1
|
Lipinska AP, Krueger-Hadfield SA, Godfroy O, Dittami S, Ayres-Ostrock L, Bonthond G, Brillet-Guéguen L, Coelho S, Corre E, Cossard G, Destombe C, Epperlein P, Faugeron S, Ficko-Blean E, Beltrán J, Lavaut E, Le Bars A, Marchi F, Mauger S, Michel G, Potin P, Scornet D, Sotka EE, Weinberger F, de Oliveira MC, Guillemin ML, Plastino EM, Valero M. The Rhodoexplorer Platform for Red Algal Genomics and Whole Genome Assemblies for Several Gracilaria Species. Genome Biol Evol 2023:evad124. [PMID: 37481260 PMCID: PMC10388701 DOI: 10.1093/gbe/evad124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/24/2023] Open
Abstract
Macroalgal (seaweed) genomic resources are generally lacking as compared to other eukaryotic taxa, and this is particularly true in the red algae (Rhodophyta). Understanding red algal genomes is critical to understanding eukaryotic evolution given that red algal genes are spread across eukaryotic lineages from secondary endosymbiosis and red algae diverged early in the Archaeplastids. The Gracilariales is a highly diverse and widely distributed order including species that can serve as ecosystem engineers in intertidal habitats and several notorious introduced species. The genus Gracilaria is cultivated worldwide, in part for its production of agar and other bioactive compounds with downstream pharmaceutical and industrial applications. This genus is also emerging as a model for algal evolutionary ecology. Here, we report new whole genome assemblies for two species (G. chilensis and G. gracilis), a draft genome assembly of G. caudata, and genome annotation of the previously published G. vermiculophylla genome. To facilitate accessibility and comparative analysis, we integrated these data in a newly created web-based portal dedicated to red algal genomics (https://rhodoexplorer.sb-roscoff.fr). These genomes will provide a resource for understanding algal biology and, more broadly, eukaryotic evolution.
Collapse
Affiliation(s)
- Agnieszka P Lipinska
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Stacy A Krueger-Hadfield
- Department of Biology, University of Alabama at Birmingham, 1300 University Blvd, Birmingham, AL, 35294, USA
| | - Olivier Godfroy
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Simon Dittami
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Lígia Ayres-Ostrock
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
- Hortimare - Breeding & Propagating Seaweed. Altonstraat 25A 1704 CC Heerhugowaard. The Netherlands
| | - Guido Bonthond
- Institute for Chemistry and Biology of the Marine Environment (ICBM), Carl von Ossietzky University Oldenburg, Schleusenstrasse 1, 26382, Wilhelmshaven, Germany
| | - Loraine Brillet-Guéguen
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
| | - Susana Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Erwan Corre
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
| | - Guillaume Cossard
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Christophe Destombe
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Paul Epperlein
- Department of Algal Development and Evolution, Max Planck Institute for Biology Tubingen, Tubingen, Germany
| | - Sylvain Faugeron
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Elizabeth Ficko-Blean
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Jessica Beltrán
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Emma Lavaut
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Arthur Le Bars
- CNRS, Sorbonne Université, FR2424, ABiMS-IFB, Station Biologique, 29680, Roscoff, France
- CNRS, Institut Français de Bioinformatique, IFB-core, UMS 3601, Évry, France
| | - Fabiana Marchi
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Stéphane Mauger
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| | - Gurvan Michel
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Philippe Potin
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Delphine Scornet
- Sorbonne Université, CNRS, UMR 8227, Laboratory of Integrative Biology of Marine Models, Station Biologique de Roscoff, Roscoff, France
| | - Erik E Sotka
- Department of Biology, College of Charleston, Charleston SC 29412
| | - Florian Weinberger
- GEOMAR Helmholtz-Zentrum für Ozeanforschung, Marine Ecology Division, Düsternbrooker Weg 20, 24105 Kiel, Germany
| | - Mariana Cabral de Oliveira
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Marie-Laure Guillemin
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
- Núcleo Milenio MASH, Facultad de Ciencias, Instituto de Ciencias Ambientales y Evolutivas, Universidad Austral de Chile, Casilla 567, Valdivia, Chile
- Centro FONDAP de Investigación de Ecosistemas Marinos de Altas Latitudes (IDEAL), Valdivia, Chile
| | - Estela M Plastino
- Departamento de Botânica, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, Cidade Universitária 05508-090, São Paulo, SP, Brasil
| | - Myriam Valero
- CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, IRL 3614, Evolutionary Biology and Ecology of Algae, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France
| |
Collapse
|
2
|
Godfroy O, Zheng M, Yao H, Henschen A, Peters AF, Scornet D, Colin S, Ronchi P, Hipp K, Nagasato C, Motomura T, Cock JM, Coelho SM. The baseless mutant links protein phosphatase 2A with basal cell identity in the brown alga Ectocarpus. Development 2023; 150:dev201283. [PMID: 36786333 PMCID: PMC10112911 DOI: 10.1242/dev.201283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/16/2023] [Indexed: 02/15/2023]
Abstract
The first mitotic division of the initial cell is a key event in all multicellular organisms and is associated with the establishment of major developmental axes and cell fates. The brown alga Ectocarpus has a haploid-diploid life cycle that involves the development of two multicellular generations: the sporophyte and the gametophyte. Each generation deploys a distinct developmental programme autonomously from an initial cell, the first cell division of which sets up the future body pattern. Here, we show that mutations in the BASELESS (BAS) gene result in multiple cellular defects during the first cell division and subsequent failure to produce basal structures during both generations. BAS encodes a type B″ regulatory subunit of protein phosphatase 2A (PP2A), and transcriptomic analysis identified potential effector genes that may be involved in determining basal cell fate. The bas mutant phenotype is very similar to that observed in distag (dis) mutants, which lack a functional Tubulin-binding co-factor Cd1 (TBCCd1) protein, indicating that TBCCd1 and PP2A are two essential components of the cellular machinery that regulates the first cell division and mediates basal cell fate determination.
