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Murphy EA, Kleiner FH, Helliwell KE, Wheeler GL. Channels of Evolution: Unveiling Evolutionary Patterns in Diatom Ca 2+ Signalling. PLANTS (BASEL, SWITZERLAND) 2024; 13:1207. [PMID: 38732422 PMCID: PMC11085791 DOI: 10.3390/plants13091207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 04/09/2024] [Accepted: 04/15/2024] [Indexed: 05/13/2024]
Abstract
Diatoms are important primary producers in marine and freshwater environments, but little is known about the signalling mechanisms they use to detect changes in their environment. All eukaryotic organisms use Ca2+ signalling to perceive and respond to environmental stimuli, employing a range of Ca2+-permeable ion channels to facilitate the movement of Ca2+ across cellular membranes. We investigated the distribution of different families of Ca2+ channels in diatom genomes, with comparison to other members of the stramenopile lineage. The four-domain voltage-gated Ca2+ channels (Cav) are present in some centric diatoms but almost completely absent in pennate diatoms, whereas single-domain voltage-gated EukCatA channels were found in all diatoms. Glutamate receptors (GLRs) and pentameric ligand-gated ion channels (pLGICs) also appear to have been lost in several pennate species. Transient receptor potential (TRP) channels are present in all diatoms, but have not undergone the significant expansion seen in brown algae. All diatom species analysed lacked the mitochondrial uniporter (MCU), a highly conserved channel type found in many eukaryotes, including several stramenopile lineages. These results highlight the unique Ca2+-signalling toolkit of diatoms and indicate that evolutionary gains or losses of different Ca2+ channels may contribute to differences in cellular-signalling mechanisms between species.
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Affiliation(s)
- Eleanor A. Murphy
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
- School of Biological Sciences, University of Bristol, Bristol BS8 1TQ, UK
| | | | - Katherine E. Helliwell
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
- Department of Biosciences, University of Exeter, Exeter EX4 4QD, UK
| | - Glen L. Wheeler
- Marine Biological Association, Plymouth PL1 2PB, UK (K.E.H.)
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2
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Murison V, Hérault J, Côme M, Guinio S, Lebon A, Chamot C, Bénard M, Galas L, Schoefs B, Marchand J, Bardor M, Ulmann L. Comparison of two Phaeodactylum tricornutum ecotypes under nitrogen starvation and resupply reveals distinct lipid accumulation strategies but a common degradation process. FRONTIERS IN PLANT SCIENCE 2023; 14:1257500. [PMID: 37810403 PMCID: PMC10556672 DOI: 10.3389/fpls.2023.1257500] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 09/04/2023] [Indexed: 10/10/2023]
Abstract
Introduction Phaeodactylum tricornutum is a model species frequently used to study lipid metabolism in diatoms. When exposed to a nutrient limitation or starvation, diatoms are known to accumulate neutral lipids in cytoplasmic lipid droplets (LDs). Those lipids are produced partly de novo and partly from the recycle of plastid membrane lipids. Under a nitrogen resupply, the accumulated lipids are catabolized, a phenomenon about which only a few data are available. Various strains of P. tricornutum have been isolated around the world that may differ in lipid accumulation patterns. Methods To get further information on this topic, two genetically distant ecotypes of P. tricornutum (Pt1 and Pt4) have been cultivated under nitrogen deprivation during 11 days followed by a resupply period of 3 days. The importance of cytoplasmic LDs relative to the plastid was assessed by a combination of confocal laser scanning microscopy and cell volume estimation using bright field microscopy pictures. Results and discussion We observed that in addition to a basal population of small LDs (0.005 μm3 to 0.7 μm3) present in both strains all along the experiment, Pt4 cells immediately produced two large LDs (up to 12 μm3 after 11 days) while Pt1 cells progressively produced a higher number of smaller LDs (up to 7 μm3 after 11 days). In this work we showed that, in addition to intracellular available space, lipid accumulation may be limited by the pre-starvation size of the plastid as a source of membrane lipids to be recycled. After resupplying nitrogen and for both ecotypes, a fragmentation of the largest LDs was observed as well as a possible migration of LDs to the vacuoles that would suggest an autophagic degradation. Altogether, our results deepen the understanding of LDs dynamics and open research avenues for a better knowledge of lipid degradation in diatoms.
