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Nelson DR, Mystikou A, Jaiswal A, Rad-Menendez C, Preston MJ, De Boever F, El Assal DC, Daakour S, Lomas MW, Twizere JC, Green DH, Ratcliff WC, Salehi-Ashtiani K. Macroalgal deep genomics illuminate multiple paths to aquatic, photosynthetic multicellularity. MOLECULAR PLANT 2024; 17:747-771. [PMID: 38614077 DOI: 10.1016/j.molp.2024.03.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 01/31/2024] [Accepted: 03/08/2024] [Indexed: 04/15/2024]
Abstract
Macroalgae are multicellular, aquatic autotrophs that play vital roles in global climate maintenance and have diverse applications in biotechnology and eco-engineering, which are directly linked to their multicellularity phenotypes. However, their genomic diversity and the evolutionary mechanisms underlying multicellularity in these organisms remain uncharacterized. In this study, we sequenced 110 macroalgal genomes from diverse climates and phyla, and identified key genomic features that distinguish them from their microalgal relatives. Genes for cell adhesion, extracellular matrix formation, cell polarity, transport, and cell differentiation distinguish macroalgae from microalgae across all three major phyla, constituting conserved and unique gene sets supporting multicellular processes. Adhesome genes show phylum- and climate-specific expansions that may facilitate niche adaptation. Collectively, our study reveals genetic determinants of convergent and divergent evolutionary trajectories that have shaped morphological diversity in macroalgae and provides genome-wide frameworks to understand photosynthetic multicellular evolution in aquatic environments.
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Affiliation(s)
- David R Nelson
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
| | - Alexandra Mystikou
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE; Biotechnology Research Center, Technology Innovation Institute, PO Box 9639, Masdar City, Abu Dhabi, UAE.
| | - Ashish Jaiswal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Cecilia Rad-Menendez
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Michael J Preston
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Frederik De Boever
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - Diana C El Assal
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE
| | - Michael W Lomas
- National Center for Marine Algae and Microbiota, Bigelow Laboratory for Ocean Sciences, East Boothbay, ME, USA
| | - Jean-Claude Twizere
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Laboratory of Viral Interactomes, GIGA Institute, University of Liege, Liege, Belgium
| | - David H Green
- Culture Collection of Algae and Protozoa, Scottish Association for Marine Science, Oban, Scotland, UK
| | - William C Ratcliff
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, USA
| | - Kourosh Salehi-Ashtiani
- Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Abu Dhabi, Abu Dhabi, UAE.
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2
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De Saeger J, Coulembier Vandelannoote E, Lee H, Park J, Blomme J. Genome editing in macroalgae: advances and challenges. Front Genome Ed 2024; 6:1380682. [PMID: 38516199 PMCID: PMC10955705 DOI: 10.3389/fgeed.2024.1380682] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 02/13/2024] [Indexed: 03/23/2024] Open
Abstract
This minireview examines the current state and challenges of genome editing in macroalgae. Despite the ecological and economic significance of this group of organisms, genome editing has seen limited applications. While CRISPR functionality has been established in two brown (Ectocarpus species 7 and Saccharina japonica) and one green seaweed (Ulva prolifera), these studies are limited to proof-of-concept demonstrations. All studies also (co)-targeted ADENINE PHOSPHORIBOSYL TRANSFERASE to enrich for mutants, due to the relatively low editing efficiencies. To advance the field, there should be a focus on advancing auxiliary technologies, particularly stable transformation, so that novel editing reagents can be screened for their efficiency. More work is also needed on understanding DNA repair in these organisms, as this is tightly linked with the editing outcomes. Developing efficient genome editing tools for macroalgae will unlock the ability to characterize their genes, which is largely uncharted terrain. Moreover, given their economic importance, genome editing will also impact breeding campaigns to develop strains that have better yields, produce more commercially valuable compounds, and show improved resilience to the impacts of global change.
