1
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Fields O, Hammond MJ, Xu X, O'Neill EC. Advances in euglenoid genomics: unravelling the fascinating biology of a complex clade. Trends Genet 2024:S0168-9525(24)00173-2. [PMID: 39147613 DOI: 10.1016/j.tig.2024.07.007] [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: 06/27/2024] [Revised: 07/23/2024] [Accepted: 07/23/2024] [Indexed: 08/17/2024]
Abstract
Euglenids have long been studied due to their unique physiology and versatile metabolism, providing underpinnings for much of our understanding of photosynthesis and biochemistry, and a growing opportunity in biotechnology. Until recently there has been a lack of genetic studies due to their large and complex genomes, but recently new technologies have begun to unveil their genetic capabilities. Whilst much research has focused on the model organism Euglena gracilis, other members of the euglenids have now started to receive due attention. Currently only poor nuclear genome assemblies of E. gracilis and Rhabdomonas costata are available, but there are many more plastid genome sequences and an increasing number of transcriptomes. As more assemblies become available, there are great opportunities to understand the fundamental biology of these organisms and to exploit them for biotechnology.
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Affiliation(s)
- Oskar Fields
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Michael J Hammond
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic; Faculty of Science, University of South Bohemia, České Budějovice (Budweis), Czech Republic; These authors contributed equally
| | - Xiao Xu
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; These authors contributed equally
| | - Ellis C O'Neill
- School of Chemistry, University of Nottingham, University Park, Nottingham, NG7 2RD, UK; Biodiscovery Institute, University of Nottingham, University Park, Nottingham, NG7 2RD, UK.
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2
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Harada R, Hirakawa Y, Yabuki A, Kim E, Yazaki E, Kamikawa R, Nakano K, Eliáš M, Inagaki Y. Encyclopedia of Family A DNA Polymerases Localized in Organelles: Evolutionary Contribution of Bacteria Including the Proto-Mitochondrion. Mol Biol Evol 2024; 41:msae014. [PMID: 38271287 PMCID: PMC10877234 DOI: 10.1093/molbev/msae014] [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: 08/29/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 01/27/2024] Open
Abstract
DNA polymerases synthesize DNA from deoxyribonucleotides in a semiconservative manner and serve as the core of DNA replication and repair machinery. In eukaryotic cells, there are 2 genome-containing organelles, mitochondria, and plastids, which were derived from an alphaproteobacterium and a cyanobacterium, respectively. Except for rare cases of genome-lacking mitochondria and plastids, both organelles must be served by nucleus-encoded DNA polymerases that localize and work in them to maintain their genomes. The evolution of organellar DNA polymerases has yet to be fully understood because of 2 unsettled issues. First, the diversity of organellar DNA polymerases has not been elucidated in the full spectrum of eukaryotes. Second, it is unclear when the DNA polymerases that were used originally in the endosymbiotic bacteria giving rise to mitochondria and plastids were discarded, as the organellar DNA polymerases known to date show no phylogenetic affinity to those of the extant alphaproteobacteria or cyanobacteria. In this study, we identified from diverse eukaryotes 134 family A DNA polymerase sequences, which were classified into 10 novel types, and explored their evolutionary origins. The subcellular localizations of selected DNA polymerases were further examined experimentally. The results presented here suggest that the diversity of organellar DNA polymerases has been shaped by multiple transfers of the PolI gene from phylogenetically broad bacteria, and their occurrence in eukaryotes was additionally impacted by secondary plastid endosymbioses. Finally, we propose that the last eukaryotic common ancestor may have possessed 2 mitochondrial DNA polymerases, POP, and a candidate of the direct descendant of the proto-mitochondrial DNA polymerase I, rdxPolA, identified in this study.
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Affiliation(s)
- Ryo Harada
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Yoshihisa Hirakawa
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Akinori Yabuki
- Deep-Sea Biodiversity Research Group, Research Institute for Global Change (RIGC), Japan Agency for Marine-Earth Science and Technology (JAMSTEC), Yokosuka, Japan
| | - Eunsoo Kim
- Division of EcoScience, Ewha Womans University, Seoul, South Korea
- Division of Invertebrate Zoology, American Museum of Natural History, New York, NY, USA
| | - Euki Yazaki
- Research Center for Advanced Analysis, National Agriculture and Food Research Organization, Tsukuba, Japan
- Interdisciplinary Theoretical and Mathematical Sciences program (iTHEMS), RIKEN, Wako, Saitama, Japan
| | - Ryoma Kamikawa
- Graduate School of Agriculture, Kyoto University, Kyoto, Japan
| | - Kentaro Nakano
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Marek Eliáš
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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3
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He S, Crans VL, Jonikas MC. The pyrenoid: the eukaryotic CO2-concentrating organelle. THE PLANT CELL 2023; 35:3236-3259. [PMID: 37279536 PMCID: PMC10473226 DOI: 10.1093/plcell/koad157] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/08/2023]
Abstract
The pyrenoid is a phase-separated organelle that enhances photosynthetic carbon assimilation in most eukaryotic algae and the land plant hornwort lineage. Pyrenoids mediate approximately one-third of global CO2 fixation, and engineering a pyrenoid into C3 crops is predicted to boost CO2 uptake and increase yields. Pyrenoids enhance the activity of the CO2-fixing enzyme Rubisco by supplying it with concentrated CO2. All pyrenoids have a dense matrix of Rubisco associated with photosynthetic thylakoid membranes that are thought to supply concentrated CO2. Many pyrenoids are also surrounded by polysaccharide structures that may slow CO2 leakage. Phylogenetic analysis and pyrenoid morphological diversity support a convergent evolutionary origin for pyrenoids. Most of the molecular understanding of pyrenoids comes from the model green alga Chlamydomonas (Chlamydomonas reinhardtii). The Chlamydomonas pyrenoid exhibits multiple liquid-like behaviors, including internal mixing, division by fission, and dissolution and condensation in response to environmental cues and during the cell cycle. Pyrenoid assembly and function are induced by CO2 availability and light, and although transcriptional regulators have been identified, posttranslational regulation remains to be characterized. Here, we summarize the current knowledge of pyrenoid function, structure, components, and dynamic regulation in Chlamydomonas and extrapolate to pyrenoids in other species.
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Affiliation(s)
- Shan He
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
| | - Victoria L Crans
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
| | - Martin C Jonikas
- Department of Molecular Biology, Princeton University, Princeton, NJ 08540, USA
- Howard Hughes Medical Institute, Princeton University, Princeton, NJ 08540, USA
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4
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Ma X, Shi X, Wang Q, Zhao M, Zhang Z, Zhong B. A Reinvestigation of Multiple Independent Evolution and Triassic-Jurassic Origins of Multicellular Volvocine Algae. Genome Biol Evol 2023; 15:evad142. [PMID: 37498572 PMCID: PMC10410301 DOI: 10.1093/gbe/evad142] [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: 12/21/2022] [Revised: 07/09/2023] [Accepted: 07/22/2023] [Indexed: 07/28/2023] Open
Abstract
The evolution of multicellular organisms is considered to be a major evolutionary transition, profoundly affecting the ecology and evolution of nearly all life on earth. The volvocine algae, a unique clade of chlorophytes with diverse cell morphology, provide an appealing model for investigating the evolution of multicellularity and development. However, the phylogenetic relationship and timescale of the volvocine algae are not fully resolved. Here, we use extensive taxon and gene sampling to reconstruct the phylogeny of the volvocine algae. Our results support that the colonial volvocine algae are not monophyletic group and multicellularity independently evolve at least twice in the volvocine algae, once in Tetrabaenaceae and another in the Goniaceae + Volvocaceae. The simulation analyses suggest that incomplete lineage sorting is a major factor for the tree topology discrepancy, which imply that the multispecies coalescent model better fits the data used in this study. The coalescent-based species tree supports that the Goniaceae is monophyletic and Crucicarteria is the earliest diverging lineage, followed by Hafniomonas and Radicarteria within the Volvocales. By considering the multiple uncertainties in divergence time estimation, the dating analyses indicate that the volvocine algae occurred during the Cryogenian to Ediacaran (696.6-551.1 Ma) and multicellularity in the volvocine algae originated from the Triassic to Jurassic. Our phylogeny and timeline provide an evolutionary framework for studying the evolution of key traits and the origin of multicellularity in the volvocine algae.
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Affiliation(s)
- Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Qiuping Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Mengru Zhao
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China
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Wetherbee R, Bringloe TT, van de Meene A, Andersen RA, Verbruggen H. Structure and formation of the perforated theca defining the Pelagophyceae (Heterokonta), and three new genera that substantiate the diverse nature of the class. JOURNAL OF PHYCOLOGY 2023; 59:126-151. [PMID: 36326615 DOI: 10.1111/jpy.13294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 10/10/2022] [Indexed: 06/16/2023]
Abstract
The pelagophytes, a morphologically diverse class of marine heterokont algae, have been historically united only by DNA sequences. Recently we described a novel perforated theca (PT) encasing cells from the Pelagophyceae and hypothesized it may be the first morphological feature to define the class. Here we consolidate that observation, describing a PT for the first time in an additional seven pelagophyte genera, including three genera new to science. We established clonal cultures of pelagophytes collected from intertidal pools located around Australia, and established phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA and psbC gene sequences that led to the discovery of three new species: Wyeophycus julieharrissiae and Chromopallida australis form a distinct lineage along with Ankylochrysis lutea within the Pelagomonadales, while Pituiglomerulus capricornicus is sister genus to Chrysocystis fragilis in the Chrysocystaceae (Sarcinochrysidales). Using fixation by high-pressure freezing for electron microscope observations, a distinctive PT was observed in the three new genera described in this paper, as well as four genera not previously investigated: Chrysoreinhardia, Sargassococcus, Sungminbooa and Andersenia. The mechanism of PT formation is novel, being fabricated from rafts in Golgi-derived vesicles before being inserted into an established PT. Extracellular wall and/or mucilage layers assemble exterior to the PT in most pelagophytes, the materials likewise secreted by Golgi-derived vesicles, though the mechanism of secretion is novel. Secretory vesicles never fuse with the plasma membrane as in classic secretion and deposition, but rather relocate extracellularly beneath the PT and disintegrate, the contents having to pass through the PT prior to wall and/or mucilage synthesis. This study substantiates the diverse nature of pelagophytes, and provides further evidence that the PT is a sound morphological feature to define the Pelagophyceae, with all 14 of the 20 known genera studied to date by TEM possessing a PT.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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6
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Every refuge has its price: Ostreobium as a model for understanding how algae can live in rock and stay in business. Semin Cell Dev Biol 2023; 134:27-36. [PMID: 35341677 DOI: 10.1016/j.semcdb.2022.03.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/20/2022] [Accepted: 03/08/2022] [Indexed: 11/23/2022]
Abstract
Ostreobium is a siphonous green alga in the Bryopsidales (Chlorophyta) that burrows into calcium carbonate (CaCO3) substrates. In this habitat, it lives under environmental conditions unusual for an alga (i.e., low light and low oxygen) and it is a major agent of carbonate reef bioerosion. In coral skeletons, Ostreobium can form conspicuous green bands recognizable by the naked eye and it is thought to contribute to the coral's nutritional needs. With coral reefs in global decline, there is a renewed focus on understanding Ostreobium biology and its roles in the coral holobiont. This review summarizes knowledge on Ostreobium's morphological structure, biodiversity and evolution, photosynthesis, mechanism of bioerosion and its role as a member of the coral holobiont. We discuss the resources available to study Ostreobium biology, lay out some of the uncharted territories in Ostreobium biology and offer perspectives for future research.
