1
|
Ishikawa T, Domergue F, Amato A, Corellou F. Characterization of Unique Eukaryotic Sphingolipids with Temperature-Dependent Δ8-Unsaturation from the Picoalga Ostreococcus tauri. PLANT & CELL PHYSIOLOGY 2024; 65:1029-1046. [PMID: 38252418 DOI: 10.1093/pcp/pcae007] [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: 09/20/2023] [Revised: 11/28/2023] [Accepted: 01/18/2024] [Indexed: 01/23/2024]
Abstract
Sphingolipids (SLs) are ubiquitous components of eukaryotic cell membranes and are found in some prokaryotic organisms and viruses. They are composed of a sphingoid backbone that may be acylated and glycosylated. Assembly of various sphingoid base, fatty acyl and glycosyl moieties results in highly diverse structures. The functional significance of variations in SL chemical diversity and abundance is still in the early stages of investigation. Among SL modifications, Δ8-desaturation of the sphingoid base occurs only in plants and fungi. In plants, SL Δ8-unsaturation is involved in cold hardiness. Our knowledge of the structure and functions of SLs in microalgae lags far behind that of animals, plants and fungi. Original SL structures have been reported from microalgae. However, functional studies are still missing. Ostreococcus tauri is a minimal microalga at the base of the green lineage and is therefore a key organism for understanding lipid evolution. In the present work, we achieved the detailed characterization of O. tauri SLs and unveiled unique glycosylceramides as sole complex SLs. The head groups are reminiscent of bacterial SLs, as they contain hexuronic acid residues and can be polyglycosylated. Ceramide backbones show a limited variety, and SL modification is restricted to Δ8-unsaturation. The Δ8-SL desaturase from O. tauri only produced E isomers. Expression of both Δ8-SL desaturase and Δ8-unsaturation of sphingolipids varied with temperature, with lower levels at 24°C than at 14°C. Overexpression of the Δ8-SL desaturase dramatically increases the level of Δ8 unsaturation at 24°C and is paralleled by a failure to increase cell size. Our work provides the first characterization of O. tauri SLs and functional evidence for the involvement of SL Δ8-unsaturation for temperature acclimation in microalgae, suggesting that this function is an ancestral feature in the green lineage.
Collapse
Affiliation(s)
- Toshiki Ishikawa
- Graduate School of Science and Engineering, Saitama University, 225 Shimo-Okubo, Sakura-ku, Saitama-city, Saitama, 338-8570 Japan
| | - Frédéric Domergue
- Laboratoire de Biogenèse Membranaire, University of Bordeaux, CNRSUMR 5200, Av. Edouard Bourlaux, Villenave d'Ornon 33140, France
| | - Alberto Amato
- Laboratoire de Physiologie Végétale et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique UMR 5168, Université Grenoble Alpes, CEA, IRIG, 17 Av. Des Martyrs, Grenoble 38000, France
| | - Florence Corellou
- Laboratoire de Physiologie Végétale et Cellulaire, Commissariat à l'Energie Atomique et aux Energies Alternatives, Institut National de Recherche pour l'Agriculture, l'Alimentation et l'Environnement, Centre National de la Recherche Scientifique UMR 5168, Université Grenoble Alpes, CEA, IRIG, 17 Av. Des Martyrs, Grenoble 38000, France
| |
Collapse
|
2
|
Goold HD, Moseley JL, Lauersen KJ. The synthetic future of algal genomes. CELL GENOMICS 2024; 4:100505. [PMID: 38395701 PMCID: PMC10943592 DOI: 10.1016/j.xgen.2024.100505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2023] [Revised: 12/18/2023] [Accepted: 01/24/2024] [Indexed: 02/25/2024]
Abstract
Algae are diverse organisms with significant biotechnological potential for resource circularity. Taking inspiration from fermentative microbes, engineering algal genomes holds promise to broadly expand their application ranges. Advances in genome sequencing with improvements in DNA synthesis and delivery techniques are enabling customized molecular tool development to confer advanced traits to algae. Efforts to redesign and rebuild entire genomes to create fit-for-purpose organisms currently being explored in heterotrophic prokaryotes and eukaryotic microbes could also be applied to photosynthetic algae. Future algal genome engineering will enhance yields of native products and permit the expression of complex biochemical pathways to produce novel metabolites from sustainable inputs. We present a historical perspective on advances in engineering algae, discuss the requisite genetic traits to enable algal genome optimization, take inspiration from whole-genome engineering efforts in other microbes for algal systems, and present candidate algal species in the context of these engineering goals.
Collapse
Affiliation(s)
- Hugh D Goold
- New South Wales Department of Primary Industries, Orange, NSW 2800, Australia; ARC Center of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia; School of Natural Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Jeffrey L Moseley
- California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA 94720, USA; Division of Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; Phycoil Biotechnology International, Inc., Fremont, CA 94538, USA
| | - Kyle J Lauersen
- Bioengineering Program, Biological and Environmental Sciences and Engineering Division, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Kingdom of Saudi Arabia.
| |
Collapse
|
3
|
Belshaw N, Grouneva I, Aram L, Gal A, Hopes A, Mock T. Efficient gene replacement by CRISPR/Cas-mediated homologous recombination in the model diatom Thalassiosira pseudonana. THE NEW PHYTOLOGIST 2023; 238:438-452. [PMID: 36307966 DOI: 10.1111/nph.18587] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Accepted: 10/18/2022] [Indexed: 06/16/2023]
Abstract
CRISPR/Cas enables targeted genome editing in many different plant and algal species including the model diatom Thalassiosira pseudonana. However, efficient gene targeting by homologous recombination (HR) to date is only reported for photosynthetic organisms in their haploid life-cycle phase. Here, a CRISPR/Cas construct, assembled using Golden Gate cloning, enabled highly efficient HR in a diploid photosynthetic organism. Homologous recombination was induced in T. pseudonana using sequence-specific CRISPR/Cas, paired with a dsDNA donor matrix, generating substitution of the silacidin, nitrate reductase and urease genes by a resistance cassette (FCP:NAT). Up to c. 85% of NAT-resistant T. pseudonana colonies screened positive for HR by nested PCR. Precise integration of FCP:NAT at each locus was confirmed using an inverse PCR approach. The knockout of the nitrate reductase and urease genes impacted growth on nitrate and urea, respectively, while the knockout of the silacidin gene in T. pseudonana caused a significant increase in cell size, confirming the role of this gene for cell-size regulation in centric diatoms. Highly efficient gene targeting by HR makes T. pseudonana as genetically tractable as Nannochloropsis and Physcomitrella, hence rapidly advancing functional diatom biology, bionanotechnology and biotechnological applications targeted on harnessing the metabolic potential of diatoms.
Collapse
Affiliation(s)
- Nigel Belshaw
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Irina Grouneva
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Lior Aram
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Assaf Gal
- Department of Plant and Environmental Sciences, Faculty of Biochemistry, Weizmann Institute of Science, Rehovot, 7610001, Israel
| | - Amanda Hopes
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| |
Collapse
|
4
|
Kuo EY, Yang RY, Chin YY, Chien YL, Chen YC, Wei CY, Kao LJ, Chang YH, Li YJ, Chen TY, Lee TM. Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae. Biotechnol J 2022; 17:e2100603. [PMID: 35467782 DOI: 10.1002/biot.202100603] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/12/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022]
Abstract
Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.