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Affiliation(s)
- Jonas De Saeger
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Emma Coulembier Vandelannoote
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
| | - Hojun Lee
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jihae Park
- Bio Environmental Science and Technology (BEST) Lab, Ghent University Global Campus, Yeonsu-gu, Republic of Korea
| | - Jonas Blomme
- Department of Biology, Phycology Research Group, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- VIB-UGent Center for Plant Systems Biology, Ghent, Belgium
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3
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Karimi E, Dittami SM. Maintaining beneficial alga-associated bacterial communities under heat stress: insights from controlled co-culture experiments using antibiotic-resistant bacterial strains. FEMS Microbiol Ecol 2023; 99:fiad130. [PMID: 37833238 DOI: 10.1093/femsec/fiad130] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/15/2023] Open
Abstract
Brown algae, like many eukaryotes, possess diverse microbial communities. Ectocarpus-a model brown alga-relies on these communities for essential processes, such as growth development. Controlled laboratory systems are needed for functional studies of these algal-bacterial interactions. We selected bacterial strains based on their metabolic networks to provide optimal completion of the algal metabolism, rendered them resistant to two antibiotics, and inoculate them to establish controlled co-cultures with Ectocarpus under continuous antibiotic treatment. We then monitored the stability of the resulting associations under control conditions and heat stress using 16S metabarcoding. Antibiotics strongly reduced bacterial diversity both in terms of taxonomy and predicted metabolic functions. In the inoculated sample, 63%-69% of reads corresponded to the inoculated strains, and the communities remained stable during temperature stress. They also partially restored the predicted metabolic functions of the natural community. Overall, the development of antibiotic-resistant helper cultures offers a promising route to fully controlled laboratory experiments with algae and microbiota and thus represents an important step towards generating experimental evidence for specific host-microbe interactions in the systems studied. Further work will be required to achieve full control and progressively expand our repertoire of helper strains including those currently 'unculturable'.
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Affiliation(s)
- Elham Karimi
- Integrative Biology of Marine Models, Sorbonne Université/CNRS, UMR8227, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
| | - Simon M Dittami
- Integrative Biology of Marine Models, Sorbonne Université/CNRS, UMR8227, Station Biologique de Roscoff, CS 90074, 29688 Roscoff Cedex, France
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4
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KleinJan H, Frioux C, Califano G, Aite M, Fremy E, Karimi E, Corre E, Wichard T, Siegel A, Boyen C, Dittami SM. Insights into the potential for mutualistic and harmful host-microbe interactions affecting brown alga freshwater acclimation. Mol Ecol 2023; 32:703-723. [PMID: 36326449 PMCID: PMC10099861 DOI: 10.1111/mec.16766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 10/25/2022] [Accepted: 10/27/2022] [Indexed: 11/05/2022]
Abstract
Microbes can modify their hosts' stress tolerance, thus potentially enhancing their ecological range. An example of such interactions is Ectocarpus subulatus, one of the few freshwater-tolerant brown algae. This tolerance is partially due to its (un)cultivated microbiome. We investigated this phenomenon by modifying the microbiome of laboratory-grown E. subulatus using mild antibiotic treatments, which affected its ability to grow in low salinity. Low salinity acclimation of these algal-bacterial associations was then compared. Salinity significantly impacted bacterial and viral gene expression, albeit in different ways across algal-bacterial communities. In contrast, gene expression of the host and metabolite profiles were affected almost exclusively in the freshwater-intolerant algal-bacterial communities. We found no evidence of bacterial protein production that would directly improve algal stress tolerance. However, vitamin K synthesis is one possible bacterial service missing specifically in freshwater-intolerant cultures in low salinity. In this condition, we also observed a relative increase in bacterial transcriptomic activity and the induction of microbial genes involved in the biosynthesis of the autoinducer AI-1, a quorum-sensing regulator. This could have resulted in dysbiosis by causing a shift in bacterial behaviour in the intolerant algal-bacterial community. Together, these results provide two promising hypotheses to be examined by future targeted experiments. Although they apply only to the specific study system, they offer an example of how bacteria may impact their host's stress response.