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Affiliation(s)
- Victor Murison
- Biology of Organisms, Stress, Health and Environment, IUT Département Génie Biologique, Le Mans Université, IUML-FR 3473 CNRS, Laval, France
| | - Josiane Hérault
- Biology of Organisms, Stress, Health and Environment, IUT Département Génie Biologique, Le Mans Université, IUML-FR 3473 CNRS, Laval, France
| | - Martine Côme
- Biology of Organisms, Stress, Health and Environment, IUT Département Génie Biologique, Le Mans Université, IUML-FR 3473 CNRS, Laval, France
| | - Sabrina Guinio
- Biology of Organisms, Stress, Health and Environment, IUT Département Génie Biologique, Le Mans Université, IUML-FR 3473 CNRS, Laval, France
| | - Alexis Lebon
- Université de Rouen Normandie, INSERM, CNRS, HeRacLeS US51 UAR2026, PRIMACEN, Rouen, France
| | - Christophe Chamot
- Université de Rouen Normandie, INSERM, CNRS, HeRacLeS US51 UAR2026, PRIMACEN, Rouen, France
| | - Magalie Bénard
- Université de Rouen Normandie, INSERM, CNRS, HeRacLeS US51 UAR2026, PRIMACEN, Rouen, France
| | - Ludovic Galas
- Université de Rouen Normandie, INSERM, CNRS, HeRacLeS US51 UAR2026, PRIMACEN, Rouen, France
| | - Benoît Schoefs
- Biology of Organisms, Stress, Health and Environment, UFR Sciences et Techniques, Le Mans Université, IUML-FR 3473 CNRS, Le Mans, France
| | - Justine Marchand
- Biology of Organisms, Stress, Health and Environment, UFR Sciences et Techniques, Le Mans Université, IUML-FR 3473 CNRS, Le Mans, France
| | - Muriel Bardor
- Université de Rouen Normandie, Laboratoire GlycoMEV UR4358, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, Rouen, France
| | - Lionel Ulmann
- Biology of Organisms, Stress, Health and Environment, IUT Département Génie Biologique, Le Mans Université, IUML-FR 3473 CNRS, Laval, France
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Debit A, Charton F, Pierre-Elies P, Bowler C, Cruz de Carvalho H. Differential expression patterns of long noncoding RNAs in a pleiomorphic diatom and relation to hyposalinity. Sci Rep 2023; 13:2440. [PMID: 36765079 PMCID: PMC9918465 DOI: 10.1038/s41598-023-29489-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2022] [Accepted: 02/06/2023] [Indexed: 02/12/2023] Open
Abstract
Long non-coding (lnc)RNAs have been shown to have central roles in stress responses, cell identity and developmental processes in multicellular organisms as well as in unicellular fungi. Previous works have shown the occurrence of lncRNAs in diatoms, namely in Phaeodactylum tricornutum, many of which being expressed under specific stress conditions. Interestingly, P. tricornutum is the only known diatom that has a demonstrated morphological plasticity, occurring in three distinct morphotypes: fusiform, triradiate and oval. Although the morphotypes are interchangeable, the fusiform is the dominant one while both the triradiate and the oval forms are less common, the latter often being associated with stress conditions such as low salinity and solid culture media, amongst others. Nonetheless, the molecular basis underpinning morphotype identity in P. tricornutum remains elusive. Using twelve previously published transcriptomic datasets originating from the three morphotypes of P. tricornutum, we sought to investigate the expression patterns of lncRNAs (lincRNAs and NATs) in these distinct morphotypes, using pairwise comparisons, in order to explore the putative involvement of these noncoding molecules in morphotype identity. We found that differentially expressed lncRNAs cluster according to morphotype, indicating that lncRNAs are not randomly expressed, but rather seem to provide a specific (noncoding) transcriptomic signature of the morphotype. We also present evidence to suggest that the major differences in DE genes (both noncoding and coding) between the stress related oval morphotype and the most common fusiform morphotype could be due, to a large extent, to the hyposaline culture conditions rather than to the morphotype itself. However, several lncRNAs associated to each one of the three morphotypes were identified, which could have a potential role in morphotype (or cell) identity in P. tricornutum, similar to what has been found in both animals and plant development.
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Affiliation(s)
- Ahmed Debit
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Florent Charton
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Priscillia Pierre-Elies
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Chris Bowler
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France
| | - Helena Cruz de Carvalho
- Institut de Biologie de L'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, 75005, Paris, France.