Collapse
Affiliation(s)
- Eva YuHua Kuo
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Ru-Yin Yang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yuan Yu Chin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Lin Chien
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu Chu Chen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Cheng-Yu Wei
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Li-Jung Kao
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Hua Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu-Jia Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Te-Yuan Chen
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| |
Collapse
|
5
|
Singh M, Mal N, Mohapatra R, Bagchi T, Parambath SD, Chavali M, Rao KM, Ramanaiah SV, Kadier A, Kumar G, Chandrasekhar K, Kim SH. Recent biotechnological developments in reshaping the microalgal genome: A signal for green recovery in biorefinery practices. CHEMOSPHERE 2022; 293:133513. [PMID: 34990720 DOI: 10.1016/j.chemosphere.2022.133513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 12/13/2021] [Accepted: 12/31/2021] [Indexed: 06/14/2023]
Abstract
The use of renewable energy sources as a substitute for nonrenewable fossil fuels is urgently required. Algae biorefinery platform provides an excellent alternate to overcome future energy problems. However, to let this viable biomass be competent with existing feedstocks, it is necessary to exploit genetic manipulation and improvement in upstream and downstream platforms for optimal bio-product recovery. Furthermore, the techno-economic strategies further maximize metabolites production for biofuel, biohydrogen, and other industrial applications. The experimental methodologies in algal photobioreactor promote high biomass production, enriched in lipid and starch content in limited environmental conditions. This review presents an optimization framework combining genetic manipulation methods to simulate microalgal growth dynamics, understand the complexity of algal biorefinery to scale up, and identify green strategies for techno-economic feasibility of algae for biomass conversion. Overall, the algal biorefinery opens up new possibilities for the valorization of algae biomass and the synthesis of various novel products.
Collapse
Affiliation(s)
- Meenakshi Singh
- Department of Botany, Faculty of Science, The Maharaja Sayajirao University of Baroda, Vadodara, 390002, Gujarat, India
| | - Navonil Mal
- Department of Botany, University of Calcutta, Kolkata, 700019, West Bengal, India
| | - Reecha Mohapatra
- Department of Life Sciences, NIT Rourkela, 769008, Odisha, India
| | - Trisha Bagchi
- Department of Botany, West Bengal State University, Barasat, 700126, West Bengal, India
| | | | - Murthy Chavali
- Office of the Dean (Research) & Division of Chemistry, Department of Science, Faculty of Science & Technology, Alliance University (Central Campus), Chandapura-Anekal Main Road, Bengaluru, 562106, Karnataka, India; NTRC-MCETRC and 109 Nano Composite Technologies Pvt. Ltd., Guntur District, 522201, Andhra Pradesh, India
| | - Kummara Madhusudana Rao
- School of Chemical Engineering, Yeungnam University, 280 Daehak-ro, Joyeong-dong, Gyeongsan-si, Gyeongsangbuk-do, 38541, South Korea; Department of Automotive Lighting Convergence Engineering, Yeungnam University, 280 Daehak-ro, Joyeong-dong, Gyeongsan-si, Gyeongsangbuk-do, 38541, South Korea
| | - S V Ramanaiah
- Food and Biotechnology Research Lab, South Ural State University (National Research University), 454080, Chelyabinsk, Russian Federation
| | - Abudukeremu Kadier
- Laboratory of Environmental Science and Technology, The Xinjiang Technical Institute of Physics and Chemistry, Key Laboratory of Functional Materials and Devices for Special Environments, Chinese Academy of Sciences, Urumqi, 830011, China; Center of Material and Opto-electronic Research, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Gopalakrishnan Kumar
- Institute of Chemistry, Bioscience and Environmental Engineering, Faculty of Science and Technology, University of Stavanger, 4036, Stavanger, Norway
| | - K Chandrasekhar
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| | - Sang-Hyoun Kim
- School of Civil and Environmental Engineering, Yonsei University, Seoul, 03722, Republic of Korea.
| |
Collapse
|
6
|
Muthukrishnan L. Bio‐engineering of microalgae: Challenges and future prospects toward industrial and environmental applications. J Basic Microbiol 2022; 62:310-329. [DOI: 10.1002/jobm.202100417] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 12/28/2021] [Accepted: 01/08/2022] [Indexed: 01/29/2023]
Affiliation(s)
- Lakshmipathy Muthukrishnan
- Department of Conservative Dentistry and Endodontics, Saveetha Dental College and Hospitals Saveetha Institute of Medical and Technical Sciences Chennai Tamil Nadu India
| |
Collapse
|
7
|
Thomy J, Sanchez F, Gut M, Cruz F, Alioto T, Piganeau G, Grimsley N, Yau S. Combining Nanopore and Illumina Sequencing Permits Detailed Analysis of Insertion Mutations and Structural Variations Produced by PEG-Mediated Transformation in Ostreococcus tauri. Cells 2021; 10:cells10030664. [PMID: 33802698 PMCID: PMC8002553 DOI: 10.3390/cells10030664] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 03/09/2021] [Accepted: 03/15/2021] [Indexed: 12/13/2022] Open
Abstract
Ostreococcus tauri is a simple unicellular green alga representing an ecologically important group of phytoplankton in oceans worldwide. Modern molecular techniques must be developed in order to understand the mechanisms that permit adaptation of microalgae to their environment. We present for the first time in O. tauri a detailed characterization of individual genomic integration events of foreign DNA of plasmid origin after PEG-mediated transformation. Vector integration occurred randomly at a single locus in the genome and mainly as a single copy. Thus, we confirmed the utility of this technique for insertional mutagenesis. While the mechanism of double-stranded DNA repair in the O. tauri model remains to be elucidated, we clearly demonstrate by genome resequencing that the integration of the vector leads to frequent structural variations (deletions/insertions and duplications) and some chromosomal rearrangements in the genome at the insertion loci. Furthermore, we often observed variations in the vector sequence itself. From these observations, we speculate that a nonhomologous end-joining-like mechanism is employed during random insertion events, as described in plants and other freshwater algal models. PEG-mediated transformation is therefore a promising molecular biology tool, not only for functional genomic studies, but also for biotechnological research in this ecologically important marine alga.
Collapse
Affiliation(s)
- Julie Thomy
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Frederic Sanchez
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Marta Gut
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Fernando Cruz
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
| | - Tyler Alioto
- CNAG-CRG, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Baldiri i Reixac 4, 08028 Barcelona, Spain; (M.G.); (F.C.); (T.A.)
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Gwenael Piganeau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
| | - Nigel Grimsley
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
- Correspondence: (N.G.); (S.Y.)
| | - Sheree Yau
- Sorbonne Université, CNRS, UMR 7232 Biologie Intégrative des Organismes Marins (BIOM), Observatoire Océanologique, F-66650 Banyuls-sur-Mer, France; (J.T.); (F.S.); (G.P.)
