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Jiang Y, Cao T, Yang Y, Zhang H, Zhang J, Li X. A chlorophyll c synthase widely co-opted by phytoplankton. Science 2023; 382:92-98. [PMID: 37797009 DOI: 10.1126/science.adg7921] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 08/30/2023] [Indexed: 10/07/2023]
Abstract
Marine and terrestrial photosynthesis exhibit a schism in the accessory chlorophyll (Chl) that complements the function of Chl a: Chl b for green plants versus Chl c for most eukaryotic phytoplankton. The enzymes that mediate Chl c biosynthesis have long remained elusive. In this work, we identified the CHLC dioxygenase (Phatr3_J43737) from the marine diatom Phaeodactylum tricornutum as the Chl c synthase. The chlc mutants lacked Chl c, instead accumulating its precursors, and exhibited growth defects. In vitro, recombinant CHLC protein converted these precursors into Chl c, thereby confirming its identity. Phylogenetic evidence demonstrates conserved use of CHLC across phyla but also the existence of distinct Chl c synthases in different algal groups. Our study addresses a long-outstanding question with implications for both contemporary and ancient marine photosynthesis.
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Affiliation(s)
- Yanyou Jiang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Tianjun Cao
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Yuqing Yang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Huan Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
| | - Jingyu Zhang
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
| | - Xiaobo Li
- Research Center for Industries of the Future, Key Laboratory of Growth Regulation and Translational Research of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Biology, Westlake Institute for Advanced Study, Hangzhou, China
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Pérez-Burillo J, Valoti G, Witkowski A, Prado P, Mann DG, Trobajo R. Assessment of marine benthic diatom communities: insights from a combined morphological-metabarcoding approach in Mediterranean shallow coastal waters. MARINE POLLUTION BULLETIN 2022; 174:113183. [PMID: 35090287 DOI: 10.1016/j.marpolbul.2021.113183] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 11/16/2021] [Accepted: 11/20/2021] [Indexed: 06/14/2023]
Abstract
We investigated the advantages and disadvantages of light microscope (LM)-based identifications and DNA metabarcoding, based on a 312-bp rbcL marker, for examining benthic diatom communities from Mediterranean shallow coastal environments. For this, we used biofilm samples collected from different substrata in the Ebro delta bays. We show that 1) Ebro delta bays harbour high-diversity diatom communities [LM identified 249 taxa] and 2) DNA metabarcoding effectively reflects this diversity at genus- but not species level, because of the incompleteness of the DNA reference library. Nevertheless, DNA metabarcoding offers new opportunities for detecting small, delicate and rare diatom species missed by LM and diatoms that lack silica frustules. The primers used, though designed for diatoms, successfully amplified rarely reported members of other stramenopile groups. Combining LM and DNA approaches offers stronger support for ecological studies of benthic microalgal communities in shallow coastal environments than using either approach on its own.
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Affiliation(s)
- Javier Pérez-Burillo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Departament de Geografia, Universitat Rovira i Virgili, C/ Joanot Martorell 15, E43500 Vila-seca, Tarragona, Spain
| | - Greta Valoti
- Università Politecnica delle Marche, Piazza Roma, 22, IT60131 Ancona, Italy
| | - Andrzej Witkowski
- Institute of Marine and Environmental Sciences, University of Szczecin, Mickiewicza 16a, 70-383 Szczecin, Poland
| | - Patricia Prado
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain
| | - David G Mann
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain; Royal Botanic Garden Edinburgh, Edinburgh EH3 5LR, Scotland, UK
| | - Rosa Trobajo
- IRTA-Institute for Food and Agricultural Research and Technology, Marine and Continental Waters Programme, Ctra de Poble Nou Km 5.5, E43540 Sant Carles de la Ràpita, Tarragona, Spain.
