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Garza EA, Bielinski VA, Espinoza JL, Orlandi K, Alfaro JR, Bolt TM, Beeri K, Weyman PD, Dupont CL. Validating a Promoter Library for Application in Plasmid-Based Diatom Genetic Engineering. ACS Synth Biol 2023; 12:3215-3228. [PMID: 37857380 PMCID: PMC10661051 DOI: 10.1021/acssynbio.3c00163] [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: 03/21/2023] [Indexed: 10/21/2023]
Abstract
While diatoms are promising synthetic biology platforms, there currently exists a limited number of validated genetic regulatory parts available for genetic engineering. The standard method for diatom transformation, nonspecific introduction of DNA into chromosomes via biolistic particle bombardment, is low throughput and suffers from clonal variability and epigenetic effects. Recent developments in diatom engineering have demonstrated that autonomously replicating episomal plasmids serve as stable expression platforms for diverse gene expression technologies. These plasmids are delivered via bacterial conjugation and, when combined with modular DNA assembly technologies, provide a flexibility and speed not possible with biolistic-mediated strain generation. In order to expand the current toolbox for plasmid-based engineering in the diatom Phaeodactylum tricornutum, a conjugation-based forward genetics screen for promoter discovery was developed, and application to a diatom genomic DNA library defined 252 P. tricornutum promoter elements. From this library, 40 promoter/terminator pairs were delivered via conjugation on episomal plasmids, characterized in vivo, and ranked across 4 orders of magnitude difference in reporter gene expression levels.
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Affiliation(s)
- Erin A. Garza
- J. Craig Venter Institute, La Jolla, California 92037, United States
| | | | - Josh L. Espinoza
- J. Craig Venter Institute, La Jolla, California 92037, United States
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2
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Krämer LC, Wasser D, Haitz F, Sabel B, Büchel C. Heterologous expression of HUP1 glucose transporter enables low-light mediated growth on glucose in Phaeodactylum tricornutum. ALGAL RES 2022. [DOI: 10.1016/j.algal.2022.102719] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
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3
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Slattery SS, Giguere DJ, Stuckless EE, Shrestha A, Briere LAK, Galbraith A, Reaume S, Boyko X, Say HH, Browne TS, Frederick MI, Lant JT, Heinemann IU, O'Donoghue P, Dsouza L, Martin S, Howard P, Jedeszko C, Ali K, Styba G, Flatley M, Karas BJ, Gloor GB, Edgell DR. Phosphate-regulated expression of the SARS-CoV-2 receptor-binding domain in the diatom Phaeodactylum tricornutum for pandemic diagnostics. Sci Rep 2022; 12:7010. [PMID: 35487958 PMCID: PMC9051505 DOI: 10.1038/s41598-022-11053-7] [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: 11/19/2021] [Accepted: 04/18/2022] [Indexed: 12/22/2022] Open
Abstract
The worldwide COVID-19 pandemic caused by the SARS-CoV-2 betacoronavirus has highlighted the need for a synthetic biology approach to create reliable and scalable sources of viral antigen for uses in diagnostics, therapeutics and basic biomedical research. Here, we adapt plasmid-based systems in the eukaryotic microalgae Phaeodactylum tricornutum to develop an inducible overexpression system for SARS-CoV-2 proteins. Limiting phosphate and iron in growth media induced expression of the receptor-binding domain (RBD) of the SARS-CoV-2 spike protein from the P. tricornutum HASP1 promoter in the wild-type strain and in a histidine auxotrophic strain that alleviates the requirement for antibiotic selection of expression plasmids. The RBD was purified from whole cell extracts (algae-RBD) with yield compromised by the finding that 90-95% of expressed RBD lacked the genetically encoded C-terminal 6X-histidine tag. Constructs that lacked the TEV protease site between the RBD and C-terminal 6X-histidine tag retained the tag, increasing yield. Purified algae-RBD was found to be N-linked glycosylated by treatment with endoglycosidases, was cross-reactive with anti-RBD polyclonal antibodies, and inhibited binding of recombinant RBD purified from mammalian cell lines to the human ACE2 receptor. We also show that the algae-RBD can be used in a lateral flow assay device to detect SARS-CoV-2 specific IgG antibodies from donor serum at sensitivity equivalent to assays performed with RBD made in mammalian cell lines. Our study shows that P. tricornutum is a scalable system with minimal biocontainment requirements for the inducible production of SARS-CoV-2 or other coronavirus antigens for pandemic diagnostics.