- Correspondence: (N.G.); (S.Y.)
| |
Collapse
|
8
|
Carrasco Flores D, Fricke M, Wesp V, Desirò D, Kniewasser A, Hölzer M, Marz M, Mittag M. A marine Chlamydomonas sp. emerging as an algal model. JOURNAL OF PHYCOLOGY 2021; 57:54-69. [PMID: 33043442 DOI: 10.1111/jpy.13083] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2020] [Revised: 08/25/2020] [Accepted: 08/26/2020] [Indexed: 06/11/2023]
Abstract
The freshwater microalga Chlamydomonas reinhardtii, which lives in wet soil, has served for decades as a model for numerous biological processes, and many tools have been introduced for this organism. Here, we have established a stable nuclear transformation for its marine counterpart, Chlamydomonas sp. SAG25.89, by fusing specific cis-acting elements from its Actin gene with the gene providing hygromycin resistance and using an elaborated electroporation protocol. Like C. reinhardtii, Chlamydomonas sp. has a high GC content, allowing reporter genes and selection markers to be applicable in both organisms. Chlamydomonas sp. grows purely photoautotrophically and requires ammonia as a nitrogen source because its nuclear genome lacks some of the genes required for nitrogen metabolism. Interestingly, it can grow well under both low and very high salinities (up to 50 g · L-1 ) rendering it as a model for osmotolerance. We further show that Chlamydomonas sp. grows well from 15 to 28°C, but halts its growth at 32°C. The genome of Chlamydomonas sp. contains some gene homologs the expression of which is regulated according to the ambient temperatures and/or confer thermal acclimation in C. reinhardtii. Thus, knowledge of temperature acclimation can now be compared to the marine species. Furthermore, Chlamydomonas sp. can serve as a model for studying marine microbial interactions and for comparing mechanisms in freshwater and marine environments. Chlamydomonas sp. was previously shown to be immobilized rapidly by a cyclic lipopeptide secreted from the antagonistic bacterium Pseudomonas protegens PF-5, which deflagellates C. reinhardtii.
Collapse
Affiliation(s)
- David Carrasco Flores
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, 07743, Germany
| | - Markus Fricke
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, 07743, Germany
| | - Valentin Wesp
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, 07743, Germany
| | - Daniel Desirò
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, 07743, Germany
| | - Anja Kniewasser
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, 07743, Germany
| | - Martin Hölzer
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, 07743, Germany
| | - Manja Marz
- RNA Bioinformatics and High-Throughput Analysis, Friedrich Schiller University, Jena, 07743, Germany
- FLI, Leibniz Institute for Age Research, Beutenbergstr. 11, Jena, 07745, Germany
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Jena, 07743, Germany
| |
Collapse
|
9
|
Sutak R, Camadro JM, Lesuisse E. Iron Uptake Mechanisms in Marine Phytoplankton. Front Microbiol 2020; 11:566691. [PMID: 33250865 PMCID: PMC7676907 DOI: 10.3389/fmicb.2020.566691] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 10/19/2020] [Indexed: 12/20/2022] Open
Abstract
Oceanic phytoplankton species have highly efficient mechanisms of iron acquisition, as they can take up iron from environments in which it is present at subnanomolar concentrations. In eukaryotes, three main models were proposed for iron transport into the cells by first studying the kinetics of iron uptake in different algal species and then, more recently, by using modern biological techniques on the model diatom Phaeodactylum tricornutum. In the first model, the rate of uptake is dependent on the concentration of unchelated Fe species, and is thus limited thermodynamically. Iron is transported by endocytosis after carbonate-dependent binding of Fe(III)' (inorganic soluble ferric species) to phytotransferrin at the cell surface. In this strategy the cells are able to take up iron from very low iron concentration. In an alternative model, kinetically limited for iron acquisition, the extracellular reduction of all iron species (including Fe') is a prerequisite for iron acquisition. This strategy allows the cells to take up iron from a great variety of ferric species. In a third model, hydroxamate siderophores can be transported by endocytosis (dependent on ISIP1) after binding to the FBP1 protein, and iron is released from the siderophores by FRE2-dependent reduction. In prokaryotes, one mechanism of iron uptake is based on the use of siderophores excreted by the cells. Iron-loaded siderophores are transported across the cell outer membrane via a TonB-dependent transporter (TBDT), and are then transported into the cells by an ABC transporter. Open ocean cyanobacteria do not excrete siderophores but can probably use siderophores produced by other organisms. In an alternative model, inorganic ferric species are transported through the outer membrane by TBDT or by porins, and are taken up by the ABC transporter system FutABC. Alternatively, ferric iron of the periplasmic space can be reduced by the alternative respiratory terminal oxidase (ARTO) and the ferrous ions can be transported by divalent metal transporters (FeoB or ZIP). After reoxidation, iron can be taken up by the high-affinity permease Ftr1.
Collapse
Affiliation(s)
- Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University, BIOCEV, Vestec, Czechia
| | | | | |
Collapse
|
10
|
Genetic tool development in marine protists: emerging model organisms for experimental cell biology. Nat Methods 2020; 17:481-494. [PMID: 32251396 PMCID: PMC7200600 DOI: 10.1038/s41592-020-0796-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 03/02/2020] [Indexed: 12/13/2022]
Abstract
Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species, which do not represent eukaryotic diversity or environmentally relevant taxa. Here, we report on the development of genetic tools in a range of protists primarily from marine environments. We present evidence for foreign DNA delivery and expression in 13 species never before transformed and for advancement of tools for eight other species, as well as potential reasons for why transformation of yet another 17 species tested was not achieved. Our resource in genetic manipulation will provide insights into the ancestral eukaryotic lifeforms, general eukaryote cell biology, protein diversification and the evolution of cellular pathways.
Collapse
|
11
|
Abstract
Algae are photosynthetic eukaryotes whose taxonomic breadth covers a range of life histories, degrees of cellular and developmental complexity, and diverse patterns of sexual reproduction. These patterns include haploid- and diploid-phase sex determination, isogamous mating systems, and dimorphic sexes. Despite the ubiquity of sexual reproduction in algae, their mating-type-determination and sex-determination mechanisms have been investigated in only a limited number of representatives. These include volvocine green algae, where sexual cycles and sex-determining mechanisms have shed light on the transition from mating types to sexes, and brown algae, which are a model for UV sex chromosome evolution in the context of a complex haplodiplontic life cycle. Recent advances in genomics have aided progress in understanding sexual cycles in less-studied taxa including ulvophyte, charophyte, and prasinophyte green algae, as well as in diatoms.
Collapse
Affiliation(s)
- James Umen
- Donald Danforth Plant Science Center, St. Louis, Missouri 63132, USA;
| | - Susana Coelho
- Algal Genetics Group, Integrative Biology of Marine Models, Station Biologique de Roscoff, Sorbonne Université, UPMC Université Paris 06, CNRS, CS 90074, F-29688 Roscoff, France;
| |
Collapse
|
12
|
Blanco-Ameijeiras S, Cabanes DJE, Hassler CS. Towards the development of a new generation of whole-cell bioreporters to sense iron bioavailability in oceanic systems-learning from the case of Synechococcus sp. PCC7002 iron bioreporter. J Appl Microbiol 2019; 127:1291-1304. [PMID: 30970168 DOI: 10.1111/jam.14277] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2018] [Revised: 02/17/2019] [Accepted: 04/04/2019] [Indexed: 12/24/2022]
Abstract
Whole-cell bioreporters are genetically modified micro-organisms designed to sense bioavailable forms of nutrients or toxic compounds in aquatic systems. As they represent the most promising cost-efficient tools available for such purpose, engineering and use of bioreporters is rapidly growing in association with wide applicability. Bioreporters are urgently needed to determine phytoplankton iron (Fe) limitation, which has been reported in up to 30% of the ocean, with consequences affecting Earth's global carbon cycle and climate. This study presents a critical evaluation and optimization of the only Cyanobacteria bioreporter available to sense Fe limitation in marine systems (Synechococcus sp. PCC7002). The nonmonotonic biphasic dose-response curve between the bioreporters' signal and Fe bioavailability impairs an appropriate data interpretation, highlighting the need for new carefully designed bioreporters. Here, limitations under low Fe concentrations were related to cellular energy stress, nonlinear expression of the targeted promoter and siderophore expression. Furthermore, we provide critical standard criteria for the development of new Fe bioreporters. Finally, based on gene expression data under a range of marine Fe concentrations, we propose novel sensor genes for the development of new Cyanobacteria Fe bioreporters for distinct marine regions.