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7
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Maciszewski K, Fells A, Karnkowska A. Challenging the Importance of Plastid Genome Structure Conservation: New Insights From Euglenophytes. Mol Biol Evol 2022; 39:6834297. [PMID: 36403966 PMCID: PMC9728796 DOI: 10.1093/molbev/msac255] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Plastids, similar to mitochondria, are organelles of endosymbiotic origin, which retained their vestigial genomes (ptDNA). Their unique architecture, commonly referred to as the quadripartite (four-part) structure, is considered to be strictly conserved; however, the bulk of our knowledge on their variability and evolutionary transformations comes from studies of the primary plastids of green algae and land plants. To broaden our perspective, we obtained seven new ptDNA sequences from freshwater species of photosynthetic euglenids-a group that obtained secondary plastids, known to have dynamically evolving genome structure, via endosymbiosis with a green alga. Our analyses have demonstrated that the evolutionary history of euglenid plastid genome structure is exceptionally convoluted, with a patchy distribution of inverted ribosomal operon (rDNA) repeats, as well as several independent acquisitions of tandemly repeated rDNA copies. Moreover, we have shown that inverted repeats in euglenid ptDNA do not share their genome-stabilizing property documented in chlorophytes. We hypothesize that the degeneration of the quadripartite structure of euglenid plastid genomes is connected to the group II intron expansion. These findings challenge the current global paradigms of plastid genome architecture evolution and underscore the often-underestimated divergence between the functionality of shared traits in primary and complex plastid organelles.
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Affiliation(s)
| | - Alicja Fells
- Institute of Evolutionary Biology, Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, 02-089 Warsaw, Poland
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8
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Matsuo E, Morita K, Nakayama T, Yazaki E, Sarai C, Takahashi K, Iwataki M, Inagaki Y. Comparative Plastid Genomics of Green-Colored Dinoflagellates Unveils Parallel Genome Compaction and RNA Editing. FRONTIERS IN PLANT SCIENCE 2022; 13:918543. [PMID: 35898209 PMCID: PMC9309888 DOI: 10.3389/fpls.2022.918543] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 06/22/2022] [Indexed: 06/15/2023]
Abstract
Dinoflagellates possess plastids that are diverse in both pigmentation and evolutionary background. One of the plastid types found in dinoflagellates is pigmented with chlorophylls a and b (Chl a + b) and originated from the endosymbionts belonging to a small group of green algae, Pedinophyceae. The Chl a + b-containing plastids have been found in three distantly related dinoflagellates Lepidodinium spp., strain MGD, and strain TGD, and were proposed to be derived from separate partnerships between a dinoflagellate (host) and a pedinophycean green alga (endosymbiont). Prior to this study, a plastid genome sequence was only available for L. chlorophorum, which was reported to bear the features that were not found in that of the pedinophycean green alga Pedinomonas minor, a putative close relative of the endosymbiont that gave rise to the current Chl a + b-containing plastid. In this study, we sequenced the plastid genomes of strains MGD and TGD to compare with those of L. chlorophorum as well as pedinophycean green algae. The mapping of the RNA-seq reads on the corresponding plastid genome identified RNA editing on plastid gene transcripts in the three dinoflagellates. Further, the comparative plastid genomics revealed that the plastid genomes of the three dinoflagellates achieved several features, which are not found in or much less obvious than the pedinophycean plastid genomes determined to date, in parallel.
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Affiliation(s)
- Eriko Matsuo
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Kounosuke Morita
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
| | - Takuro Nakayama
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
| | | | - Chihiro Sarai
- Graduate School of Science and Engineering, Yamagata University, Yamagata, Japan
| | - Kazuya Takahashi
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | - Mitsunori Iwataki
- Asian Natural Environmental Science Center, The University of Tokyo, Tokyo, Japan
| | - Yuji Inagaki
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tsukuba, Japan
- Center for Computational Sciences, University of Tsukuba, Tsukuba, Japan
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9
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Hou Z, Ma X, Shi X, Li X, Yang L, Xiao S, De Clerck O, Leliaert F, Zhong B. Phylotranscriptomic insights into a Mesoproterozoic-Neoproterozoic origin and early radiation of green seaweeds (Ulvophyceae). Nat Commun 2022; 13:1610. [PMID: 35318329 PMCID: PMC8941102 DOI: 10.1038/s41467-022-29282-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 03/09/2022] [Indexed: 01/09/2023] Open
Abstract
The Ulvophyceae, a major group of green algae, is of particular evolutionary interest because of its remarkable morphological and ecological diversity. Its phylogenetic relationships and diversification timeline, however, are still not fully resolved. In this study, using an extensive nuclear gene dataset, we apply coalescent- and concatenation-based approaches to reconstruct the phylogeny of the Ulvophyceae and to explore the sources of conflict in previous phylogenomic studies. The Ulvophyceae is recovered as a paraphyletic group, with the Bryopsidales being a sister group to the Chlorophyceae, and the remaining taxa forming a clade (Ulvophyceae sensu stricto). Molecular clock analyses with different calibration strategies emphasize the large impact of fossil calibrations, and indicate a Meso-Neoproterozoic origin of the Ulvophyceae (sensu stricto), earlier than previous estimates. The results imply that ulvophyceans may have had a profound influence on oceanic redox structures and global biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition. “Ulvophyceae is a remarkably morphologically and ecologically diverse clade of green algae. Here, the authors reconstruct the Ulvophyceae phylogeny, showing that these algae originated earlier than expected and may have influenced biogeochemical cycles at the Mesoproterozoic-Neoproterozoic transition.”
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Affiliation(s)
- Zheng Hou
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xuan Shi
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Xi Li
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, Nanjing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA
| | - Olivier De Clerck
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium
| | - Frederik Leliaert
- Phycology Research Group and Center for Molecular Phylogenetics and Evolution, Ghent University, Ghent, Belgium.,Meise Botanic Garden, Meise, Belgium
| | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, Nanjing, China.
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10
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Repetti SI, Iha C, Uthanumallian K, Jackson CJ, Chen Y, Chan CX, Verbruggen H. Nuclear genome of a pedinophyte pinpoints genomic innovation and streamlining in the green algae. THE NEW PHYTOLOGIST 2022; 233:2144-2154. [PMID: 34923642 DOI: 10.1111/nph.17926] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Accepted: 12/06/2021] [Indexed: 06/14/2023]
Abstract
The genomic diversity underpinning high ecological and species diversity in the green algae (Chlorophyta) remains little known. Here, we aimed to track genome evolution in the Chlorophyta, focusing on loss and gain of homologous genes, and lineage-specific innovations of the core Chlorophyta. We generated a high-quality nuclear genome for pedinophyte YPF701, a sister lineage to others in the core Chlorophyta and incorporated this genome in a comparative analysis with 25 other genomes from diverse Viridiplantae taxa. The nuclear genome of pedinophyte YPF701 has an intermediate size and gene number between those of most prasinophytes and the remainder of the core Chlorophyta. Our results suggest positive selection for genome streamlining in the Pedinophyceae, independent from genome minimisation observed among prasinophyte lineages. Genome expansion was predicted along the branch leading to the UTC clade (classes Ulvophyceae, Trebouxiophyceae and Chlorophyceae) after divergence from their last common ancestor with pedinophytes, with genomic novelty implicated in a range of basic biological functions. Results emphasise multiple independent signals of genome minimisation within the Chlorophyta, as well as the genomic novelty arising before diversification in the UTC clade, which may underpin the success of this species-rich clade in a diversity of habitats.
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Affiliation(s)
- Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
| | | | | | - Yibi Chen
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Cheong Xin Chan
- School of Chemistry and Molecular Biosciences, Australian Centre for Ecogenomics, The University of Queensland, Brisbane, Qld, 4072, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Vic, 3010, Australia
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11
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Dougan KE, González-Pech RA, Stephens TG, Shah S, Chen Y, Ragan MA, Bhattacharya D, Chan CX. Genome-powered classification of microbial eukaryotes: focus on coral algal symbionts. Trends Microbiol 2022; 30:831-840. [DOI: 10.1016/j.tim.2022.02.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 01/20/2022] [Accepted: 02/01/2022] [Indexed: 12/20/2022]
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12
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Uthanumallian K, Iha C, Repetti SI, Chan CX, Bhattacharya D, Duchene S, Verbruggen H. Tightly Constrained Genome Reduction and Relaxation of Purifying Selection during Secondary Plastid Endosymbiosis. Mol Biol Evol 2022; 39:msab295. [PMID: 34613411 PMCID: PMC8763093 DOI: 10.1093/molbev/msab295] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Endosymbiosis, the establishment of a former free-living prokaryotic or eukaryotic cell as an organelle inside a host cell, can dramatically alter the genomic architecture of the endosymbiont. Plastids or chloroplasts, the light-harvesting organelle of photosynthetic eukaryotes, are excellent models to study this phenomenon because plastid origin has occurred multiple times in evolution. Here, we investigate the genomic signature of molecular processes acting through secondary plastid endosymbiosis-the origination of a new plastid from a free-living eukaryotic alga. We used phylogenetic comparative methods to study gene loss and changes in selective regimes on plastid genomes, focusing on green algae that have given rise to three independent lineages with secondary plastids (euglenophytes, chlorarachniophytes, and Lepidodinium). Our results show an overall increase in gene loss associated with secondary endosymbiosis, but this loss is tightly constrained by the retention of genes essential for plastid function. The data show that secondary plastids have experienced temporary relaxation of purifying selection during secondary endosymbiosis. However, this process is tightly constrained, with selection relaxed only relative to the background in primary plastids. Purifying selection remains strong in absolute terms even during the endosymbiosis events. Selection intensity rebounds to pre-endosymbiosis levels following endosymbiosis events, demonstrating the changes in selection efficiency during different origin phases of secondary plastids. Independent endosymbiosis events in the euglenophytes, chlorarachniophytes, and Lepidodinium differ in their degree of relaxation of selection, highlighting the different evolutionary contexts of these events. This study reveals the selection-drift interplay during secondary endosymbiosis and evolutionary parallels during organellogenesis.