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Affiliation(s)
- Samuel S Slattery
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Daniel J Giguere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Emily E Stuckless
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Arina Shrestha
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Lee-Ann K Briere
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Alexa Galbraith
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Stephen Reaume
- Lambton College, 1457 London Rd, Sarnia, ON, N7S 6K4, Canada
| | - Xenia Boyko
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Henry H Say
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Tyler S Browne
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Mallory I Frederick
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Jeremy T Lant
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Ilka U Heinemann
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Patrick O'Donoghue
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
- Department of Chemistry, Western University, London, ON, N6A 3K7, Canada
| | - Liann Dsouza
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Steven Martin
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Peter Howard
- Pond Technologies Inc., Markham, ON, L3R 9W7, Canada
| | - Christopher Jedeszko
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Kinza Ali
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Garth Styba
- International Point of Care Inc., 135 The West Mall Unit 9, Toronto, ON, M9C 1C2, Canada
| | - Martin Flatley
- Suncor Energy Inc., Sarnia Refinery, 1900 River Road, Sarnia, ON, N7T 7J3, Canada
| | - Bogumil J Karas
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada
| | - Gregory B Gloor
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
| | - David R Edgell
- Department of Biochemistry, Schlich School of Medicine and Dentistry, Western University, London, ON, N6A 5C1, Canada.
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Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
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Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
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Erdene‐Ochir E, Shin B, Huda MN, Lee EH, Song D, Jung C, Pan C. Characterization of endogenous promoters of GapC1 and GS for recombinant protein expression in Phaeodactylum tricornutum. Microbiologyopen 2021; 10:e1239. [PMID: 34713604 PMCID: PMC8545674 DOI: 10.1002/mbo3.1239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 09/14/2021] [Indexed: 11/11/2022] Open
Abstract
Although diatoms have been utilized as a cellular factory to produce biopharmaceuticals, recombinant proteins, and biofuels, only a few numbers of gene promoters are available. Therefore, the development of novel endogenous promoters is essential for the production of a range of bioactive substances. Here, we characterized the activities of endogenous promoters glyceraldehyde-3-phosphate dehydrogenase (GapC1) and glutamine synthetase (GS) of Phaeodactylum tricornutum using green fluorescent protein (GFP) under different culture conditions. Compared with the widely used fucoxanthin chlorophyll-binding protein A (fcpA) promoter, the GS promoter constitutively drove the expression of GFP throughout all growth phases of P. tricornutum, regardless of culture conditions. Additionally, the GFP level driven by the GapC1 promoter was the highest at the log phase, similar to the fcpA promoter, and increased light and nitrogen-starvation conditions reduced GFP levels by inhibiting promoter activity. These results suggested that the GS promoter could be utilized as a strong endogenous promoter for the genetic engineering of P. tricornutum.
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Affiliation(s)
- Erdenedolgor Erdene‐Ochir
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
| | | | - Md Nazmul Huda
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
| | - Eun Ha Lee
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
| | - Dae‐Geun Song
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
| | - Choonkyun Jung
- Department of International Agricultural Technology and Crop Biotechnology Institute/GreenBio Science and TechnologySeoul National UniversityPyeongchangRepublic of Korea
- Department of Agriculture, Forestry, and Bioresources and Integrated Major in Global Smart Farm, College of Agriculture and Life SciencesSeoul National UniversitySeoulRepublic of Korea
| | - Cheol‐Ho Pan
- Natural Product Informatics Research CenterKIST Gangneung Institute of Natural ProductsGangneungRepublic of Korea
- Division of Bio‐Medical Science and Technology, KIST SchoolKorea University of Science and TechnologySeoulRepublic of Korea
- Microalgae Ask Us Co., Ltd.GangneungRepublic of Korea
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6
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de Grahl I, Reumann S. Stramenopile microalgae as "green biofactories" for recombinant protein production. World J Microbiol Biotechnol 2021; 37:163. [PMID: 34453200 PMCID: PMC8397651 DOI: 10.1007/s11274-021-03126-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2021] [Accepted: 08/06/2021] [Indexed: 12/23/2022]
Abstract
Photoautotrophic microalgae have become intriguing hosts for recombinant protein production because they offer important advantages of both prokaryotic and eukaryotic expression systems. Advanced molecular tools have recently been established for the biotechnologically relevant group of stramenopile microalgae, particularly for several Nannochloropsis species and diatoms. Strategies for the selection of powerful genetic elements and for optimization of protein production have been reported. Much needed high-throughput techniques required for straight-forward identification and selection of the best expression constructs and transformants have become available and are discussed. The first recombinant proteins have already been produced successfully in stramenopile microalgae and include not only several subunit vaccines but also one antimicrobial peptide, a fish growth hormone, and an antibody. These research results offer interesting future applications in aquaculture and as biopharmaceuticals. In this review we highlight recent progress in genetic technology development for recombinant protein production in the most relevant Nannochloropsis species and diatoms. Diverse realistic biotechnological applications of these proteins are emphasized that have the potential to establish stramenopile algae as sustainable green factories for an economically competitive production of high-value biomolecules.