Collapse
Affiliation(s)
- S Blanco-Ameijeiras
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - D J E Cabanes
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| | - C S Hassler
- Department F.-A. Forel for Environmental and Aquatic Sciences, Faculty of Science, University of Geneva, Geneva, Switzerland
| |
Collapse
|
13
|
Sanchez F, Geffroy S, Norest M, Yau S, Moreau H, Grimsley N. Simplified Transformation of Ostreococcus tauri Using Polyethylene Glycol. Genes (Basel) 2019; 10:E399. [PMID: 31130696 PMCID: PMC6562926 DOI: 10.3390/genes10050399] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2019] [Revised: 05/16/2019] [Accepted: 05/21/2019] [Indexed: 12/21/2022] Open
Abstract
Ostreococcustauri is an easily cultured representative of unicellular algae (class Mamiellophyceae) that abound in oceans worldwide. Eight complete 13-22 Mb genomes of phylogenetically divergent species within this class are available, and their DNA sequences are nearly always present in metagenomic data produced from marine samples. Here we describe a simplified and robust transformation protocol for the smallest of these algae (O. tauri). Polyethylene glycol (PEG) treatment was much more efficient than the previously described electroporation protocol. Short (2 min or less) incubation times in PEG gave >104 transformants per microgram DNA. The time of cell recovery after transformation could be reduced to a few hours, permitting the experiment to be done in a day rather than overnight as used in previous protocols. DNA was randomly inserted in the O. tauri genome. In our hands PEG was 20-40-fold more efficient than electroporation for the transformation of O. tauri, and this improvement will facilitate mutagenesis of all of the dispensable genes present in the tiny O. tauri genome.
Collapse
Affiliation(s)
- Frédéric Sanchez
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Solène Geffroy
- IFREMER, Centre Atlantique, 44331 Nantes CEDEX 03, France.
| | - Manon Norest
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Sheree Yau
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Hervé Moreau
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| | - Nigel Grimsley
- CNRS UMR7232 BIOM (Biologie Intégrative des Organismes Marin) Sorbonne University, 66650 Banyuls sur Mer, France.
| |
Collapse
|
14
|
Marine Natural Products from Microalgae: An -Omics Overview. Mar Drugs 2019; 17:md17050269. [PMID: 31067655 PMCID: PMC6562964 DOI: 10.3390/md17050269] [Citation(s) in RCA: 57] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2019] [Revised: 04/30/2019] [Accepted: 05/04/2019] [Indexed: 12/19/2022] Open
Abstract
Over the last decade, genome sequences and other -omics datasets have been produced for a wide range of microalgae, and several others are on the way. Marine microalgae possess distinct and unique metabolic pathways, and can potentially produce specific secondary metabolites with biological activity (e.g., antipredator, allelopathic, antiproliferative, cytotoxic, anticancer, photoprotective, as well as anti-infective and antifouling activities). Because microalgae are very diverse, and adapted to a broad variety of environmental conditions, the chances to find novel and unexplored bioactive metabolites with properties of interest for biotechnological and biomedical applications are high. This review presents a comprehensive overview of the current efforts and of the available solutions to produce, explore and exploit -omics datasets, with the aim of identifying species and strains with the highest potential for the identification of novel marine natural products. In addition, funding efforts for the implementation of marine microalgal -omics resources and future perspectives are presented as well.
Collapse
|
15
|
Scheiber IF, Pilátová J, Malych R, Kotabova E, Krijt M, Vyoral D, Mach J, Léger T, Camadro JM, Prášil O, Lesuisse E, Sutak R. Copper and iron metabolism in Ostreococcus tauri – the role of phytotransferrin, plastocyanin and a chloroplast copper-transporting ATPase. Metallomics 2019; 11:1657-1666. [DOI: 10.1039/c9mt00078j] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We have identified Ostreococcus tauri major iron uptake mediating protein, phytotransferrin (Ot-FEA1), whose expression and binding of iron is copper dependent.
Collapse
|
16
|
Khatiwada B, Kautto L, Sunna A, Sun A, Nevalainen H. Nuclear transformation of the versatile microalga Euglena gracilis. ALGAL RES 2019. [DOI: 10.1016/j.algal.2018.11.022] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
|
17
|
Paerl RW, Bertrand EM, Rowland E, Schatt P, Mehiri M, Niehaus TD, Hanson AD, Riemann L, Bouget FY. Carboxythiazole is a key microbial nutrient currency and critical component of thiamin biosynthesis. Sci Rep 2018; 8:5940. [PMID: 29654239 PMCID: PMC5899164 DOI: 10.1038/s41598-018-24321-2] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/28/2018] [Indexed: 11/25/2022] Open
Abstract
Almost all cells require thiamin, vitamin B1 (B1), which is synthesized via the coupling of thiazole and pyrimidine precursors. Here we demonstrate that 5-(2-hydroxyethyl)-4-methyl-1,3-thiazole-2-carboxylic acid (cHET) is a useful in vivo B1 precursor for representatives of ubiquitous marine picoeukaryotic phytoplankton and Escherichia coli – drawing attention to cHET as a valuable exogenous micronutrient for microorganisms with ecological, industrial, and biomedical value. Comparative utilization experiments with the terrestrial plant Arabidopsis thaliana revealed that it can also use exogenous cHET, but notably, picoeukaryotic marine phytoplankton and E. coli were adapted to grow on low (picomolar) concentrations of exogenous cHET. Our results call for the modification of the conventional B1 biosynthesis model to incorporate cHET as a key precursor for B1 biosynthesis in two domains of life, and for consideration of cHET as a microbial micronutrient currency modulating marine primary productivity and community interactions in human gut-hosted microbiomes.