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Affiliation(s)
- Hetty KleinJan
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
- CEBEDEAU, Research and Expertise Centre for WaterQuartier Polytech 1LiègeBelgium
| | - Clémence Frioux
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
- InriaUniversity of Bordeaux, INRAETalenceFrance
| | - Gianmaria Califano
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller University JenaJenaGermany
| | - Méziane Aite
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Enora Fremy
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Elham Karimi
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
| | - Erwan Corre
- Station BiologiqueFR2424, ABiMS, Sorbonne Université, CNRSRoscoffFrance
| | - Thomas Wichard
- Institute for Inorganic and Analytical ChemistryFriedrich Schiller University JenaJenaGermany
| | - Anne Siegel
- Inria, CNRS, IRISAUniversity of RennesRennesFrance
| | - Catherine Boyen
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
| | - Simon M. Dittami
- Station Biologique de Roscoff, Laboratory of Integrative Biology of Marine ModelsSorbonne University, CNRSRoscoffFrance
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5
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Mazéas L, Yonamine R, Barbeyron T, Henrissat B, Drula E, Terrapon N, Nagasato C, Hervé C. Assembly and synthesis of the extracellular matrix in brown algae. Semin Cell Dev Biol 2023; 134:112-124. [PMID: 35307283 DOI: 10.1016/j.semcdb.2022.03.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Revised: 02/03/2022] [Accepted: 03/04/2022] [Indexed: 12/23/2022]
Abstract
In brown algae, the extracellular matrix (ECM) and its constitutive polymers play crucial roles in specialized functions, including algal growth and development. In this review we offer an integrative view of ECM construction in brown algae. We briefly report the chemical composition of its main constituents, and how these are interlinked in a structural model. We examine the ECM assembly at the tissue and cell level, with consideration on its structure in vivo and on the putative subcellular sites for the synthesis of its main constituents. We further discuss the biosynthetic pathways of two major polysaccharides, alginates and sulfated fucans, and the progress made beyond the candidate genes with the biochemical validation of encoded proteins. Key enzymes involved in the elongation of the glycan chains are still unknown and predictions have been made at the gene level. Here, we offer a re-examination of some glycosyltransferases and sulfotransferases from published genomes. Overall, our analysis suggests novel investigations to be performed at both the cellular and biochemical levels. First, to depict the location of polysaccharide structures in tissues. Secondly, to identify putative actors in the ECM synthesis to be functionally studied in the future.
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Affiliation(s)
- Lisa Mazéas
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Rina Yonamine
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Tristan Barbeyron
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France
| | - Bernard Henrissat
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France; Department of Biological Sciences, King Abdulaziz University, Jeddah, Saudi Arabia; Technical University of Denmark, DTU Bioengineering, DK-2800 Kgs., Lyngby, Denmark
| | - Elodie Drula
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Nicolas Terrapon
- CNRS, Aix Marseille Univ, UMR 7257 AFMB, 13288 Marseille, France; INRAE, USC1408 AFMB, 13288 Marseille, France
| | - Chikako Nagasato
- Muroran Marine Station, Field Science Center for Northern Biosphere, Hokkaido University, Muroran 051-0013, Japan
| | - Cécile Hervé
- CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France; Sorbonne Universités, UPMC Univ Paris 06, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, Roscoff, France.
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6
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Marine macroalgae polysaccharides-based nanomaterials: an overview with respect to nanoscience applications. BENI-SUEF UNIVERSITY JOURNAL OF BASIC AND APPLIED SCIENCES 2022. [DOI: 10.1186/s43088-022-00335-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Abstract
Background
Exploration of marine macroalgae poly-saccharide-based nanomaterials is emerging in the nanotechnology field, such as wound dressing, water treatment, environmental engineering, biosensor, and food technology.
Main body
In this article, the current innovation and encroachments of marine macroalgae polysaccharide-based nanoparticles (NPs), and their promising opportunities, for future prospect in different industries are briefly reviewed. The extraction and advancement of various natural sources from marine polysaccharides, including carrageenan, agarose, fucoidan, and ulvan, are highlighted in order to provide a wide range of impacts on the nanofood technology. Further, seaweed or marine macroalgae is an unexploited natural source of polysaccharides, which involves numerous different phytonutrients in the outermost layer of the cell and is rich in sulphated polysaccharides (SP), SP-based nanomaterial which has an enhanced potential value in the nanotechnology field.