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Affiliation(s)
| | - Cintia Iha
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Cheong Xin Chan
- Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, The University of Queensland, Brisbane, QLD, Australia
| | | | - Sebastian Duchene
- Deptartment of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, University of Melbourne, Melbourne, VIC, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
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13
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Gain G, Vega de Luna F, Cordoba J, Perez E, Degand H, Morsomme P, Thiry M, Baurain D, Pierangelini M, Cardol P. Trophic state alters the mechanism whereby energetic coupling between photosynthesis and respiration occurs in Euglena gracilis. THE NEW PHYTOLOGIST 2021; 232:1603-1617. [PMID: 34392544 PMCID: PMC9292222 DOI: 10.1111/nph.17677] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 08/06/2021] [Indexed: 06/13/2023]
Abstract
The coupling between mitochondrial respiration and photosynthesis plays an important role in the energetic physiology of green plants and some secondary-red photosynthetic eukaryotes (diatoms), allowing an efficient CO2 assimilation and optimal growth. Using the flagellate Euglena gracilis, we first tested if photosynthesis-respiration coupling occurs in this species harbouring secondary green plastids (i.e. originated from an endosymbiosis between a green alga and a phagotrophic euglenozoan). Second, we tested how the trophic state (mixotrophy and photoautotrophy) of the cell alters the mechanisms involved in the photosynthesis-respiration coupling. Energetic coupling between photosynthesis and respiration was determined by testing the effect of respiratory inhibitors on photosynthesis, and measuring the simultaneous variation of photosynthesis and respiration rates as a function of temperature (i.e. thermal response curves). The mechanism involved in the photosynthesis-respiration coupling was assessed by combining proteomics, biophysical and cytological analyses. Our work shows that there is photosynthesis-respiration coupling and membrane contacts between mitochondria and chloroplasts in E. gracilis. However, whereas in mixotrophy adjustment of the chloroplast ATP/NADPH ratio drives the interaction, in photoautotrophy the coupling is conditioned by CO2 limitation and photorespiration. This indicates that maintenance of photosynthesis-respiration coupling, through plastic metabolic responses, is key to E. gracilis functioning under changing environmental conditions.
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Affiliation(s)
- Gwenaëlle Gain
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Félix Vega de Luna
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Javier Cordoba
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Emilie Perez
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Hervé Degand
- Louvain Institute of Biomolecular Science and Technology (LIBST)UCLouvainLouvain‐la‐NeuveB‐1348Belgium
| | - Pierre Morsomme
- Louvain Institute of Biomolecular Science and Technology (LIBST)UCLouvainLouvain‐la‐NeuveB‐1348Belgium
| | - Marc Thiry
- Laboratoire de Biologie Cellulaire et TissulaireGiga‐NeurosciencesULiègeLiègeB‐4000Belgium
| | - Denis Baurain
- InBioS – PhytoSYSTEMSEukaryotic PhylogenomicsULiègeLiègeB‐4000Belgium
| | - Mattia Pierangelini
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
| | - Pierre Cardol
- InBioS – PhytoSYSTEMSLaboratoire de Génétique et Physiologie des MicroalguesULiègeLiègeB‐4000Belgium
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14
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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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15
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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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16
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Záhonová K, Lax G, Sinha SD, Leonard G, Richards TA, Lukeš J, Wideman JG. Single-cell genomics unveils a canonical origin of the diverse mitochondrial genomes of euglenozoans. BMC Biol 2021; 19:103. [PMID: 34001130 PMCID: PMC8130358 DOI: 10.1186/s12915-021-01035-y] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 04/22/2021] [Indexed: 12/28/2022] Open
Abstract
Background The supergroup Euglenozoa unites heterotrophic flagellates from three major clades, kinetoplastids, diplonemids, and euglenids, each of which exhibits extremely divergent mitochondrial characteristics. Mitochondrial genomes (mtDNAs) of euglenids comprise multiple linear chromosomes carrying single genes, whereas mitochondrial chromosomes are circular non-catenated in diplonemids, but circular and catenated in kinetoplastids. In diplonemids and kinetoplastids, mitochondrial mRNAs require extensive and diverse editing and/or trans-splicing to produce mature transcripts. All known euglenozoan mtDNAs exhibit extremely short mitochondrial small (rns) and large (rnl) subunit rRNA genes, and absence of tRNA genes. How these features evolved from an ancestral bacteria-like circular mitochondrial genome remains unanswered. Results We sequenced and assembled 20 euglenozoan single-cell amplified genomes (SAGs). In our phylogenetic and phylogenomic analyses, three SAGs were placed within kinetoplastids, 14 within diplonemids, one (EU2) within euglenids, and two SAGs with nearly identical small subunit rRNA gene (18S) sequences (EU17/18) branched as either a basal lineage of euglenids, or as a sister to all euglenozoans. Near-complete mitochondrial genomes were identified in EU2 and EU17/18. Surprisingly, both EU2 and EU17/18 mitochondrial contigs contained multiple genes and one tRNA gene. Furthermore, EU17/18 mtDNA possessed several features unique among euglenozoans including full-length rns and rnl genes, six mitoribosomal genes, and nad11, all likely on a single chromosome. Conclusions Our data strongly suggest that EU17/18 is an early-branching euglenozoan with numerous ancestral mitochondrial features. Collectively these data contribute to untangling the early evolution of euglenozoan mitochondria. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01035-y.
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Affiliation(s)
- Kristína Záhonová
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic.,Faculty of Science, Charles University, BIOCEV, Vestec, Czech Republic
| | - Gordon Lax
- Department of Botany, University of British Columbia, Vancouver, Canada
| | - Savar D Sinha
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA
| | - Guy Leonard
- Department of Zoology, University of Oxford, Oxford, UK
| | | | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice (Budweis), Czech Republic. .,Faculty of Sciences, University of South Bohemia, České Budějovice (Budweis), Czech Republic.
| | - Jeremy G Wideman
- Center for Mechanisms of Evolution, Biodesign Institute, School of Life Sciences, Arizona State University, Tempe, USA.
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17
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Strother PK, Brasier MD, Wacey D, Timpe L, Saunders M, Wellman CH. A possible billion-year-old holozoan with differentiated multicellularity. Curr Biol 2021; 31:2658-2665.e2. [PMID: 33852871 DOI: 10.1016/j.cub.2021.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Revised: 12/07/2020] [Accepted: 03/15/2021] [Indexed: 02/05/2023]
Abstract
Sediments of the Torridonian sequence of the Northwest Scottish Highlands contain a wide array of microfossils, documenting life in a non-marine setting a billion years ago (1 Ga).1-4 Phosphate nodules from the Diabaig Formation at Loch Torridon preserve microorganisms with cellular-level fidelity,5,6 allowing for partial reconstruction of the developmental stages of a new organism, Bicellum brasieri gen. et sp. nov. The mature form of Bicellum consists of a solid, spherical ball of tightly packed cells (a stereoblast) of isodiametric cells enclosed in a monolayer of elongated, sausage-shaped cells. However, two populations of naked stereoblasts show mixed cell shapes, which we infer to indicate incipient development of elongated cells that were migrating to the periphery of the cell mass. These simple morphogenetic movements could be explained by differential cell-cell adhesion.7,8 In fact, the basic morphology of Bicellum is topologically similar to that of experimentally produced cell masses that were shown to spontaneously segregate into two distinct domains based on differential cadherin-based cell adhesion.9 The lack of rigid cell walls in the stereoblast renders an algal affinity for Bicellum unlikely: its overall morphology is more consistent with a holozoan origin. Unicellular holozoans are known today to form multicellular stages within complex life cycles,10-13 so the occurrence of such simple levels of transient multicellularity seen here is consistent with a holozoan affinity. Regardless of precise phylogenetic placement, these fossils demonstrate simple cell differentiation and morphogenic processes that are similar to those seen in some metazoans today.
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Affiliation(s)
- Paul K Strother
- Department of Earth & Environmental Sciences, Weston Observatory of Boston College, 381 Concord Road, Weston, MA 02493, USA.
| | - Martin D Brasier
- Department of Earth Sciences, University of Oxford, South Parks Road, Oxford OX1 3AN, UK
| | - David Wacey
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Leslie Timpe
- Department of Biology, San Francisco State University, San Francisco, CA 94132, USA
| | - Martin Saunders
- Centre for Microscopy, Characterisation and Analysis, The University of Western Australia, 35 Stirling Highway, Perth, WA 6009, Australia
| | - Charles H Wellman
- Department of Animal & Plant Sciences, University of Sheffield, Alfred Denny Building, Western Bank, Sheffield S10 2TN, UK
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18
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Wetherbee R, Bringloe TT, Costa JF, van de Meene A, Andersen RA, Verbruggen H. New pelagophytes show a novel mode of algal colony development and reveal a perforated theca that may define the class. JOURNAL OF PHYCOLOGY 2021; 57:396-411. [PMID: 32975327 DOI: 10.1111/jpy.13074] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Revised: 07/20/2020] [Accepted: 08/18/2020] [Indexed: 06/11/2023]
Abstract
Pelagophytes (Heterokonta) are a morphologically diverse class of marine algae historically united only by DNA sequences. We established clonal cultures of sand-dwelling pelagophytes collected from intertidal pools around Australia. Phylogenetic trees based on nuclear 18S rDNA and plastid rbcL, psaA, psaB, psbA, and psbC sequences revealed two new genera, Gazia and Glomerochrysis, related to Aureoumbra in a distinct lineage within the Sarcinochrysidaceae (Pelagophyceae). The three new species (Gazia saundersii, Gazia australica, and Glomerochrysis psammophila), along with an Australian strain of Aureoumbra geitleri, are characterized by dominant benthic stages that differ significantly from one another, while occasionally producing classic heterokont zoospores. The benthic stage of Ga. saundersii has a novel development not observed in any other colonial alga, consisting of large, spherical colonies (up to 140 μm in diameter) containing c. 2,500 cells that eventually differentiate and segregate into a large number of daughter colonies that are subsequently liberated. Alternatively, colonies may differentiate into a mass of zoospores that escape and settle to develop into new colonies. In Gl. psammophila, cubic packets of cells form large sticky clusters that bind sand together, while Ga. australica and A. geitleri are unicellular species. Using fixation by high-pressure freezing, a distinctive perforated theca was observed by TEM in all genera of this lineage, and we hypothesize this unique covering may be the first morphological feature to characterize most, if not all, pelagophytes. This study substantiates the diverse nature of sand-dwelling pelagophytes as well as their mechanisms for thriving in a dynamic habitat.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Trevor T Bringloe
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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19
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Roux P, Siano R, Collin K, Bilien G, Sinquin C, Marchand L, Zykwinska A, Delbarre-Ladrat C, Schapira M. Bacteria enhance the production of extracellular polymeric substances by the green dinoflagellate Lepidodinium chlorophorum. Sci Rep 2021; 11:4795. [PMID: 33637819 PMCID: PMC7910647 DOI: 10.1038/s41598-021-84253-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2020] [Accepted: 02/03/2021] [Indexed: 11/22/2022] Open
Abstract
High biomasses of the marine dinoflagellate Lepidodinium chlorophorum cause green seawater discolorations along Southern Brittany (NE Atlantic, France). The viscosity associated to these phenomena has been related to problems in oyster cultivation. The harmful effect of L. chlorophorum might originate from the secretion of Extracellular Polymeric Substances (EPS). To understand whether the EPS are produced by L. chlorophorum or its associated bacteria, or if they are a product of their interaction, batch cultures were performed under non-axenic and pseudo-axenic conditions for three strains. Maximum dinoflagellate cell abundances were observed in pseudo-axenic cultures. The non-sinking fraction of polymers (Soluble Extracellular Polymers, SEP), mainly composed of proteins and the exopolysaccharide sulphated galactan, slightly increased in pseudo-axenic cultures. The amount of Transparent Exopolymer Particles (TEP) per cell increased under non-axenic conditions. Despite the high concentrations of Particulate Organic Carbon (POC) measured, viscosity did not vary. These results suggest that the L. chlorophorum-bacteria interaction could have a detrimental consequence on the dinoflagellate, translating in a negative effect on L. chlorophorum growth, as well as EPS overproduction by the dinoflagellate, at concentrations that should not affect seawater viscosity.