Collapse
Affiliation(s)
- Olivier Godfroy
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Min Zheng
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Haiqin Yao
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Agnes Henschen
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | | | - Delphine Scornet
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Sebastien Colin
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Paolo Ronchi
- Electron Microscopy Core Facility, European Molecular Biology Laboratory, 69117 Heidelberg, Germany
| | - Katharina Hipp
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - J. Mark Cock
- Laboratory of Integrative Biology of Marine Models, Sorbonne Université, UPMC University of Paris 06, CNRS, UMR 8227, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M. Coelho
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany
| |
Collapse
|
3
|
Bourdareau S, Godfroy O, Gueno J, Scornet D, Coelho SM, Tirichine L, Cock JM. An Efficient Chromatin Immunoprecipitation Protocol for the Analysis of Histone Modification Distributions in the Brown Alga Ectocarpus. Methods Protoc 2022; 5:mps5030036. [PMID: 35645344 PMCID: PMC9149930 DOI: 10.3390/mps5030036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2022] [Revised: 04/19/2022] [Accepted: 04/20/2022] [Indexed: 11/16/2022] Open
Abstract
The brown algae are an important but understudied group of multicellular marine organisms. A number of genetic and genomic tools have been developed for the model brown alga Ectocarpus; this includes, most recently, chromatin immunoprecipitation methodology, which allows genome-wide detection and analysis of histone post-translational modifications. Post-translational modifications of histone molecules have been shown to play an important role in gene regulation in organisms from other major eukaryotic lineages, and this methodology will therefore be a very useful tool to investigate genome function in the brown algae. This article provides a detailed, step-by-step description of the Ectocarpus ChIP protocol, which effectively addresses the difficult problem of efficiently extracting chromatin from cells protected by a highly resistant cell wall. The protocol described here will be an essential tool for the future application of chromatin analysis methodologies in brown algal research.
Collapse
Affiliation(s)
- Simon Bourdareau
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Olivier Godfroy
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Josselin Gueno
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Delphine Scornet
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Susana M. Coelho
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
| | - Leila Tirichine
- Nantes Université, CNRS, US2B, UMR 6286, F-44000 Nantes, France
- Correspondence: (L.T.); (J.M.C.); Tel.: +33-2-98-29-23-60 (J.M.C.)
| | - J. Mark Cock
- Algal Genetics Group, Integrative Biology of Marine Models Laboratory, CNRS, Sorbonne Université, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff, France; (S.B.); (O.G.); (J.G.); (D.S.); (S.M.C.)
- Correspondence: (L.T.); (J.M.C.); Tel.: +33-2-98-29-23-60 (J.M.C.)
| |
Collapse
|
4
|
Badis Y, Scornet D, Harada M, Caillard C, Godfroy O, Raphalen M, Gachon CMM, Coelho SM, Motomura T, Nagasato C, Cock JM. Targeted CRISPR-Cas9-based gene knockouts in the model brown alga Ectocarpus. New Phytol 2021; 231:2077-2091. [PMID: 34076889 DOI: 10.1111/nph.17525] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Accepted: 05/20/2021] [Indexed: 06/12/2023]
Abstract
Brown algae are an important group of multicellular eukaryotes, phylogenetically distinct from both the animal and land plant lineages. Ectocarpus has emerged as a model organism to study diverse aspects of brown algal biology, but this system currently lacks an effective reverse genetics methodology to analyse the functions of selected target genes. Here, we report that mutations at specific target sites are generated following the introduction of CRISPR-Cas9 ribonucleoproteins into Ectocarpus cells, using either biolistics or microinjection as the delivery method. Individuals with mutations affecting the ADENINE PHOSPHORIBOSYL TRANSFERASE (APT) gene were isolated following treatment with 2-fluoroadenine, and this selection system was used to isolate individuals in which mutations had been introduced simultaneously at APT and at a second gene. This double mutation approach could potentially be used to isolate mutants affecting any Ectocarpus gene, providing an effective reverse genetics tool for this model organism. The availability of this tool will significantly enhance the utility of Ectocarpus as a model organism for this ecologically and economically important group of marine organisms. Moreover, the methodology described here should be readily transferable to other brown algal species.
Collapse
Affiliation(s)
- Yacine Badis
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll,, PA37 1QA, UK
| | - Delphine Scornet
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Minori Harada
- Graduate School of Environmental Science, Hokkaido University, Sapporo, 060-0810, Japan
| | - Céline Caillard
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Olivier Godfroy
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Morgane Raphalen
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| | - Claire M M Gachon
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll,, PA37 1QA, UK
- UMR 7245 Molécules de Communication et Adaptation des Micro-organismes, Muséum National d'Histoire Naturelle, CP 54, 57 rue Cuvier, Paris, 75005, France
| | - Susana M Coelho
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
- Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, Tübingen, 72076, Germany
| | - Taizo Motomura
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran, 051-0013, Japan
| | - J Mark Cock
- Roscoff Biological Station, Place Georges Teissier, Roscoff, 29680, France
| |
Collapse
|
5
|
Yao H, Scornet D, Jam M, Hervé C, Potin P, Oliveira Correia L, Coelho SM, Cock JM. Biochemical characteristics of a diffusible factor that induces gametophyte to sporophyte switching in the brown alga Ectocarpus. J Phycol 2021; 57:742-753. [PMID: 33432598 DOI: 10.1111/jpy.13126] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 11/16/2020] [Accepted: 11/16/2020] [Indexed: 06/12/2023]
Abstract
The haploid-diploid life cycle of the filamentous brown alga Ectocarpus involves alternation between two independent and morphologically distinct multicellular generations, the sporophyte and the gametophyte. Deployment of the sporophyte developmental program requires two TALE homeodomain transcription factors OUROBOROS and SAMSARA. In addition, the sporophyte generation has been shown to secrete a diffusible factor that can induce uni-spores to switch from the gametophyte to the sporophyte developmental program. Here, we determine optimal conditions for production, storage, and detection of this diffusible factor and show that it is a heat-resistant, high molecular weight molecule. Based on a combined approach involving proteomic analysis of sporophyte-conditioned medium and the use of biochemical tools to characterize arabinogalactan proteins, we present evidence that sporophyte-conditioned medium contains AGP epitopes and suggest that the diffusible factor may belong to this family of glycoproteins.