Conclusion
At the end of this article, the promising prospect of SP-based NPs and their applications in the food sector is briefly addressed.
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7
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Goecke F, Gómez Garreta A, Martín-Martín R, Rull Lluch J, Skjermo J, Ergon Å. Nuclear DNA Content Variation in Different Life Cycle Stages of Sugar Kelp, Saccharina latissima. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2022; 24:706-721. [PMID: 35882688 PMCID: PMC9385784 DOI: 10.1007/s10126-022-10137-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 06/20/2022] [Indexed: 06/15/2023]
Abstract
Ploidy variants can be utilized to increase yield, introduce sterility, and modify specific traits with an economic impact. Despite economic importance of Saccharina species, their nuclear DNA content in different cell types and life stages remain unclear. The present research was initiated to determine the nuclear DNA content and intraindividual variation at different life cycle stages of the Laminarialean kelp Saccharina latissima. Nuclear DNA content in embryonic and mature sporophytes, released and unreleased zoospores, female, and male gametophytes from Sør-Trøndelag county in Norway were estimated by image analysis using the DNA-localizing fluorochrome DAPI and chicken's red blood cells as a standard. DNA content of a total of 6905 DAPI-stained nuclei was estimated. This is the first study of nuclear DNA content which covered the life cycle of kelp. The lowest level of DNA content (1C) was observed in zoospores with an average of 0.76 pg. Male and female single spore gametophyte cultures presented higher average DNA content, more than double that of zoospores, suggesting the presence of polyteny. Female gametophyte nuclei were slightly larger and more variable in size than those of male gametophytes. The DNA content observed in embryonic sporophytes and in meristoderm cells from older sporophytes (1.51 pg) was 2C as expected and in the range of previously published studies of sporophytes of S. latissima. Mature sporophytes showed intra-plant variation with DNA content values ranging from 2-16C. The main difference was between meristoderm cells (mostly 2C) and cortical and medullary cells (2-16C).
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Affiliation(s)
- Franz Goecke
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway.
| | - Amelia Gómez Garreta
- Laboratori de Botànica, Facultat de Farmàcia I Ciències de L'Alimentació, Institut de Recerca de La Biodiversitat (IRBio) & Centre de Documentació de Biodiversitat Vegetal (CeDocBiV), Universitat de Barcelona, Barcelona, Spain
| | - Rafael Martín-Martín
- Laboratori de Botànica, Facultat de Farmàcia I Ciències de L'Alimentació, Institut de Recerca de La Biodiversitat (IRBio) & Centre de Documentació de Biodiversitat Vegetal (CeDocBiV), Universitat de Barcelona, Barcelona, Spain
| | - Jordi Rull Lluch
- Laboratori de Botànica, Facultat de Farmàcia I Ciències de L'Alimentació, Institut de Recerca de La Biodiversitat (IRBio) & Centre de Documentació de Biodiversitat Vegetal (CeDocBiV), Universitat de Barcelona, Barcelona, Spain
| | - Jorunn Skjermo
- Department of Fisheries and New Biomarine Industries, SINTEF Ocean, Trondheim, Norway
| | - Åshild Ergon
- Department of Plant Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, Norway
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8
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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. JOURNAL OF PHYCOLOGY 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] [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.
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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
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9
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Darnet S, Blary A, Chevalier Q, Schaller H. Phytosterol Profiles, Genomes and Enzymes - An Overview. FRONTIERS IN PLANT SCIENCE 2021; 12:665206. [PMID: 34093623 PMCID: PMC8172173 DOI: 10.3389/fpls.2021.665206] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/20/2021] [Indexed: 05/12/2023]
Abstract
The remarkable diversity of sterol biosynthetic capacities described in living organisms is enriched at a fast pace by a growing number of sequenced genomes. Whereas analytical chemistry has produced a wealth of sterol profiles of species in diverse taxonomic groups including seed and non-seed plants, algae, phytoplanktonic species and other unicellular eukaryotes, functional assays and validation of candidate genes unveils new enzymes and new pathways besides canonical biosynthetic schemes. An overview of the current landscape of sterol pathways in the tree of life is tentatively assembled in a series of sterolotypes that encompass major groups and provides also peculiar features of sterol profiles in bacteria, fungi, plants, and algae.