Collapse
Affiliation(s)
- Ryan W Paerl
- Department of Marine Earth and Atmospheric Sciences, North Carolina State University, Raleigh, NC, USA 27695, USA. .,Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark.
| | - Erin M Bertrand
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Elden Rowland
- Department of Biology, Dalhousie University, Halifax, NS, Canada
| | - Phillippe Schatt
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls/mer, France
| | - Mohamed Mehiri
- University Nice Côte d'Azur, CNRS, Institute of Chemistry of Nice, UMR 7272, Marine Natural Products Team, Nice, France
| | - Thomas D Niehaus
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA 32611, USA
| | - Andrew D Hanson
- Horticultural Sciences Department, University of Florida, Gainesville, FL, USA 32611, USA
| | - Lasse Riemann
- Department of Biology, University of Copenhagen, 3000, Helsingør, Denmark
| | - Francois-Yves Bouget
- University Nice Côte d'Azur, CNRS, Institute of Chemistry of Nice, UMR 7272, Marine Natural Products Team, Nice, France
| |
Collapse
|
18
|
Guyon JB, Vergé V, Schatt P, Lozano JC, Liennard M, Bouget FY. Comparative Analysis of Culture Conditions for the Optimization of Carotenoid Production in Several Strains of the Picoeukaryote Ostreococcus. Mar Drugs 2018; 16:md16030076. [PMID: 29495580 PMCID: PMC5867620 DOI: 10.3390/md16030076] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 02/16/2018] [Accepted: 02/16/2018] [Indexed: 01/09/2023] Open
Abstract
Microalgae are promising sources for the sustainable production of compounds of interest for biotechnologies. Compared to higher plants, microalgae have a faster growth rate and can be grown in industrial photobioreactors. The microalgae biomass contains specific metabolites of high added value for biotechnology such as lipids, polysaccharides or carotenoid pigments. Studying carotenogenesis is important for deciphering the mechanisms of adaptation to stress tolerance as well as for biotechnological production. In recent years, the picoeukaryote Ostreococcustauri has emerged as a model organism thanks to the development of powerful genetic tools. Several strains of Ostreococcus isolated from different environments have been characterized with respect to light response or iron requirement. We have compared the carotenoid contents and growth rates of strains of Ostreococcus (OTTH595, RCC802 and RCC809) under a wide range of light, salinity and temperature conditions. Carotenoid profiles and productivities varied in a strain-specific and stress-dependent manner. Our results also illustrate that phylogenetically related microalgal strains originating from different ecological niches present specific interests for the production of specific molecules under controlled culture conditions.
Collapse
Affiliation(s)
- Jean-Baptiste Guyon
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| | - Valérie Vergé
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| | - Philippe Schatt
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| | - Jean-Claude Lozano
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| | - Marion Liennard
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| | - François-Yves Bouget
- Observatoire Océanologique, UMR 7621 Laboratoire d'Océanographie Microbienne, Université de Pierre et Marie Curie (Paris 06), Sorbonne Universités, 66650 Banyuls-sur-Mer, France.
| |
Collapse
|
19
|
Brodie J, Chan CX, De Clerck O, Cock JM, Coelho SM, Gachon C, Grossman AR, Mock T, Raven JA, Smith AG, Yoon HS, Bhattacharya D. The Algal Revolution. TRENDS IN PLANT SCIENCE 2017; 22:726-738. [PMID: 28610890 DOI: 10.1016/j.tplants.2017.05.005] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 05/04/2017] [Accepted: 05/16/2017] [Indexed: 05/28/2023]
Abstract
Algae are (mostly) photosynthetic eukaryotes that occupy multiple branches of the tree of life, and are vital for planet function and health. In this review, we highlight a transformative period in studies of the evolution and functioning of this extraordinary group of organisms and their potential for novel applications, wrought by high-throughput 'omic' and reverse genetic methods. We cover the origin and diversification of algal groups, explore advances in understanding the link between phenotype and genotype, consider algal sex determination, and review progress in understanding the roots of algal multicellularity. Experimental evolution studies to determine how algae evolve in changing environments are highlighted, as is their potential as production platforms for compounds of commercial interest, such as biofuel precursors, nutraceuticals, or therapeutics.
Collapse
Affiliation(s)
- Juliet Brodie
- Natural History Museum, Department of Life Sciences, London SW7 5BD, UK
| | - Cheong Xin Chan
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD 4072, Australia
| | - Olivier De Clerck
- Research Group Phycology, Ghent University, Krijgslaan 281, S8, 9000 Ghent, Belgium
| | - 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
| | - 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
| | - Claire Gachon
- Scottish Association for Marine Science, Scottish Marine Institute, Oban, PA37 1QA, UK
| | - Arthur R Grossman
- Department of Plant Biology, The Carnegie Institution, Stanford, CA 94305, USA
| | - Thomas Mock
- School of Environmental Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - John A Raven
- Permanent address: Division of Plant Sciences, University of Dundee at the James Hutton Institute, Dundee DD2 5DA, UK; School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
| | - Alison G Smith
- Department of Plant Sciences, University of Cambridge, Cambridge, CB2 3EA, UK
| | - Hwan Su Yoon
- Department of Biological Sciences, Sungkyunkwan University, Suwon 16419, Korea
| | - Debashish Bhattacharya
- Department of Biochemistry and Microbiology, Rutgers University, New Brunswick, NJ 08901, USA.
| |
Collapse
|
20
|
Fujiwara T, Ohnuma M, Kuroiwa T, Ohbayashi R, Hirooka S, Miyagishima SY. Development of a Double Nuclear Gene-Targeting Method by Two-Step Transformation Based on a Newly Established Chloramphenicol-Selection System in the Red Alga Cyanidioschyzon merolae. FRONTIERS IN PLANT SCIENCE 2017; 8:343. [PMID: 28352279 PMCID: PMC5348525 DOI: 10.3389/fpls.2017.00343] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 02/27/2017] [Indexed: 05/24/2023]
Abstract
The unicellular red alga Cyanidioschyzon merolae possesses a simple cellular architecture that consists of one mitochondrion, one chloroplast, one peroxisome, one Golgi apparatus, and several lysosomes. The nuclear genome content is also simple, with very little genetic redundancy (16.5 Mbp, 4,775 genes). In addition, molecular genetic tools such as gene targeting and inducible gene expression systems have been recently developed. These cytological features and genetic tractability have facilitated various omics analyses. However, only a single transformation selection marker URA has been made available and thus the application of genetic modification has been limited. Here, we report the development of a nuclear targeting method by using chloramphenicol and the chloramphenicol acetyltransferase (CAT) gene. In addition, we found that at least 200-bp homologous arms are required and 500-bp arms are sufficient for a targeted single-copy insertion of the CAT selection marker into the nuclear genome. By means of a combination of the URA and CAT transformation systems, we succeeded in producing a C. merolae strain that expresses HA-cyclin 1 and FLAG-CDKA from the chromosomal CYC1 and CDKA loci, respectively. These methods of multiple nuclear targeting will facilitate genetic manipulation of C. merolae.