Collapse
Affiliation(s)
- Haiqin Yao
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Delphine Scornet
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Murielle Jam
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
- Marine Glycobiology, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
| | - Cécile Hervé
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
- Marine Glycobiology, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
| | - Philippe Potin
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
- Algal Biology and Environmental Interactions, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
| | - Lydie Oliveira Correia
- PAPPSO, INRA, AgroParisTech, Micalis Institute, Université Paris-Saclay, 78350, Jouy-en-Josas, France
| | - Susana M Coelho
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - J Mark Cock
- Algal Genetics Group, UMR 8227, CNRS, Sorbonne Université, UPMC University Paris 06, Paris, France
- Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| |
Collapse
|
6
|
Bourdareau S, Tirichine L, Lombard B, Loew D, Scornet D, Wu Y, Coelho SM, Cock JM. Histone modifications during the life cycle of the brown alga Ectocarpus. Genome Biol 2021; 22:12. [PMID: 33397407 PMCID: PMC7784034 DOI: 10.1186/s13059-020-02216-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2020] [Accepted: 12/02/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Brown algae evolved complex multicellularity independently of the animal and land plant lineages and are the third most developmentally complex phylogenetic group on the planet. An understanding of developmental processes in this group is expected to provide important insights into the evolutionary events necessary for the emergence of complex multicellularity. Here, we focus on mechanisms of epigenetic regulation involving post-translational modifications of histone proteins. RESULTS A total of 47 histone post-translational modifications are identified, including a novel mark H2AZR38me1, but Ectocarpus lacks both H3K27me3 and the major polycomb complexes. ChIP-seq identifies modifications associated with transcription start sites and gene bodies of active genes and with transposons. H3K79me2 exhibits an unusual pattern, often marking large genomic regions spanning several genes. Transcription start sites of closely spaced, divergently transcribed gene pairs share a common nucleosome-depleted region and exhibit shared histone modification peaks. Overall, patterns of histone modifications are stable through the life cycle. Analysis of histone modifications at generation-biased genes identifies a correlation between the presence of specific chromatin marks and the level of gene expression. CONCLUSIONS The overview of histone post-translational modifications in the brown alga presented here will provide a foundation for future studies aimed at understanding the role of chromatin modifications in the regulation of brown algal genomes.
Collapse
Affiliation(s)
- Simon Bourdareau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Leila Tirichine
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Bérangère Lombard
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Damarys Loew
- Institut Curie, PSL Research University, Centre de Recherche, Laboratoire de Spectrométrie de Masse Protéomique, 26 rue d'Ulm, 75248, Paris, Cedex 05, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yue Wu
- Université de Nantes, CNRS, UFIP, UMR 6286, F-44000, Nantes, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
- Current address: Max Planck Institute for Developmental Biology, Max-Planck-Ring 5, 72076, Tübingen, Germany.
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.
| |
Collapse
|
7
|
Yao H, Scornet D, Badis Y, Peters AF, Jam M, Hervé C, Potin P, Coelho SM, Cock JM. Production and Bioassay of a Diffusible Factor That Induces Gametophyte-to-Sporophyte Developmental Reprogramming in the Brown Alga Ectocarpus. Bio Protoc 2020; 10:e3753. [PMID: 33659412 DOI: 10.21769/bioprotoc.3753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Revised: 07/13/2020] [Accepted: 07/29/2020] [Indexed: 11/02/2022] Open
Abstract
The brown alga Ectocarpus has a haploid-diploid life cycle that involves alternation between two multicellular generations, the sporophyte and the gametophyte. Life cycle generation is not determined by ploidy but by a genetic system that includes two different three amino acid loop extension homeodomain transcription factors called OUROBOROS and SAMSARA. In addition, sporophytes have been shown to secrete a diffusible factor into the medium that can induce gametophyte initial cells to switch from the gametophyte to the sporophyte developmental program. The protocol presented here describes how to produce sporophyte-conditioned medium containing the diffusible sporophyte-inducing factor and how to assay for activity of the factor using a meio-spore-based bioassay. The protocol, which describes how several steps of these procedures can be optimised, will represent a useful tool for future work aimed at characterising the diffusible factor and investigating its mode of action.
Collapse
Affiliation(s)
- Haiqin Yao
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Yacine Badis
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France.,The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll PA37 1QA, United Kingdom
| | | | - Murielle Jam
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Cécile Hervé
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Philippe Potin
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688, Roscoff, France
| |
Collapse
|
8
|
Mignerot L, Nagasato C, Peters AF, Perrineau MM, Scornet D, Pontheaux F, Djema W, Badis Y, Motomura T, Coelho SM, Cock JM. Unusual Patterns of Mitochondrial Inheritance in the Brown Alga Ectocarpus. Mol Biol Evol 2019; 36:2778-2789. [PMID: 31504759 DOI: 10.1093/molbev/msz186] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Most eukaryotes inherit their mitochondria from only one of their parents. When there are different sexes, it is almost always the maternal mitochondria that are transmitted. Indeed, maternal uniparental inheritance has been reported for the brown alga Ectocarpus but we show in this study that different strains of Ectocarpus can exhibit different patterns of inheritance: Ectocarpus siliculosus strains showed maternal uniparental inheritance, as expected, but crosses using different Ectocarpus species 7 strains exhibited either paternal uniparental inheritance or an unusual pattern of transmission where progeny inherited either maternal or paternal mitochondria, but not both. A possible correlation between the pattern of mitochondrial inheritance and male gamete parthenogenesis was investigated. Moreover, in contrast to observations in the green lineage, we did not detect any change in the pattern of mitochondrial inheritance in mutant strains affected in life cycle progression. Finally, an analysis of field-isolated strains provided evidence of mitochondrial genome recombination in both Ectocarpus species.
Collapse
Affiliation(s)
- Laure Mignerot
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | | | | | - Marie-Mathilde Perrineau
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland
| | - Delphine Scornet
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Florian Pontheaux
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - Walid Djema
- Inria Sophia-Antipolis, Côte d'Azur University, Bicore and McTAO Teams, France
| | - Yacine Badis
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
- The Scottish Association for Marine Science, Scottish Marine Institute, Oban, Argyll, Scotland
| | | | - Susana M Coelho
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| | - J Mark Cock
- Sorbonne Université, CNRS, Algal Genetics Group, UMR 8227 Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), Roscoff, France
| |
Collapse
|
9
|
Arun A, Coelho SM, Peters AF, Bourdareau S, Pérès L, Scornet D, Strittmatter M, Lipinska AP, Yao H, Godfroy O, Montecinos GJ, Avia K, Macaisne N, Troadec C, Bendahmane A, Cock JM. Convergent recruitment of TALE homeodomain life cycle regulators to direct sporophyte development in land plants and brown algae. eLife 2019; 8:e43101. [PMID: 30644818 PMCID: PMC6368402 DOI: 10.7554/elife.43101] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/13/2019] [Indexed: 01/21/2023] Open
Abstract
Three amino acid loop extension homeodomain transcription factors (TALE HD TFs) act as life cycle regulators in green algae and land plants. In mosses these regulators are required for the deployment of the sporophyte developmental program. We demonstrate that mutations in either of two TALE HD TF genes, OUROBOROS or SAMSARA, in the brown alga Ectocarpus result in conversion of the sporophyte generation into a gametophyte. The OUROBOROS and SAMSARA proteins heterodimerise in a similar manner to TALE HD TF life cycle regulators in the green lineage. These observations demonstrate that TALE-HD-TF-based life cycle regulation systems have an extremely ancient origin, and that these systems have been independently recruited to regulate sporophyte developmental programs in at least two different complex multicellular eukaryotic supergroups, Archaeplastida and Chromalveolata.
