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Toustou C, Boulogne I, Gonzalez AA, Bardor M. Comparative RNA-Seq of Ten Phaeodactylum tricornutum Accessions: Unravelling Criteria for Robust Strain Selection from a Bioproduction Point of View. Mar Drugs 2024; 22:353. [PMID: 39195469 DOI: 10.3390/md22080353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 07/26/2024] [Accepted: 07/29/2024] [Indexed: 08/29/2024] Open
Abstract
The production of biologics in mammalian cells is hindered by some limitations including high production costs, prompting the exploration of other alternative expression systems that are cheaper and sustainable like microalgae. Successful productions of biologics such as monoclonal antibodies have already been demonstrated in the diatom Phaeodactylum tricornutum; however, limited production yields still remain compared to mammalian cells. Therefore, efforts are needed to make this microalga more competitive as a cell biofactory. Among the seventeen reported accessions of P. tricornutum, ten have been mainly studied so far. Among them, some have already been used to produce high-value-added molecules such as biologics. The use of "omics" is increasingly being described as useful for the improvement of both upstream and downstream steps in bioprocesses using mammalian cells. Therefore, in this context, we performed an RNA-Seq analysis of the ten most used P. tricornutum accessions (Pt1 to Pt10) and deciphered the differential gene expression in pathways that could affect bioproduction of biologics in P. tricornutum. Our results highlighted the benefits of certain accessions such as Pt9 or Pt4 for the production of biologics. Indeed, these accessions seem to be more advantageous. Moreover, these results contribute to a better understanding of the molecular and cellular biology of P. tricornutum.
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Affiliation(s)
- Charlotte Toustou
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Isabelle Boulogne
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
| | - Anne-Alicia Gonzalez
- MGX-Montpellier GenomiX, Univ. Montpellier, CNRS, INSERM, 34094 Montpellier, France
| | - Muriel Bardor
- Laboratoire GlycoMEV UR 4358, Université de Rouen Normandie, SFR Normandie Végétal FED 4277, Innovation Chimie Carnot, 76000 Rouen, France
- ALGA BIOLOGICS, CURIB, 25 rue Tesnières, 76821 Mont-Saint-Aignan, France
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2
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Madhuri S, Lepetit B, Fürst AH, Kroth PG. A Knockout of the Photoreceptor PtAureo1a Results in Altered Diel Expression of Diatom Clock Components. PLANTS (BASEL, SWITZERLAND) 2024; 13:1465. [PMID: 38891274 PMCID: PMC11174801 DOI: 10.3390/plants13111465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Revised: 05/10/2024] [Accepted: 05/17/2024] [Indexed: 06/21/2024]
Abstract
Plants and algae use light not only for driving photosynthesis but also to sense environmental cues and to adjust their circadian clocks via photoreceptors. Aureochromes are blue-light-dependent photoreceptors that also function as transcription factors, possessing both a LOV and a bZIP domain. Aureochromes so far have only been detected in Stramenopile algae, which include the diatoms. Four paralogues of aureochromes have been identified in the pennate model diatom Phaeodactylum tricornutum: PtAureo1a, 1b, 1c, and 2. While it was shown recently that diatoms have a diel rhythm, the molecular mechanisms and components regulating it are still largely unknown. Diel gene expression analyses of wild-type P. tricornutum, a PtAureo1a knockout strain, and the respective PtAureo1 complemented line revealed that all four aureochromes have a different diel regulation and that PtAureo1a has a strong co-regulatory influence on its own transcription, as well as on that of other genes encoding different blue-light photoreceptors (CPF1, 2 and 4), proteins involved in photoprotection (Lhcx1), and specific bHLH transcription factors (RITMO1). Some of these genes completely lost their circadian expression in the PtAureo1a KO mutant. Our results suggest a major involvement of aureochromes in the molecular clock of diatoms.
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Affiliation(s)
| | | | | | - Peter G. Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany; (S.M.); (B.L.); (A.H.F.)
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3
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Im SH, Lepetit B, Mosesso N, Shrestha S, Weiss L, Nymark M, Roellig R, Wilhelm C, Isono E, Kroth PG. Identification of promoter targets by Aureochrome 1a in the diatom Phaeodactylum tricornutum. JOURNAL OF EXPERIMENTAL BOTANY 2024; 75:1834-1851. [PMID: 38066674 DOI: 10.1093/jxb/erad478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/04/2023] [Accepted: 12/04/2023] [Indexed: 03/28/2024]
Abstract
Aureochromes (AUREOs) are unique blue light receptors and transcription factors found only in stramenopile algae. While each of the four AUREOs identified in the diatom Phaeodactylum tricornutum may have a specific function, PtAUREO1a has been shown to have a strong impact on overall gene regulation, when light changes from red to blue light conditions. Despite its significance, the molecular mechanism of PtAUREO1a is largely unexplored. To comprehend the overall process of gene regulation by PtAUREO1a, we conducted a series of in vitro and in vivo experiments, including pull-down assays, yeast one-hybrid experiments, and phenotypical characterization using recombinant PtAUREOs and diatom mutant lines expressing a modified PtAureo1a gene. We describe the distinct light absorption properties of four PtAUREOs and the formation of all combinations of their potential dimers. We demonstrate the capability of PtAUREO1a and 1b to activate the genes, diatom-specific cyclin 2, PtAureo1a, and PtAureo1c under both light and dark conditions. Using mutant lines expressing a modified PtAUREO1a protein with a considerably reduced light absorption, we found novel evidence that PtAUREO1a regulates the expression of PtLHCF15, which is essential for red light acclimation. Based on current knowledge, we present a working model of PtAUREO1a gene regulation properties.
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Affiliation(s)
- Soo Hyun Im
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
- Molecular Stress Physiology, Institute of Biological Sciences, University of Rostock, D-18059 Rostock, Germany
| | - Niccolò Mosesso
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Sandeep Shrestha
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Laura Weiss
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Marianne Nymark
- Department of Biology, Norwegian University of Science and Technology, Trondheim, N-7491, Norway
| | - Robert Roellig
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Erika Isono
- Plant Physiology and Biochemistry, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, D-78457 Konstanz, Germany
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4
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Yin W, Hu H. CRISPR/Cas9-Mediated Genome Editing via Homologous Recombination in a Centric Diatom Chaetoceros muelleri. ACS Synth Biol 2023; 12:1287-1296. [PMID: 37031406 DOI: 10.1021/acssynbio.3c00051] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2023]
Abstract
Chaetoceros, the most abundant genus of marine planktonic diatoms, can be used in mariculture. An effective genetic transformation system with a short transformation period was established in Chaetoceros muelleri by electroporation in our previous study. In this study, a sequence-specific clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 vector applicable for C. muelleri was constructed, and the expressions of sgRNA, resistance gene, and Cas9 gene were driven by the endogenous promoters U6, acetyl-CoA acetyltransferase, and fucoxanthin chlorophyll a/c binding protein, respectively, in the vector. Nitrate reductase (NR) and urease (URE) genes were edited in C. muelleri, and the NR knockout and NR/URE double-knockout lines displayed the strict auxotrophic phenotype. In addition, the DNA double-strand break was repaired by homologous recombination when a donor DNA was introduced. CRISPR/Cas9 technology was successfully applied to C. muelleri with an editing efficiency of up to 86%, providing a molecular tool for the study of basic biology in C. muelleri and its synthetic biology applications.
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Affiliation(s)
- Wenxiu Yin
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hanhua Hu
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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5
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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.