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Affiliation(s)
| | | | | | - Hubert Schaller
- Plant Isoprenoid Biology Team, Institut de Biologie Moléculaire des Plantes du CNRS, Université de Strasbourg, Strasbourg, France
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10
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Karimi E, Geslain E, Belcour A, Frioux C, Aïte M, Siegel A, Corre E, Dittami SM. Robustness analysis of metabolic predictions in algal microbial communities based on different annotation pipelines. PeerJ 2021; 9:e11344. [PMID: 33996285 PMCID: PMC8106915 DOI: 10.7717/peerj.11344] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 04/03/2021] [Indexed: 01/29/2023] Open
Abstract
Animals, plants, and algae rely on symbiotic microorganisms for their development and functioning. Genome sequencing and genomic analyses of these microorganisms provide opportunities to construct metabolic networks and to analyze the metabolism of the symbiotic communities they constitute. Genome-scale metabolic network reconstructions rest on information gained from genome annotation. As there are multiple annotation pipelines available, the question arises to what extent differences in annotation pipelines impact outcomes of these analyses. Here, we compare five commonly used pipelines (Prokka, MaGe, IMG, DFAST, RAST) from predicted annotation features (coding sequences, Enzyme Commission numbers, hypothetical proteins) to the metabolic network-based analysis of symbiotic communities (biochemical reactions, producible compounds, and selection of minimal complementary bacterial communities). While Prokka and IMG produced the most extensive networks, RAST and DFAST networks produced the fewest false positives and the most connected networks with the fewest dead-end metabolites. Our results underline differences between the outputs of the tested pipelines at all examined levels, with small differences in the draft metabolic networks resulting in the selection of different microbial consortia to expand the metabolic capabilities of the algal host. However, the consortia generated yielded similar predicted producible compounds and could therefore be considered functionally interchangeable. This contrast between selected communities and community functions depending on the annotation pipeline needs to be taken into consideration when interpreting the results of metabolic complementarity analyses. In the future, experimental validation of bioinformatic predictions will likely be crucial to both evaluate and refine the pipelines and needs to be coupled with increased efforts to expand and improve annotations in reference databases.
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Affiliation(s)
- Elham Karimi
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Enora Geslain
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France.,FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Arnaud Belcour
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | | | - Méziane Aïte
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Anne Siegel
- Equipe Dyliss, Univ Rennes, Inria, CNRS, IRISA, Rennes, France
| | - Erwan Corre
- FR2424, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
| | - Simon M Dittami
- UMR8227, Integrative Biology of Marine Models, Sorbonne Université/CNRS, Station Biologique de Roscoff, Roscoff, France
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11
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Patwary ZP, Paul NA, Nishitsuji K, Campbell AH, Shoguchi E, Zhao M, Cummins SF. Application of omics research in seaweeds with a focus on red seaweeds. Brief Funct Genomics 2021; 20:148-161. [PMID: 33907795 DOI: 10.1093/bfgp/elab023] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/24/2021] [Accepted: 03/25/2021] [Indexed: 01/01/2023] Open
Abstract
Targeted 'omics' research for seaweeds, utilizing various computational and informatics frameworks, has the potential to rapidly develop our understanding of biological processes at the molecular level and contribute to solutions for the most pressing environmental and social issues of our time. Here, a systematic review into the current status of seaweed omics research was undertaken to evaluate the biological diversity of seaweed species investigated (red, green and brown phyla), the levels to which the work was undertaken (from full genome to transcripts, proteins or metabolites) and the field of research to which it has contributed. We report that from 1994 to 2021 the majority of seaweed omics research has been performed on the red seaweeds (45% of total studies), with more than half of these studies based upon two genera Pyropia and Gracilaria. A smaller number of studies examined brown seaweed (key genera Saccharina and Sargassum) and green seaweed (primarily Ulva). Overall, seaweed omics research is most highly associated with the field of evolution (46% of total studies), followed by the fields of ecology, natural products and their biosynthesis, omics methodology and seaweed-microbe interactions. Synthesis and specific outcomes derived from omics studies in the red seaweeds are provided. Together, these studies have provided a broad-scale interrogation of seaweeds, facilitating our ability to answer fundamental queries and develop applied outcomes. Crucial to the next steps will be establishing analytical tools and databases that can be more broadly utilized by practitioners and researchers across the globe because of their shared interest in the key seaweed genera.