- Faculté des Sciences et Technologie, Université Paris Est-Créteil (UPEC), 61, Avenue du Général De Gaulle, 94000, Créteil, France.
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Jiang EY, Fan Y, Phung NV, Xia WY, Hu GR, Li FL. Overexpression of plastid lipid-associated protein in marine diatom enhances the xanthophyll synthesis and storage. Front Microbiol 2023; 14:1143017. [PMID: 37152729 PMCID: PMC10160619 DOI: 10.3389/fmicb.2023.1143017] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 04/04/2023] [Indexed: 05/09/2023] Open
Abstract
Plastoglobules, which are lipoprotein structures surrounded by a single hydrophobic phospholipid membrane, are subcellular organelles in plant chromoplasts and chloroplasts. They contain neutral lipids, tocopherols, quinones, chlorophyll metabolites, carotenoids and their derivatives. Proteomic studies indicated that plastoglobules are involved in carotenoid metabolism and storage. In this study, one of the plastid lipid-associated proteins (PAP), the major protein in plastoglobules, was selected and overexpressed in Phaeodactylum tricornutum. The diameter of the plastoglobules in mutants was decreased by a mean of 19.2% versus the wild-type, while the fucoxanthin level was increased by a mean of 51.2%. All mutants exhibited morphological differences from the wild-type, including a prominent increase in the transverse diameter. Moreover, the unsaturated fatty acid levels were increased in different mutants, including an 18.9-59.3% increase in eicosapentaenoic acid content. Transcriptomic analysis revealed that PAP expression and the morphological changes altered xanthophyll synthesis and storage, which affected the assembly of the fucoxanthin chlorophyll a/c-binding protein and expression of antenna proteins as well as reduced the non-photochemical quenching activity of diatom cells. Therefore, metabolic regulation at the suborganelle level can be achieved by modulating PAP expression. These findings provide a subcellular structural site and target for synthetic biology to modify pigment and lipid metabolism in microalgae chassis cells.
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Affiliation(s)
- Er-Ying Jiang
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yong Fan
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- *Correspondence: Yong Fan,
| | - Nghi-Van Phung
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Wan-Yue Xia
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Guang-Rong Hu
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Fu-Li Li
- Shandong Provincial Key Laboratory of Synthetic Biology, Qingdao C1 Refinery Engineering Research Center, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
- Shandong Energy Institute, Qingdao, China
- Qingdao New Energy Shandong Laboratory, Qingdao, China
- Fu-Li Li,
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Gao S, Zhou L, Yang W, Wang L, Liu X, Gong Y, Hu Q, Wang G. Overexpression of a novel gene (Pt2015) endows the commercial diatom Phaeodactylum tricornutum high lipid content and grazing resistance. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2022; 15:131. [PMID: 36435813 PMCID: PMC9701398 DOI: 10.1186/s13068-022-02221-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 11/04/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND The marine diatom Phaeodactylum tricornutum is a commercially viable species due to its bioactive substances and lipid productivity. Increasing attention has been paid to the isolation or genetic modification of species or strains with a rapid growth rate and large quantities of lipids. Furthermore, contamination of microzooplankton has been one of the major constraints in P. tricornutum large-scale cultivation, which adversely affects growth and greatly impedes the course of biomass production industrialization. RESULTS Here, based on our previous transcriptomics of P. tricornutum, we found a novel gene (ID: 7202015, hereafter called Pt2015) which affects morphotype of P. tricornutum. Pt2015 protein is located in the plastid, which is highly homologous to part of the sequences of exosome component. The morphotype of the Pt2015 knockout strain (termed 2015KO) using CRISPR/Cas9 method is fusiform, but the Pt2015 overexpression strain (termed oeT) demonstrates a majority triradiate morphotype (approximately 95%) which is stable and has been cultured for more than 200 generations. In addition, the oeT strain demonstrated a similar growth rate to the WT and simultaneously accumulated larger lipids droplets that increased by approximately 30% compared to that of the WT. More importantly, the grazing rate of the amoebae cultured in the oeT strain significantly decreased in comparison with that cultured in WT, suggesting that the oeT can effectively avoid being eaten by microzooplankton. CONCLUSIONS Therefore, the oeT strain not only improves our understanding of morphotype conversion in diatoms but also demonstrates potential applications for large-scale cultivation of P. tricornutum.