Collapse
Affiliation(s)
- Alok Arun
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Susana M Coelho
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | | | - Simon Bourdareau
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Laurent Pérès
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Delphine Scornet
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Martina Strittmatter
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Agnieszka P Lipinska
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Haiqin Yao
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Olivier Godfroy
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Gabriel J Montecinos
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Komlan Avia
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Nicolas Macaisne
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| | - Christelle Troadec
- Institut National de la Recherche Agronomique (INRA), Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-SudOrsayFrance
| | - Abdelhafid Bendahmane
- Institut National de la Recherche Agronomique (INRA), Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, Université Paris-SudOrsayFrance
| | - J Mark Cock
- Sorbonne Université, CNRS, Algal Genetics Group, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR)RoscoffFrance
| |
Collapse
|
10
|
Godfroy O, Uji T, Nagasato C, Lipinska AP, Scornet D, Peters AF, Avia K, Colin S, Mignerot L, Motomura T, Cock JM, Coelho SM. DISTAG/TBCCd1 Is Required for Basal Cell Fate Determination in Ectocarpus. Plant Cell 2017; 29:3102-3122. [PMID: 29208703 PMCID: PMC5757272 DOI: 10.1105/tpc.17.00440] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2017] [Revised: 11/14/2017] [Accepted: 12/04/2017] [Indexed: 05/09/2023]
Abstract
Brown algae are one of the most developmentally complex groups within the eukaryotes. As in many land plants and animals, their main body axis is established early in development, when the initial cell gives rise to two daughter cells that have apical and basal identities, equivalent to shoot and root identities in land plants, respectively. We show here that mutations in the Ectocarpus DISTAG (DIS) gene lead to loss of basal structures during both the gametophyte and the sporophyte generations. Several abnormalities were observed in the germinating initial cell in dis mutants, including increased cell size, disorganization of the Golgi apparatus, disruption of the microtubule network, and aberrant positioning of the nucleus. DIS encodes a TBCCd1 protein, which has a role in internal cell organization in animals, Chlamydomonas reinhardtii, and trypanosomes. Our study highlights the key role of subcellular events within the germinating initial cell in the determination of apical/basal cell identities in a brown alga and emphasizes the remarkable functional conservation of TBCCd1 in regulating internal cell organization across extremely distant eukaryotic groups.
Collapse
Affiliation(s)
- Olivier Godfroy
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Toshiki Uji
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Chikako Nagasato
- Muroran Marine Station, Hokkaido University, Hokkaido 060-0808, Japan
| | - Agnieszka P Lipinska
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Delphine Scornet
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | | | - Komlan Avia
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Universités, UPMC, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique Roscoff, 29688 Roscoff, France
| | - Sebastien Colin
- Sorbonne Universités, UPMC Université Paris 06, CNRS, UMR7144, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Laure Mignerot
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Taizo Motomura
- Muroran Marine Station, Hokkaido University, Hokkaido 060-0808, Japan
| | - J Mark Cock
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| | - Susana M Coelho
- Sorbonne Université, UPMC Université Paris 06, CNRS, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, F-29688 Roscoff, France
| |
Collapse
|
11
|
Macaisne N, Liu F, Scornet D, Peters AF, Lipinska A, Perrineau MM, Henry A, Strittmatter M, Coelho SM, Cock JM. The Ectocarpus IMMEDIATE UPRIGHT gene encodes a member of a novel family of cysteine-rich proteins with an unusual distribution across the eukaryotes. Development 2017; 144:409-418. [PMID: 28049657 DOI: 10.1242/dev.141523] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 12/12/2016] [Indexed: 01/09/2023]
Abstract
The sporophyte generation of the brown alga Ectocarpus sp. exhibits an unusual pattern of development compared with the majority of brown algae. The first cell division is symmetrical and the apical-basal axis is established late in development. In the immediate upright (imm) mutant, the initial cell undergoes an asymmetric division to immediately establish the apical-basal axis. We provide evidence which suggests that this phenotype corresponds to the ancestral state of the sporophyte. The IMM gene encodes a protein of unknown function that contains a repeated motif also found in the EsV-1-7 gene of the Ectocarpus virus EsV-1. Brown algae possess large families of EsV-1-7 domain genes but these genes are rare in other stramenopiles, suggesting that the expansion of this family might have been linked with the emergence of multicellular complexity. EsV-1-7 domain genes have a patchy distribution across eukaryotic supergroups and occur in several viral genomes, suggesting possible horizontal transfer during eukaryote evolution.
Collapse
Affiliation(s)
- Nicolas Macaisne
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Fuli Liu
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Delphine Scornet
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | | | - Agnieszka Lipinska
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Marie-Mathilde Perrineau
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Antoine Henry
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Martina Strittmatter
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - Susana M Coelho
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| | - J Mark Cock
- CNRS, Sorbonne Université, UPMC University Paris 06, Algal Genetics Group, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff F-29688, France
| |
Collapse
|
12
|
Dittami SM, Barbeyron T, Boyen C, Cambefort J, Collet G, Delage L, Gobet A, Groisillier A, Leblanc C, Michel G, Scornet D, Siegel A, Tapia JE, Tonon T. Genome and metabolic network of "Candidatus Phaeomarinobacter ectocarpi" Ec32, a new candidate genus of Alphaproteobacteria frequently associated with brown algae. Front Genet 2014; 5:241. [PMID: 25120558 PMCID: PMC4110880 DOI: 10.3389/fgene.2014.00241] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2014] [Accepted: 07/07/2014] [Indexed: 11/18/2022] Open
Abstract
Rhizobiales and related orders of Alphaproteobacteria comprise several genera of nodule-inducing symbiotic bacteria associated with plant roots. Here we describe the genome and the metabolic network of “Candidatus Phaeomarinobacter ectocarpi” Ec32, a member of a new candidate genus closely related to Rhizobiales and found in association with cultures of the filamentous brown algal model Ectocarpus. The “Ca. P. ectocarpi” genome encodes numerous metabolic pathways that may be relevant for this bacterium to interact with algae. Notably, it possesses a large set of glycoside hydrolases and transporters, which may serve to process and assimilate algal metabolites. It also harbors several proteins likely to be involved in the synthesis of algal hormones such as auxins and cytokinins, as well as the vitamins pyridoxine, biotin, and thiamine. As of today, “Ca. P. ectocarpi” has not been successfully cultured, and identical 16S rDNA sequences have been found exclusively associated with Ectocarpus. However, related sequences (≥97% identity) have also been detected free-living and in a Fucus vesiculosus microbiome barcoding project, indicating that the candidate genus “Phaeomarinobacter” may comprise several species, which may colonize different niches.