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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
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6
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Yu G, Nakajima K, Gruber A, Rio Bartulos C, Schober AF, Lepetit B, Yohannes E, Matsuda Y, Kroth PG. Mitochondrial phosphoenolpyruvate carboxylase contributes to carbon fixation in the diatom Phaeodactylum tricornutum at low inorganic carbon concentrations. THE NEW PHYTOLOGIST 2022; 235:1379-1393. [PMID: 35596716 DOI: 10.1111/nph.18268] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Photosynthetic carbon fixation is often limited by CO2 availability, which led to the evolution of CO2 concentrating mechanisms (CCMs). Some diatoms possess CCMs that employ biochemical fixation of bicarbonate, similar to C4 plants, but whether biochemical CCMs are commonly found in diatoms is a subject of debate. In the diatom Phaeodactylum tricornutum, phosphoenolpyruvate carboxylase (PEPC) is present in two isoforms, PEPC1 in the plastids and PEPC2 in the mitochondria. We used real-time quantitative polymerase chain reaction, Western blots, and enzymatic assays to examine PEPC expression and PEPC activity, under low and high concentrations of dissolved inorganic carbon (DIC). We generated and analyzed individual knockout cell lines of PEPC1 and PEPC2, as well as a PEPC1/2 double-knockout strain. While we could not detect an altered phenotype in the PEPC1 knockout strains at ambient, low or high DIC concentrations, PEPC2 and the double-knockout strains grown under ambient air or lower DIC availability conditions showed reduced growth and photosynthetic affinity for DIC while behaving similarly to wild-type (WT) cells at high DIC concentrations. These mutants furthermore exhibited significantly lower 13 C/12 C ratios compared to the WT. Our data imply that in P. tricornutum at least parts of the CCM rely on biochemical bicarbonate fixation catalyzed by the mitochondrial PEPC2.
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Affiliation(s)
- Guilan Yu
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
| | - Kensuke Nakajima
- Department of Bioscience, School of Biological and Environmental Sciences, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
- Institute of Parasitology, Biology Centre, Czech Academy of Sciences, 370 05, České Budějovice, Czech Republic
| | | | | | - Bernard Lepetit
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
| | | | - Yusuke Matsuda
- Department of Bioscience, School of Biological and Environmental Sciences, 1 Gakuen Uegahara, Sanda, Hyogo, 669-1330, Japan
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany
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Xu Y, Du X, Yu X, Jiang Q, Zheng K, Xu J, Wang P. Recent Advances in the Heterologous Expression of Biosynthetic Gene Clusters for Marine Natural Products. Mar Drugs 2022; 20:341. [PMID: 35736144 PMCID: PMC9225448 DOI: 10.3390/md20060341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2022] [Revised: 05/11/2022] [Accepted: 05/20/2022] [Indexed: 12/29/2022] Open
Abstract
Marine natural products (MNPs) are an important source of biologically active metabolites, particularly for therapeutic agent development after terrestrial plants and nonmarine microorganisms. Sequencing technologies have revealed that the number of biosynthetic gene clusters (BGCs) in marine microorganisms and the marine environment is much higher than expected. Unfortunately, the majority of them are silent or only weakly expressed under traditional laboratory culture conditions. Furthermore, the large proportion of marine microorganisms are either uncultivable or cannot be genetically manipulated. Efficient heterologous expression systems can activate cryptic BGCs and increase target compound yield, allowing researchers to explore more unknown MNPs. When developing heterologous expression of MNPs, it is critical to consider heterologous host selection as well as genetic manipulations for BGCs. In this review, we summarize current progress on the heterologous expression of MNPs as a reference for future research.
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Affiliation(s)
- Yushan Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xinhua Du
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Xionghui Yu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Qian Jiang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Kaiwen Zheng
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Jinzhong Xu
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
| | - Pinmei Wang
- Ocean College, Zhejiang University, Zhoushan 316021, China; (Y.X.); (X.D.); (X.Y.); (Q.J.); (K.Z.); (J.X.)
- State Key Laboratory of Motor Vehicle Biofuel Technology, Zhejiang University, Zhoushan 316021, China
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8
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Chen J, Huang Y, Shu Y, Hu X, Wu D, Jiang H, Wang K, Liu W, Fu W. Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity. Front Bioeng Biotechnol 2022; 10:908804. [PMID: 35646842 PMCID: PMC9136054 DOI: 10.3389/fbioe.2022.908804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.
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Affiliation(s)
- Jiwei Chen
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Yifan Huang
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Yuexuan Shu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Xiaoyue Hu
- Center for Data Science, Zhejiang University, Hangzhou, China
- School of Mathematical Sciences, Zhejiang University, Hangzhou, China
| | - Di Wu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, China
| | - Kui Wang
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Weihua Liu
- School of Mathematical Sciences, Zhejiang University, Hangzhou, China
| | - Weiqi Fu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
- 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
- *Correspondence: Weiqi Fu,
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9
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Knockout of Cia5 gene using CRISPR/Cas9 technique in Chlamydomonas reinhardtii and evaluating CO2 sequestration in control and mutant isolates. J Genet 2022. [DOI: 10.1007/s12041-021-01350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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10
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Non-Photochemical Quenching: From Light Perception to Photoprotective Gene Expression. Int J Mol Sci 2022; 23:ijms23020687. [PMID: 35054872 PMCID: PMC8775618 DOI: 10.3390/ijms23020687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2021] [Revised: 01/05/2022] [Accepted: 01/05/2022] [Indexed: 02/06/2023] Open
Abstract
Light is essential for photosynthesis but light levels that exceed an organism's assimilation capacity can cause serious damage or even cell death. Plants and microalgae have developed photoprotective mechanisms collectively referred to as non-photochemical quenching to minimize such potential damage. One such mechanism is energy-dependent quenching (qE), which dissipates excess light energy as heat. Over the last 30 years, much has been learned about the molecular mechanism of qE in green algae and plants. However, the steps between light perception and qE represented a gap in our knowledge until the recent identification of light-signaling pathways that function in these processes in the green alga Chlamydomonas reinhardtii. In this review, we summarize the high light and UV-mediated signaling pathways for qE in Chlamydomonas. We discuss key questions remaining about the pathway from light perception to photoprotective gene expression in Chlamydomonas. We detail possible differences between green algae and plants in light-signaling mechanisms for qE and emphasize the importance of research on light-signaling mechanisms for qE in plants.
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Taparia Y, Dolui AK, Boussiba S, Khozin-Goldberg I. Multiplexed Genome Editing via an RNA Polymerase II Promoter-Driven sgRNA Array in the Diatom Phaeodactylum tricornutum: Insights Into the Role of StLDP. FRONTIERS IN PLANT SCIENCE 2022; 12:784780. [PMID: 35058949 PMCID: PMC8763850 DOI: 10.3389/fpls.2021.784780] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 11/29/2021] [Indexed: 06/14/2023]
Abstract
CRISPR/Cas9-mediated genome editing has been demonstrated in the model diatom P. tricornutum, yet the currently available genetic tools do not combine the various advantageous features into a single, easy-to-assemble, modular construct that would allow the multiplexed targeting and creation of marker-free genome-edited lines. In this report, we describe the construction of the first modular two-component transcriptional unit system expressing SpCas9 from a diatom episome, assembled using the Universal Loop plasmid kit for Golden Gate assembly. We compared the editing efficiency of two constructs with orthogonal promoter-terminator combinations targeting the StLDP gene, encoding the major lipid droplet protein of P. tricornutum. Multiplexed targeting of the StLDP gene was confirmed via PCR screening, and lines with homozygous deletions were isolated from primary exconjugants. An editing efficiency ranging from 6.7 to 13.8% was observed in the better performing construct. Selected gene-edited lines displayed growth impairment, altered morphology, and the formation of lipid droplets during nutrient-replete growth. Under nitrogen deprivation, oversized lipid droplets were observed; the recovery of cell proliferation and degradation of lipid droplets were impaired after nitrogen replenishment. The results are consistent with the key role played by StLDP in the regulation of lipid droplet size and lipid homeostasis.