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20
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Lax G, Kolisko M, Eglit Y, Lee WJ, Yubuki N, Karnkowska A, Leander BS, Burger G, Keeling PJ, Simpson AGB. Multigene phylogenetics of euglenids based on single-cell transcriptomics of diverse phagotrophs. Mol Phylogenet Evol 2021; 159:107088. [PMID: 33545276 DOI: 10.1016/j.ympev.2021.107088] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 01/24/2021] [Accepted: 01/26/2021] [Indexed: 12/22/2022]
Abstract
Euglenids are a well-known group of single-celled eukaryotes, with phototrophic, osmotrophic and phagotrophic members. Phagotrophs represent most of the phylogenetic diversity of euglenids, and gave rise to the phototrophs and osmotrophs, but their evolutionary relationships are poorly understood. Symbiontids, in contrast, are anaerobes that are alternatively inferred to be derived euglenids, or a separate euglenozoan group. Most phylogenetic studies of euglenids have examined the SSU rDNA only, which is often highly divergent. Also, many phagotrophic euglenids (and symbiontids) are uncultured, restricting collection of other molecular data. We generated transcriptome data for 28 taxa, mostly using a single-cell approach, and conducted the first multigene phylogenetic analyses of euglenids to include phagotrophs and symbiontids. Euglenids are recovered as monophyletic, with symbiontids forming an independent branch within Euglenozoa. Spirocuta, the clade of flexible euglenids that contains both the phototrophs (Euglenophyceae) and osmotrophs (Aphagea), is robustly resolved, with the ploeotid Olkasia as its sister group, forming the new taxon Olkaspira. Ploeotids are paraphyletic, although Ploeotiidae (represented by Ploeotia spp.), Lentomonas, and Keelungia form a robust clade (new taxon Alistosa). Petalomonadida branches robustly as sister to other euglenids in outgroup-rooted analyses. Within Spirocuta, Euglenophyceae is a robust clade that includes Rapaza, and Anisonemia is a well-supported monophyletic group containing Anisonemidae (Anisonema and Dinema spp.), 'Heteronema II' (represented by H. vittatum), and a clade of Neometanema plus Aphagea. Among 'peranemid' phagotrophs, Chasmostoma branches with included Urceolus, and Peranema with the undescribed 'Jenningsia II', while other relationships are weakly supported and consequently the closest sister group to Euglenophyceae remains unresolved. Our results are inconsistent with recent inferences that Entosiphon is the evolutionarily pivotal sister either to other euglenids, or to Spirocuta. At least three transitions between posterior and anterior flagellar gliding occurred in euglenids, with the phylogenetic positions and directions of those transitions remaining ambiguous.
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Affiliation(s)
- G Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada; Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - M Kolisko
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Y Eglit
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada
| | - W J Lee
- Department of Environment and Energy Engineering, Kyungnam University, Changwon, Republic of Korea
| | - N Yubuki
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, Orsay, France; Department of Zoology, University of British Columbia, Vancouver, Canada
| | - A Karnkowska
- Institute of Evolutionary Biology, Faculty of Biology, University of Warsaw, Poland
| | - B S Leander
- Department of Zoology, University of British Columbia, Vancouver, Canada
| | - G Burger
- Robert-Cedergren Centre for Bioinformatics and Genomics, Biochemistry Department, Université de Montréal, Montréal, Canada
| | - P J Keeling
- Department of Botany, University of British Columbia, Vancouver, Canada(1)
| | - A G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, Canada.
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21
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Fang J, Liu B, Liu G, Verbruggen H, Zhu H. Six Newly Sequenced Chloroplast Genomes From Trentepohliales: The Inflated Genomes, Alternative Genetic Code and Dynamic Evolution. FRONTIERS IN PLANT SCIENCE 2021; 12:780054. [PMID: 34956275 PMCID: PMC8692980 DOI: 10.3389/fpls.2021.780054] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/15/2021] [Indexed: 05/17/2023]
Abstract
Cephaleuros is often known as an algal pathogen with 19 taxonomically valid species, some of which are responsible for red rust and algal spot diseases in vascular plants. No chloroplast genomes have yet been reported in this genus, and the limited genetic information is an obstacle to understanding the evolution of this genus. In this study, we sequenced six new Trentepohliales chloroplast genomes, including four Cephaleuros and two Trentepohlia. The chloroplast genomes of Trentepohliales are large compared to most green algae, ranging from 216 to 408 kbp. They encode between 93 and 98 genes and have a GC content of 26-36%. All new chloroplast genomes were circular-mapping and lacked a quadripartite structure, in contrast to the previously sequenced Trentepohlia odorata, which does have an inverted repeat. The duplicated trnD -GTC, petD, and atpA genes in C. karstenii may be remnants of the IR region and shed light on its reduction. Chloroplast genes of Trentepohliales show elevated rates of evolution, strong rearrangement dynamics and several genes display an alternative genetic code with reassignment of the UGA/UAG codon presumably coding for arginine. Our results present the first whole chloroplast genome of the genus Cephaleuros and enrich the chloroplast genome resources of Trentepohliales.
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Affiliation(s)
- Jiao Fang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Benwen Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Guoxiang Liu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, VIC, Australia
| | - Huan Zhu
- State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- *Correspondence: Huan Zhu,
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22
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Raven JA, Suggett DJ, Giordano M. Inorganic carbon concentrating mechanisms in free-living and symbiotic dinoflagellates and chromerids. JOURNAL OF PHYCOLOGY 2020; 56:1377-1397. [PMID: 32654150 DOI: 10.1111/jpy.13050] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 06/23/2020] [Indexed: 06/11/2023]
Abstract
Photosynthetic dinoflagellates are ecologically and biogeochemically important in marine and freshwater environments. However, surprisingly little is known of how this group acquires inorganic carbon or how these diverse processes evolved. Consequently, how CO2 availability ultimately influences the success of dinoflagellates over space and time remains poorly resolved compared to other microalgal groups. Here we review the evidence. Photosynthetic core dinoflagellates have a Form II RuBisCO (replaced by Form IB or Form ID in derived dinoflagellates). The in vitro kinetics of the Form II RuBisCO from dinoflagellates are largely unknown, but dinoflagellates with Form II (and other) RuBisCOs have inorganic carbon concentrating mechanisms (CCMs), as indicated by in vivo internal inorganic C accumulation and affinity for external inorganic C. However, the location of the membrane(s) at which the essential active transport component(s) of the CCM occur(s) is (are) unresolved; isolation and characterization of functionally competent chloroplasts would help in this respect. Endosymbiotic Symbiodiniaceae (in Foraminifera, Acantharia, Radiolaria, Ciliata, Porifera, Acoela, Cnidaria, and Mollusca) obtain inorganic C by transport from seawater through host tissue. In corals this transport apparently provides an inorganic C concentration around the photobiont that obviates the need for photobiont CCM. This is not the case for tridacnid bivalves, medusae, or, possibly, Foraminifera. Overcoming these long-standing knowledge gaps relies on technical advances (e.g., the in vitro kinetics of Form II RuBisCO) that can functionally track the fate of inorganic C forms.
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Affiliation(s)
- John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Invergowrie, Dundee, DD2 5DA, UK
- Faculty of Science, University of Technology, Sydney, Climate Change Cluster, Ultimo, Sydney, New South Wales, 2007, Australia
- School of Biological Science, University of Western Australia, 35 Stirling Highway, Crawley, Western Australia, 6009, Australia
| | - David J Suggett
- Faculty of Science, University of Technology, Sydney, Climate Change Cluster, Ultimo, Sydney, New South Wales, 2007, Australia
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Via Brecce Bianche, 60131, Ancona, Italy
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Algatech, Trebon, Czech Republic
- National Research Council, Institute of Marine Science ISMAR, Venezia, Italy
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23
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Abstract
Most secondary nonphotosynthetic eukaryotes have retained residual plastids whose physiological role is often still unknown. One such example is Euglena longa, a close nonphotosynthetic relative of Euglena gracilis harboring a plastid organelle of enigmatic function. By mining transcriptome data from E. longa, we finally provide an overview of metabolic processes localized to its elusive plastid. The organelle plays no role in the biosynthesis of isoprenoid precursors and fatty acids and has a very limited repertoire of pathways concerning nitrogen-containing metabolites. In contrast, the synthesis of phospholipids and glycolipids has been preserved, curiously with the last step of sulfoquinovosyldiacylglycerol synthesis being catalyzed by the SqdX form of an enzyme so far known only from bacteria. Notably, we show that the E. longa plastid synthesizes tocopherols and a phylloquinone derivative, the first such report for nonphotosynthetic plastids studied so far. The most striking attribute of the organelle could be the presence of a linearized Calvin-Benson (CB) pathway, including RuBisCO yet lacking the gluconeogenetic part of the standard cycle, together with ferredoxin-NADP+ reductase (FNR) and the ferredoxin/thioredoxin system. We hypothesize that the ferredoxin/thioredoxin system activates the linear CB pathway in response to the redox status of the E. longa cell and speculate on the role of the pathway in keeping the redox balance of the cell. Altogether, the E. longa plastid defines a new class of relic plastids that is drastically different from the best-studied organelle of this category, the apicoplast.IMPORTANCE Colorless plastids incapable of photosynthesis evolved in many plant and algal groups, but what functions they perform is still unknown in many cases. Here, we study the elusive plastid of Euglena longa, a nonphotosynthetic cousin of the familiar green flagellate Euglena gracilis We document an unprecedented combination of metabolic functions that the E. longa plastid exhibits in comparison with previously characterized nonphotosynthetic plastids. For example, and truly surprisingly, it has retained the synthesis of tocopherols (vitamin E) and a phylloquinone (vitamin K) derivative. In addition, we offer a possible solution of the long-standing conundrum of the presence of the CO2-fixing enzyme RuBisCO in E. longa Our work provides a detailed account on a unique variant of relic plastids, the first among nonphotosynthetic plastids that evolved by secondary endosymbiosis from a green algal ancestor, and suggests that it has persisted for reasons not previously considered in relation to nonphotosynthetic plastids.