Collapse
Affiliation(s)
- Simon M Dittami
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Tristan Barbeyron
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Boyen
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Jeanne Cambefort
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Guillaume Collet
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Ludovic Delage
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Angélique Gobet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Agnès Groisillier
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Catherine Leblanc
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Gurvan Michel
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Delphine Scornet
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| | - Anne Siegel
- CNRS, IRISA UMR 6074 Rennes, France ; IRISA UMR 6074, Université de Rennes 1 Rennes, France ; INRIA, Centre Rennes-Bretagne-Atlantique, Projet Dyliss Rennes, France
| | - Javier E Tapia
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile Santiago, Chile
| | - Thierry Tonon
- Sorbonne Universités, UPMC Univ. Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France ; CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff Roscoff, France
| |
Collapse
|
13
|
Arun A, Peters NT, Scornet D, Peters AF, Mark Cock J, Coelho SM. Non-cell autonomous regulation of life cycle transitions in the model brown alga Ectocarpus. New Phytol 2013; 197:503-510. [PMID: 23106314 DOI: 10.1111/nph.12007] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2012] [Accepted: 09/24/2012] [Indexed: 05/29/2023]
Abstract
The model brown alga Ectocarpus has a haploid-diploid life cycle, involving alternation between two independent multicellular generations, the gametophyte and the sporophyte. Recent work has shown that alternation of generations is not determined by ploidy but is rather under genetic control, involving at least one master regulatory locus, OUROBOROS (ORO). Using cell biology approaches combined with measurements of generation-specific transcript abundance we provide evidence that alternation of generations can also be regulated by non-cell autonomous mechanisms. The Ectocarpus sporophyte produces a diffusible factor that causes major developmental reprogramming in gametophyte cells. Cells become resistant to reprogramming when the cell wall is synthetized, suggesting that the cell wall may play a role in locking an individual into the developmental program that has been engaged. A functional ORO gene is necessary for the induction of the developmental switch. Our results highlight the role of the cell wall in maintaining the differentiated generation stage once the appropriate developmental program has been engaged and also indicate that ORO is a key member of the developmental pathway triggered by the sporophyte factor. Alternation between gametophyte and sporophyte generations in Ectocarpus is surprisingly labile, perhaps reflecting an adaptation to the variable seashore environment inhabited by this alga.
Collapse
Affiliation(s)
- Alok Arun
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
- The Marine Plants and Biomolecules Laboratory, UMR 7139, UPMC Université Paris 06, Station Biologique de Roscoff, BP74, 29682, Roscoff Cedex, France
| | - Nick T Peters
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
- The Marine Plants and Biomolecules Laboratory, UMR 7139, UPMC Université Paris 06, Station Biologique de Roscoff, BP74, 29682, Roscoff Cedex, France
- Department of Biology, University of Utah, Salt Lake City, Utah, USA
| | - Delphine Scornet
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
| | - Akira F Peters
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
- The Marine Plants and Biomolecules Laboratory, UMR 7139, UPMC Université Paris 06, Station Biologique de Roscoff, BP74, 29682, Roscoff Cedex, France
- Bezhin Rosko, 29250, Santec, France
| | - J Mark Cock
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
- The Marine Plants and Biomolecules Laboratory, UMR 7139, UPMC Université Paris 06, Station Biologique de Roscoff, BP74, 29682, Roscoff Cedex, France
| | - Susana M Coelho
- UMR 7139, Laboratoire International Associé Dispersal and Adaptation in Marine Species, Station Biologique de Roscoff, CNRS, Place Georges Teissier, BP74, 29682, Roscoff Cedex, France
- The Marine Plants and Biomolecules Laboratory, UMR 7139, UPMC Université Paris 06, Station Biologique de Roscoff, BP74, 29682, Roscoff Cedex, France
| |
Collapse
|
14
|
Coelho SM, Scornet D, Rousvoal S, Peters N, Dartevelle L, Peters AF, Cock JM. Isolation and regeneration of protoplasts from Ectocarpus. Cold Spring Harb Protoc 2012; 2012:361-4. [PMID: 22383637 DOI: 10.1101/pdb.prot067959] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
This article describes how to obtain isolated cells with no surrounding cell wall by enzymatic digestion of Ectocarpus filaments. The resultant protoplasts are totipotent and regenerate to produce individual algae under appropriate culture conditions. The yield of protoplasts and their capacity to regenerate are highly dependent on the Ectocarpus strain used, the stage of the life cycle, and the culture conditions. The highest yields are obtained with young gametophyte filaments cultivated at low density. The naked, wall-less cells produced by this protocol can be used for several applications, including studies of cell wall regeneration, investigation of the role of the cell wall in determining cell fate, and as a source of naked cells for the development of methods for introducing diverse molecules into the cell.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | |
Collapse
|
15
|
Coelho SM, Scornet D, Rousvoal S, Peters N, Dartevelle L, Peters AF, Cock JM. Extraction of high-quality genomic DNA from Ectocarpus. Cold Spring Harb Protoc 2012; 2012:365-8. [PMID: 22383638 DOI: 10.1101/pdb.prot067967] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
For some applications, such as genome sequencing and high-throughput genotyping with multiple markers, it is necessary to use high-quality genomic DNA. This article describes how to obtain several micrograms of high-quality, cesium chloride-purified DNA from 1 g of Ectocarpus filaments. We also recommend using DNA of this quality for quantitative RT-PCR control reactions. However, simpler, more rapid, kit-based methods are preferable for experiments that involve the treatment of large numbers of individuals, such as genotyping large populations with a small number of markers or PCR screening of large populations.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | |
Collapse
|
16
|
Abstract
This article describes an immunostaining protocol for Ectocarpus that was optimized for the detection of tubulin but could be used with any suitable antibody. Ectocarpus has small but relatively transparent cells and the uniseriate filaments can be grown directly attached to the surface of microscope slides. These features make Ectocarpus particularly suitable for high resolution imaging approaches, both in vivo or after fixation. All incubations described below are carried out on a platform shaker at room temperature. Use high-quality microscope slides to avoid imperfections in the glass that can be a problem for confocal laserscan microscopy analysis.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | |
