (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany;
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10
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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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11
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Extensive gain and loss of photosystem I subunits in chromerid algae, photosynthetic relatives of apicomplexans. Sci Rep 2017; 7:13214. [PMID: 29038514 PMCID: PMC5643376 DOI: 10.1038/s41598-017-13575-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 09/26/2017] [Indexed: 12/16/2022] Open
Abstract
In oxygenic photosynthesis the initial photochemical processes are carried out by photosystem I (PSI) and II (PSII). Although subunit composition varies between cyanobacterial and plastid photosystems, the core structures of PSI and PSII are conserved throughout photosynthetic eukaryotes. So far, the photosynthetic complexes have been characterised in only a small number of organisms. We performed in silico and biochemical studies to explore the organization and evolution of the photosynthetic apparatus in the chromerids Chromera velia and Vitrella brassicaformis, autotrophic relatives of apicomplexans. We catalogued the presence and location of genes coding for conserved subunits of the photosystems as well as cytochrome b6f and ATP synthase in chromerids and other phototrophs and performed a phylogenetic analysis. We then characterised the photosynthetic complexes of Chromera and Vitrella using 2D gels combined with mass-spectrometry and further analysed the purified Chromera PSI. Our data suggest that the photosynthetic apparatus of chromerids underwent unique structural changes. Both photosystems (as well as cytochrome b6f and ATP synthase) lost several canonical subunits, while PSI gained one superoxide dismutase (Vitrella) or two superoxide dismutases and several unknown proteins (Chromera) as new regular subunits. We discuss these results in light of the extraordinarily efficient photosynthetic processes described in Chromera.
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12
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Reductive evolution of chloroplasts in non-photosynthetic plants, algae and protists. Curr Genet 2017; 64:365-387. [DOI: 10.1007/s00294-017-0761-0] [Citation(s) in RCA: 54] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/22/2017] [Accepted: 10/04/2017] [Indexed: 11/24/2022]
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13
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Bodył A. Did some red alga-derived plastids evolveviakleptoplastidy? A hypothesis. Biol Rev Camb Philos Soc 2017; 93:201-222. [DOI: 10.1111/brv.12340] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2017] [Revised: 04/24/2017] [Accepted: 04/25/2017] [Indexed: 12/31/2022]
Affiliation(s)
- Andrzej Bodył
- Laboratory of Evolutionary Protistology, Department of Invertebrate Biology, Evolution and Conservation, Institute of Environmental Biology; University of Wrocław, ul. Przybyszewskiego 65; 51-148 Wrocław Poland
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14
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Hadariová L, Vesteg M, Birčák E, Schwartzbach SD, Krajčovič J. An intact plastid genome is essential for the survival of colorless Euglena longa but not Euglena gracilis. Curr Genet 2016; 63:331-341. [PMID: 27553633 DOI: 10.1007/s00294-016-0641-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Revised: 08/02/2016] [Accepted: 08/13/2016] [Indexed: 12/18/2022]
Abstract
Euglena gracilis growth with antibacterial agents leads to bleaching, permanent plastid gene loss. Colorless Euglena (Astasia) longa resembles a bleached E. gracilis. To evaluate the role of bleaching in E. longa evolution, the effect of streptomycin, a plastid protein synthesis inhibitor, and ofloxacin, a plastid DNA gyrase inhibitor, on E. gracilis and E. longa growth and plastid DNA content were compared. E. gracilis growth was unaffected by streptomycin and ofloxacin. Quantitative PCR analyses revealed a time dependent loss of plastid genes in E. gracilis demonstrating that bleaching agents produce plastid gene deletions without affecting cell growth. Streptomycin and ofloxacin inhibited E. longa growth indicating that it requires plastid genes to survive. This suggests that evolutionary divergence of E. longa from E. gracilis was triggered by the loss of a cytoplasmic metabolic activity also occurring in the plastid. Plastid metabolism has become obligatory for E. longa cell growth. A process termed "intermittent bleaching", short term exposure to subsaturating concentrations of reversible bleaching agents followed by growth in the absence of a bleaching agent, is proposed as the molecular mechanism for E. longa plastid genome reduction. Various non-photosynthetic lineages could have independently arisen from their photosynthetic ancestors via a similar process.
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Affiliation(s)
- Lucia Hadariová
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic
| | - Matej Vesteg
- Department of Biology and Ecology, Faculty of Natural Sciences, Matej Bel University, 974 01, Banská Bystrica, Slovakia
| | - Erik Birčák
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic
| | | | - Juraj Krajčovič
- Department of Genetics, Faculty of Natural Sciences, Comenius University, Mlynská dolina G-1, 842 15, Bratislava, Slovak Republic. .,Department of Biology, Faculty of Natural Sciences, University of ss. Cyril and Methodius, 917 01, Trnava, Slovakia.