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 PMCID: PMC7594059 DOI: 10.3390/v12101180] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 12/14/2022] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia; (R.W.); (H.V.)
| | - Edward C. Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia; (J.C.); (V.R.M.)
- Correspondence: ; Tel.: +61-2-9351-5591
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25
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Charon J, Marcelino VR, Wetherbee R, Verbruggen H, Holmes EC. Metatranscriptomic Identification of Diverse and Divergent RNA Viruses in Green and Chlorarachniophyte Algae Cultures. Viruses 2020; 12:v12101180. [PMID: 33086653 DOI: 10.1101/2020.06.08.141184] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Revised: 10/12/2020] [Accepted: 10/14/2020] [Indexed: 05/26/2023] Open
Abstract
Our knowledge of the diversity and evolution of the virosphere will likely increase dramatically with the study of microbial eukaryotes, including the microalgae within which few RNA viruses have been documented. By combining total RNA sequencing with sequence and structural-based homology detection, we identified 18 novel RNA viruses in cultured samples from two major groups of microbial algae: the chlorophytes and the chlorarachniophytes. Most of the RNA viruses identified in the green algae class Ulvophyceae were related to the Tombusviridae and Amalgaviridae viral families commonly associated with land plants. This suggests that the evolutionary history of these viruses extends to divergence events between algae and land plants. Seven Ostreobium sp-associated viruses exhibited sequence similarity to the mitoviruses most commonly found in fungi, compatible with horizontal virus transfer between algae and fungi. We also document, for the first time, RNA viruses associated with chlorarachniophytes, including the first negative-sense (bunya-like) RNA virus in microalgae, as well as a distant homolog of the plant virus Virgaviridae, potentially signifying viral inheritance from the secondary chloroplast endosymbiosis that marked the origin of the chlorarachniophytes. More broadly, these data suggest that the scarcity of RNA viruses in algae results from limited investigation rather than their absence.
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Affiliation(s)
- Justine Charon
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
| | - Vanessa Rossetto Marcelino
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, NSW 2145, Australia
| | - Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, VIC 3010, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, School of Life and Environmental Sciences and School of Medical Sciences, The University of Sydney, Sydney, NSW 2006, Australia
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26
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Lax G, Simpson AGB. The Molecular Diversity of Phagotrophic Euglenids Examined Using Single-cell Methods. Protist 2020; 171:125757. [PMID: 33126020 DOI: 10.1016/j.protis.2020.125757] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Revised: 07/29/2020] [Accepted: 08/05/2020] [Indexed: 01/16/2023]
Abstract
Euglenids are a diverse group of euglenozoan flagellates that includes phototrophs, osmotrophs, and phagotrophs. Despite making up most of the phylogenetic diversity of euglenids, phagotrophs remain understudied, and recent work has focused on 'deep-branching' groups. Spirocuta is the large clade encompassing all flexible euglenids including the phototroph and primary osmotroph clades, plus various phagotrophs. Understanding the phylogenetic diversity of phagotrophic spirocutes is crucial for tracing euglenid evolution, including how phototrophs arose. We used single-cell approaches to greatly increase sampling of SSU rDNA for phagotrophic euglenids, particularly spirocutes, including the first sequences from Urceolus, Jenningsia, Chasmostoma, and Sphenomonas, and expanded coverage for Dinema and Heteronema sensu lato, amongst others. Urceolus monophyly is unconfirmed. Organisms referred to Jenningsia form two distinct clades. Heteronema vittatum and similar cells branch separately from Heteronema (c.f.) globuliferum and Teloprocta/Heteronema scaphurum, while Dinema appears as 2-3 clades. Sphenomonas is monophyletic and the deepest branch within Petalomonadida. The census of genera markedly underestimates the phylogenetic diversity of phagotrophs, but taxonomic restraint is necessary when sequences are not available from type species or reasonable surrogates. SSU rDNA phylogenies do not resolve most deep relationships within Spirocuta, but identify units of diversity to sample in future multigene analyses.
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Affiliation(s)
- Gordon Lax
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada
| | - Alastair G B Simpson
- Department of Biology, and Centre for Comparative Genomics and Evolutionary Bioinformatics, Dalhousie University, Halifax, NS, Canada.
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27
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Zhang Z, Qu C, Zhang K, He Y, Zhao X, Yang L, Zheng Z, Ma X, Wang X, Wang W, Wang K, Li D, Zhang L, Zhang X, Su D, Chang X, Zhou M, Gao D, Jiang W, Leliaert F, Bhattacharya D, De Clerck O, Zhong B, Miao J. Adaptation to Extreme Antarctic Environments Revealed by the Genome of a Sea Ice Green Alga. Curr Biol 2020; 30:3330-3341.e7. [PMID: 32619486 DOI: 10.1016/j.cub.2020.06.029] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 05/13/2020] [Accepted: 06/08/2020] [Indexed: 01/21/2023]
Abstract
The unicellular green alga Chlamydomonas sp. ICE-L thrives in polar sea ice, where it tolerates extreme low temperatures, high salinity, and broad seasonal fluctuations in light conditions. Despite the high interest in biotechnological uses of this species, little is known about the adaptations that allow it to thrive in this harsh and complex environment. Here, we assembled a high-quality genome sequence of ∼542 Mb and found that retrotransposon proliferation contributed to the relatively large genome size of ICE-L when compared to other chlorophytes. Genomic features that may support the extremophilic lifestyle of this sea ice alga include massively expanded gene families involved in unsaturated fatty acid biosynthesis, DNA repair, photoprotection, ionic homeostasis, osmotic homeostasis, and reactive oxygen species detoxification. The acquisition of multiple ice binding proteins through putative horizontal gene transfer likely contributed to the origin of the psychrophilic lifestyle in ICE-L. Additional innovations include the significant upregulation under abiotic stress of several expanded ICE-L gene families, likely reflecting adaptive changes among diverse metabolic processes. Our analyses of the genome, transcriptome, and functional assays advance general understanding of the Antarctic green algae and offer potential explanations for how green plants adapt to extreme environments.
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Affiliation(s)
- Zhenhua Zhang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Changfeng Qu
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Kaijian Zhang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Yingying He
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xing Zhao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Lingxiao Yang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Zhou Zheng
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China
| | - Xiaoya Ma
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xixi Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Wenyu Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Kai Wang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Dan Li
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Liping Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Xin Zhang
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China
| | - Danyan Su
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Xin Chang
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China
| | - Mengyan Zhou
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Dan Gao
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Wenkai Jiang
- Novogene Bioinformatics Institute, 100083 Beijing, China
| | - Frederik Leliaert
- Biology Department, Ghent University, 9000 Ghent, Belgium; Meise Botanic Garden, Nieuwelaan 38, 1860 Meise, Belgium
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA
| | | | - Bojian Zhong
- College of Life Sciences, Nanjing Normal University, 210023 Nanjing, China.
| | - Jinlai Miao
- First Institute of Oceanography, Ministry of Natural Resources, 266061 Qingdao, China; Laboratory for Marine Drugs and Bioproducts of Qingdao National Laboratory for Marine Science and Technology, 266237 Qingdao, China.
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28
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Dinoflagellates with relic endosymbiont nuclei as models for elucidating organellogenesis. Proc Natl Acad Sci U S A 2020; 117:5364-5375. [PMID: 32094181 DOI: 10.1073/pnas.1911884117] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Nucleomorphs are relic endosymbiont nuclei so far found only in two algal groups, cryptophytes and chlorarachniophytes, which have been studied to model the evolutionary process of integrating an endosymbiont alga into a host-governed plastid (organellogenesis). However, past studies suggest that DNA transfer from the endosymbiont to host nuclei had already ceased in both cryptophytes and chlorarachniophytes, implying that the organellogenesis at the genetic level has been completed in the two systems. Moreover, we have yet to pinpoint the closest free-living relative of the endosymbiotic alga engulfed by the ancestral chlorarachniophyte or cryptophyte, making it difficult to infer how organellogenesis altered the endosymbiont genome. To counter the above issues, we need novel nucleomorph-bearing algae, in which endosymbiont-to-host DNA transfer is on-going and for which endosymbiont/plastid origins can be inferred at a fine taxonomic scale. Here, we report two previously undescribed dinoflagellates, strains MGD and TGD, with green algal endosymbionts enclosing plastids as well as relic nuclei (nucleomorphs). We provide evidence for the presence of DNA in the two nucleomorphs and the transfer of endosymbiont genes to the host (dinoflagellate) genomes. Furthermore, DNA transfer between the host and endosymbiont nuclei was found to be in progress in both the MGD and TGD systems. Phylogenetic analyses successfully resolved the origins of the endosymbionts at the genus level. With the combined evidence, we conclude that the host-endosymbiont integration in MGD/TGD is less advanced than that in cryptophytes/chrorarachniophytes, and propose the two dinoflagellates as models for elucidating organellogenesis.
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29
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Tang Q, Pang K, Yuan X, Xiao S. A one-billion-year-old multicellular chlorophyte. Nat Ecol Evol 2020; 4:543-549. [PMID: 32094536 PMCID: PMC8668152 DOI: 10.1038/s41559-020-1122-9] [Citation(s) in RCA: 51] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2019] [Accepted: 01/20/2020] [Indexed: 11/09/2022]
Abstract
Chlorophytes (representing a clade within the Viridiplantae and a sister group of the Streptophyta) probably dominated marine export bioproductivity and played a key role in facilitating ecosystem complexity before the Mesozoic diversification of phototrophic eukaryotes such as diatoms, coccolithophorans and dinoflagellates. Molecular clock and biomarker data indicate that chlorophytes diverged in the Mesoproterozoic or early Neoproterozoic, followed by their subsequent phylogenetic diversification, multicellular evolution and ecological expansion in the late Neoproterozoic and Palaeozoic. This model, however, has not been rigorously tested with palaeontological data because of the scarcity of Proterozoic chlorophyte fossils. Here we report abundant millimetre-sized, multicellular and morphologically differentiated macrofossils from rocks approximately 1,000 million years ago. These fossils are described as Proterocladus antiquus new species and are interpreted as benthic siphonocladalean chlorophytes, suggesting that chlorophytes acquired macroscopic size, multicellularity and cellular differentiation nearly a billion years ago, much earlier than previously thought.