Collapse
|
17
|
Abstract
This article describes the standard procedure for growing Ectocarpus in the laboratory. The culture is started with partheno-sporophyte (or sporophyte) filaments because this is the stage that is usually maintained in strain collections. The standard medium is Provasoli-enriched natural seawater (PES), but Ectocarpus can also be grown in artificial seawater, which allows more precise control over the culture conditions. The algae can be cultivated either in plastic Petri dishes or in 10-L bottles with bubbling, if large amounts of biomass are required. Standard growth conditions are 13°C with a 12h/12h d/night cycle and 20 µmol photons m(-2) s(-1) irradiance using daylight-type fluorescent tubes. All manipulations of Ectocarpus cultures should be performed in a clean environment (if possible, under a laminar flow hood). Forceps should be dipped in ethanol and allowed to dry under the hood.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, BP74, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | |
Collapse
|
18
|
Abstract
This article describes a procedure for conducting crosses between different strains of Ectocarpus. Crossing gametophytes to obtain the sporophyte generation is the most technically challenging stage of this process because diploid sporophytes have to be distinguished from the haploid partheno-sporophytes that result from the parthenogenetic germination of unfused gametes. This requires careful monitoring of the progeny of the genetic cross until they have developed sufficiently to be transferred to a separate Petri dish. Genetic crosses allow several classical genetic methodologies to be applied in Ectocarpus, including allelic complementation tests, backcrosses, combination of different genetic mutations, and outcrosses to create mapping populations.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, BP74, 29682 Roscoff Cedex, France.
| | | | | | | | | | | | | |
Collapse
|
19
|
Abstract
The brown algae are an interesting group of organisms from several points of view. They are the dominant organisms in many coastal ecosystems, where they often form large, underwater forests. They also have an unusual evolutionary history, being members of the stramenopiles, which are very distantly related to well-studied animal and green plant models. As a consequence of this history, brown algae have evolved many novel features, for example in terms of their cell biology and metabolic pathways. They are also one of only a small number of eukaryotic groups to have independently evolved complex multicellularity. Despite these interesting features, the brown algae have remained a relatively poorly studied group. This situation has started to change over the last few years, however, with the emergence of the filamentous brown alga Ectocarpus as a model system that is amenable to the genomic and genetic approaches that have proved to be so powerful in more classical model organisms such as Drosophila and Arabidopsis.
Collapse
Affiliation(s)
- Susana M Coelho
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, BP74, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | |
Collapse
|
20
|
Michel G, Tonon T, Scornet D, Cock JM, Kloareg B. The cell wall polysaccharide metabolism of the brown alga Ectocarpus siliculosus. Insights into the evolution of extracellular matrix polysaccharides in Eukaryotes. New Phytol 2010; 188:82-97. [PMID: 20618907 DOI: 10.1111/j.1469-8137.2010.03374.x] [Citation(s) in RCA: 250] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
• Brown algal cell walls share some components with plants (cellulose) and animals (sulfated fucans), but they also contain some unique polysaccharides (alginates). Analysis of the Ectocarpus genome provides a unique opportunity to decipher the molecular bases of these crucial metabolisms. • An extensive bioinformatic census of the enzymes potentially involved in the biogenesis and remodeling of cellulose, alginate and fucans was performed, and completed by phylogenetic analyses of key enzymes. • The routes for the biosynthesis of cellulose, alginates and sulfated fucans were reconstructed. Surprisingly, known families of cellulases, expansins and alginate lyases are absent in Ectocarpus, suggesting the existence of novel mechanisms and/or proteins for cell wall expansion in brown algae. • Altogether, our data depict a complex evolutionary history for the main components of brown algal cell walls. Cellulose synthesis was inherited from the ancestral red algal endosymbiont, whereas the terminal steps for alginate biosynthesis were acquired by horizontal gene transfer from an Actinobacterium. This horizontal gene transfer event also contributed genes for hemicellulose biosynthesis. By contrast, the biosynthetic route for sulfated fucans is an ancestral pathway, conserved with animals. These findings shine a new light on the origin and evolution of cell wall polysaccharides in other Eukaryotes.
Collapse
Affiliation(s)
- Gurvan Michel
- UPMC University Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France.
| | | | | | | | | |
Collapse
|
21
|
Michel G, Tonon T, Scornet D, Cock JM, Kloareg B. Central and storage carbon metabolism of the brown alga Ectocarpus siliculosus: insights into the origin and evolution of storage carbohydrates in Eukaryotes. New Phytol 2010; 188:67-81. [PMID: 20618908 DOI: 10.1111/j.1469-8137.2010.03345.x] [Citation(s) in RCA: 122] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
• Brown algae exhibit a unique carbon (C) storage metabolism. The photoassimilate D-fructose 6-phosphate is not used to produce sucrose but is converted into D-mannitol. These seaweeds also store C as β-1,3-glucan (laminarin), thus markedly departing from most living organisms, which use α-1,4-glucans (glycogen or starch). • Using a combination of bioinformatic and phylogenetic approaches, we identified the candidate genes for the enzymes involved in C storage in the genome of the brown alga Ectocarpus siliculosus and traced their evolutionary origins. • Ectocarpus possesses a complete set of enzymes for synthesis of mannitol, laminarin and trehalose. By contrast, the pathways for sucrose, starch and glycogen are completely absent. • The synthesis of β-1,3-glucans appears to be a very ancient eukaryotic pathway. Brown algae inherited the trehalose pathway from the red algal progenitor of phaeoplasts, while the mannitol pathway was acquired by lateral gene transfer from Actinobacteria. The starch metabolism of the red algal endosymbiont was entirely lost in the ancestor of Stramenopiles. In light of these novel findings we question the validity of the 'Chromalveolate hypothesis'.