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Affiliation(s)
| | | | | | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture and Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Midreshet Ben-Gurion, Sede Boqer, Israel
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12
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Shokravi H, Shokravi Z, Heidarrezaei M, Ong HC, Rahimian Koloor SS, Petrů M, Lau WJ, Ismail AF. Fourth generation biofuel from genetically modified algal biomass: Challenges and future directions. CHEMOSPHERE 2021; 285:131535. [PMID: 34329137 DOI: 10.1016/j.chemosphere.2021.131535] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/27/2021] [Accepted: 07/09/2021] [Indexed: 06/13/2023]
Abstract
Genetic engineering applications in the field of biofuel are rapidly expanding due to their potential to boost biomass productivity while lowering its cost and enhancing its quality. Recently, fourth-generation biofuel (FGB), which is biofuel obtained from genetically modified (GM) algae biomass, has gained considerable attention from academic and industrial communities. However, replacing fossil resources with FGB is still beset with many challenges. Most notably, technical aspects of genetic modification operations need to be more fully articulated and elaborated. However, relatively little attention has been paid to GM algal biomass. There is a limited number of reviews on the progress and challenges faced in the algal genetics of FGB. Therefore, the present review aims to fill this gap in the literature by recapitulating the findings of recent studies and achievements on safe and efficient genetic manipulation in the production of FGB. Then, the essential issues and parameters related to genome editing in algal strains are highlighted. Finally, the main challenges to FGB pertaining to the diffusion risk and regulatory frameworks are addressed. This review concluded that the technical and biosafety aspects of FGB, as well as the complexity and diversity of the related regulations, legitimacy concerns, and health and environmental risks, are among the most important challenges that require a strong commitment at the national/international levels to reach a global consensus.
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Affiliation(s)
- Hoofar Shokravi
- School of Civil Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia
| | - Zahra Shokravi
- Department of Microbiology, Faculty of Basic Science, Islamic Azad University, Science and Research Branch of Tehran, Markazi, Iran
| | - Mahshid Heidarrezaei
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Institute of Bioproduct Development (IBD), Universiti Teknologi Malaysia, Johor Bahru, 81310, Malaysia
| | - Hwai Chyuan Ong
- Centre for Green Technology, Faculty of Engineering and Information Technology, University of Technology Sydney, NSW, 2007, Australia.
| | - Seyed Saeid Rahimian Koloor
- Institute for Nanomaterials, Advanced Technologies, and Innovation (CXI), Technical University of Liberec (TUL), Studentska 2, 461 17, Liberec, Czech Republic
| | - Michal Petrů
- Institute for Nanomaterials, Advanced Technologies, and Innovation (CXI), Technical University of Liberec (TUL), Studentska 2, 461 17, Liberec, Czech Republic
| | - Woei Jye Lau
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
| | - Ahmad Fauzi Ismail
- School of Chemical & Energy Engineering, Faculty of Engineering, Universiti Teknologi Malaysia, 81310, UTM Skudai, Johor Bahru, Johor, Malaysia; Advanced Membrane Technology Research Centre (AMTEC), Universiti Teknologi Malaysia, 81310, Skudai, Johor, Malaysia
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13
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Chrysafoudi A, Maity S, Kleinekathöfer U, Daskalakis V. Robust Strategy for Photoprotection in the Light-Harvesting Antenna of Diatoms: A Molecular Dynamics Study. J Phys Chem Lett 2021; 12:9626-9633. [PMID: 34585934 DOI: 10.1021/acs.jpclett.1c02498] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Diatoms generate a large portion of the oxygen produced on earth due to their exceptional light-harvesting properties involving fucoxanthin and chlorophyll-binding proteins (FCP). At the same time, an efficient adaptation of these complexes to fluctuating light conditions is necessary to protect the diatoms against photodamage. So far, structural and dynamic data for the interaction between FCP and the photoprotective LHCX family of proteins in diatoms are lacking. In this computational study, we provide a structural basis for a remarkable pH-dependent adaptation at the molecular level. Upon binding of the LHCX1 protein to the FCP complex together with a change in pH, conformational changes within the FCP protein result in a variation of the electronic coupling in a specific chlorophyll-fucoxanthin pair, leading to a change in the exciton transfer rate by almost an order of magnitude. A common strategy for photoprotection between diatoms and higher plants is identified and discussed.
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Affiliation(s)
- Anthi Chrysafoudi
- Department of Biology, University of Crete, Voutes University Campus, GR-70013 Heraklion, Crete, Greece
| | - Sayan Maity
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Ulrich Kleinekathöfer
- Department of Physics and Earth Sciences, Jacobs University Bremen, Campus Ring 1, 28759 Bremen, Germany
| | - Vangelis Daskalakis
- Department of Chemical Engineering, Cyprus University of Technology, 30 Archbishop Kyprianou Str., 3603 Limassol, Cyprus
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14
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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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15
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Bhattacharjya R, Tiwari A, Marella TK, Bansal H, Srivastava S. New paradigm in diatom omics and genetic manipulation. BIORESOURCE TECHNOLOGY 2021; 325:124708. [PMID: 33487514 DOI: 10.1016/j.biortech.2021.124708] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2020] [Revised: 01/07/2021] [Accepted: 01/08/2021] [Indexed: 06/12/2023]
Abstract
Diatoms are one of the most heterogeneous eukaryotic plankton known for regulating earth's biogeochemical cycles and maintaining the marine ecosystems ever since the late Eocene epoch. The advent of multidisciplinary omics approach has both epitomized and revolutionized the nature of their chimeric genetic toolkit, ecophysiology, and metabolic adaptability as well as their interaction with other communities. In addition, advanced functional annotation of transcriptomic and proteomic data using cutting edge bioinformatics tools together with high-resolution genome-scale mathematical modeling has effectively proven as the catapult in solving genetic bottlenecks in microbial as well as diatom exploration. In this review, a corroborative summation of the robust work done in manipulating, engineering, and sequencing of the diatom genomes besides underpinning the holistic application of omics in transcription and translation has been discussed in order to shrewd their multifarious novel potential in the field of biotechnology and provide an insight into their dynamic evolutionary relevance.
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Affiliation(s)
- Raya Bhattacharjya
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
| | - Archana Tiwari
- Diatom Research Laboratory, Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India.
| | - Thomas Kiran Marella
- Algae Biomass Energy System Development Research Center (ABES), Tennodai, University of Tsukuba, Tsukuba, Ibaraki 305-8572, Japan
| | - Hina Bansal
- Amity Institute of Biotechnology, Amity University, Noida, Uttar Pradesh 201313, India
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16
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Synthetic Biology Approaches To Enhance Microalgal Productivity. Trends Biotechnol 2021; 39:1019-1036. [PMID: 33541719 DOI: 10.1016/j.tibtech.2020.12.010] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Revised: 12/22/2020] [Accepted: 12/29/2020] [Indexed: 12/15/2022]
Abstract
The major bottleneck in commercializing biofuels and other commodities produced by microalgae is the high cost associated with phototrophic cultivation. Improving microalgal productivities could be a solution to this problem. Synthetic biology methods have recently been used to engineer the downstream production pathways in several microalgal strains. However, engineering upstream photosynthetic and carbon fixation metabolism to enhance growth, productivity, and yield has barely been explored in microalgae. We describe strategies to improve the generation of reducing power from light, as well as to improve the assimilation of CO2 by either the native Calvin cycle or synthetic alternatives. Overall, we are optimistic that recent technological advances will prompt long-awaited breakthroughs in microalgal research.