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Raven JA, Giordano M. Acquisition and metabolism of carbon in the Ochrophyta other than diatoms. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160400. [PMID: 28717026 PMCID: PMC5516109 DOI: 10.1098/rstb.2016.0400] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/09/2017] [Indexed: 11/12/2022] Open
Abstract
The acquisition and assimilation of inorganic C have been investigated in several of the 15 clades of the Ochrophyta other than diatoms, with biochemical, physiological and genomic data indicating significant mechanistic variation. Form ID Rubiscos in the Ochrophyta are characterized by a broad range of kinetics values. In spite of relatively high K0.5CO2 and low CO2 : O2 selectivity, diffusive entry of CO2 occurs in the Chrysophyceae and Synurophyceae. Eustigmatophyceae and Phaeophyceae, on the contrary, have CO2 concentrating mechanisms, usually involving the direct or indirect use of [Formula: see text] This variability is possibly due to the ecological contexts of the organism. In brown algae, C fixation generally takes place through a classical C3 metabolism, but there are some hints of the occurrence of C4 metabolism and low amplitude CAM in a few members of the Fucales. Genomic data show the presence of a number of potential C4 and CAM genes in Ochrophyta other than diatoms, but the other core functions of many of these genes give a very limited diagnostic value to their presence and are insufficient to conclude that C4 photosynthesis is present in these algae.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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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
- Climate Change Cluster, University of Technology Sydney, Ultimo, New South Wales 2007, Australia
| | - Mario Giordano
- Dipartimento di Scienze della Vita e dell'Ambiente, Università Politecnica delle Marche, Ancona 60131, Italy
- Institute of Microbiology, Academy of Sciences of the Czech Republic, Trěboň 37901, Czech Republic
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Derelle R, López-García P, Timpano H, Moreira D. A Phylogenomic Framework to Study the Diversity and Evolution of Stramenopiles (=Heterokonts). Mol Biol Evol 2016; 33:2890-2898. [PMID: 27512113 DOI: 10.1093/molbev/msw168] [Citation(s) in RCA: 82] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Stramenopiles or heterokonts constitute one of the most speciose and diverse clades of protists. It includes ecologically important algae (such as diatoms or large multicellular brown seaweeds), as well as heterotrophic (e.g., bicosoecids, MAST groups) and parasitic (e.g., Blastocystis, oomycetes) species. Despite their evolutionary and ecological relevance, deep phylogenetic relationships among stramenopile groups, inferred mostly from small-subunit rDNA phylogenies, remain unresolved, especially for the heterotrophic taxa. Taking advantage of recently released stramenopile transcriptome and genome sequences, as well as data from the genomic assembly of the MAST-3 species Incisomonas marina generated in our laboratory, we have carried out the first extensive phylogenomic analysis of stramenopiles, including representatives of most major lineages. Our analyses, based on a large data set of 339 widely distributed proteins, strongly support a root of stramenopiles lying between two clades, Bigyra and Gyrista (Pseudofungi plus Ochrophyta). Additionally, our analyses challenge the Phaeista-Khakista dichotomy of photosynthetic stramenopiles (ochrophytes) as two groups previously considered to be part of the Phaeista (Pelagophyceae and Dictyochophyceae), branch with strong support with the Khakista (Bolidophyceae and Diatomeae). We propose a new classification of ochrophytes within the two groups Chrysista and Diatomista to reflect the new phylogenomic results. Our stramenopile phylogeny provides a robust phylogenetic framework to investigate the evolution and diversification of this group of ecologically relevant protists.
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Affiliation(s)
- Romain Derelle
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-García
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - Hélène Timpano
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
| | - David Moreira
- Unité d'Ecologie, Systématique et Evolution, Centre National de la Recherche Scientifique (CNRS), Université Paris-Sud/Paris-Saclay, AgroParisTech, Orsay, France
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A paneukaryotic genomic analysis of the small GTPase RABL2 underscores the significance of recurrent gene loss in eukaryote evolution. Biol Direct 2016; 11:5. [PMID: 26832778 PMCID: PMC4736243 DOI: 10.1186/s13062-016-0107-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/27/2016] [Indexed: 12/30/2022] Open
Abstract