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Affiliation(s)
| | | | - Koki Nishitsuji
- marine genomics unit in the Okinawa Institute of Science and Technology Graduate University
| | | | - Eiichi Shoguchi
- marine genomics unit in the Okinawa Institute of Science and Technology Graduate University
| | - Min Zhao
- University of the Sunshine Coast
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12
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Girard J, Lanneau G, Delage L, Leroux C, Belcour A, Got J, Collén J, Boyen C, Siegel A, Dittami SM, Leblanc C, Markov GV. Semi-Quantitative Targeted Gas Chromatography-Mass Spectrometry Profiling Supports a Late Side-Chain Reductase Cycloartenol-to-Cholesterol Biosynthesis Pathway in Brown Algae. FRONTIERS IN PLANT SCIENCE 2021; 12:648426. [PMID: 33986764 PMCID: PMC8112355 DOI: 10.3389/fpls.2021.648426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Accepted: 04/06/2021] [Indexed: 05/08/2023]
Abstract
Sterols are biologically important molecules that serve as membrane fluidity regulators and precursors of signaling molecules, either endogenous or involved in biotic interactions. There is currently no model of their biosynthesis pathways in brown algae. Here, we benefit from the availability of genome data and gas chromatography-mass spectrometry (GC-MS) sterol profiling using a database of internal standards to build such a model. We expand the set of identified sterols in 11 species of red, brown, and green macroalgae and integrate these new data with genomic data. Our analyses suggest that some metabolic reactions may be conserved despite the loss of canonical eukaryotic enzymes, like the sterol side-chain reductase (SSR). Our findings are consistent with the principle of metabolic pathway drift through enzymatic replacement and show that cholesterol synthesis from cycloartenol may be a widespread but variable pathway among chlorophyllian eukaryotes. Among the factors contributing to this variability, one could be the recruitment of cholesterol biosynthetic intermediates to make signaling molecules, such as the mozukulins. These compounds were found in some brown algae belonging to Ectocarpales, and we here provide a first mozukulin biosynthetic model. Our results demonstrate that integrative approaches can already be used to infer experimentally testable models, which will be useful to further investigate the biological roles of those newly identified algal pathways.
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Affiliation(s)
- Jean Girard
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Goulven Lanneau
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
- CNRS, Plateforme Corsaire-METABOMER (FR2424), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Ludovic Delage
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Cédric Leroux
- CNRS, Plateforme Corsaire-METABOMER (FR2424), Station Biologique de Roscoff, Sorbonne Université, Roscoff, France
| | - Arnaud Belcour
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Jeanne Got
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Jonas Collén
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Catherine Boyen
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Simon M. Dittami
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Catherine Leblanc
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
| | - Gabriel V. Markov
- CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), Sorbonne Université, Roscoff, France
- *Correspondence: Gabriel V. Markov,
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13
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Abstract
Model organisms are extensively used in research as accessible and convenient systems for studying a particular area or question in biology. Traditionally, only a limited number of organisms have been studied in detail, but modern genomic tools are enabling researchers to extend beyond the set of classical model organisms to include novel species from less-studied phylogenetic groups. This review focuses on model species for an important group of multicellular organisms, the brown algae. The development of genetic and genomic tools for the filamentous brown alga Ectocarpus has led to it emerging as a general model system for this group, but additional models, such as Fucus or Dictyota dichotoma, remain of interest for specific biological questions. In addition, Saccharina japonica has emerged as a model system to directly address applied questions related to algal aquaculture. We discuss the past, present, and future of brown algal model organisms in relation to the opportunities and challenges in brown algal research.