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Affiliation(s)
- Shan Gao
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‑Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Lu Zhou
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‑Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
- College of Earth Sciences, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Wenting Yang
- College of Life Science, Qingdao Agricultural University, Qingdao, China
| | - Lijun Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‑Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Xuehua Liu
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‑Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China
| | - Yingchun Gong
- Center for Microalgal Biotechnology and Biofuels, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Qiang Hu
- CAS Key Laboratory of Quantitative Engineering Biology, Shenzhen Institute of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
- Faculty of Synthetic Biology, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China
| | - Guangce Wang
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Center for Ocean Mega‑Science, Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao, China.
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Understanding quantitative polymerase chain reaction bioanalysis issues before validation planning: Japan Bioanalysis Forum discussion group. Bioanalysis 2022; 14:1391-1405. [PMID: 36621859 DOI: 10.4155/bio-2022-0190] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
Investigating the biodistribution of cell and gene therapy products may play an important role in evaluating their safety and pharmacology. As quantitative polymerase chain reaction (qPCR) is often used for these analyses, it is essential to improve the reliability of bioanalysis performed using qPCR. In this report, the authors discuss the use of qPCR in nonclinical studies, as it can be used to detect target DNA/RNA and it is quantitative and applicable for long-term analysis. The authors also discuss points to consider during bioanalysis using qPCR and present appropriate validation items and their criteria. The authors anticipate the discussion provided herein to contribute to the development of validation and sample analysis for pharmaceuticals analyzed using qPCR.
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Chuberre C, Chan P, Walet-Balieu ML, Thiébert F, Burel C, Hardouin J, Gügi B, Bardor M. Comparative Proteomic Analysis of the Diatom Phaeodactylum tricornutum Reveals New Insights Into Intra- and Extra-Cellular Protein Contents of Its Oval, Fusiform, and Triradiate Morphotypes. FRONTIERS IN PLANT SCIENCE 2022; 13:673113. [PMID: 35386671 PMCID: PMC8977783 DOI: 10.3389/fpls.2022.673113] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 02/01/2022] [Indexed: 06/14/2023]
Abstract
Phaeodactylum tricornutum is an atypical diatom since it can display three main morphotypes: fusiform, triradiate, and oval. Such pleomorphism is possible thanks to an original metabolism, which is tightly regulated in order to acclimate to environmental conditions. Currently, studies dedicated to the comparison of each morphotype issued from one specific strain are scarce and little information is available regarding the physiological significance of this morphogenesis. In this study, we performed a comparative proteomic analysis of the three morphotypes from P. tricornutum. Cultures highly enriched in one dominant morphotype (fusiform, triradiate, or oval) of P. tricornutum Pt3 strain were used. Pairwise comparisons highlighted biological processes, which are up- and down-regulated in the oval (e.g., purine and cellular amino acid metabolism) and triradiate morphotypes (e.g., oxido-reduction and glycolytic processes) compared to the fusiform one used as a reference. Intersection analysis allowed us to identify the specific features of the oval morphotype. Results from this study confirmed previous transcriptomic RNA sequencing observation showing that the oval cells present a distinct metabolism with specific protein enrichment compared to fusiform and triradiate cells. Finally, the analysis of the secretome of each morphotype was also performed.