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Affiliation(s)
- Qing Tang
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
| | - Ke Pang
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xunlai Yuan
- State Key Laboratory of Palaeobiology and Stratigraphy, Nanjing Institute of Geology and Palaeontology and Center for Excellence in Life and Paleoenvironment, Chinese Academy of Sciences, Nanjing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Shuhai Xiao
- Department of Geosciences and Global Change Center, Virginia Tech, Blacksburg, VA, USA.
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30
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Del Cortona A, Jackson CJ, Bucchini F, Van Bel M, D'hondt S, Škaloud P, Delwiche CF, Knoll AH, Raven JA, Verbruggen H, Vandepoele K, De Clerck O, Leliaert F. Neoproterozoic origin and multiple transitions to macroscopic growth in green seaweeds. Proc Natl Acad Sci U S A 2020; 117:2551-2559. [PMID: 31911467 PMCID: PMC7007542 DOI: 10.1073/pnas.1910060117] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The Neoproterozoic Era records the transition from a largely bacterial to a predominantly eukaryotic phototrophic world, creating the foundation for the complex benthic ecosystems that have sustained Metazoa from the Ediacaran Period onward. This study focuses on the evolutionary origins of green seaweeds, which play an important ecological role in the benthos of modern sunlit oceans and likely played a crucial part in the evolution of early animals by structuring benthic habitats and providing novel niches. By applying a phylogenomic approach, we resolve deep relationships of the core Chlorophyta (Ulvophyceae or green seaweeds, and freshwater or terrestrial Chlorophyceae and Trebouxiophyceae) and unveil a rapid radiation of Chlorophyceae and the principal lineages of the Ulvophyceae late in the Neoproterozoic Era. Our time-calibrated tree points to an origin and early diversification of green seaweeds in the late Tonian and Cryogenian periods, an interval marked by two global glaciations with strong consequent changes in the amount of available marine benthic habitat. We hypothesize that unicellular and simple multicellular ancestors of green seaweeds survived these extreme climate events in isolated refugia, and diversified in benthic environments that became increasingly available as ice retreated. An increased supply of nutrients and biotic interactions, such as grazing pressure, likely triggered the independent evolution of macroscopic growth via different strategies, including true multicellularity, and multiple types of giant-celled forms.
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Affiliation(s)
- Andrea Del Cortona
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | | | - François Bucchini
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Michiel Van Bel
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
| | - Sofie D'hondt
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium
| | - Pavel Škaloud
- Department of Botany, Faculty of Science, Charles University, CZ-12800 Prague 2, Czech Republic
| | - Charles F Delwiche
- Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD 20742
| | - Andrew H Knoll
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA 02138
| | - John A Raven
- Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, United Kingdom
- School of Biological Sciences, University of Western Australia, WA 6009, Australia
- Climate Change Cluster, University of Technology, Ultimo, NSW 2006, Australia
| | - Heroen Verbruggen
- School of Biosciences, University of Melbourne, Melbourne, VIC 3010, Australia
| | - Klaas Vandepoele
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Zwijnaarde, Belgium;
- Vlaams Instituut voor Biotechnologie Center for Plant Systems Biology, 9052 Zwijnaarde, Belgium
- Bioinformatics Institute Ghent, Ghent University, 9052 Zwijnaarde, Belgium
| | - Olivier De Clerck
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
| | - Frederik Leliaert
- Department of Biology, Phycology Research Group, Ghent University, 9000 Ghent, Belgium;
- Meise Botanic Garden, 1860 Meise, Belgium
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31
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Novák Vanclová AMG, Zoltner M, Kelly S, Soukal P, Záhonová K, Füssy Z, Ebenezer TE, Lacová Dobáková E, Eliáš M, Lukeš J, Field MC, Hampl V. Metabolic quirks and the colourful history of the Euglena gracilis secondary plastid. THE NEW PHYTOLOGIST 2020; 225:1578-1592. [PMID: 31580486 DOI: 10.1111/nph.16237] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/03/2019] [Accepted: 09/25/2019] [Indexed: 05/20/2023]
Abstract
Euglena spp. are phototrophic flagellates with considerable ecological presence and impact. Euglena gracilis harbours secondary green plastids, but an incompletely characterised proteome precludes accurate understanding of both plastid function and evolutionary history. Using subcellular fractionation, an improved sequence database and MS we determined the composition, evolutionary relationships and hence predicted functions of the E. gracilis plastid proteome. We confidently identified 1345 distinct plastid protein groups and found that at least 100 proteins represent horizontal acquisitions from organisms other than green algae or prokaryotes. Metabolic reconstruction confirmed previously studied/predicted enzymes/pathways and provided evidence for multiple unusual features, including uncoupling of carotenoid and phytol metabolism, a limited role in amino acid metabolism, and dual sets of the SUF pathway for FeS cluster assembly, one of which was acquired by lateral gene transfer from Chlamydiae. Plastid paralogues of trafficking-associated proteins potentially mediating fusion of transport vesicles with the outermost plastid membrane were identified, together with derlin-related proteins, potential translocases across the middle membrane, and an extremely simplified TIC complex. The Euglena plastid, as the product of many genomes, combines novel and conserved features of metabolism and transport.
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Affiliation(s)
| | - Martin Zoltner
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Petr Soukal
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
| | - Kristína Záhonová
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Zoltán Füssy
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Eva Lacová Dobáková
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Marek Eliáš
- Faculty of Science, University of Ostrava, Ostrava, 710 00, Czechia
| | - Julius Lukeš
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
- Faculty of Science, University of South Bohemia, České Budějovice, 370 05, Czechia
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, 370 05, Czechia
| | - Vladimír Hampl
- Faculty of Science, Charles University, BIOCEV, Vestec, 252 50, Czechia
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32
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Lukešová S, Karlicki M, Tomečková Hadariová L, Szabová J, Karnkowska A, Hampl V. Analyses of environmental sequences and two regions of chloroplast genomes revealed the presence of new clades of photosynthetic euglenids in marine environments. ENVIRONMENTAL MICROBIOLOGY REPORTS 2020; 12:78-91. [PMID: 31845515 DOI: 10.1111/1758-2229.12817] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 11/23/2019] [Accepted: 11/30/2019] [Indexed: 06/10/2023]
Abstract
Euglenophyceae are unicellular algae with the majority of their diversity known from small freshwater reservoirs. Only two dozen species have been described to occur in marine habitats, but their abundance and diversity remain unexplored. Phylogenetic studies revealed marine prasinophyte green alga, Pyramimonas parkeae, as the closest extant relative of the euglenophytes' plastid, but similarly to euglenophytes, our knowledge about the diversity of Pyramimonadales is limited. Here we explored Euglenophyceae and Pyramimonadales phylogenetic diversity in marine environmental samples. We yielded 18S rDNA and plastid 16S rDNA sequences deposited in public repositories and reconstructed Euglenophyceae reference trees. We searched high-throughput environmental sequences from the TARA Oceans expedition and Ocean Sampling Day initiative for 18S rDNA and 16S rDNA, placed them in the phylogenetic context and estimated their relative abundances. To avoid polymerase chain reaction (PCR) bias, we also exploited metagenomic data from the TARA Oceans expedition for the presence of rRNA sequences from these groups. Finally, we targeted these protists in coastal samples by specific PCR amplification of two parts of the plastid genome uniquely shared between euglenids and Pyramimonadales. All approaches revealed previously undetected, but relatively low-abundant lineages of marine Euglenophyceae. Surprisingly, some of those lineages are branching within the freshwater or brackish genera.
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Affiliation(s)
- Soňa Lukešová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Michał Karlicki
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Lucia Tomečková Hadariová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Jana Szabová
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
| | - Anna Karnkowska
- Faculty of Biology, Biological and Chemical Research Centre, University of Warsaw, Żwirki i Wigury 101, Warsaw, 02 089, Poland
| | - Vladimír Hampl
- Faculty of Science, Department of Parasitology, BIOCEV, Charles University, Průmyslová, 595, Vestec, 25250, Czech Republic
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Mathieu-Rivet E, Mati-Baouche N, Walet-Balieu ML, Lerouge P, Bardor M. N- and O-Glycosylation Pathways in the Microalgae Polyphyletic Group. FRONTIERS IN PLANT SCIENCE 2020; 11:609993. [PMID: 33391324 PMCID: PMC7773692 DOI: 10.3389/fpls.2020.609993] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 11/23/2020] [Indexed: 05/15/2023]
Abstract
The term microalga refers to various unicellular and photosynthetic organisms representing a polyphyletic group. It gathers numerous species, which can be found in cyanobacteria (i.e., Arthrospira) as well as in distinct eukaryotic groups, such as Chlorophytes (i.e., Chlamydomonas or Chlorella) and Heterokonts (i.e., diatoms). This phylogenetic diversity results in an extraordinary variety of metabolic pathways, offering large possibilities for the production of natural compounds like pigments or lipids that can explain the ever-growing interest of industrials for these organisms since the middle of the last century. More recently, several species have received particular attention as biofactories for the production of recombinant proteins. Indeed, microalgae are easy to grow, safe and cheap making them attractive alternatives as heterologous expression systems. In this last scope of applications, the glycosylation capacity of these organisms must be considered as this post-translational modification of proteins impacts their structural and biological features. Although these mechanisms are well known in various Eukaryotes like mammals, plants or insects, only a few studies have been undertaken for the investigation of the protein glycosylation in microalgae. Recently, significant progresses have been made especially regarding protein N-glycosylation, while O-glycosylation remain poorly known. This review aims at summarizing the recent data in order to assess the state-of-the art knowledge in glycosylation processing in microalgae.