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Affiliation(s)
- Susana M Coelho
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
- Current affiliation: Department of Algal Development and Evolution, Max Planck Institute for Developmental Biology, 72076 Tübingen, Germany;
| | - J Mark Cock
- Laboratory of Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff (SBR), CNRS, Sorbonne Université, 29680 Roscoff, France;
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14
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Coelho SM, Peters AF, Müller D, Cock JM. Ectocarpus: an evo-devo model for the brown algae. EvoDevo 2020; 11:19. [PMID: 32874530 PMCID: PMC7457493 DOI: 10.1186/s13227-020-00164-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/13/2020] [Indexed: 12/15/2022] Open
Abstract
Ectocarpus is a genus of filamentous, marine brown algae. Brown algae belong to the stramenopiles, a large supergroup of organisms that are only distantly related to animals, land plants and fungi. Brown algae are also one of only a small number of eukaryotic lineages that have evolved complex multicellularity. For many years, little information was available concerning the molecular mechanisms underlying multicellular development in the brown algae, but this situation has changed with the emergence of Ectocarpus as a model brown alga. Here we summarise some of the main questions that are being addressed and areas of study using Ectocarpus as a model organism and discuss how the genomic information, genetic tools and molecular approaches available for this organism are being employed to explore developmental questions in an evolutionary context.
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Affiliation(s)
- 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, 29688 Roscoff, France
| | | | - Dieter Müller
- Fachbereich Biologie der Universitat Konstanz, 78457 Konstanz, 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, 29688 Roscoff, France
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15
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Dittami SM, Peters AF, West JA, Cariou T, KleinJan H, Burgunter-Delamare B, Prechoux A, Egan S, Boyen C. Revisiting Australian Ectocarpus subulatus (Phaeophyceae) From the Hopkins River: Distribution, Abiotic Environment, and Associated Microbiota. JOURNAL OF PHYCOLOGY 2020; 56:719-729. [PMID: 31965565 DOI: 10.1111/jpy.12970] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Accepted: 01/07/2020] [Indexed: 05/24/2023]
Abstract
In 1995 a strain of Ectocarpus was isolated from Hopkins River Falls, Victoria, Australia, constituting one of few available freshwater or nearly freshwater brown algae, and the only one belonging to the genus Ectocarpus. It has since been used as a model to study acclimation and adaptation to low salinities and the role of its microbiota in these processes. To provide more background information on this model, we assessed if Ectocarpus was still present in the Hopkins river 22 years after the original finding, estimated its present distribution, described its abiotic environment, and determined its in situ microbial composition. We sampled for Ectocarpus at 15 sites along the Hopkins River as well as 10 neighboring sites and found individuals with ITS and cox1 sequences identical to the original isolate at three sites upstream of Hopkins River Falls. The salinity of the water at these sites ranged from 3.1 to 6.9, and it was rich in sulfate (1-5 mM). The diversity of bacteria associated with the algae in situ (1312 operational taxonomic units) was one order of magnitude higher than in previous studies of the original laboratory culture, and 95 alga-associated bacterial strains were isolated from algal filaments on site. In particular, species of Planctomycetes were abundant in situ but rare in laboratory cultures. Our results confirmed that Ectocarpus was still present in the Hopkins River, and the newly isolated algal and bacterial strains offer new possibilities to study the adaptation of Ectocarpus to low salinity and its interactions with its microbiome.