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17
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Mann M, Serif M, Wrobel T, Eisenhut M, Madhuri S, Flachbart S, Weber APM, Lepetit B, Wilhelm C, Kroth PG. The Aureochrome Photoreceptor PtAUREO1a Is a Highly Effective Blue Light Switch in Diatoms. iScience 2020; 23:101730. [PMID: 33235981 PMCID: PMC7670200 DOI: 10.1016/j.isci.2020.101730] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 09/30/2020] [Accepted: 10/21/2020] [Indexed: 02/08/2023] Open
Abstract
Aureochromes represent a unique type of blue light photoreceptors that possess a blue light sensing flavin-binding LOV-domain and a DNA-binding bZIP domain, thus being light-driven transcription factors. The diatom Phaeodactylum tricornutum, a member of the essential marine primary producers, possesses four aureochromes (PtAUREO1a, 1b, 1c, 2). Here we show a dramatic change in the global gene expression pattern of P. tricornutum wild-type cells after a shift from red to blue light. About 75% of the genes show significantly changed transcript levels already after 10 and 60 min of blue light exposure, which includes genes of major transcription factors as well as other photoreceptors. Very surprisingly, this light-induced regulation of gene expression is almost completely inhibited in independent PtAureo1a knockout lines. Such a massive and fast transcriptional change depending on one single photoreceptor is so far unprecedented. We conclude that PtAUREO1a plays a key role in diatoms upon blue light exposure. Blue light induces a very fast transcriptional response in the diatom P. tricornutum This strong response is almost completely inhibited when Aureochrome 1a is absent The results imply a key role of PtAureo1a in blue light-induced responses in diatoms
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Affiliation(s)
- Marcus Mann
- Institut für Biologie, Universität Leipzig, 04009 Leipzig, Germany
| | - Manuel Serif
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Thomas Wrobel
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Marion Eisenhut
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Shvaita Madhuri
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Samantha Flachbart
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Andreas P M Weber
- Institut für Biochemie der Pflanzen, Cluster of Excellence on Plant Science (CEPLAS), Heinrich-Heine-Universität, 40225 Düsseldorf, Germany
| | - Bernard Lepetit
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | | | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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18
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Teng SY, Yew GY, Sukačová K, Show PL, Máša V, Chang JS. Microalgae with artificial intelligence: A digitalized perspective on genetics, systems and products. Biotechnol Adv 2020; 44:107631. [PMID: 32931875 DOI: 10.1016/j.biotechadv.2020.107631] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2020] [Revised: 09/08/2020] [Accepted: 09/08/2020] [Indexed: 12/18/2022]
Abstract
With recent advances in novel gene-editing tools such as RNAi, ZFNs, TALENs, and CRISPR-Cas9, the possibility of altering microalgae toward designed properties for various application is becoming a reality. Alteration of microalgae genomes can modify metabolic pathways to give elevated yields in lipids, biomass, and other components. The potential of such genetically optimized microalgae can give a "domino effect" in further providing optimization leverages down the supply chain, in aspects such as cultivation, processing, system design, process integration, and revolutionary products. However, the current level of understanding the functional information of various microalgae gene sequences is still primitive and insufficient as microalgae genome sequences are long and complex. From this perspective, this work proposes to link up this knowledge gap between microalgae genetic information and optimized bioproducts using Artificial Intelligence (AI). With the recent acceleration of AI research, large and complex data from microalgae research can be properly analyzed by combining the cutting-edge of both fields. In this work, the most suitable class of AI algorithms (such as active learning, semi-supervised learning, and meta-learning) are discussed for different cases of microalgae applications. This work concisely reviews the current state of the research milestones and highlight some of the state-of-art that has been carried out, providing insightful future pathways. The utilization of AI algorithms in microalgae cultivation, system optimization, and other aspects of the supply chain is also discussed. This work opens the pathway to a digitalized future for microalgae research and applications.
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Affiliation(s)
- Sin Yong Teng
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Guo Yong Yew
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Kateřina Sukačová
- Global Change Research Institute of the Czech Academy of Sciences, Bělidla 986/4a, Brno 603 00, Czech Republic.
| | - Pau Loke Show
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor, Malaysia.
| | - Vítězslav Máša
- Brno University of Technology, Institute of Process Engineering, Technická 2896/2, 616 69, Brno, Czech Republic.
| | - Jo-Shu Chang
- Department of Chemical and Materials Engineering, College of Engineering, Tunghai University, Taichung 407, Taiwan; Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan.
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19
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Slattery SS, Wang H, Giguere DJ, Kocsis C, Urquhart BL, Karas BJ, Edgell DR. Plasmid-based complementation of large deletions in Phaeodactylum tricornutum biosynthetic genes generated by Cas9 editing. Sci Rep 2020; 10:13879. [PMID: 32807825 PMCID: PMC7431573 DOI: 10.1038/s41598-020-70769-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 07/27/2020] [Indexed: 11/09/2022] Open
Abstract
The model diatom Phaeodactylum tricornutum is an attractive candidate for synthetic biology applications. Development of auxotrophic strains of P. tricornutum would provide alternative selective markers to commonly used antibiotic resistance genes. Here, using CRISPR/Cas9, we show successful editing of genes in the uracil, histidine, and tryptophan biosynthetic pathways. Nanopore long-read sequencing indicates that editing events are characterized by the occurrence of large deletions of up to ~ 2.7 kb centered on the editing site. The uracil and histidine-requiring phenotypes can be complemented by plasmid-based copies of the intact genes after curing of the Cas9-editing plasmid. Growth of uracil auxotrophs on media supplemented with 5-fluoroorotic acid and uracil results in loss of the complementing plasmid, providing a facile method for plasmid curing with potential applications in strain engineering and CRISPR editing. Metabolomic characterization of uracil auxotrophs revealed changes in cellular orotate concentrations consistent with partial or complete loss of orotate phosphoribosyltransferase activity. Our results expand the range of P. tricornutum auxotrophic strains and demonstrate that auxotrophic complementation markers provide a viable alternative to traditionally used antibiotic selection markers. Plasmid-based auxotrophic markers should expand the range of genome engineering applications and provide a means for biocontainment of engineered P. tricornutum strains.
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Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Helen Wang
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Csanad Kocsis
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bradley L Urquhart
- Department of Physiology and Pharmacology, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada
| | - David R Edgell
- Department of Biochemistry, Schulich School of Medicine and Dentistry, Western University, London, Canada.
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20
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Kadono T, Tomaru Y, Suzuki K, Yamada K, Adachi M. The possibility of using marine diatom-infecting viral promoters for the engineering of marine diatoms. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2020; 296:110475. [PMID: 32540005 DOI: 10.1016/j.plantsci.2020.110475] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Revised: 02/26/2020] [Accepted: 03/18/2020] [Indexed: 06/11/2023]
Abstract
Marine diatoms constitute a major group of unicellular photosynthetic eukaryotes. Diatoms are widely applicable for both basic studies and applied studies. Molecular tools and techniques have been developed for diatom research. Among these tools, several endogenous gene promoters (e.g., the fucoxanthin chlorophyll a/c-binding protein gene promoter) have become available for expressing transgenes in diatoms. Gene promoters that drive transgene expression at a high level are very important for the metabolic engineering of diatoms. Various marine diatom-infecting viruses (DIVs), including both DNA viruses and RNA viruses, have recently been isolated, and their genome sequences have been characterized. Promoters from viruses that infect plants and mammals are widely used as constitutive promoters to achieve high expression of transgenes. Thus, we recently investigated the activity of promoters derived from marine DIVs in the marine diatom, Phaeodactylum tricornutum. We discuss novel viral promoters that will be useful for the future metabolic engineering of diatoms.
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Affiliation(s)
- Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan
| | - Yuji Tomaru
- National Research Institute of Fisheries and Environment of Inland Sea, Japan Fisheries Research and Education Agency, 2-17-5 Maruishi, Hatsukaichi, Hiroshima, 739-0452, Japan
| | - Kengo Suzuki
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Koji Yamada
- euglena Co., Ltd., G-BASE Tamachi 2nd and 3rd Floor 5-29-11 Shiba Minato-ku, Tokyo, 108-0014, Japan
| | - Masao Adachi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi, 783-8502, Japan.
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21
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George J, Kahlke T, Abbriano RM, Kuzhiumparambil U, Ralph PJ, Fabris M. Metabolic Engineering Strategies in Diatoms Reveal Unique Phenotypes and Genetic Configurations With Implications for Algal Genetics and Synthetic Biology. Front Bioeng Biotechnol 2020; 8:513. [PMID: 32582656 PMCID: PMC7290003 DOI: 10.3389/fbioe.2020.00513] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2019] [Accepted: 04/30/2020] [Indexed: 12/23/2022] Open
Abstract
Diatoms are photosynthetic microeukaryotes that dominate phytoplankton populations and have increasing applicability in biotechnology. Uncovering their complex biology and elevating strains to commercial standards depends heavily on robust genetic engineering tools. However, engineering microalgal genomes predominantly relies on random integration of transgenes into nuclear DNA, often resulting in detrimental “position-effects” such as transgene silencing, integration into transcriptionally-inactive regions, and endogenous sequence disruption. With the recent development of extrachromosomal transgene expression via independent episomes, it is timely to investigate both strategies at the phenotypic and genomic level. Here, we engineered the model diatom Phaeodactylum tricornutum to produce the high-value heterologous monoterpenoid geraniol, which, besides applications as fragrance and insect repellent, is a key intermediate of high-value pharmaceuticals. Using high-throughput phenotyping we confirmed the suitability of episomes for synthetic biology applications and identified superior geraniol-yielding strains following random integration. We used third generation long-read sequencing technology to generate a complete analysis of all transgene integration events including their genomic locations and arrangements associated with high-performing strains at a genome-wide scale with subchromosomal detail, never before reported in any microalga. This revealed very large, highly concatenated insertion islands, offering profound implications on diatom functional genetics and next generation genome editing technologies, and is key for developing more precise genome engineering approaches in diatoms, including possible genomic safe harbour locations to support high transgene expression for targeted integration approaches. Furthermore, we have demonstrated that exogenous DNA is not integrated inadvertently into the nuclear genome of extrachromosomal-expression clones, an important characterisation of this novel engineering approach that paves the road to synthetic biology applications.