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Affiliation(s)
| | | | | | - Patrice Lerouge
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Muriel Bardor
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
- Unité de Glycobiologie Structurale et Fonctionnelle (UGSF), UMR 8576, CNRS, Université de Lille, Lille, France
- *Correspondence: Muriel Bardor,
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Wetherbee R, Rossetto Marcelino V, Costa JF, Grant B, Crawford S, Waller RF, Andersen RA, Berry D, McFadden GI, Verbruggen H. A new marine prasinophyte genus alternates between a flagellate and a dominant benthic stage with microrhizoids for adhesion. JOURNAL OF PHYCOLOGY 2019; 55:1210-1225. [PMID: 31393007 DOI: 10.1111/jpy.12909] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/29/2019] [Accepted: 06/13/2019] [Indexed: 06/10/2023]
Abstract
Prasinophytes (Chlorophyta) are a diverse, paraphyletic group of planktonic microalgae for which benthic species are largely unknown. Here, we report a sand-dwelling, marine prasinophyte with several novel features observed in clonal cultures established from numerous locations around Australia. The new genus and species, which we name Microrhizoidea pickettheapsiorum (Mamiellophyceae), alternates between a benthic palmelloid colony, where cell division occurs, and a planktonic flagellate. Flagellates are short lived, settle and quickly resorb their flagella, the basal bodies then nucleate novel tubular appendages, termed "microrhizoids", that lack an axoneme and function to anchor benthic cells to the substratum. To our knowledge, microrhizoids have not been observed in any other green alga or protist, are slightly smaller in diameter than flagella, generally contain nine microtubules, are long (3-5 times the length of flagella) and are not encased in scales. Following settlement, cell divisions result in a loose, palmelloid colony, each cell connected to the substratum by two microrhizoids. Flagellates are round to bean-shaped with two long, slightly uneven flagella. Both benthic cells and flagellates, along with their flagella, are encased in thin scales. Phylogenies based on the complete chloroplast genome of Microrhizoidea show that it is clearly a member of the Mamiellophyceae, most closely related to Dolichomastix tenuilepsis. More taxon-rich phylogenetic analyses of the 18S rRNA gene, including metabarcodes from the Tara Oceans and Ocean Sampling Day projects, confidently show the distinctive nature of Microrhizoidea, and that the described biodiversity of the Mamiellophyceae is a fraction of its real biodiversity. The discovery of a largely benthic prasinophyte changes our perspective on this group of algae and, along with the observation of other potential benthic lineages in environmental sequences, illustrates that benthic habitats can be a rich ground for algal biodiscovery.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Vanessa Rossetto Marcelino
- Westmead Institute for Medical Research, The University of Sydney, Westmead, New South Wales, 2145, Australia
| | - Joana F Costa
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Brenna Grant
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Simon Crawford
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Ross F Waller
- Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Robert A Andersen
- Friday Harbor Laboratories, University of Washington, Seattle, Washington, USA
| | - Drew Berry
- The Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, 3052, Australia
| | - Geoffrey I McFadden
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Parkville, Victoria, 3010, Australia
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Ponce-Toledo RI, López-García P, Moreira D. Horizontal and endosymbiotic gene transfer in early plastid evolution. THE NEW PHYTOLOGIST 2019; 224:618-624. [PMID: 31135958 PMCID: PMC6759420 DOI: 10.1111/nph.15965] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2018] [Accepted: 05/17/2019] [Indexed: 05/03/2023]
Abstract
Plastids evolved from a cyanobacterium that was engulfed by a heterotrophic eukaryotic host and became a stable organelle. Some of the resulting eukaryotic algae entered into a number of secondary endosymbioses with diverse eukaryotic hosts. These events had major consequences on the evolution and diversification of life on Earth. Although almost all plastid diversity derives from a single endosymbiotic event, the analysis of nuclear genomes of plastid-bearing lineages has revealed a mosaic origin of plastid-related genes. In addition to cyanobacterial genes, plastids recruited for their functioning eukaryotic proteins encoded by the host nucleus and also bacterial proteins of noncyanobacterial origin. Therefore, plastid proteins and plastid-localised metabolic pathways evolved by tinkering and using gene toolkits from different sources. This mixed heritage seems especially complex in secondary algae containing green plastids, the acquisition of which appears to have been facilitated by many previous acquisitions of red algal genes (the 'red carpet hypothesis').
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Affiliation(s)
- Rafael I Ponce-Toledo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Sud, AgroParisTech, Université Paris-Saclay, 91400, Orsay, France
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36
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Inwongwan S, Kruger NJ, Ratcliffe RG, O'Neill EC. Euglena Central Metabolic Pathways and Their Subcellular Locations. Metabolites 2019; 9:E115. [PMID: 31207935 PMCID: PMC6630311 DOI: 10.3390/metabo9060115] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/03/2019] [Accepted: 06/11/2019] [Indexed: 01/16/2023] Open
Abstract
Euglenids are a group of algae of great interest for biotechnology, with a large and complex metabolic capability. To study the metabolic network, it is necessary to know where the component enzymes are in the cell, but despite a long history of research into Euglena, the subcellular locations of many major pathways are only poorly defined. Euglena is phylogenetically distant from other commonly studied algae, they have secondary plastids bounded by three membranes, and they can survive after destruction of their plastids. These unusual features make it difficult to assume that the subcellular organization of the metabolic network will be equivalent to that of other photosynthetic organisms. We analysed bioinformatic, biochemical, and proteomic information from a variety of sources to assess the subcellular location of the enzymes of the central metabolic pathways, and we use these assignments to propose a model of the metabolic network of Euglena. Other than photosynthesis, all major pathways present in the chloroplast are also present elsewhere in the cell. Our model demonstrates how Euglena can synthesise all the metabolites required for growth from simple carbon inputs, and can survive in the absence of chloroplasts.
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Affiliation(s)
- Sahutchai Inwongwan
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Nicholas J Kruger
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - R George Ratcliffe
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
| | - Ellis C O'Neill
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK.
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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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Abstract
Over 100 whole-genome sequences from algae are published or soon to be published. The rapidly increasing availability of these fundamental resources is changing how we understand one of the most diverse, complex, and understudied groups of photosynthetic eukaryotes. Genome sequences provide a window into the functional potential of individual algae, with phylogenomics and functional genomics as tools for contextualizing and transferring knowledge from reference organisms into less well-characterized systems. Remarkably, over half of the proteins encoded by algal genomes are of unknown function, highlighting the volume of functional capabilities yet to be discovered. In this review, we provide an overview of publicly available algal genomes, their associated protein inventories, and their quality, with a summary of the statuses of protein function understanding and predictions.
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Affiliation(s)
| | - Sabeeha S Merchant
- Departments of Plant and Microbial Biology and Molecular and Cell Biology, University of California, Berkeley, California 94720, USA
- Institute for Genomics and Proteomics, University of California, Los Angeles, California 90095, USA
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Wetherbee R, Jackson CJ, Repetti SI, Clementson LA, Costa JF, van de Meene A, Crawford S, Verbruggen H. The golden paradox - a new heterokont lineage with chloroplasts surrounded by two membranes. JOURNAL OF PHYCOLOGY 2019; 55:257-278. [PMID: 30536815 DOI: 10.1111/jpy.12822] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Accepted: 10/23/2018] [Indexed: 06/09/2023]
Abstract
A marine, sand-dwelling, golden-brown alga is described from clonal cultures established from a high intertidal pool in southeastern Australia. This tiny, unicellular species, which we call the "golden paradox" (Chrysoparadoxa australica gen. et sp. nov.), is benthic, surrounded by a multilayered cell wall and attached to the substratum by a complex adhesive plug. Each vegetative cell gives rise to a single, naked zoospore with heterokont flagella that settles and may become briefly amoeboid prior to dividing. Daughter cells are initially amoeboid, then either permanently attach and return to the benthic stage or become motile again prior to final settlement. Two deeply lobed chloroplasts occupy opposite ends of the cell and are surrounded by only two membranes. The outer chloroplast membrane is continuous between the two chloroplasts via the outer membrane of the nuclear envelope. Only two membranes occupy the chloroplast-nucleus interface, the inner membrane of the nuclear envelope and the inner chloroplast membrane. A small pyrenoid is found in each chloroplast and closely abuts the nucleus or protrudes into it. It contains an unusual, membrane-bound inclusion that stains with SYBR green but is unlikely to be a nucleomorph. Phylogenies inferred from a 10-gene concatenated alignment show an early-branching position within the PX clade. The unusual morphological features and phylogenetic position indicate C. australica should be classified as a new class, Chrysoparadoxophyceae. Despite an atypical plastid, exploration of the C. australica transcriptome revealed typical heterokont protein targeting to the plastid.
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Affiliation(s)
- Richard Wetherbee
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Christopher J Jackson
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Sonja I Repetti
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | | | - Joana F Costa
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Allison van de Meene
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Simon Crawford
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
| | - Heroen Verbruggen
- School of BioSciences, University of Melbourne, Melbourne, Victoria, 3010, Australia
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40
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Ebenezer TE, Zoltner M, Burrell A, Nenarokova A, Novák Vanclová AMG, Prasad B, Soukal P, Santana-Molina C, O'Neill E, Nankissoor NN, Vadakedath N, Daiker V, Obado S, Silva-Pereira S, Jackson AP, Devos DP, Lukeš J, Lebert M, Vaughan S, Hampl V, Carrington M, Ginger ML, Dacks JB, Kelly S, Field MC. Transcriptome, proteome and draft genome of Euglena gracilis. BMC Biol 2019; 17:11. [PMID: 30732613 PMCID: PMC6366073 DOI: 10.1186/s12915-019-0626-8] [Citation(s) in RCA: 83] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2018] [Accepted: 01/08/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Photosynthetic euglenids are major contributors to fresh water ecosystems. Euglena gracilis in particular has noted metabolic flexibility, reflected by an ability to thrive in a range of harsh environments. E. gracilis has been a popular model organism and of considerable biotechnological interest, but the absence of a gene catalogue has hampered both basic research and translational efforts. RESULTS We report a detailed transcriptome and partial genome for E. gracilis Z1. The nuclear genome is estimated to be around 500 Mb in size, and the transcriptome encodes over 36,000 proteins and the genome possesses less than 1% coding sequence. Annotation of coding sequences indicates a highly sophisticated endomembrane system, RNA processing mechanisms and nuclear genome contributions from several photosynthetic lineages. Multiple gene families, including likely signal transduction components, have been massively expanded. Alterations in protein abundance are controlled post-transcriptionally between light and dark conditions, surprisingly similar to trypanosomatids. CONCLUSIONS Our data provide evidence that a range of photosynthetic eukaryotes contributed to the Euglena nuclear genome, evidence in support of the 'shopping bag' hypothesis for plastid acquisition. We also suggest that euglenids possess unique regulatory mechanisms for achieving extreme adaptability, through mechanisms of paralog expansion and gene acquisition.