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Affiliation(s)
- Simon M Dittami
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Akira F Peters
- Bezhin Rosko, 40 Rue des Pêcheurs, 29250, Santec, France
| | - John A West
- Biosciences 2, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Thierry Cariou
- CNRS, FR2424, Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Hetty KleinJan
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Bertille Burgunter-Delamare
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Aurélie Prechoux
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Catherine Boyen
- CNRS, Integrative Biology of Marine Models (LBI2M), Station Biologique de Roscoff, Sorbonne Université, 29680, Roscoff, France
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16
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Belcour A, Girard J, Aite M, Delage L, Trottier C, Marteau C, Leroux C, Dittami SM, Sauleau P, Corre E, Nicolas J, Boyen C, Leblanc C, Collén J, Siegel A, Markov GV. Inferring Biochemical Reactions and Metabolite Structures to Understand Metabolic Pathway Drift. iScience 2020; 23:100849. [PMID: 32058961 PMCID: PMC6997860 DOI: 10.1016/j.isci.2020.100849] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 11/11/2019] [Accepted: 01/13/2020] [Indexed: 11/03/2022] Open
Abstract
Inferring genome-scale metabolic networks in emerging model organisms is challenged by incomplete biochemical knowledge and partial conservation of biochemical pathways during evolution. Therefore, specific bioinformatic tools are necessary to infer biochemical reactions and metabolic structures that can be checked experimentally. Using an integrative approach combining genomic and metabolomic data in the red algal model Chondrus crispus, we show that, even metabolic pathways considered as conserved, like sterols or mycosporine-like amino acid synthesis pathways, undergo substantial turnover. This phenomenon, here formally defined as "metabolic pathway drift," is consistent with findings from other areas of evolutionary biology, indicating that a given phenotype can be conserved even if the underlying molecular mechanisms are changing. We present a proof of concept with a methodological approach to formalize the logical reasoning necessary to infer reactions and molecular structures, abstracting molecular transformations based on previous biochemical knowledge.
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Affiliation(s)
- Arnaud Belcour
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Jean Girard
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Méziane Aite
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | | | - Cédric Leroux
- Sorbonne Université, CNRS, Plateforme METABOMER-Corsaire (FR2424), Station Biologique de Roscoff, Roscoff, France
| | - Simon M Dittami
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | | | - Erwan Corre
- Sorbonne Université, CNRS, Plateforme ABiMS (FR2424), Station Biologique de Roscoff, Roscoff, France
| | - Jacques Nicolas
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Catherine Boyen
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Jonas Collén
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France
| | - Anne Siegel
- Univ Rennes, Inria, CNRS, IRISA, Equipe Dyliss, Rennes, France
| | - Gabriel V Markov
- Sorbonne Université, CNRS, Integrative Biology of Marine Models (LBI2M, UMR8227), Station Biologique de Roscoff (SBR), 29680 Roscoff, France.
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17
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Siméon A, Kridi S, Kloareg B, Hervé C. Presence of Exogenous Sulfate Is Mandatory for Tip Growth in the Brown Alga Ectocarpus subulatus. FRONTIERS IN PLANT SCIENCE 2020; 11:1277. [PMID: 33013948 PMCID: PMC7461865 DOI: 10.3389/fpls.2020.01277] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 08/05/2020] [Indexed: 05/08/2023]
Abstract
Brown algae (Phaeophyceae) are multicellular photoautrophic organisms and the largest biomass producers in coastal regions. A variety of observations indicate that their extracellular matrix (ECM) is involved with screening of salts, development, cell fate selection, and defense responses. It is likely that these functionalities are related to its constitutive structures. The major components of the ECM of brown algae are β-glucans, alginates, and fucose-containing sulfated polysaccharides. The genus Ectocarpus comprises a wide range of species that have adapted to different environments, including isolates of Ectocarpus subulatus, a species highly resistant to low salinity. Previous studies on a freshwater strain of E. subulatus indicated that the sulfate remodeling of fucans is related to the external salt concentration. Here we show that the sulfate content of the surrounding medium is a key parameter influencing both the patterning of the alga and the occurrence of the BAM4 sulfated fucan epitope in walls of apical cells. These results indicate that sulfate uptake and incorporation in the sulfated fucans from apical cells is an essential parameter to sustain tip growth, and we discuss its influence on the architectural plasticity of Ectocarpus.
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