Collapse
Affiliation(s)
- Takayuki Fujiwara
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Genetics, Graduate University for Advanced StudiesShizuoka, Japan
| | - Mio Ohnuma
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- National Institute of Technology, Hiroshima CollegeHiroshima, Japan
| | - Tsuneyoshi Kuroiwa
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Chemical and Biological Science, Faculty of Science, Japan Women’s UniversityTokyo, Japan
| | - Ryudo Ohbayashi
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
| | - Shunsuke Hirooka
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
| | - Shin-Ya Miyagishima
- Department of Cell Genetics, National Institute of GeneticsShizuoka, Japan
- Japan Science and Technology Agency, Core Research for Evolutional Science and TechnologySaitama, Japan
- Department of Genetics, Graduate University for Advanced StudiesShizuoka, Japan
| |
Collapse
|
21
|
Hirth M, Liverani S, Mahlow S, Bouget FY, Pohnert G, Sasso S. Metabolic profiling identifies trehalose as an abundant and diurnally fluctuating metabolite in the microalga Ostreococcus tauri. Metabolomics 2017; 13:68. [PMID: 28473745 PMCID: PMC5392535 DOI: 10.1007/s11306-017-1203-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/31/2017] [Indexed: 12/18/2022]
Abstract
INTRODUCTION The picoeukaryotic alga Ostreococcus tauri (Chlorophyta) belongs to the widespread group of marine prasinophytes. Despite its ecological importance, little is known about the metabolism of this alga. OBJECTIVES In this work, changes in the metabolome were quantified when O. tauri was grown under alternating cycles of 12 h light and 12 h darkness. METHODS Algal metabolism was analyzed by gas chromatography-mass spectrometry. Using fluorescence-activated cell sorting, the bacteria associated with O. tauri were depleted to below 0.1% of total cells at the time of metabolic profiling. RESULTS Of 111 metabolites quantified over light-dark cycles, 20 (18%) showed clear diurnal variations. The strongest fluctuations were found for trehalose. With an intracellular concentration of 1.6 mM in the dark, this disaccharide was six times more abundant at night than during the day. This fluctuation pattern of trehalose may be a consequence of starch degradation or of the synchronized cell cycle. On the other hand, maltose (and also sucrose) was below the detection limit (~10 μM). Accumulation of glycine in the light is in agreement with the presence of a classical glycolate pathway of photorespiration. We also provide evidence for the presence of fatty acid methyl and ethyl esters in O. tauri. CONCLUSIONS This study shows how the metabolism of O. tauri adapts to day and night and gives new insights into the configuration of the carbon metabolism. In addition, several less common metabolites were identified.
Collapse
Affiliation(s)
- Matthias Hirth
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - Silvia Liverani
- 0000 0001 0724 6933grid.7728.aDepartment of Mathematics, Brunel University London, Uxbridge, UK
| | - Sebastian Mahlow
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| | - François-Yves Bouget
- 0000 0001 2369 4306grid.463752.1Sorbonne Universités, UPMC Univ Paris 06 & Centre National pour la Recherche Scientifique CNRS, UMR 7621, Laboratoire d’Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Georg Pohnert
- 0000 0001 1939 2794grid.9613.dInstitute for Inorganic and Analytical Chemistry, Friedrich Schiller University, Jena, Germany
- 0000 0004 0491 7131grid.418160.aMax Planck Institute for Chemical Ecology, Jena, Germany
| | - Severin Sasso
- 0000 0001 1939 2794grid.9613.dInstitute of General Botany and Plant Physiology, Friedrich Schiller University, Jena, Germany
| |
Collapse
|
22
|
Paerl RW, Bouget FY, Lozano JC, Vergé V, Schatt P, Allen EE, Palenik B, Azam F. Use of plankton-derived vitamin B1 precursors, especially thiazole-related precursor, by key marine picoeukaryotic phytoplankton. ISME JOURNAL 2016; 11:753-765. [PMID: 27935586 PMCID: PMC5322297 DOI: 10.1038/ismej.2016.145] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2016] [Revised: 08/18/2016] [Accepted: 09/14/2016] [Indexed: 12/19/2022]
Abstract
Several cosmopolitan marine picoeukaryotic phytoplankton are B1 auxotrophs requiring exogenous vitamin B1 or precursor to survive. From genomic evidence, representatives of picoeukaryotic phytoplankton (Ostreococcus and Micromonas spp.) were predicted to use known thiazole and pyrimidine B1 precursors to meet their B1 demands, however, recent culture-based experiments could not confirm this assumption. We hypothesized these phytoplankton strains could grow on precursors alone, but required a thiazole-related precursor other the well-known and extensively tested 4-methyl-5-thiazoleethanol. This hypothesis was tested using bioassays and co-cultures of picoeukaryotic phytoplankton and bacteria. We found that specific B1-synthesizing proteobacteria and phytoplankton are sources of a yet-to-be chemically identified thiazole-related precursor(s) that, along with pyrimidine B1 precursor 4-amino-5-hydroxymethyl-2-methylpyrimidine, can support growth of Ostreococcus spp. (also Micromonas spp.) without B1. We additionally found that the B1-synthesizing plankton do not require contact with picoeukaryotic phytoplankton cells to produce thiazole-related precursor(s). Experiments with wild-type and genetically engineered Ostreococcus lines revealed that the thiazole kinase, ThiM, is required for growth on precursors, and that thiazole-related precursor(s) accumulate to appreciable levels in the euphotic ocean. Overall, our results point to thiazole-related B1 precursors as important micronutrients promoting the survival of abundant phytoplankton influencing surface ocean production and biogeochemical cycling.
Collapse
Affiliation(s)
- Ryan W Paerl
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Francois-Yves Bouget
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Jean-Claude Lozano
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Valérie Vergé
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Philippe Schatt
- Sorbonne Universités, Université Pierre and Marie Curie (Paris 06), UMR 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Banyuls-sur-Mer, France
| | - Eric E Allen
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Brian Palenik
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| | - Farooq Azam
- Marine Biology Research Division, Scripps Institution of Oceanography, University of California at San Diego, La Jolla, CA, USA
| |
Collapse
|
23
|
Wang Q, Lu Y, Xin Y, Wei L, Huang S, Xu J. Genome editing of model oleaginous microalgae Nannochloropsis spp. by CRISPR/Cas9. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:1071-1081. [PMID: 27538728 DOI: 10.1111/tpj.13307] [Citation(s) in RCA: 141] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Revised: 08/04/2016] [Accepted: 08/05/2016] [Indexed: 05/18/2023]
Abstract
Microalgae are promising feedstock for biofuels yet mechanistic probing of their cellular network and industrial strain development have been hindered by lack of genome-editing tools. Nannochloropsis spp. are emerging model microalgae for scalable oil production and carbon sequestration. Here we established a CRISPR/Cas9-based precise genome-editing approach for the industrial oleaginous microalga Nannochloropsis oceanica, using nitrate reductase (NR; g7988) as example. A new screening procedure that compares between restriction enzyme-digested nested PCR (nPCR) products derived from enzyme-digested and not-digested genomic DNA of transformant pools was developed to quickly, yet reliably, detect genome-engineered mutants. Deep sequencing of nPCR products directly amplified from pooled genomic DNA revealed over an 1% proportion of 5-bp deletion mutants and a lower frequency of 12-bp deletion mutants, with both types of editing precisely located at the targeted site. The isolated mutants, in which precise deletion of five bases caused a frameshift in NR translation, grow normally under NH4 Cl but fail to grow under NaNO3 , and thus represent a valuable chassis strain for transgenic-strain development. This demonstration of CRISPR/Cas9-based genome editing in industrial microalgae opens many doors for microalgae-based biotechnological applications.