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Affiliation(s)
- Jestin George
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Tim Kahlke
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Raffaela M Abbriano
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | | | - Peter J Ralph
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia
| | - Michele Fabris
- University of Technology Sydney, Climate Change Cluster, Faculty of Science, Ultimo, NSW, Australia.,CSIRO Synthetic Biology Future Science Platform, Brisbane, QLD, Australia
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22
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Nawaly H, Tsuji Y, Matsuda Y. Rapid and precise genome editing in a marine diatom, Thalassiosira pseudonana by Cas9 nickase (D10A). ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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23
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Marter P, Schmidt S, Kiontke S, Moog D. Optimized mRuby3 is a Suitable Fluorescent Protein for in vivo Co-localization Studies with GFP in the Diatom Phaeodactylum tricornutum. Protist 2020; 171:125715. [PMID: 32062589 DOI: 10.1016/j.protis.2020.125715] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Revised: 12/19/2019] [Accepted: 12/27/2019] [Indexed: 11/19/2022]
Abstract
Phaeodactylum tricornutum is an ecologically and evolutionarily relevant microalga that has developed into an important model for molecular biological studies on organisms with complex plastids. The diatom is particularly suitable for in vivo protein localization analyses via fluorescence microscopy in which the green fluorescent protein (GFP) and its derivatives are dominantly used. Whereas GFP fluorescence emission is usually measured between 500 and 520nm in confocal microscopy, the autofluorescence of the P. tricornutum plastid is detected above 625nm. Here we established the fluorescent protein mRuby3 as tag for efficient in vivo protein localization studies by expressing a codon-optimized gene in P. tricornutum. mRuby3 was directed to seven different subcellular localizations by means of full-length marker protein or N-/C-terminal targeting signal fusions; its emission was detected efficiently between 580 and 605nm, being unequivocally distinguishable from the plastid autofluorescence in vivo. Moreover, mRuby3 proved to be highly suitable for co-localization experiments using confocal laser scanning microscopy in which mRuby3 fusion proteins were expressed in parallel with GFP-tagged proteins. Our results show the potential of mRuby3 for its application in studying protein targeting and localization in P. tricornutum, particularly underlining its compatibility with GFP and the plastid autofluorescence in signal detection.
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Affiliation(s)
- Pia Marter
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Sebastian Schmidt
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Stephan Kiontke
- Molecular Plant Physiology and Photobiology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany
| | - Daniel Moog
- Laboratory for Cell Biology, Philipps University Marburg, Karl-von-Frisch-Str. 8, 35032 Marburg, Germany; SYNMIKRO Research Center, Hans-Meerwein-Str. 6, 35032 Marburg, Germany.
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24
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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: 90] [Impact Index Per Article: 22.5] [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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25
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Buck JM, Sherman J, Bártulos CR, Serif M, Halder M, Henkel J, Falciatore A, Lavaud J, Gorbunov MY, Kroth PG, Falkowski PG, Lepetit B. Lhcx proteins provide photoprotection via thermal dissipation of absorbed light in the diatom Phaeodactylum tricornutum. Nat Commun 2019; 10:4167. [PMID: 31519883 PMCID: PMC6744471 DOI: 10.1038/s41467-019-12043-6] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Accepted: 08/16/2019] [Indexed: 11/15/2022] Open
Abstract
Diatoms possess an impressive capacity for rapidly inducible thermal dissipation of excess absorbed energy (qE), provided by the xanthophyll diatoxanthin and Lhcx proteins. By knocking out the Lhcx1 and Lhcx2 genes individually in Phaeodactylum tricornutum strain 4 and complementing the knockout lines with different Lhcx proteins, multiple mutants with varying qE capacities are obtained, ranging from zero to high values. We demonstrate that qE is entirely dependent on the concerted action of diatoxanthin and Lhcx proteins, with Lhcx1, Lhcx2 and Lhcx3 having similar functions. Moreover, we establish a clear link between Lhcx1/2/3 mediated inducible thermal energy dissipation and a reduction in the functional absorption cross-section of photosystem II. This regulation of the functional absorption cross-section can be tuned by altered Lhcx protein expression in response to environmental conditions. Our results provide a holistic understanding of the rapidly inducible thermal energy dissipation process and its mechanistic implications in diatoms.
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Affiliation(s)
- Jochen M Buck
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jonathan Sherman
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Carolina Río Bártulos
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Manuel Serif
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Marc Halder
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Jan Henkel
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3001, Bern, Switzerland
| | - Angela Falciatore
- Sorbonne Université, Centre National de la Recherche Scientifique, Institut de Biologie Paris-Seine, Laboratory of Computational and Quantitative Biology, F-75005, Paris, France
| | - Johann Lavaud
- UMI 3376 Takuvik, CNRS/ULaval, Département de Biologie, Pavillon Alexandre-Vachon, Université Laval, Québec (Québec), G1V 0A6, Canada
| | - Maxim Y Gorbunov
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Peter G Kroth
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany
| | - Paul G Falkowski
- Environmental Biophysics and Molecular Ecology Program, Department of Marine and Coastal Sciences, Rutgers, The State University of New Jersey, New Brunswick, NJ, 08901, USA
| | - Bernard Lepetit
- Plant Ecophysiology, Department of Biology, University of Konstanz, 78457, Konstanz, Germany.
- Zukunftskolleg, University of Konstanz, 78457, Konstanz, Germany.
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Taparia Y, Zarka A, Leu S, Zarivach R, Boussiba S, Khozin-Goldberg I. A novel endogenous selection marker for the diatom Phaeodactylum tricornutum based on a unique mutation in phytoene desaturase 1. Sci Rep 2019; 9:8217. [PMID: 31160749 PMCID: PMC6546710 DOI: 10.1038/s41598-019-44710-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 05/21/2019] [Indexed: 01/10/2023] Open
Abstract
Phaeodactylum tricornutum is a well-developed model diatom for both marine ecology and microalgal biotechnology, which has been enabled by the sequenced genome and the availability of gene delivery tools, such as biolistic transformation and E. coli-mediated conjugation. Till now, these tools have mainly relied on two selectable markers of bacterial origin which confer resistance to antibiotics Zeocin and nourseothricin. An alternative cost-effective and preferably endogenous selectable marker would facilitate gene stacking efforts through successive transformation or conjugation. We performed UV-mutagenesis of P. tricornutum to obtain mutations in the phytoene desaturase (PDS) gene, conferring resistance to the bleaching herbicide norflurazon. Two mutants displaying high tolerance to norflurazon and carrying unique mutations in PtPDS1 (PHATRDRAFT_45735) were selected. These mutants revealed novel point mutations at a conserved residue Gly290 to Ser/Arg. Homology-based structural modeling of mutated PDS1, over a resolved crystallographic model of rice PDS1 complexed with norflurazon, suggests steric hindrance by bulkier residue substitution may confer herbicide resistance. We report the characterization of PtPDS1 mutants and the development of the first endogenous selectable marker in diatoms suitable for industrial strain development, with the added benefit of biocontainment. The plasmid carrying the mutated PDS1 as a selection marker and eGFP as a reporter was created. An optimized biolistic transformation system is reported which allowed the isolation of positive transgenic events at the rate of 96.7%. Additionally, the ease of in vivo UV-mutagenesis may be employed as a strategy to create PDS-norflurazon-based selectable markers for other diatoms.