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Affiliation(s)
- Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany.
| | - Sigrun Reumann
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, 22609, Hamburg, Germany
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7
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Avilan L, Lebrun R, Puppo C, Citerne S, Cuiné S, Li‐Beisson Y, Menand B, Field B, Gontero B. ppGpp influences protein protection, growth and photosynthesis in Phaeodactylum tricornutum. THE NEW PHYTOLOGIST 2021; 230:1517-1532. [PMID: 33595847 PMCID: PMC8252717 DOI: 10.1111/nph.17286] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 02/08/2021] [Indexed: 05/08/2023]
Abstract
Chloroplasts retain elements of a bacterial stress response pathway that is mediated by the signalling nucleotides guanosine penta- and tetraphosphate ((p)ppGpp). In the model flowering plant Arabidopsis, ppGpp acts as a potent regulator of plastid gene expression and influences photosynthesis, plant growth and development. However, little is known about ppGpp metabolism or its evolution in other photosynthetic eukaryotes. Here, we studied the function of ppGpp in the diatom Phaeodactylum tricornutum using transgenic lines containing an inducible system for ppGpp accumulation. We used these lines to investigate the effects of ppGpp on growth, photosynthesis, lipid metabolism and protein expression. We demonstrate that ppGpp accumulation reduces photosynthetic capacity and promotes a quiescent-like state with reduced proliferation and ageing. Strikingly, using nontargeted proteomics, we discovered that ppGpp accumulation also leads to the coordinated upregulation of a protein protection response in multiple cellular compartments. Our findings highlight the importance of ppGpp as a fundamental regulator of chloroplast function across different domains of life, and lead to new questions about the molecular mechanisms and roles of (p)ppGpp signalling in photosynthetic eukaryotes.
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Affiliation(s)
- Luisana Avilan
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
- Centre for Enzyme InnovationSchool of Biological SciencesInstitute of Biological and Biomedical SciencesUniversity of PortsmouthPortsmouthPO1 2DYUK
| | - Regine Lebrun
- Plate‐forme ProtéomiqueMarseille Protéomique (MaP)IMM FR 3479, 31 Chemin Joseph AiguierMarseille13009France
| | - Carine Puppo
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
| | - Sylvie Citerne
- Institut Jean‐Pierre BourginINRAEAgroParisTechUniversité Paris‐SaclayVersailles78000France
| | - Stephane Cuiné
- CEA, CNRS, UMR7265 BIAMCEA CadaracheAix‐Marseille UnivSaint‐Paul‐lez Durance13108France
| | - Yonghua Li‐Beisson
- CEA, CNRS, UMR7265 BIAMCEA CadaracheAix‐Marseille UnivSaint‐Paul‐lez Durance13108France
| | - Benoît Menand
- CEA, CNRS, UMR7265 BIAMAix‐Marseille UnivMarseille13009France
| | - Ben Field
- CEA, CNRS, UMR7265 BIAMAix‐Marseille UnivMarseille13009France
| | - Brigitte Gontero
- CNRSBIPUMR 7281IMM FR 3479Aix Marseille Univ31 Chemin Joseph AiguierMarseille13009France
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Moog D, Zarzycki J, Rexer KH, Erb TJ, Maier UG. Engineering microalgae as a whole cell catalyst for PET degradation. Methods Enzymol 2021; 648:435-455. [PMID: 33579415 DOI: 10.1016/bs.mie.2020.12.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Plastic pollution has become a serious issue on Earth. Although efficient industrial recycling processes exist, a significant fraction of plastic waste still ends up in nature, where it can endure for centuries. Slow mechanical and chemical decay lead to the formation of micro- and nanoplastics, which are washed from land into rivers and finally end up in the oceans. As such particles cannot be efficiently removed from the environment, biological degradation mechanisms are highly desirable. Several enzymes have been described that are capable of degrading certain plastic materials such as polyethylene terephthalate (PET). Such enzymes have a huge potential for future biotechnology applications. However, they require model systems that can be efficiently adapted to very specific conditions. Here, we present detailed instructions, how to convert the model diatom Phaeodactylum into a solar-fueled microbial cell factory for PETase expression, resulting in a whole cell catalyst for PET degradation at moderate temperatures under saltwater conditions.