Collapse
Affiliation(s)
- Qintao Wang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yandu Lu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- State Key Laboratory of Marine Resource Utilization in South China Sea, College of Oceanology, Hainan University, 570228, Haikou, Hainan, China
| | - Yi Xin
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Li Wei
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
| | - Shi Huang
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian Xu
- Single-Cell Center, CAS Key Laboratory of Biofuels and Shandong Key Laboratory of Energy Genetics, Qingdao Institute of BioEnergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, Shandong, 266101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| |
Collapse
|
24
|
Yau S, Hemon C, Derelle E, Moreau H, Piganeau G, Grimsley N. A Viral Immunity Chromosome in the Marine Picoeukaryote, Ostreococcus tauri. PLoS Pathog 2016; 12:e1005965. [PMID: 27788272 PMCID: PMC5082852 DOI: 10.1371/journal.ppat.1005965] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Accepted: 09/29/2016] [Indexed: 12/22/2022] Open
Abstract
Micro-algae of the genus Ostreococcus and related species of the order Mamiellales are globally distributed in the photic zone of world's oceans where they contribute to fixation of atmospheric carbon and production of oxygen, besides providing a primary source of nutrition in the food web. Their tiny size, simple cells, ease of culture, compact genomes and susceptibility to the most abundant large DNA viruses in the sea render them attractive as models for integrative marine biology. In culture, spontaneous resistance to viruses occurs frequently. Here, we show that virus-producing resistant cell lines arise in many independent cell lines during lytic infections, but over two years, more and more of these lines stop producing viruses. We observed sweeping over-expression of all genes in more than half of chromosome 19 in resistant lines, and karyotypic analyses showed physical rearrangements of this chromosome. Chromosome 19 has an unusual genetic structure whose equivalent is found in all of the sequenced genomes in this ecologically important group of green algae. We propose that chromosome 19 of O. tauri is specialized in defence against viral attack, a constant threat for all planktonic life, and that the most likely cause of resistance is the over-expression of numerous predicted glycosyltransferase genes. O. tauri thus provides an amenable model for molecular analysis of genome evolution under environmental stress and for investigating glycan-mediated host-virus interactions, such as those seen in herpes, influenza, HIV, PBCV and mimivirus.
Collapse
Affiliation(s)
- Sheree Yau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Claire Hemon
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Evelyne Derelle
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Hervé Moreau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Gwenaël Piganeau
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
| | - Nigel Grimsley
- Sorbonne Universités, UPMC Univ Paris 06, CNRS, Biologie Intégrative des Organismes Marins (BIOM, UMR 7232), Observatoire Océanologique, Banyuls sur Mer, France
- * E-mail:
| |
Collapse
|
25
|
Abstract
The genetic, physiological and metabolic diversity of microalgae has driven fundamental research into photosynthesis, flagella structure and function, and eukaryotic evolution. Within the last 10 years these organisms have also been investigated as potential biotechnology platforms, for example to produce high value compounds such as long chain polyunsaturated fatty acids, pigments and antioxidants, and for biodiesel precursors, in particular triacylglycerols (TAGs). Transformation protocols, molecular tools and genome sequences are available for a number of model species including the green alga Chlamydomonas reinhardtii and the diatom Phaeodactylum tricornutum, although for both species there are bottlenecks to be overcome to allow rapid and predictable genetic manipulation. One approach to do this would be to apply the principles of synthetic biology to microalgae, namely the cycle of Design-Build-Test, which requires more robust, predictable and high throughput methods. In this mini-review we highlight recent progress in the areas of improving transgene expression, genome editing, identification and design of standard genetic elements (parts), and the use of microfluidics to increase throughput. We suggest that combining these approaches will provide the means to establish algal synthetic biology, and that application of standard parts and workflows will avoid parallel development and capitalize on lessons learned from other systems.
Collapse
|
26
|
Lelandais G, Scheiber I, Paz-Yepes J, Lozano JC, Botebol H, Pilátová J, Žárský V, Léger T, Blaiseau PL, Bowler C, Bouget FY, Camadro JM, Sutak R, Lesuisse E. Ostreococcus tauri is a new model green alga for studying iron metabolism in eukaryotic phytoplankton. BMC Genomics 2016; 17:319. [PMID: 27142620 PMCID: PMC4855317 DOI: 10.1186/s12864-016-2666-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 04/26/2016] [Indexed: 11/17/2022] Open
Abstract
Background Low iron bioavailability is a common feature of ocean surface water and therefore micro-algae developed original strategies to optimize iron uptake and metabolism. The marine picoeukaryotic green alga Ostreococcus tauri is a very good model for studying physiological and genetic aspects of the adaptation of the green algal lineage to the marine environment: it has a very compact genome, is easy to culture in laboratory conditions, and can be genetically manipulated by efficient homologous recombination. In this study, we aimed at characterizing the mechanisms of iron assimilation in O. tauri by combining genetics and physiological tools. Specifically, we wanted to identify and functionally characterize groups of genes displaying tightly orchestrated temporal expression patterns following the exposure of cells to iron deprivation and day/night cycles, and to highlight unique features of iron metabolism in O. tauri, as compared to the freshwater model alga Chalamydomonas reinhardtii. Results We used RNA sequencing to investigated the transcriptional responses to iron limitation in O. tauri and found that most of the genes involved in iron uptake and metabolism in O. tauri are regulated by day/night cycles, regardless of iron status. O. tauri lacks the classical components of a reductive iron uptake system, and has no obvious iron regulon. Iron uptake appears to be copper-independent, but is regulated by zinc. Conversely, iron deprivation resulted in the transcriptional activation of numerous genes encoding zinc-containing regulation factors. Iron uptake is likely mediated by a ZIP-family protein (Ot-Irt1) and by a new Fea1-related protein (Ot-Fea1) containing duplicated Fea1 domains. The adaptation of cells to iron limitation involved an iron-sparing response tightly coordinated with diurnal cycles to optimize cell functions and synchronize these functions with the day/night redistribution of iron orchestrated by ferritin, and a stress response based on the induction of thioredoxin-like proteins, of peroxiredoxin and of tesmin-like methallothionein rather than ascorbate. We briefly surveyed the metabolic remodeling resulting from iron deprivation. Conclusions The mechanisms of iron uptake and utilization by O. tauri differ fundamentally from those described in C. reinhardtii. We propose this species as a new model for investigation of iron metabolism in marine microalgae. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2666-6) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Gaëlle Lelandais
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Ivo Scheiber
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Javier Paz-Yepes
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - Jean-Claude Lozano
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Hugo Botebol
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jana Pilátová
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Vojtěch Žárský
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic
| | - Thibaut Léger
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Pierre-Louis Blaiseau
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Chris Bowler
- Ecole Normale Supérieure, PSL Research University, Institut de Biologie de l'Ecole Normale Supérieure (IBENS), CNRS UMR 8197, INSERM U1024, 46 rue d'Ulm, F-75005, Paris, France
| | - François-Yves Bouget
- Sorbonne Universités, University Pierre et Marie Curie, University of Paris VI, CNRS, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, F-66650, Banyuls-sur-Mer, France
| | - Jean-Michel Camadro
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France
| | - Robert Sutak
- Department of Parasitology, Faculty of Science, Charles University in Prague, 12844, Prague, Czech Republic.
| | - Emmanuel Lesuisse
- CNRS, Institut Jacques Monod, Université Paris Diderot-Paris 7, F-75013, Paris, France.
| |
Collapse
|
27
|
Central role for ferritin in the day/night regulation of iron homeostasis in marine phytoplankton. Proc Natl Acad Sci U S A 2015; 112:14652-7. [PMID: 26553998 DOI: 10.1073/pnas.1506074112] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In large regions of the open ocean, iron is a limiting resource for phytoplankton. The reduction of iron quota and the recycling of internal iron pools are among the diverse strategies that phytoplankton have evolved to allow them to grow under chronically low ambient iron levels. Phytoplankton species also have evolved strategies to cope with sporadic iron supply such as long-term storage of iron in ferritin. In the picophytoplanktonic species Ostreococcus we report evidence from observations both in the field and in laboratory cultures that ferritin and the main iron-binding proteins involved in photosynthesis and nitrate assimilation pathways show opposite diurnal expression patterns, with ferritin being maximally expressed during the night. Biochemical and physiological experiments using a ferritin knock-out line subsequently revealed that this protein plays a central role in the diel regulation of iron uptake and recycling and that this regulation of iron homeostasis is essential for cell survival under iron limitation.