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Affiliation(s)
- Yogesh Taparia
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture & Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Aliza Zarka
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture & Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Stefan Leu
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture & Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Raz Zarivach
- Department of Life Sciences, Faculty of Natural Sciences, Ben-Gurion University of the Negev, Beer-Sheva, 8410501, Israel
| | - Sammy Boussiba
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture & Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel
| | - Inna Khozin-Goldberg
- Microalgal Biotechnology Laboratory, French Associates Institute for Agriculture & Biotechnology of Drylands, The Jacob Blaustein Institutes for Desert Research, Ben-Gurion University of the Negev, Sede-Boqer Campus, Midreshet Ben-Gurion, 8499000, Israel.
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Luan H, Yao J, Chen Z, Duan D. The 40S Ribosomal Protein S6 Response to Blue Light by Interaction with SjAUREO in Saccharina japonica. Int J Mol Sci 2019; 20:E2414. [PMID: 31096691 PMCID: PMC6566693 DOI: 10.3390/ijms20102414] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Accepted: 05/14/2019] [Indexed: 02/06/2023] Open
Abstract
Blue light (BL) plays an important role in regulation of the growth and development of aquatic plants and land plants. Aureochrome (AUREO), the recent BL photoreceptor identified in photosynthetic stramenopile algae, is involved in the photomorphogenesis and early development of Saccharina japonica porophytes (kelp). However the factors that interact with the SjAUREO under BL conditions specifically are not clear. Here in our study, three high quality cDNA libraries with CFU over 5 × 106 and a recombination rate of 100% were constructed respectively through white light (WL), BL and darkness (DK) treatments to the juvenile sporophytes. Based on the constructed cDNA libraries, the interactors of SjAUREO were screened and analyzed. There are eighty-four genes encoding the sixteen predicted proteins from the BL cDNA library, sixty-eight genes encoding eighteen predicted proteins from the DK cDNA library, and seventy-four genes encoding nineteen proteins from the WL cDNA library. All the predicted proteins are presumed to interact with SjAUREO when co-expressed with SjAUREO seperately. The 40S ribosomal protein S6 (RPS6), which only exists in the BL treated cDNA library except for two other libraries, and which is essential for cell proliferation and is involved in cell cycle progression, was selected for detailed analysis. We showed that its transcription was up-regulated by BL, and was highly transcribed in the basal blade (meristem region) of juvenile sporophytes but less in the distal part. Taken together, our results indicated that RPS6 was highly involved in BL-mediated kelp cellular division and photomorphogenesis by interacting with SjAUREO.
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Affiliation(s)
- Hexiang Luan
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Jianting Yao
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
| | - Zhihang Chen
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
- University of the Chinese Academy of Sciences, Beijing 100093, China.
| | - Delin Duan
- Key Laboratory of Experimental Marine Biology, Chinese Academy of Sciences, Qingdao 266071, China.
- Center for Ocean Mega-Science, Chinese Academy of Sciences, No.7 Nanhai Road, Qingdao 266071, China.
- Laboratory for Marine Biology and Biotechnology, Qingdao National Laboratory for Marine Science and Technology, Qingdao 266237, China.
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Zhang YT, Jiang JY, Shi TQ, Sun XM, Zhao QY, Huang H, Ren LJ. Application of the CRISPR/Cas system for genome editing in microalgae. Appl Microbiol Biotechnol 2019; 103:3239-3248. [PMID: 30877356 DOI: 10.1007/s00253-019-09726-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2018] [Revised: 02/25/2019] [Accepted: 02/25/2019] [Indexed: 12/12/2022]
Abstract
Microalgae are arguably the most abundant single-celled eukaryotes and are widely distributed in oceans and freshwater lakes. Moreover, microalgae are widely used in biotechnology to produce bioenergy and high-value products such as polyunsaturated fatty acids (PUFAs), bioactive peptides, proteins, antioxidants and so on. In general, genetic editing techniques were adapted to increase the production of microalgal metabolites. The main genome editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas nuclease system. Due to its high genome editing efficiency, the CRISPR/Cas system is emerging as the most important genome editing method. In this review, we summarized the available literature on the application of CRISPR/Cas in microalgal genetic engineering, including transformation methods, strategies for the expression of Cas9 and sgRNA, the CRISPR/Cas9-mediated gene knock-in/knock-out strategies, and CRISPR interference expression modification strategies.
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Affiliation(s)
- Yu-Ting Zhang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Jia-Yi Jiang
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Tian-Qiong Shi
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Xiao-Man Sun
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - Quan-Yu Zhao
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
| | - He Huang
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- School of Pharmaceutical Sciences, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China
- State Key Laboratory of Materials-Oriented Chemical Engineering, Nanjing Tech University, No. 5 Xinmofan Road, Nanjing, 210009, People's Republic of China
- School of Food Science and Pharmaceutical Engineering, Nanjing Normal University, Wenyuan Road, Nanjing, 210023, People's Republic of China
| | - Lu-Jing Ren
- College of Biotechnology and Pharmaceutical Engineering, Nanjing Tech University, No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.
- Jiangsu National Synergetic Innovation Center for Advanced Materials (SICAM), No. 30 South Puzhu Road, Nanjing, 211816, People's Republic of China.
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30
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Buck JM, Río Bártulos C, Gruber A, Kroth PG. Blasticidin-S deaminase, a new selection marker for genetic transformation of the diatom Phaeodactylum tricornutum. PeerJ 2018; 6:e5884. [PMID: 30488015 PMCID: PMC6250098 DOI: 10.7717/peerj.5884] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 10/08/2018] [Indexed: 01/25/2023] Open
Abstract
Most genetic transformation protocols for the model diatom Phaeodactylum tricornutum rely on one of two available antibiotics as selection markers: Zeocin (a formulation of phleomycin D1) or nourseothricin. This limits the number of possible consecutive genetic transformations that can be performed. In order to expand the biotechnological possibilities for P. tricornutum, we searched for additional antibiotics and corresponding resistance genes that might be suitable for use with this diatom. Among the three different antibiotics tested in this study, blasticidin-S and tunicamycin turned out to be lethal to wild-type cells at low concentrations, while voriconazole had no detectable effect on P. tricornutum. Testing the respective resistance genes, we found that the blasticidin-S deaminase gene (bsr) effectively conferred resistance against blasticidin-S to P. tricornutum. Furthermore, we could show that expression of bsr did not lead to cross-resistances against Zeocin or nourseothricin, and that genetically transformed cell lines with resistance against Zeocin or nourseothricin were not resistant against blasticidin-S. In a proof of concept, we also successfully generated double resistant (against blasticidin-S and nourseothricin) P. tricornutum cell lines by co-delivering the bsr vector with a vector conferring nourseothricin resistance to wild-type cells.
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Affiliation(s)
- Jochen M Buck
- Department of Biology, University of Konstanz, Konstanz, Germany
| | | | - Ansgar Gruber
- Department of Biology, University of Konstanz, Konstanz, Germany.,Institute of Parasitology, Biology Centre, Czech Academy of Sciences, České Budějovice, Czech Republic
| | - Peter G Kroth
- Department of Biology, University of Konstanz, Konstanz, Germany
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Kroth PG, Bones AM, Daboussi F, Ferrante MI, Jaubert M, Kolot M, Nymark M, Río Bártulos C, Ritter A, Russo MT, Serif M, Winge P, Falciatore A. Genome editing in diatoms: achievements and goals. PLANT CELL REPORTS 2018; 37:1401-1408. [PMID: 30167805 DOI: 10.1007/s00299-018-2334-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/28/2018] [Accepted: 08/07/2018] [Indexed: 05/20/2023]
Abstract
Diatoms are major components of phytoplankton and play a key role in the ecology of aquatic ecosystems. These algae are of great scientific importance for a wide variety of research areas, ranging from marine ecology and oceanography to biotechnology. During the last 20 years, the availability of genomic information on selected diatom species and a substantial progress in genetic manipulation, strongly contributed to establishing diatoms as molecular model organisms for marine biology research. Recently, tailored TALEN endonucleases and the CRISPR/Cas9 system were utilized in diatoms, allowing targeted genetic modifications and the generation of knockout strains. These approaches are extremely valuable for diatom research because breeding, forward genetic screens by random insertion, and chemical mutagenesis are not applicable to the available model species Phaeodactylum tricornutum and Thalassiosira pseudonana, which do not cross sexually in the lab. Here, we provide an overview of the genetic toolbox that is currently available for performing stable genetic modifications in diatoms. We also discuss novel challenges that need to be addressed to fully exploit the potential of these technologies for the characterization of diatom biology and for metabolic engineering.