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Affiliation(s)
- Daniel Moog
- Laboratory for Cell Biology, University of Marburg, Marburg, Germany; SYNMIKRO Research Center, Marburg, Germany.
| | - Jan Zarzycki
- Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Karl-Heinz Rexer
- Department for Evolutionary Ecology of Plants, University of Marburg, Marburg, Germany
| | - Tobias J Erb
- SYNMIKRO Research Center, Marburg, Germany; Max Planck Institute for Terrestrial Microbiology, Marburg, Germany
| | - Uwe G Maier
- Laboratory for Cell Biology, University of Marburg, Marburg, Germany; SYNMIKRO Research Center, Marburg, Germany
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de Grahl I, Rout SS, Maple-Grødem J, Reumann S. Development of a constitutive and an auto-inducible high-yield expression system for recombinant protein production in the microalga Nannochloropsis oceanica. Appl Microbiol Biotechnol 2020; 104:8747-8760. [PMID: 32902683 PMCID: PMC7502441 DOI: 10.1007/s00253-020-10789-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 07/10/2020] [Accepted: 07/19/2020] [Indexed: 01/28/2023]
Abstract
Photoautotrophic microalgae offer a great potential as novel hosts for efficient recombinant protein production. Nannochloropsis oceanica produces an extraordinarily high content of polyunsaturated fatty acids, and its robust growth characteristics, published genome sequence and efficient nuclear transformation make N. oceanica a promising candidate for biotechnological applications. To establish a robust and flexible system for recombinant protein production, we cloned six endogenous, potentially constitutive or inducible promoters from N. oceanica strain CCMP1779 and investigated their strength using monomeric Venus as reporter gene. Microscopic pre-screening of individual transformants revealed that the promoters of elongation factor (EF), tubulin (TUB) and nitrate reductase (NR) enabled high reporter gene expression. Comparative quantitative analyses of transformant populations by flow cytometry and qRT-PCR demonstrated the highest Venus expression from the EF promoter and the NR promoter if extended by an N-terminal 14-amino acid leader sequence. The kinetics of reporter gene expression were analysed during photobioreactor cultivation, achieving Venus yields of 0.3% (for EF) and 4.9% (for NR::LS) of total soluble protein. Since inducible expression systems enable the production of toxic proteins, we developed an auto-induction medium for the NR promoter transformants. By switching the N source from ammonium to nitrate in the presence of low ammonium concentrations, the starting point of Venus induction could be fine-tuned and shifted towards exponential growth phase while maintaining high recombinant protein yields. Taken together, we demonstrate that a model recombinant protein can be produced robustly and at very high levels in N. oceanica not only under constitutive but also under auto-inducible cultivation conditions. KEY POINTS: • Nannochloropsis oceanica might serve as host for recombinant protein production. • Comparative promoter strength analyses were conducted for twelve different constructs. • Robust high-yield recombinant protein production was achieved under constitutive conditions. • The nitrate reductase promoter enabled protein production under auto-induction conditions.
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Affiliation(s)
- Imke de Grahl
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, D-22609, Hamburg, Germany
| | - Sweta Suman Rout
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, D-22609, Hamburg, Germany
| | - Jodi Maple-Grødem
- The Norwegian Centre for Movement Disorders, Stavanger University Hospital, N-4021, Stavanger, Norway.,Department of Chemistry, Bioscience and Environmental Engineering, University of Stavanger, N-4036, Stavanger, Norway
| | - Sigrun Reumann
- Plant Biochemistry and Infection Biology, Institute of Plant Science and Microbiology, Universität Hamburg, Ohnhorststr. 18, D-22609, Hamburg, Germany.