Background The cilium (flagellum) is a complex cellular structure inherited from the last eukaryotic common ancestor (LECA). A large number of ciliary proteins have been characterized in a few model organisms, but their evolutionary history often remains unexplored. One such protein is the small GTPase RABL2, recently implicated in the assembly of the sperm tail in mammals. Results Using the wealth of currently available genome and transcriptome sequences, including data from our on-going sequencing projects, we systematically analyzed the phylogenetic distribution and evolutionary history of RABL2 orthologs. Our dense taxonomic sampling revealed the presence of RABL2 genes in nearly all major eukaryotic lineages, including small “obscure” taxa such as breviates, ancyromonads, malawimonads, jakobids, picozoans, or palpitomonads. The phyletic pattern of RABL2 genes indicates that it was present already in the LECA. However, some organisms lack RABL2 as a result of secondary loss and our present sampling predicts well over 30 such independent events during the eukaryote evolution. The distribution of RABL2 genes correlates with the presence/absence of cilia: not a single well-established cilium-lacking species has retained a RABL2 ortholog. However, several ciliated taxa, most notably nematodes, some arthropods and platyhelminths, diplomonads, and ciliated subgroups of apicomplexans and embryophytes, lack RABL2 as well, suggesting some simplification in their cilium-associated functions. On the other hand, several algae currently unknown to form cilia, e.g., the “prasinophytes” of the genus Prasinoderma or the ochrophytes Pelagococcus subviridis and Pinguiococcus pyrenoidosus, turned out to encode not only RABL2, but also homologs of some hallmark ciliary proteins, suggesting the existence of a cryptic flagellated stage in their life cycles. We additionally obtained insights into the evolution of the RABL2 gene architecture, which seems to have ancestrally consisted of eight exons subsequently modified not only by lineage-specific intron loss and gain, but also by recurrent loss of the terminal exon encoding a poorly conserved C-terminal extension. Conclusions Our comparative analysis supports the notion that RABL2 is an ancestral component of the eukaryotic cilium and underscores the still underappreciated magnitude of recurrent gene loss, or reductive evolution in general, in the history of eukaryotic genomes and cells. Reviewers This article was reviewed by Berend Snel and James O. McInerney. Electronic supplementary material The online version of this article (doi:10.1186/s13062-016-0107-8) contains supplementary material, which is available to authorized users.
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Schmidt M, Horn S, Ehlers K, Wilhelm C, Schnetter R. Guanchochroma wildpretii gen. et spec. nov. (Ochrophyta) Provides New Insights into the Diversification and Evolution of the Algal Class Synchromophyceae. PLoS One 2015; 10:e0131821. [PMID: 26135124 PMCID: PMC4489749 DOI: 10.1371/journal.pone.0131821] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Accepted: 06/06/2015] [Indexed: 12/04/2022] Open
Abstract
A new relative of the chrysophyte genus Chrysopodocystis was found in Tenerife and termed Guanchochroma wildpretii. This unicellular alga was most noticeably discernible from Chrysopodocystis socialis (the only species of this genus) by the presence of a cyst-like stage with a multilayered lorica, which also functions as a dispersal unit and shows secondary wall growth. Secondary expansion of loricae (cell casings not involved in cell division, usually with a more or less pronounced opening) has never been observed previously and marks a unique feature of the new taxon. Plastids are non-randomly distributed within cells of G. wildpretii. 18S rRNA gene analyses identified the two species as sister lineages and placed them in a monophyletic group with the Synchromophyceae, a heterokont algal (Ochrophyta) class characterized by the presence of chloroplast complexes. Yet, neither Chrysopodocystis nor Guanchochroma showed this feature in ultrastructure analyses. Additionally, their 18S rRNA genes possessed distinct inserts, the highest GC-content known for Ochrophyta and exceptionally long branches on the Ochrophyta 18S rDNA phylogenetic tree, suggesting substantially increased substitution rates along their branch compared to Synchromophyceae. Plastid marker data (rbcL) recovered a monophyletic clade of Chrysopodocystis, Guanchochroma and Synchromophyceae as well, yet with lower supports for internal split order due to limited resolution of the marker. Evidence for the sequence of events leading to the formation of the plastid complex of Synchromophyceae still remains ambiguous because of the apparently short timeframe in which they occurred.
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Affiliation(s)
- Maria Schmidt
- Universität Leipzig, Department of Plant Physiology, Johannisallee 21–23, 04103 Leipzig, Germany
- * E-mail:
| | - Susanne Horn
- Universitätsklinikum Essen, Klinik für Dermatologie, Forschungslabor, Hufelandstr. 55, 45447 Essen, Germany
| | - Katrin Ehlers
- Justus-Liebig-Universität Gießen, Institut für Botanik, Heinrich-Buff-Ring 38, 35392 Giessen, Germany
| | - Christian Wilhelm
- Universität Leipzig, Department of Plant Physiology, Johannisallee 21–23, 04103 Leipzig, Germany
| | - Reinhard Schnetter
- Justus-Liebig-Universität Gießen, Institut für Botanik, Heinrich-Buff-Ring 38, 35392 Giessen, Germany
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