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Affiliation(s)
- Coralie Chuberre
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Philippe Chan
- UNIROUEN, PISSARO Proteomic Facility, Institute for Research and Innovation in Biomedicine, Normandie Université, Mont-Saint-Aignan, France
- Normandie University, UNIROUEN, INSERM US 51, CNRS UAR 2026, HeRacLeS-PISSARO, Rouen, France
- UNIROUEN, Institute for Research and Innovation in Biomedicine, Normandie Université, Rouen, France
| | | | - François Thiébert
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Carole Burel
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Julie Hardouin
- UNIROUEN, PISSARO Proteomic Facility, Institute for Research and Innovation in Biomedicine, Normandie Université, Mont-Saint-Aignan, France
- Normandie University, UNIROUEN, INSERM US 51, CNRS UAR 2026, HeRacLeS-PISSARO, Rouen, France
- Polymers, Biopolymers, Surface Laboratory, UMR 6270 CNRS, University of Rouen, Mont-Saint-Aignan, France
| | - Bruno Gügi
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
| | - Muriel Bardor
- UNIROUEN, Laboratoire Glyco-MEV EA4358, Normandie Université, Rouen, France
- Institut Universitaire de France, Paris, France
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Liu X, Wang L, Wu S, Zhou L, Gao S, Xie X, Wang L, Gu W, Wang G. Formation of resting cells is accompanied with enrichment of ferritin in marine diatom Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2021.102567] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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9
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Galas L, Burel C, Schapman D, Ropitaux M, Bernard S, Bénard M, Bardor M. Comparative Structural and Functional Analyses of the Fusiform, Oval, and Triradiate Morphotypes of Phaeodactylum tricornutum Pt3 Strain. FRONTIERS IN PLANT SCIENCE 2021; 12:638181. [PMID: 33912207 PMCID: PMC8072121 DOI: 10.3389/fpls.2021.638181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2020] [Accepted: 03/16/2021] [Indexed: 05/24/2023]
Abstract
The diatom Phaeodactylum tricornutum is a marine unicellular microalga that exists under three main morphotypes: oval, fusiform, and triradiate. Previous works have demonstrated that the oval morphotype of P. tricornutum Pt3 strain presents specific metabolic features. Here, we compared the cellular organization of the main morphotypes of the diatom P. tricornutum Pt3 strain through transmission electron and advanced light microscopies. The three morphotypes share similarities including spectral characteristics of the plastid, the location of the nucleus, the organization of mitochondria around the plastid as well as the existence of both a F-actin cortex, and an intracellular network of F-actin. In contrast, compared to fusiform and triradiate cells, oval cells spontaneously release proteins more rapidly. In addition, comparison of whole transcriptomes of oval versus fusiform or triradiate cells revealed numerous differential expression of positive and negative regulators belonging to the complex dynamic secretory machinery. This study highlights the specificities occurring within the oval morphotype underlying that the oval cells secrete proteins more rapidly.
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Affiliation(s)
- Ludovic Galas
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Carole Burel
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Damien Schapman
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Marc Ropitaux
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Sophie Bernard
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
| | - Magalie Bénard
- Normandie University, UNIROUEN, INSERM, PRIMACEN, Rouen, France
| | - Muriel Bardor
- Normandie University, UNIROUEN, Laboratoire Glycobiologie et Matrice Extracellulaire Végétale (Glyco-MEV) EA4358, Rouen, France
- Institut Universitaire de France, Paris, France
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Zhao X, Rastogi A, Deton Cabanillas AF, Ait Mohamed O, Cantrel C, Lombard B, Murik O, Genovesio A, Bowler C, Bouyer D, Loew D, Lin X, Veluchamy A, Vieira FRJ, Tirichine L. Genome wide natural variation of H3K27me3 selectively marks genes predicted to be important for cell differentiation in Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2021; 229:3208-3220. [PMID: 33533496 DOI: 10.1111/nph.17129] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 11/24/2020] [Indexed: 05/28/2023]
Abstract
In multicellular organisms, Polycomb Repressive Complex2 (PRC2) is known to deposit tri-methylation of lysine 27 of histone H3 (H3K27me3) to establish and maintain gene silencing, critical for developmentally regulated processes. The PRC2 complex is absent in both widely studied model yeasts, which initially suggested that PRC2 arose with the emergence of multicellularity. However, its discovery in several unicellular species including microalgae questions its role in unicellular eukaryotes. Here, we use Phaeodactylum tricornutum enhancer of zeste E(z) knockouts and show that P. tricornutum E(z) is responsible for di- and tri-methylation of lysine 27 of histone H3. H3K27me3 depletion abolishes cell morphology in P. tricornutum providing evidence for its role in cell differentiation. Genome-wide profiling of H3K27me3 in fusiform and triradiate cells further revealed genes that may specify cell identity. These results suggest a role for PRC2 and its associated mark in cell differentiation in unicellular species, and highlight their ancestral function in a broader evolutionary context than currently is appreciated.