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15
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Markunas CM, Triemer RE. Evolutionary History of the Enzymes Involved in the Calvin–Benson Cycle in Euglenids. J Eukaryot Microbiol 2016; 63:326-39. [DOI: 10.1111/jeu.12282] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2015] [Revised: 10/28/2015] [Accepted: 10/28/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Chelsea M. Markunas
- Department of Plant Biology Michigan State University 612 Wilson Road 166 Plant Biology Labs East Lansing Michigan 48824
| | - Richard E. Triemer
- Department of Plant Biology Michigan State University 612 Wilson Road 166 Plant Biology Labs East Lansing Michigan 48824
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16
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Waller RF, Gornik SG, Koreny L, Pain A. Metabolic pathway redundancy within the apicomplexan-dinoflagellate radiation argues against an ancient chromalveolate plastid. Commun Integr Biol 2015; 9:e1116653. [PMID: 27066182 PMCID: PMC4802802 DOI: 10.1080/19420889.2015.1116653] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Revised: 10/30/2015] [Accepted: 10/30/2015] [Indexed: 11/06/2022] Open
Abstract
The chromalveolate hypothesis presents an attractively simple explanation for the presence of red algal-derived secondary plastids in 5 major eukaryotic lineages: “chromista” phyla, cryptophytes, haptophytes and ochrophytes; and alveolate phyla, dinoflagellates and apicomplexans. It posits that a single secondary endosymbiotic event occurred in a common ancestor of these diverse groups, and that this ancient plastid has since been maintained by vertical inheritance only. Substantial testing of this hypothesis by molecular phylogenies has, however, consistently failed to provide support for the predicted monophyly of the host organisms that harbour these plastids—the “chromalveolates.” This lack of support does not disprove the chromalveolate hypothesis per se, but rather drives the proposed endosymbiosis deeper into the eukaryotic tree, and requires multiple plastid losses to have occurred within intervening aplastidic lineages. An alternative perspective on plastid evolution is offered by considering the metabolic partnership between the endosymbiont and its host cell. A recent analysis of metabolic pathways in a deep-branching dinoflagellate indicates a high level of pathway redundancy in the common ancestor of apicomplexans and dinoflagellates, and differential losses of these pathways soon after radiation of the major extant lineages. This suggests that vertical inheritance of an ancient plastid in alveolates is highly unlikely as it would necessitate maintenance of redundant pathways over very long evolutionary timescales.
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Affiliation(s)
- Ross F Waller
- Department of Biochemistry, University of Cambridge , Cambridge, UK
| | - Sebastian G Gornik
- School of Natural Sciences, National University of Ireland Galway , Galway, Ireland
| | - Ludek Koreny
- Department of Biochemistry, University of Cambridge , Cambridge, UK
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology , Thuwal, Saudi Arabia
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Burns JA, Paasch A, Narechania A, Kim E. Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition. Genome Biol Evol 2015. [PMID: 26224703 PMCID: PMC5741210 DOI: 10.1093/gbe/evv144] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Cymbomonas tetramitiformis—a marine prasinophyte—is one of only a few green algae that still retain an ancestral particulate-feeding mechanism while harvesting energy through photosynthesis. The genome of the alga is estimated to be 850 Mb–1.2 Gb in size—the bulk of which is filled with repetitive sequences—and is annotated with 37,366 protein-coding gene models. A number of unusual metabolic pathways (for the Chloroplastida) are predicted for C. tetramitiformis, including pathways for Lipid-A and peptidoglycan metabolism. Comparative analyses of the predicted peptides of C. tetramitiformis to sets of other eukaryotes revealed that nonphagocytes are depleted in a number of genes, a proportion of which have known function in feeding. In addition, our analysis suggests that obligatory phagotrophy is associated with the loss of genes that function in biosynthesis of small molecules (e.g., amino acids). Further, C. tetramitiformis and at least one other phago-mixotrophic alga are thus unique, compared with obligatory heterotrophs and nonphagocytes, in that both feeding and small molecule synthesis-related genes are retained in their genomes. These results suggest that early, ancestral host eukaryotes that gave rise to phototrophs had the capacity to assimilate building block molecules from inorganic substances (i.e., prototrophy). The loss of biosynthesis genes, thus, may at least partially explain the apparent lack of instances of permanent incorporation of photosynthetic endosymbionts in later-divergent, auxotrophic eukaryotic lineages, such as metazoans and ciliates.