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Affiliation(s)
- Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457, Konstanz, Germany.
| | - Atle M Bones
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Fayza Daboussi
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Maria I Ferrante
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Marianne Jaubert
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Misha Kolot
- Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, 76100, Rehovot, Israel
- Department of Biochemistry and Molecular Biology, Tel-Aviv University, Tel-Aviv, 69978, Israel
| | - Marianne Nymark
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | | | - Andrés Ritter
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France
| | - Monia T Russo
- Integrative Marine Ecology, Stazione Zoologica Anton Dohrn, Villa Comunale 1, Naples, 80121, Italy
| | - Manuel Serif
- LISBP, Université de Toulouse, CNRS, INSA, 135 Avenue de Rangueil, 31077, Toulouse, France
| | - Per Winge
- Cell, Molecular Biology and Genomics Group, Department of Biology, Norwegian University of Science and Technology, 7491, Trondheim, Norway
| | - Angela Falciatore
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Paris-Seine, Sorbonne Université, CNRS, 75005, Paris, France.
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32
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Serif M, Dubois G, Finoux AL, Teste MA, Jallet D, Daboussi F. One-step generation of multiple gene knock-outs in the diatom Phaeodactylum tricornutum by DNA-free genome editing. Nat Commun 2018; 9:3924. [PMID: 30254261 PMCID: PMC6156588 DOI: 10.1038/s41467-018-06378-9] [Citation(s) in RCA: 72] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Accepted: 08/31/2018] [Indexed: 01/24/2023] Open
Abstract
Recently developed transgenic techniques to explore and exploit the metabolic potential of microalgae present several drawbacks associated with the delivery of exogenous DNA into the cells and its subsequent integration at random sites within the genome. Here, we report a highly efficient multiplex genome-editing method in the diatom Phaeodactylum tricornutum, relying on the biolistic delivery of CRISPR-Cas9 ribonucleoproteins coupled with the identification of two endogenous counter-selectable markers, PtUMPS and PtAPT. First, we demonstrate the functionality of RNP delivery by positively selecting the disruption of each of these genes. Then, we illustrate the potential of the approach for multiplexing by generating double-gene knock-out strains, with 65% to 100% efficiency, using RNPs targeting one of these markers and PtAureo1a, a photoreceptor-encoding gene. Finally, we created triple knock-out strains in one step by delivering six RNP complexes into Phaeodactylum cells. This approach could readily be applied to other hard-to-transfect organisms of biotechnological interest. The manipulation of diatom genomes is essential for industrial applications based on their metabolic abilities. Here the authors present an efficient multiplex DNA-free gene editing method using CRISPR-Cas9 and counter-selectable markers.
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Affiliation(s)
- Manuel Serif
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Gwendoline Dubois
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Anne-Laure Finoux
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Marie-Ange Teste
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Denis Jallet
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France.,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France.,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France
| | - Fayza Daboussi
- INSA, UPS, INP, LISBP, Université de Toulouse, 135 Avenue de Rangueil, F-31077, Toulouse, France. .,INRA, LISBP, UMR792, 135 Avenue de Rangueil, F-31077, Toulouse, France. .,CNRS, LISBP, UMR5504, 135 Avenue de Rangueil, F-31077, Toulouse, France.
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Matiiv AB, Chekunova EM. Aureochromes - Blue Light Receptors. BIOCHEMISTRY (MOSCOW) 2018; 83:662-673. [PMID: 30195323 DOI: 10.1134/s0006297918060044] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A variety of living organisms including bacteria, fungi, animals, and plants use blue light (BL) to adapt to changing ambient light. Photosynthetic forms (plants and algae) require energy of light for photosynthesis, movements, development, and regulation of activity. Several complex light-sensitive systems evolved in eukaryotic cells to use the information of light efficiently with photoreceptors selectively absorbing various segments of the solar spectrum, being the first components in the light signal transduction chain. They are most diverse in algae. Photosynthetic stramenopiles, which received chloroplasts from red algae during secondary symbiosis, play an important role in ecosystems and aquaculture, being primary producers. These taxa acquired the ability to use BL for regulation of such processes as phototropism, chloroplast photo-relocation movement, and photomorphogenesis. A new type of BL receptor - aureochrome (AUREO) - was identified in Vaucheria frigida in 2007. AUREO consists of two domains: bZIP (basic-region leucine zipper) domain and LOV (light-oxygen-voltage-sensing) domain, and thus this photoreceptor is a BL-sensitive transcription factor. This review presents current data on the structure, mechanisms of action, and biochemical features of aureochromes.
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Affiliation(s)
- A B Matiiv
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia
| | - E M Chekunova
- St. Petersburg State University, Faculty of Biology, St. Petersburg, 199034, Russia.
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34
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The evolution of the photoprotective antenna proteins in oxygenic photosynthetic eukaryotes. Biochem Soc Trans 2018; 46:1263-1277. [DOI: 10.1042/bst20170304] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2018] [Revised: 07/02/2018] [Accepted: 07/04/2018] [Indexed: 12/24/2022]
Abstract
Photosynthetic organisms require rapid and reversible down-regulation of light harvesting to avoid photodamage. Response to unpredictable light fluctuations is achieved by inducing energy-dependent quenching, qE, which is the major component of the process known as non-photochemical quenching (NPQ) of chlorophyll fluorescence. qE is controlled by the operation of the xanthophyll cycle and accumulation of specific types of proteins, upon thylakoid lumen acidification. The protein cofactors so far identified to modulate qE in photosynthetic eukaryotes are the photosystem II subunit S (PsbS) and light-harvesting complex stress-related (LHCSR/LHCX) proteins. A transition from LHCSR- to PsbS-dependent qE took place during the evolution of the Viridiplantae (also known as ‘green lineage’ organisms), such as green algae, mosses and vascular plants. Multiple studies showed that LHCSR and PsbS proteins have distinct functions in the mechanism of qE. LHCX(-like) proteins are closely related to LHCSR proteins and found in ‘red lineage’ organisms that contain secondary red plastids, such as diatoms. Although LHCX proteins appear to control qE in diatoms, their role in the mechanism remains poorly understood. Here, we present the current knowledge on the functions and evolution of these crucial proteins, which evolved in photosynthetic eukaryotes to optimise light harvesting.
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Li X, Pan Y, Hu H. Identification of the triacylglycerol lipase in the chloroplast envelope of the diatom Phaeodactylum tricornutum. ALGAL RES 2018. [DOI: 10.1016/j.algal.2018.06.023] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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36
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Maeda Y, Yoshino T, Matsunaga T, Matsumoto M, Tanaka T. Marine microalgae for production of biofuels and chemicals. Curr Opin Biotechnol 2018; 50:111-120. [DOI: 10.1016/j.copbio.2017.11.018] [Citation(s) in RCA: 76] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Revised: 11/27/2017] [Accepted: 11/28/2017] [Indexed: 01/17/2023]
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37
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Stukenberg D, Zauner S, Dell’Aquila G, Maier UG. Optimizing CRISPR/Cas9 for the Diatom Phaeodactylum tricornutum. FRONTIERS IN PLANT SCIENCE 2018; 9:740. [PMID: 29928285 PMCID: PMC5998643 DOI: 10.3389/fpls.2018.00740] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2018] [Accepted: 05/15/2018] [Indexed: 05/18/2023]
Abstract
CRISPR/Cas9 is a powerful tool for genome editing. We constructed an easy-to-handle expression vector for application in the model organism Phaeodactylum tricornutum and tested its capabilities in order to apply CRISPR/Cas9 technology for our purpose. In our experiments, we targeted two different genes, screened for mutations and analyzed mutated diatoms in a three-step process. In the end, we identified cells, showing either monoallelic or homo-biallelic targeted mutations. Thus, we confirm that application of the CRISPR/Cas9 system for P. tricornutum is very promising, although, as discussed, overlooked pitfalls have to be considered.