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Affiliation(s)
- Xue Zhao
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
| | - Achal Rastogi
- Corteva AgriscienceTM, Ascendas IT Park, 12th floor, Atria, V, Madhapur, Telangana, 500081, India
| | - Anne Flore Deton Cabanillas
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Ouardia Ait Mohamed
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Catherine Cantrel
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Berangère Lombard
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Omer Murik
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Auguste Genovesio
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Chris Bowler
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Daniel Bouyer
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Damarys Loew
- Laboratoire de Spectrométrie de Masse Protéomique, Centre de Recherche, Institut Curie, PSL Research University, 26 rue d'Ulm, Cedex 05 Paris, 75248, France
| | - Xin Lin
- State Key Laboratory of Marine Environmental Science, Centre de Recherche, College of Ocean Camp; Earth Sciences,, Xiamen University, Xiamen, 361102, China
| | - Alaguraj Veluchamy
- Laboratory of Chromatin Biochemistry, 4700 King Abdullah University of Science and Technology (KAUST), BESE Division Building 2, Level 3, Office B2-3327, Thuwal, 23955-6900, Saudi Arabia
| | - Fabio Rocha Jimenez Vieira
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
| | - Leila Tirichine
- Institut de Biologie de l'ENS (IBENS), Département de Biologie, École Normale Supérieure, CNRS, INSERM, Université PSL, Paris, 75005, France
- CNRS UMR6286, UFIP UFR Sciences et Techniques, Université de Nantes, 2 rue de la Houssinière 44322, Nantes Cedex 03, France
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11
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Fu W, Chaiboonchoe A, Dohai B, Sultana M, Baffour K, Alzahmi A, Weston J, Al Khairy D, Daakour S, Jaiswal A, Nelson DR, Mystikou A, Brynjolfsson S, Salehi-Ashtiani K. GPCR Genes as Activators of Surface Colonization Pathways in a Model Marine Diatom. iScience 2020; 23:101424. [PMID: 32798972 PMCID: PMC7452957 DOI: 10.1016/j.isci.2020.101424] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 04/25/2020] [Accepted: 07/28/2020] [Indexed: 11/30/2022] Open
Abstract
Surface colonization allows diatoms, a dominant group of phytoplankton in oceans, to adapt to harsh marine environments while mediating biofoulings to human-made underwater facilities. The regulatory pathways underlying diatom surface colonization, which involves morphotype switching in some species, remain mostly unknown. Here, we describe the identification of 61 signaling genes, including G-protein-coupled receptors (GPCRs) and protein kinases, which are differentially regulated during surface colonization in the model diatom species, Phaeodactylum tricornutum. We show that the transformation of P. tricornutum with constructs expressing individual GPCR genes induces cells to adopt the surface colonization morphology. P. tricornutum cells transformed to express GPCR1A display 30% more resistance to UV light exposure than their non-biofouling wild-type counterparts, consistent with increased silicification of cell walls associated with the oval biofouling morphotype. Our results provide a mechanistic definition of morphological shifts during surface colonization and identify candidate target proteins for the screening of eco-friendly, anti-biofouling molecules. The model diatom Phaeodactylum tricornutum shifts morphology to form biofilms G-protein-coupled receptors (GPCRs) can modulate diatom surface colonization GPCR1A expression can induce biofouling morphotype and UV resistance Identified genes and pathways can serve as targets for anti-biofouling discoveries
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Affiliation(s)
- Weiqi Fu
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland.
| | - Amphun Chaiboonchoe
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Bushra Dohai
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Mehar Sultana
- Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Kristos Baffour
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Amnah Alzahmi
- Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE; Department of Biology, United Arab Emirates University (UAEU), Al Ain, UAE
| | - James Weston
- Core Technology Platforms, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Dina Al Khairy
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sarah Daakour
- Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Ashish Jaiswal
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE
| | - David R Nelson
- Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Alexandra Mystikou
- Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE
| | - Sigurdur Brynjolfsson
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Kourosh Salehi-Ashtiani
- Laboratory of Algal, Systems, and Synthetic Biology (LASSB), Division of Science and Math, New York University Abu Dhabi, Abu Dhabi, UAE; Center for Genomics and Systems Biology (CGSB), New York University Research Institute, New York University Abu Dhabi, Abu Dhabi, UAE.
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12
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Song Z, Lye GJ, Parker BM. Morphological and biochemical changes in Phaeodactylum tricornutum triggered by culture media: Implications for industrial exploitation. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101822] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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13
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Butler T, Kapoore RV, Vaidyanathan S. Phaeodactylum tricornutum: A Diatom Cell Factory. Trends Biotechnol 2020; 38:606-622. [PMID: 31980300 DOI: 10.1016/j.tibtech.2019.12.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.
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Affiliation(s)
- Thomas Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK
| | - Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK; Present address: Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK.