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Affiliation(s)
- John A Burns
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| | - Amber Paasch
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| | - Apurva Narechania
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
| | - Eunsoo Kim
- Sackler Institute for Comparative Genomics and Division of Invertebrate Zoology, American Museum of Natural History, New York, NY
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18
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Ševčíková T, Horák A, Klimeš V, Zbránková V, Demir-Hilton E, Sudek S, Jenkins J, Schmutz J, Přibyl P, Fousek J, Vlček Č, Lang BF, Oborník M, Worden AZ, Eliáš M. Updating algal evolutionary relationships through plastid genome sequencing: did alveolate plastids emerge through endosymbiosis of an ochrophyte? Sci Rep 2015; 5:10134. [PMID: 26017773 PMCID: PMC4603697 DOI: 10.1038/srep10134] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2015] [Accepted: 03/31/2015] [Indexed: 01/15/2023] Open
Abstract
Algae with secondary plastids of a red algal origin, such as ochrophytes (photosynthetic stramenopiles), are diverse and ecologically important, yet their evolutionary history remains controversial. We sequenced plastid genomes of two ochrophytes, Ochromonas sp. CCMP1393 (Chrysophyceae) and Trachydiscus minutus (Eustigmatophyceae). A shared split of the clpC gene as well as phylogenomic analyses of concatenated protein sequences demonstrated that chrysophytes and eustigmatophytes form a clade, the Limnista, exhibiting an unexpectedly elevated rate of plastid gene evolution. Our analyses also indicate that the root of the ochrophyte phylogeny falls between the recently redefined Khakista and Phaeista assemblages. Taking advantage of the expanded sampling of plastid genome sequences, we revisited the phylogenetic position of the plastid of Vitrella brassicaformis, a member of Alveolata with the least derived plastid genome known for the whole group. The results varied depending on the dataset and phylogenetic method employed, but suggested that the Vitrella plastids emerged from a deep ochrophyte lineage rather than being derived vertically from a hypothetical plastid-bearing common ancestor of alveolates and stramenopiles. Thus, we hypothesize that the plastid in Vitrella, and potentially in other alveolates, may have been acquired by an endosymbiosis of an early ochrophyte.
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Affiliation(s)
- Tereza Ševčíková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Aleš Horák
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Vladimír Klimeš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Veronika Zbránková
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
| | - Elif Demir-Hilton
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Sebastian Sudek
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA
| | - Jerry Jenkins
- US Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA
| | - Jeremy Schmutz
- HudsonAlpha Institute for Biotechnology, 601 Genome Way NW, Huntsville, Alabama 35806, USA
| | - Pavel Přibyl
- Centre for Algology and Biorefinery Research Centre of Competence, Institute of Botany, Czech Academy of Sciences, Dukelská 135, 379 82 Třeboň, Czech Republic
| | - Jan Fousek
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - Čestmír Vlček
- Institute of Molecular Genetics, Czech Academy of Sciences, Vídeňská 1083, 142 20 Prague 4, Czech Republic
| | - B Franz Lang
- Département de Biochimie, Centre Robert-Cedergren, Université de Montréal, 2900 Boulevard Edouard Montpetit, Montréal, Québec, H3C 3J7, Canada
| | - Miroslav Oborník
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, Branišovská 31, 370 05 České Budějovice, Czech Republic.,University of South Bohemia, Faculty of Science, Branišovská 1760, 370 05 České Budějovice, Czech Republic
| | - Alexandra Z Worden
- Monterey Bay Aquarium Research Institute (MBARI), Moss Landing, CA 95039, USA.,Integrated Microbial Biodiversity Program, Canadian Institute for Advanced Research, Toronto, M5G 1Z8, Canada
| | - Marek Eliáš
- University of Ostrava, Faculty of Science, Department of Biology and Ecology, Life Science Research Centre, Chittussiho 10, 710 00 Ostrava, Czech Republic
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Sassenhagen I, Rengefors K, Richardson TL, Pinckney JL. Pigment composition and photoacclimation as keys to the ecological success of Gonyostomum semen (Raphidophyceae, Stramenopiles). JOURNAL OF PHYCOLOGY 2014; 50:1146-1154. [PMID: 26988794 DOI: 10.1111/jpy.12246] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 07/21/2014] [Indexed: 06/05/2023]
Abstract
Aquatic habitats are usually structured by light attenuation with depth resulting in different microalgal communities, each one adapted to a certain light regime by their specific pigment composition. Several taxa contain pigments restricted to one phylogenetic group, making them useful as marker pigments in phytoplankton community studies. The nuisance and invasive freshwater microalga Gonyostomum semen (Raphidophyceae) is mainly found in brown water lakes with sharp vertical gradients in light intensity and color. However, its pigment composition and potential photoadaptations have not been comprehensively studied. We analyzed the photopigment composition of 12 genetically different strains of G. semen by high performance liquid chromatography after acclimation to different light conditions. We confirmed the pigments chl a, chl c1c2, diadinoxanthin, trans-neoxanthin, cis-neoxanthin, α and β carotene, which have already been reported for G. semen. In addition, we identified, for the first time, the pigments violaxan-thin, zeaxanthin, and alloxanthin in this species. Alloxanthin has never been observed in raphidophytes before, suggesting differences in evolutionary plastid acquisition between freshwater lineages and the well-described marine species. The amount of total chl a per cell generally decreased with increasing light intensity. In contrast, the increasing ratios of the prominent pigments diadinoxanthin and alloxanthin per chl a with light intensity suggest photoprotective functions. In addition, we found significant variation in cell-specific pigment concentration among strains, grouped by lake of origin, which might correspond to genetic differences between strains and populations.
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Affiliation(s)
- Ingrid Sassenhagen
- Aquatic Ecology, Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Karin Rengefors
- Aquatic Ecology, Department of Biology, Lund University, Sölvegatan 37, Lund, 22362, Sweden
| | - Tammi L Richardson
- Department of Biological Science, University of South Carolina, 712 Sumter Street, Columbia, South Carolina, 29208, USA
| | - James L Pinckney
- Department of Biological Science, University of South Carolina, 712 Sumter Street, Columbia, South Carolina, 29208, USA
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