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Affiliation(s)
- ThankGod E Ebenezer
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK.,Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Martin Zoltner
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK
| | - Alana Burrell
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Anna Nenarokova
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Anna M G Novák Vanclová
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Binod Prasad
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Petr Soukal
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Carlos Santana-Molina
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Ellis O'Neill
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK
| | - Nerissa N Nankissoor
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada
| | - Nithya Vadakedath
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Viktor Daiker
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Samson Obado
- Laboratory of Cellular and Structural Biology, The Rockefeller University, New York, NY, 10065, USA
| | - Sara Silva-Pereira
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Andrew P Jackson
- Department of Infection Biology, Institute of Infection and Global Health, University of Liverpool, Liverpool, UK
| | - Damien P Devos
- Centro Andaluz de Biología del Desarrollo (CABD)-CSIC, Pablo de Olavide University, Seville, Spain
| | - Julius Lukeš
- Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic
| | - Michael Lebert
- Cell Biology Division, Department of Biology, University of Erlangen-Nuremberg, 91058, Erlangen, Germany
| | - Sue Vaughan
- Department of Biological and Medical Sciences, Faculty of Health and Life Sciences, Oxford Brookes University, Oxford, OX3 0BP, UK
| | - Vladimίr Hampl
- Department of Parasitology, Faculty of Science,, Charles University, BIOCEV, 252 50, Vestec, Czech Republic
| | - Mark Carrington
- Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UK
| | - Michael L Ginger
- Department of Biological and Geographical Sciences, School of Applied Sciences, University of Huddersfield, Queensgate, Huddersfield, HD1 3DH, UK
| | - Joel B Dacks
- Division of Infectious Disease, Department of Medicine, University of Alberta, Edmonton, Alberta, T6G, Canada. .,Department of Life Sciences, The Natural History Museum, Cromwell Road, London, SW7 5BD, UK.
| | - Steven Kelly
- Department of Plant Sciences, University of Oxford, Oxford, OX1 3RB, UK.
| | - Mark C Field
- School of Life Sciences, University of Dundee, Dundee, DD1 5EH, UK. .,Biology Centre, Institute of Parasitology, Czech Academy of Sciences, and Faculty of Sciences, University of South Bohemia, 37005, České Budějovice, Czech Republic.
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Ševcíková T, Yurchenko T, Fawley KP, Amaral R, Strnad H, Santos LMA, Fawley MW, Eliáš M. Plastid Genomes and Proteins Illuminate the Evolution of Eustigmatophyte Algae and Their Bacterial Endosymbionts. Genome Biol Evol 2019; 11:362-379. [PMID: 30629162 PMCID: PMC6367104 DOI: 10.1093/gbe/evz004] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/05/2019] [Indexed: 12/26/2022] Open
Abstract
Eustigmatophytes, a class of stramenopile algae (ochrophytes), include not only the extensively studied biotechnologically important genus Nannochloropsis but also a rapidly expanding diversity of lineages with much less well characterized biology. Recent discoveries have led to exciting additions to our knowledge about eustigmatophytes. Some proved to harbor bacterial endosymbionts representing a novel genus, Candidatus Phycorickettsia, and an operon of unclear function (ebo) obtained by horizontal gene transfer from the endosymbiont lineage was found in the plastid genomes of still other eustigmatophytes. To shed more light on the latter event, as well as to generally improve our understanding of the eustigmatophyte evolutionary history, we sequenced plastid genomes of seven phylogenetically diverse representatives (including new isolates representing undescribed taxa). A phylogenomic analysis of plastid genome-encoded proteins resolved the phylogenetic relationships among the main eustigmatophyte lineages and provided a framework for the interpretation of plastid gene gains and losses in the group. The ebo operon gain was inferred to have probably occurred within the order Eustigmatales, after the divergence of the two basalmost lineages (a newly discovered hitherto undescribed strain and the Pseudellipsoidion group). When looking for nuclear genes potentially compensating for plastid gene losses, we noticed a gene for a plastid-targeted acyl carrier protein that was apparently acquired by horizontal gene transfer from Phycorickettsia. The presence of this gene in all eustigmatophytes studied, including representatives of both principal clades (Eustigmatales and Goniochloridales), is a genetic footprint indicating that the eustigmatophyte-Phycorickettsia partnership started no later than in the last eustigmatophyte common ancestor.
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Affiliation(s)
- Tereza Ševcíková
- Department of Biology and Ecology Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Tatiana Yurchenko
- Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Ostrava, Czech Republic
| | - Karen P Fawley
- Division of Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas
| | - Raquel Amaral
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Hynek Strnad
- Laboratory of Genomics and Bioinformatics, Institute of Molecular Genetics of the CAS, v.v.i., Prague, Czech Republic
| | - Lilia M A Santos
- Coimbra Collection of Algae (ACOI), Department of Life Sciences, University of Coimbra, Coimbra, Portugal
| | - Marvin W Fawley
- Division of Sciences and Mathematics, University of the Ozarks, Clarksville, Arkansas.,School of Mathematical and Natural Sciences, University of Arkansas at Monticello, Monticello, Arkansas
| | - Marek Eliáš
- Department of Biology and Ecology Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Faculty of Science, Institute of Environmental Technologies, University of Ostrava, Ostrava, Czech Republic
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42
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Graham LE. Digging deeper: why we need more Proterozoic algal fossils and how to get them. JOURNAL OF PHYCOLOGY 2019; 55:1-6. [PMID: 30270424 DOI: 10.1111/jpy.12790] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/09/2018] [Accepted: 09/24/2018] [Indexed: 06/08/2023]
Abstract
Known Proterozoic algal fossils raise compelling questions about the origin and diversification of cyanobacteria and eukaryotic algae, and their ecological influence in deep time. This Perspectives article describes particular examples of persistent evolutionary and biogeochemical issues whose resolution would be aided by additional algal fossil evidence from Proterozoic deposits, which have been the subjects of recent intensive study. New Proterozoic geosciences literature relevant to the early diversification of algae is surveyed. Previously underappreciated algal traits that might improve taxonomic attributions of fossil remains are highlighted. Processes that phycologists could use to improve detection of algal fossils are recommended. Potential geological sources of new Proterozoic fossils are suggested.
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Affiliation(s)
- Linda E Graham
- Department of Botany, University of Wisconsin-Madison, 430 Lincoln Drive, Madison, Wisconsin, 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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Peculiar features of the plastids of the colourless alga Euglena longa and photosynthetic euglenophytes unveiled by transcriptome analyses. Sci Rep 2018; 8:17012. [PMID: 30451959 PMCID: PMC6242988 DOI: 10.1038/s41598-018-35389-1] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 11/02/2018] [Indexed: 12/17/2022] Open
Abstract
Euglenophytes are a familiar algal group with green alga-derived secondary plastids, but the knowledge of euglenophyte plastid function and evolution is still highly incomplete. With this in mind we sequenced and analysed the transcriptome of the non-photosynthetic species Euglena longa. The transcriptomic data confirmed the absence of genes for the photosynthetic machinery, but provided candidate plastid-localised proteins bearing N-terminal bipartite topogenic signals (BTSs) of the characteristic euglenophyte type. Further comparative analyses including transcriptome assemblies available for photosynthetic euglenophytes enabled us to unveil salient aspects of the basic euglenophyte plastid infrastructure, such as plastidial targeting of several proteins as C-terminal translational fusions with other BTS-bearing proteins or replacement of the conventional eubacteria-derived plastidial ribosomal protein L24 by homologs of archaeo-eukaryotic origin. Strikingly, no homologs of any key component of the TOC/TIC system and the plastid division apparatus are discernible in euglenophytes, and the machinery for intraplastidial protein targeting has been simplified by the loss of the cpSRP/cpFtsY system and the SEC2 translocon. Lastly, euglenophytes proved to encode a plastid-targeted homolog of the termination factor Rho horizontally acquired from a Lambdaproteobacteria-related donor. Our study thus further documents a substantial remodelling of the euglenophyte plastid compared to its green algal progenitor.
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Matsuo E, Inagaki Y. Patterns in evolutionary origins of heme, chlorophyll a and isopentenyl diphosphate biosynthetic pathways suggest non-photosynthetic periods prior to plastid replacements in dinoflagellates. PeerJ 2018; 6:e5345. [PMID: 30083465 PMCID: PMC6078071 DOI: 10.7717/peerj.5345] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2017] [Accepted: 07/03/2018] [Indexed: 11/20/2022] Open
Abstract
Background The ancestral dinoflagellate most likely established a peridinin-containing plastid, which have been inherited in the extant photosynthetic descendants. However, kareniacean dinoflagellates and Lepidodinium species were known to bear “non-canonical” plastids lacking peridinin, which were established through haptophyte and green algal endosymbioses, respectively. For plastid function and maintenance, the aforementioned dinoflagellates were known to use nucleus-encoded proteins vertically inherited from the ancestral dinoflagellates (vertically inherited- or VI-type), and those acquired from non-dinoflagellate organisms (including the endosymbiont). These observations indicated that the proteomes of the non-canonical plastids derived from a haptophyte and a green alga were modified by “exogenous” genes acquired from non-dinoflagellate organisms. However, there was no systematic evaluation addressing how “exogenous” genes reshaped individual metabolic pathways localized in a non-canonical plastid. Results In this study, we surveyed transcriptomic data from two kareniacean species (Karenia brevis and Karlodinium veneficum) and Lepidodinium chlorophorum, and identified proteins involved in three plastid metabolic pathways synthesizing chlorophyll a (Chl a), heme and isoprene. The origins of the individual proteins of our interest were investigated, and we assessed how the three pathways were modified before and after the algal endosymbioses, which gave rise to the current non-canonical plastids. We observed a clear difference in the contribution of VI-type proteins across the three pathways. In both Karenia/Karlodinium and Lepidodinium, we observed a substantial contribution of VI-type proteins to the isoprene and heme biosynthesises. In sharp contrast, VI-type protein was barely detected in the Chl a biosynthesis in the three dinoflagellates. Discussion Pioneering works hypothesized that the ancestral kareniacean species had lost the photosynthetic activity prior to haptophyte endosymbiosis. The absence of VI-type proteins in the Chl a biosynthetic pathway in Karenia or Karlodinium is in good agreement with the putative non-photosynthetic nature proposed for their ancestor. The dominance of proteins with haptophyte origin in the Karenia/Karlodinium pathway suggests that their ancestor rebuilt the particular pathway by genes acquired from the endosymbiont. Likewise, we here propose that the ancestral Lepidodinium likely experienced a non-photosynthetic period and discarded the entire Chl a biosynthetic pathway prior to the green algal endosymbiosis. Nevertheless, Lepidodinium rebuilt the pathway by genes transferred from phylogenetically diverse organisms, rather than the green algal endosymbiont. We explore the reasons why green algal genes were barely utilized to reconstruct the Lepidodinium pathway.
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Affiliation(s)
- Eriko Matsuo
- Graduate School of Biological and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Yuji Inagaki
- Graduate School of Biological and Environmental Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan.,Center for Computational Sciences, University of Tsukuba, Tsukuba, Ibaraki, Japan
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Yubuki N, Leander BS. Diversity and Evolutionary History of the Symbiontida (Euglenozoa). Front Ecol Evol 2018. [DOI: 10.3389/fevo.2018.00100] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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