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Affiliation(s)
- Daniel Stukenberg
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | - Stefan Zauner
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
| | | | - Uwe G. Maier
- Department for Cell Biology, Philipps-Universität Marburg, Marburg, Germany
- LOEWE-Zentrum für Synthetische Mikrobiologie (SYNMIKRO), Philipps-Universität Marburg, Marburg, Germany
- *Correspondence: Uwe G. Maier,
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Kroth PG, Wilhelm C, Kottke T. An update on aureochromes: Phylogeny - mechanism - function. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:20-26. [PMID: 28797596 DOI: 10.1016/j.jplph.2017.06.010] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2017] [Revised: 06/21/2017] [Accepted: 06/23/2017] [Indexed: 05/20/2023]
Abstract
Light is important for algae, as it warrants metabolic independence via photosynthesis. In addition to the absorption of light by the photosystems, algae possess a variety of specific photoreceptors that allow the quantification of the light fluxes as well as the assessment of light qualities. About a decade ago, aureochromes have been described in the xanthophyte alga Vaucheria frigida. These proteins represent a new type of blue light photoreceptor as they possess both a light-oxygen-voltage (LOV) domain for light reception as well as a basic region leucine zipper (bZIP) domain for DNA binding, indicating that they represent light-driven transcription factors. Aureochromes so far have been detected only in a single group of algae, photosynthetic stramenopiles, but not in any other prokaryotic or eukaryotic organisms. Recent biophysical work on aureochromes in the absence and the presence of DNA revealed the mechanism of allosteric communication between the sensor and effector domains despite their unusual inversed arrangement. Different molecular models have been proposed to describe the effect of light on DNA binding. Functional characterization of mutants of the diatom Phaeodactylum tricornutum, in which the aureochrome genes have been silenced or deleted, indicate that different aureochromes may have different functions, being involved in central processes like light acclimation and regulation of the cell cycle.
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Affiliation(s)
- Peter G Kroth
- Department of Biology, University of Konstanz, 78457 Konstanz, Germany.
| | - Christian Wilhelm
- Institute of Biology, University of Leipzig, Johannisallee 21-23, 04103 Leipzig, Germany
| | - Tilman Kottke
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
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Mann M, Serif M, Jakob T, Kroth PG, Wilhelm C. PtAUREO1a and PtAUREO1b knockout mutants of the diatom Phaeodactylum tricornutum are blocked in photoacclimation to blue light. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:44-48. [PMID: 28610707 DOI: 10.1016/j.jplph.2017.05.020] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2017] [Revised: 05/22/2017] [Accepted: 05/29/2017] [Indexed: 05/20/2023]
Abstract
Aureochromes are blue light receptors specifically found in photosynthetic Stramenopiles (algae). Four different Aureochromes have been identified in the marine diatom Phaeodactylum tricornutum (PtAUREO 1a, 1b, 1c, and 2). Since blue light is necessary for high light acclimation in diatoms, it has been hypothesized that Aureochromes might play an important role in the light acclimation capacity of diatoms. This hypothesis was supported by an RNAi knockdown line of PtAUREO1a, which showed a phenotype different from wild type cells when grown in either blue or red light. Here, we show for the first time the phenotype and the photoacclimation reaction of TALEN-mediated knockout mutants of PtAUREO1a and PtAUREO1b, clearly proving the necessity of Aureochromes for light acclimation under blue light. However, both mutants do also show specific differences in their respective phenotypes. Hence, PtAUREO1a and 1b are not functionally redundant in photoacclimation to blue light, and their specific contribution needs to be clarified further.
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Affiliation(s)
- Marcus Mann
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany.
| | - Manuel Serif
- Plant Ecophysiology, Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Torsten Jakob
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
| | - Peter G Kroth
- Plant Ecophysiology, Fachbereich Biologie, Universität Konstanz, D-78457 Konstanz, Germany
| | - Christian Wilhelm
- Institute of Biology, Department of Plant Physiology, University of Leipzig, D-04103 Leipzig, Germany
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Gruber A, Kroth PG. Intracellular metabolic pathway distribution in diatoms and tools for genome-enabled experimental diatom research. Philos Trans R Soc Lond B Biol Sci 2017; 372:20160402. [PMID: 28717012 PMCID: PMC5516111 DOI: 10.1098/rstb.2016.0402] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/21/2017] [Indexed: 11/12/2022] Open
Abstract
Diatoms are important primary producers in the oceans and can also dominate other aquatic habitats. One reason for the success of this phylogenetically relatively young group of unicellular organisms could be the impressive redundancy and diversity of metabolic isoenzymes in diatoms. This redundancy is a result of the evolutionary origin of diatom plastids by a eukaryote-eukaryote endosymbiosis, a process that implies temporary redundancy of functionally complete eukaryotic genomes. During the establishment of the plastids, this redundancy was partially reduced via gene losses, and was partially retained via gene transfer to the nucleus of the respective host cell. These gene transfers required re-assignment of intracellular targeting signals, a process that simultaneously altered the intracellular distribution of metabolic enzymes compared with the ancestral cells. Genome annotation, the correct assignment of the gene products and the prediction of putative function, strongly depends on the correct prediction of the intracellular targeting of a gene product. Here again diatoms are very peculiar, because the targeting systems for organelle import are partially different to those in land plants. In this review, we describe methods of predicting intracellular enzyme locations, highlight findings of metabolic peculiarities in diatoms and present genome-enabled approaches to study their metabolism.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Ansgar Gruber
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
| | - Peter G Kroth
- Fachbereich Biologie, Universität Konstanz, 78457 Konstanz, Germany
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Hess SK, Lepetit B, Kroth PG, Mecking S. Production of chemicals from microalgae lipids - status and perspectives. EUR J LIPID SCI TECH 2017. [DOI: 10.1002/ejlt.201700152] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Sandra K. Hess
- Department of Chemistry; Chair of Chemical Materials Science; University of Konstanz; Konstanz Germany
| | - Bernard Lepetit
- Department of Biology; Plant Ecology; University of Konstanz; Konstanz Germany
| | - Peter G. Kroth
- Department of Biology; Plant Ecology; University of Konstanz; Konstanz Germany
| | - Stefan Mecking
- Department of Chemistry; Chair of Chemical Materials Science; University of Konstanz; Konstanz Germany
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Allorent G, Petroutsos D. Photoreceptor-dependent regulation of photoprotection. CURRENT OPINION IN PLANT BIOLOGY 2017; 37:102-108. [PMID: 28472717 DOI: 10.1016/j.pbi.2017.03.016] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/26/2017] [Accepted: 03/28/2017] [Indexed: 05/05/2023]
Abstract
In photosynthetic organisms, proteins in the light-harvesting complex (LHC) harvest light energy to fuel photosynthesis, whereas photoreceptor proteins are activated by the different wavelengths of the light spectrum to regulate cellular functions. Under conditions of excess light, blue-light photoreceptors activate chloroplast avoidance movements in sessile plants, and blue- and green-light photoreceptors cause motile algae to swim away from intense light. Simultaneously, LHCs switch from light-harvesting mode to energy-dissipation mode, which was thought to be independent of photoreceptor-signaling up until recently. Recent advances, however, indicate that energy dissipation in green algae is controlled by photoreceptors activated by blue and UV-B light, and new molecular links have been established between photoreception and photoprotection.
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Affiliation(s)
- Guillaume Allorent
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France
| | - Dimitris Petroutsos
- Laboratoire de Physiologie Cellulaire et Végétale, UMR 5168, Centre National de la Recherche Scientifique (CNRS), Commissariat à l'Energie Atomique et aux Energies Alternatives (CEA), Université Grenoble Alpes, Institut National Recherche Agronomique (INRA), Institut de Biosciences et Biotechnologies de Grenoble, (BIG), CEA Grenoble, 17 rue des Martyrs F-38054 Grenoble Cedex 9, France.
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