Collapse
|
28
|
Hlavova M, Turoczy Z, Bisova K. Improving microalgae for biotechnology — From genetics to synthetic biology. Biotechnol Adv 2015; 33:1194-203. [DOI: 10.1016/j.biotechadv.2015.01.009] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2014] [Revised: 01/11/2015] [Accepted: 01/17/2015] [Indexed: 01/01/2023]
|
29
|
Thommen Q, Pfeuty B, Schatt P, Bijoux A, Bouget FY, Lefranc M. Probing entrainment of Ostreococcus tauri circadian clock by green and blue light through a mathematical modeling approach. Front Genet 2015; 6:65. [PMID: 25774167 PMCID: PMC4343026 DOI: 10.3389/fgene.2015.00065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2014] [Accepted: 02/09/2015] [Indexed: 12/22/2022] Open
Abstract
Most organisms anticipate daily environmental variations and orchestrate cellular functions thanks to a circadian clock which entrains robustly to the day/night cycle, despite fluctuations in light intensity due to weather or seasonal variations. Marine organisms are also subjected to fluctuations in light spectral composition as their depth varies, due to differential absorption of different wavelengths by sea water. Studying how light input pathways contribute to circadian clock robustness is therefore important. Ostreococcus tauri, a unicellular picoplanktonic marine green alga with low genomic complexity and simple cellular organization, has become a promising model organism for systems biology. Functional and modeling approaches have shown that a core circadian oscillator based on orthologs of Arabidopsis TOC1 and CCA1 clock genes accounts for most experimental data acquired under a wide range of conditions. Some evidence points at putative light input pathway(s) consisting of a two-component signaling system (TCS) controlled by the only two histidine kinases (HK) of O. tauri. LOV-HK is a blue light photoreceptor under circadian control, that is required for circadian clock function. An involvement of Rhodopsin-HK (Rhod-HK) is also conceivable since rhodopsin photoreceptors mediate blue to green light input in animal circadian clocks. Here, we probe the role of LOV-HK and Rhod-HK in mediating light input to the TOC1-CCA1 oscillator using a mathematical model incorporating the TCS hypothesis. This model agrees with clock gene expression time series representative of multiple environmental conditions in blue or green light, characterizing entrainment by light/dark cycles, free-running in constant light, and resetting. Experimental and theoretical results indicate that both blue and green light can reset O. tauri circadian clock. Moreover, our mathematical analysis suggests that Rhod-HK is a blue-green light receptor and drives the clock together with LOV-HK.
Collapse
Affiliation(s)
- Quentin Thommen
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
| | - Benjamin Pfeuty
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
| | - Philippe Schatt
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - Amandine Bijoux
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - François-Yves Bouget
- Unité Mixte de Recherche 7621, Laboratoire d'Océanographie Microbienne, Observatoire Océanologique de Banyuls, Centre National de la Recherche Scientifique, Université Pierre et Marie Curie (Paris 06), Sorbonne Universités Banyuls sur Mer, France
| | - Marc Lefranc
- Laboratoire de Physique, Lasers, Atomes, Molécules, Université Lille 1 Sciences et Technologies, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 8523 Villeneuve d'Ascq, France
| |
Collapse
|
30
|
Abstract
As major contributors to global oxygen levels and producers of fatty acids, carotenoids, sterols, and phycocolloids, algae have significant ecological and commercial roles. Early algal models have contributed much to our understanding of circadian clocks at physiological and biochemical levels. The genetic and molecular approaches that identified clock components in other taxa have not been as widely applied to algae. We review results from seven species: the chlorophytes Chlamydomonas reinhardtii, Ostreococcus tauri, and Acetabularia spp.; the dinoflagellates Lingulodinium polyedrum and Symbiodinium spp.; the euglenozoa Euglena gracilis; and the red alga Cyanidioschyzon merolae. The relative simplicity, experimental tractability, and ecological and evolutionary diversity of algal systems may now make them particularly useful in integrating quantitative data from "omic" technologies (e.g., genomics, transcriptomics, metabolomics, and proteomics) with computational and mathematical methods.
Collapse
Affiliation(s)
- Zeenat B Noordally
- SynthSys and School of Biological Sciences, University of Edinburgh , Edinburgh EH9 3BF, United Kingdom
| | | |
Collapse
|
31
|
Blanc-Mathieu R, Verhelst B, Derelle E, Rombauts S, Bouget FY, Carré I, Château A, Eyre-Walker A, Grimsley N, Moreau H, Piégu B, Rivals E, Schackwitz W, Van de Peer Y, Piganeau G. An improved genome of the model marine alga Ostreococcus tauri unfolds by assessing Illumina de novo assemblies. BMC Genomics 2014; 15:1103. [PMID: 25494611 PMCID: PMC4378021 DOI: 10.1186/1471-2164-15-1103] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2014] [Accepted: 11/19/2014] [Indexed: 12/17/2022] Open
Abstract
Background Cost effective next generation sequencing technologies now enable the production of genomic datasets for many novel planktonic eukaryotes, representing an understudied reservoir of genetic diversity. O. tauri is the smallest free-living photosynthetic eukaryote known to date, a coccoid green alga that was first isolated in 1995 in a lagoon by the Mediterranean sea. Its simple features, ease of culture and the sequencing of its 13 Mb haploid nuclear genome have promoted this microalga as a new model organism for cell biology. Here, we investigated the quality of genome assemblies of Illumina GAIIx 75 bp paired-end reads from Ostreococcus tauri, thereby also improving the existing assembly and showing the genome to be stably maintained in culture. Results The 3 assemblers used, ABySS, CLCBio and Velvet, produced 95% complete genomes in 1402 to 2080 scaffolds with a very low rate of misassembly. Reciprocally, these assemblies improved the original genome assembly by filling in 930 gaps. Combined with additional analysis of raw reads and PCR sequencing effort, 1194 gaps have been solved in total adding up to 460 kb of sequence. Mapping of RNAseq Illumina data on this updated genome led to a twofold reduction in the proportion of multi-exon protein coding genes, representing 19% of the total 7699 protein coding genes. The comparison of the DNA extracted in 2001 and 2009 revealed the fixation of 8 single nucleotide substitutions and 2 deletions during the approximately 6000 generations in the lab. The deletions either knocked out or truncated two predicted transmembrane proteins, including a glutamate-receptor like gene. Conclusion High coverage (>80 fold) paired-end Illumina sequencing enables a high quality 95% complete genome assembly of a compact ~13 Mb haploid eukaryote. This genome sequence has remained stable for 6000 generations of lab culture. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-1103) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | - Gwenaël Piganeau
- CNRS, UMR 7232, Observatoire Océanologique, Avenue du Fontaulé, BP44, 66650 Banyuls-sur-Mer, France.
| |
Collapse
|