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Kumar G, Shekh A, Jakhu S, Sharma Y, Kapoor R, Sharma TR. Bioengineering of Microalgae: Recent Advances, Perspectives, and Regulatory Challenges for Industrial Application. Front Bioeng Biotechnol 2020; 8:914. [PMID: 33014997 PMCID: PMC7494788 DOI: 10.3389/fbioe.2020.00914] [Citation(s) in RCA: 84] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 07/15/2020] [Indexed: 01/14/2023] Open
Abstract
Microalgae, due to their complex metabolic capacity, are being continuously explored for nutraceuticals, pharmaceuticals, and other industrially important bioactives. However, suboptimal yield and productivity of the bioactive of interest in local and robust wild-type strains are of perennial concerns for their industrial applications. To overcome such limitations, strain improvement through genetic engineering could play a decisive role. Though the advanced tools for genetic engineering have emerged at a greater pace, they still remain underused for microalgae as compared to other microorganisms. Pertaining to this, we reviewed the progress made so far in the development of molecular tools and techniques, and their deployment for microalgae strain improvement through genetic engineering. The recent availability of genome sequences and other omics datasets form diverse microalgae species have remarkable potential to guide strategic momentum in microalgae strain improvement program. This review focuses on the recent and significant improvements in the omics resources, mutant libraries, and high throughput screening methodologies helpful to augment research in the model and non-model microalgae. Authors have also summarized the case studies on genetically engineered microalgae and highlight the opportunities and challenges that are emerging from the current progress in the application of genome-editing to facilitate microalgal strain improvement. Toward the end, the regulatory and biosafety issues in the use of genetically engineered microalgae in commercial applications are described.
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Affiliation(s)
- Gulshan Kumar
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ajam Shekh
- Plant Cell Biotechnology Department, CSIR-Central Food Technological Research Institute (CFTRI), Mysuru, India
| | - Sunaina Jakhu
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Yogesh Sharma
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Ritu Kapoor
- Agricultural Biotechnology Division, National Agri-Food Biotechnology Institute (NABI), Sahibzada Ajit Singh Nagar, India
| | - Tilak Raj Sharma
- Division of Crop Science, Indian Council of Agricultural Research, New Delhi, India
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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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Pollak B, Matute T, Nuñez I, Cerda A, Lopez C, Vargas V, Kan A, Bielinski V, von Dassow P, Dupont CL, Federici F. Universal loop assembly: open, efficient and cross-kingdom DNA fabrication. Synth Biol (Oxf) 2020; 5:ysaa001. [PMID: 32161816 PMCID: PMC7052795 DOI: 10.1093/synbio/ysaa001] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 12/04/2019] [Accepted: 12/23/2019] [Indexed: 01/22/2023] Open
Abstract
Standardized type IIS DNA assembly methods are becoming essential for biological engineering and research. These methods are becoming widespread and more accessible due to the proposition of a 'common syntax' that enables higher interoperability between DNA libraries. Currently, Golden Gate (GG)-based assembly systems, originally implemented in host-specific vectors, are being made compatible with multiple organisms. We have recently developed the GG-based Loop assembly system for plants, which uses a small library and an intuitive strategy for hierarchical fabrication of large DNA constructs (>30 kb). Here, we describe 'universal Loop' (uLoop) assembly, a system based on Loop assembly for use in potentially any organism of choice. This design permits the use of a compact number of plasmids (two sets of four odd and even vectors), which are utilized repeatedly in alternating steps. The elements required for transformation/maintenance in target organisms are also assembled as standardized parts, enabling customization of host-specific plasmids. Decoupling of the Loop assembly logic from the host-specific propagation elements enables universal DNA assembly that retains high efficiency regardless of the final host. As a proof-of-concept, we show the engineering of multigene expression vectors in diatoms, yeast, plants and bacteria. These resources are available through the OpenMTA for unrestricted sharing and open access.