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14
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Font-Muñoz JS, Jeanneret R, Arrieta J, Anglès S, Jordi A, Tuval I, Basterretxea G. Collective sinking promotes selective cell pairing in planktonic pennate diatoms. Proc Natl Acad Sci U S A 2019; 116:15997-16002. [PMID: 31346087 PMCID: PMC6689993 DOI: 10.1073/pnas.1904837116] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Finding a partner in an inherently unsteady 3-dimensional system, such as the planktonic marine environment, is a difficult task for nonswimming organisms with poor control over their orientation. We experimentally investigate the process of cell pairing in pennate marine diatoms and present field evidence of its occurrence in the ocean. We describe the mechanism as a 3-step process in which pennate diatoms (i) vertically reorient while sinking from surface turbulent waters to a more stable environment (i.e., under the seasonal pycnocline), (ii) segregate from incompatible partners (e.g., dead or different sized cells), and (iii) pair with other partners as a result of the hydrodynamic instabilities generated by collective cell sinking. This is, eminently, a cell abundance-dependent process, therefore being more effective when population sinking is synchronized. We suggest that this selective process, enabling matching of size-compatible healthy partners, could be fundamental in understanding sexual reproduction in pennate diatoms.
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Affiliation(s)
- Joan S Font-Muñoz
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain;
| | - Raphaël Jeanneret
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain
| | - Jorge Arrieta
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain
| | - Sílvia Anglès
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain
| | | | - Idan Tuval
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain
| | - Gotzon Basterretxea
- Department of Marine Ecology, Institut Mediterrani d'Estudis Avançats, Universitat de les Illes Balears-Consejo Superior de Investigaciones Científicas, 07190 Esporles, Illes Balears, Spain
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15
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Zhang P, Burel C, Plasson C, Kiefer-Meyer MC, Ovide C, Gügi B, Wan C, Teo G, Mak A, Song Z, Driouich A, Lerouge P, Bardor M. Characterization of a GDP-Fucose Transporter and a Fucosyltransferase Involved in the Fucosylation of Glycoproteins in the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2019; 10:610. [PMID: 31164895 PMCID: PMC6536626 DOI: 10.3389/fpls.2019.00610] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 04/25/2019] [Indexed: 05/21/2023]
Abstract
Although Phaeodactylum tricornutum is gaining importance in plant molecular farming for the production of high-value molecules such as monoclonal antibodies, little is currently known about key cell metabolism occurring in this diatom such as protein glycosylation. For example, incorporation of fucose residues in the glycans N-linked to protein in P. tricornutum is questionable. Indeed, such epitope has previously been found on N-glycans of endogenous glycoproteins in P. tricornutum. Meanwhile, the potential immunogenicity of the α(1,3)-fucose epitope present on plant-derived biopharmaceuticals is still a matter of debate. In this paper, we have studied molecular actors potentially involved in the fucosylation of the glycoproteins in P. tricornutum. Based on sequence similarities, we have identified a putative P. tricornutum GDP-L-fucose transporter and three fucosyltransferase (FuT) candidates. The putative P. tricornutum GDP-L-fucose transporter coding sequence was expressed in the Chinese Hamster Ovary (CHO)-gmt5 mutant lacking its endogenous GDP-L-fucose transporter activity. We show that the P. tricornutum transporter is able to rescue the fucosylation of proteins in this CHO-gmt5 mutant cell line, thus demonstrating the functional activity of the diatom transporter and its appropriate Golgi localization. In addition, we overexpressed one of the three FuT candidates, namely the FuT54599, in P. tricornutum and investigated its localization within Golgi stacks of the diatom. Our findings show that overexpression of the FuT54599 leads to a significant increase of the α(1,3)-fucosylation of the diatom endogenous glycoproteins.
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Affiliation(s)
- Peiqing Zhang
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Carole Burel
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Carole Plasson
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Marie-Christine Kiefer-Meyer
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Clément Ovide
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Bruno Gügi
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Corrine Wan
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Gavin Teo
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Amelia Mak
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Zhiwei Song
- Bioprocessing Technology Institute, Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
| | - Azeddine Driouich
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Patrice Lerouge
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
| | - Muriel Bardor
- Laboratoire Glyco-MEV EA4358, UNIROUEN, Normandy University, Rouen, France
- Fédération de Recherche Normandie-Végétal – FED 4277, Rouen, France
- Institut Universitaire de France (I.U.F.), Paris, France
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