Collapse
Affiliation(s)
- Gurvan Michel
- UPMC University Paris 6, UMR 7139 Marine Plants and Biomolecules, Station Biologique de Roscoff, F-29682 Roscoff, Bretagne, France.
| | | | | | | | | |
Collapse
|
22
|
Cock JM, Sterck L, Rouzé P, Scornet D, Allen AE, Amoutzias G, Anthouard V, Artiguenave F, Aury JM, Badger JH, Beszteri B, Billiau K, Bonnet E, Bothwell JH, Bowler C, Boyen C, Brownlee C, Carrano CJ, Charrier B, Cho GY, Coelho SM, Collén J, Corre E, Da Silva C, Delage L, Delaroque N, Dittami SM, Doulbeau S, Elias M, Farnham G, Gachon CMM, Gschloessl B, Heesch S, Jabbari K, Jubin C, Kawai H, Kimura K, Kloareg B, Küpper FC, Lang D, Le Bail A, Leblanc C, Lerouge P, Lohr M, Lopez PJ, Martens C, Maumus F, Michel G, Miranda-Saavedra D, Morales J, Moreau H, Motomura T, Nagasato C, Napoli CA, Nelson DR, Nyvall-Collén P, Peters AF, Pommier C, Potin P, Poulain J, Quesneville H, Read B, Rensing SA, Ritter A, Rousvoal S, Samanta M, Samson G, Schroeder DC, Ségurens B, Strittmatter M, Tonon T, Tregear JW, Valentin K, von Dassow P, Yamagishi T, Van de Peer Y, Wincker P. The Ectocarpus genome and the independent evolution of multicellularity in brown algae. Nature 2010; 465:617-21. [PMID: 20520714 DOI: 10.1038/nature09016] [Citation(s) in RCA: 518] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2009] [Accepted: 03/15/2010] [Indexed: 01/05/2023]
Abstract
Brown algae (Phaeophyceae) are complex photosynthetic organisms with a very different evolutionary history to green plants, to which they are only distantly related. These seaweeds are the dominant species in rocky coastal ecosystems and they exhibit many interesting adaptations to these, often harsh, environments. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity (Fig. 1). We report the 214 million base pair (Mbp) genome sequence of the filamentous seaweed Ectocarpus siliculosus (Dillwyn) Lyngbye, a model organism for brown algae, closely related to the kelps (Fig. 1). Genome features such as the presence of an extended set of light-harvesting and pigment biosynthesis genes and new metabolic processes such as halide metabolism help explain the ability of this organism to cope with the highly variable tidal environment. The evolution of multicellularity in this lineage is correlated with the presence of a rich array of signal transduction genes. Of particular interest is the presence of a family of receptor kinases, as the independent evolution of related molecules has been linked with the emergence of multicellularity in both the animal and green plant lineages. The Ectocarpus genome sequence represents an important step towards developing this organism as a model species, providing the possibility to combine genomic and genetic approaches to explore these and other aspects of brown algal biology further.
Collapse
Affiliation(s)
- J Mark Cock
- UPMC Université Paris 6, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France.
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
23
|
Le Bail A, Billoud B, Kowalczyk N, Kowalczyk M, Gicquel M, Le Panse S, Stewart S, Scornet D, Cock JM, Ljung K, Charrier B. Auxin metabolism and function in the multicellular brown alga Ectocarpus siliculosus. Plant Physiol 2010; 153:128-44. [PMID: 20200071 PMCID: PMC2862433 DOI: 10.1104/pp.109.149708] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2009] [Accepted: 02/17/2010] [Indexed: 05/20/2023]
Abstract
Ectocarpus siliculosus is a small brown alga that has recently been developed as a genetic model. Its thallus is filamentous, initially organized as a main primary filament composed of elongated cells and round cells, from which branches differentiate. Modeling of its early development suggests the involvement of very local positional information mediated by cell-cell recognition. However, this model also indicates that an additional mechanism is required to ensure proper organization of the branching pattern. In this paper, we show that auxin indole-3-acetic acid (IAA) is detectable in mature E. siliculosus organisms and that it is present mainly at the apices of the filaments in the early stages of development. An in silico survey of auxin biosynthesis, conjugation, response, and transport genes showed that mainly IAA biosynthesis genes from land plants have homologs in the E. siliculosus genome. In addition, application of exogenous auxins and 2,3,5-triiodobenzoic acid had different effects depending on the developmental stage of the organism, and we propose a model in which auxin is involved in the negative control of progression in the developmental program. Furthermore, we identified an auxin-inducible gene called EsGRP1 from a small-scale microarray experiment and showed that its expression in a series of morphogenetic mutants was positively correlated with both their elongated-to-round cell ratio and their progression in the developmental program. Altogether, these data suggest that IAA is used by the brown alga Ectocarpus to relay cell-cell positional information and induces a signaling pathway different from that known in land plants.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | - Bénédicte Charrier
- CNRS-Université Pierre et Marie Curie, UMR 7139 Marine Plants and Biomolecules (A.L.B., B.B., N.K., M.G., S.S., D.S., J.M.C., B.C.), and Platform of Cytology, CNRS FR2424 (S.L.P.), Station Biologique de Roscoff, 29682 Roscoff cedex, France; Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University for Agricultural Sciences, S–901 83 Umea, Sweden (M.K., K.L.)
| |
Collapse
|
24
|
Dittami SM, Scornet D, Petit JL, Ségurens B, Da Silva C, Corre E, Dondrup M, Glatting KH, König R, Sterck L, Rouzé P, Van de Peer Y, Cock JM, Boyen C, Tonon T. Global expression analysis of the brown alga Ectocarpus siliculosus (Phaeophyceae) reveals large-scale reprogramming of the transcriptome in response to abiotic stress. Genome Biol 2009; 10:R66. [PMID: 19531237 PMCID: PMC2718500 DOI: 10.1186/gb-2009-10-6-r66] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2008] [Revised: 02/04/2009] [Accepted: 06/16/2009] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Brown algae (Phaeophyceae) are phylogenetically distant from red and green algae and an important component of the coastal ecosystem. They have developed unique mechanisms that allow them to inhabit the intertidal zone, an environment with high levels of abiotic stress. Ectocarpus siliculosus is being established as a genetic and genomic model for the brown algal lineage, but little is known about its response to abiotic stress. RESULTS Here we examine the transcriptomic changes that occur during the short-term acclimation of E. siliculosus to three different abiotic stress conditions (hyposaline, hypersaline and oxidative stress). Our results show that almost 70% of the expressed genes are regulated in response to at least one of these stressors. Although there are several common elements with terrestrial plants, such as repression of growth-related genes, switching from primary production to protein and nutrient recycling processes, and induction of genes involved in vesicular trafficking, many of the stress-regulated genes are either not known to respond to stress in other organisms or are have been found exclusively in E. siliculosus. CONCLUSIONS This first large-scale transcriptomic study of a brown alga demonstrates that, unlike terrestrial plants, E. siliculosus undergoes extensive reprogramming of its transcriptome during the acclimation to mild abiotic stress. We identify several new genes and pathways with a putative function in the stress response and thus pave the way for more detailed investigations of the mechanisms underlying the stress tolerance of brown algae.
Collapse
Affiliation(s)
- Simon M Dittami
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
| | - Delphine Scornet
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
| | - Jean-Louis Petit
- CEA, DSV, Institut de Génomique, Génoscope, rue Gaston Crémieux, CP5706, 91057 Evry, France
- CNRS, UMR 8030 Génomique métabolique des genomes, rue Gaston Crémieux, CP5706, 91057 Evry, France
- Université d'Evry, UMR 8030 Génomique métabolique des genomes, 91057 Evry, France
| | - Béatrice Ségurens
- CEA, DSV, Institut de Génomique, Génoscope, rue Gaston Crémieux, CP5706, 91057 Evry, France
- CNRS, UMR 8030 Génomique métabolique des genomes, rue Gaston Crémieux, CP5706, 91057 Evry, France
- Université d'Evry, UMR 8030 Génomique métabolique des genomes, 91057 Evry, France
| | - Corinne Da Silva
- CEA, DSV, Institut de Génomique, Génoscope, rue Gaston Crémieux, CP5706, 91057 Evry, France
- CNRS, UMR 8030 Génomique métabolique des genomes, rue Gaston Crémieux, CP5706, 91057 Evry, France
- Université d'Evry, UMR 8030 Génomique métabolique des genomes, 91057 Evry, France
| | - Erwan Corre
- SIG-FR 2424 CNRS UPMC, Station Biologique, 29680 Roscoff, France
| | - Michael Dondrup
- Center for Biotechnology (CeBiTec), University of Bielefeld, 33594 Bielefeld, Germany
| | - Karl-Heinz Glatting
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Rainer König
- German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120 Heidelberg, Germany
| | - Lieven Sterck
- VIB Department of Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - Pierre Rouzé
- VIB Department of Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - Yves Van de Peer
- VIB Department of Plant Systems Biology, Ghent University, 9052 Ghent, Belgium
| | - J Mark Cock
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
| | - Catherine Boyen
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
| | - Thierry Tonon
- UPMC Univ Paris 6, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
- CNRS, UMR 7139 Végétaux marins et Biomolécules, Station Biologique, 29680 Roscoff, France
| |
Collapse
|
25
|
Peters AF, Scornet D, Ratin M, Charrier B, Monnier A, Merrien Y, Corre E, Coelho SM, Cock JM. Life-cycle-generation-specific developmental processes are modified in the immediate upright mutant of the brown alga Ectocarpus siliculosus. Development 2008; 135:1503-12. [PMID: 18339673 DOI: 10.1242/dev.016303] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Development of the sporophyte and gametophyte generations of the brown alga E. siliculosus involves two different patterns of early development, which begin with either a symmetric or an asymmetric division of the initial cell, respectively. A mutant, immediate upright (imm), was isolated that exhibited several characteristics typical of the gametophyte during the early development of the sporophyte generation. Genetic analyses showed that imm is a recessive, single-locus Mendelian factor and analysis of gene expression in this mutant indicated that the regulation of a number of life-cycle-regulated genes is specifically modified in imm mutant sporophytes. Thus, IMM appears to be a regulatory locus that controls part of the sporophyte-specific developmental programme, the mutant exhibiting partial homeotic conversion of the sporophyte into the gametophyte, a phenomenon that has not been described previously.
Collapse
Affiliation(s)
- Akira F Peters
- UPMC Université Paris 06, The Marine Plants and Biomolecules Laboratory, UMR 7139, Station Biologique de Roscoff, Place Georges Teissier, BP74, 29682 Roscoff Cedex, France
| | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Peters AF, Marie D, Scornet D, Kloareg B, Mark Cock J. PROPOSAL OF ECTOCARPUS SILICULOSUS(ECTOCARPALES, PHAEOPHYCEAE) AS A MODEL ORGANISM FOR BROWN ALGAL GENETICS AND GENOMICS. Journal of Phycology 2004; 40:1079-1088. [PMID: 0 DOI: 10.1111/j.1529-8817.2004.04058.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
|
27
|
Nyvall P, Corre E, Boisset C, Barbeyron T, Rousvoal S, Scornet D, Kloareg B, Boyen C. Characterization of mannuronan C-5-epimerase genes from the brown alga Laminaria digitata. Plant Physiol 2003; 133:726-35. [PMID: 14526115 PMCID: PMC219047 DOI: 10.1104/pp.103.025981] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2003] [Revised: 06/09/2003] [Accepted: 07/11/2003] [Indexed: 05/07/2023]
Abstract
Alginate is an industrially important polysaccharide obtained commercially by harvesting brown algae. The final step in alginate biosynthesis, the epimerization of beta-1,4-d-mannuronic acid to alpha-1,4-l-guluronic acid, a structural change that controls the physicochemical properties of the alginate, is catalyzed by the enzyme mannuronan C-5-epimerase. Six different cDNAs with homology to bacterial mannuronan C-5-epimerases were isolated from the brown alga Laminaria digitata (Phaeophyceae). Hydrophobic cluster analysis indicated that the proteins encoded by the L. digitata sequences have important structural similarities to the bacterial mannuronan C-5-epimerases, including conservation of the catalytic site. The expression of the C-5-epimerase genes was examined by northern-blot analysis and reverse transcriptase-polymerase chain reaction in L. digitata throughout a year. Expression was also monitored in protoplast cultures by northern and western blot, reverse transcriptase-polymerase chain reaction, and activity measurements. From both the structural comparisons and the expression pattern, it appears that the cDNAs isolated from L. digitata encode functional mannuronan C-5-epimerases. The phylogenetic relationships of the bacterial and brown algal enzymes and the inferences on the origin of alginate biosynthetic machinery are discussed.
Collapse
Affiliation(s)
- Pi Nyvall
- Unité Mixte de Recherche 1931, Centre National de la Recherche Scientifique and Laboratoires Goëmar, Station Biologique de Roscoff, BP 74, 29682 Roscoff cedex, Brittany, France
| | | | | | | | | | | | | | | |
Collapse
|