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Affiliation(s)
- Bernardo Pollak
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Fundación Ciencia y Vida, Santiago, Chile
| | - Tamara Matute
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Isaac Nuñez
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Department of Chemical and Bioprocess Engineering, School of Engineering, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Ariel Cerda
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Constanza Lopez
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Valentina Vargas
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Anton Kan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA
| | - Vincent Bielinski
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Peter von Dassow
- Departamento de Ecología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto Milenio de Oceanografía de Chile, Concepción, Chile
- UMI 3614 Evolutionary Biology and Ecology of Algae, CNRS, Sorbonne Université, Pontificia Universidad Católica de Chile, Universidad Austral de Chile, Station Biologique de Roscoff, 29680 Roscoff, France
| | - Chris L Dupont
- Microbial and Environmental Genomics Department, J. Craig Venter Institute, La Jolla, CA 92037, USA
| | - Fernán Federici
- Millennium Institute for Integrative Biology (iBio), Santiago, Chile
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Fondo de Desarrollo de Áreas Prioritarias, Center for Genome Regulation, Santiago, Chile
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13
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Butler T, Kapoore RV, Vaidyanathan S. Phaeodactylum tricornutum: A Diatom Cell Factory. Trends Biotechnol 2020; 38:606-622. [PMID: 31980300 DOI: 10.1016/j.tibtech.2019.12.023] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 12/17/2019] [Accepted: 12/18/2019] [Indexed: 01/12/2023]
Abstract
A switch from a petroleum-based to a biobased economy requires the capacity to produce both high-value low-volume and low-value high-volume products. Recent evidence supports the development of microalgae-based microbial cell factories with the objective of establishing environmentally sustainable manufacturing solutions. Diatoms display rich diversity and potential in this regard. We focus on Phaeodactylum tricornutum, a pennate diatom that is commonly found in marine ecosystems, and discuss recent trends in developing the diatom chassis for the production of a suite of natural and genetically engineered products. Both upstream and downstream developments are reviewed for the commercial development of P. tricornutum as a cell factory for a spectrum of marketable products.
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Affiliation(s)
- Thomas Butler
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK
| | - Rahul Vijay Kapoore
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK; Present address: Department of Biosciences, College of Science, Swansea University, Swansea, SA2 8PP, UK
| | - Seetharaman Vaidyanathan
- Department of Chemical and Biological Engineering, The University of Sheffield, Sheffield, S1 3JD, UK.
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14
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Abstract
Microalgae are unicellular organisms that act as the crucial primary producers all over the world, typically found in marine and freshwater environments. Most of them can live photo-autotrophically, reproduce rapidly, and accumulate biomass in a short period efficiently. To adapt to the uninterrupted change of the environment, they evolve and differentiate continuously. As a result, some of them evolve special abilities such as toleration of extreme environment, generation of sophisticated structure to adapt to the environment, and avoid predators. Microalgae are believed to be promising bioreactors because of their high lipid and pigment contents. Genetic engineering technologies have given revolutions in the microalgal industry, which decoded the secrets of microalgal genes, express recombinant genes in microalgal genomes, and largely soar the accumulation of interested components in transgenic microalgae. However, owing to several obstructions, the industry of transgenic microalgae is still immature. Here, we provide an overview to emphasize the advantage and imperfection of the existing transgenic microalgal bioreactors.
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Affiliation(s)
- Zhi-Cong Liang
- College of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Ming-Hua Liang
- College of Food Science and Engineering, South China University of Technology, Guangzhou, China
| | - Jian-Guo Jiang
- College of Food Science and Engineering, South China University of Technology, Guangzhou, China
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15
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Vavitsas K, Crozet P, Vinde MH, Davies F, Lemaire SD, Vickers CE. The Synthetic Biology Toolkit for Photosynthetic Microorganisms. PLANT PHYSIOLOGY 2019; 181:14-27. [PMID: 31262955 PMCID: PMC6716251 DOI: 10.1104/pp.19.00345] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/09/2019] [Indexed: 05/10/2023]
Abstract
Photosynthetic microorganisms offer novel characteristics as synthetic biology chassis, and the toolbox of components and techniques for cyanobacteria and algae is rapidly increasing.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Marcos Hamborg Vinde
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Fiona Davies
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
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16
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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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18
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Watanabe Y, Kadono T, Kira N, Suzuki K, Iwata O, Ohnishi K, Yamaguchi H, Adachi M. Development of endogenous promoters that drive high-level expression of introduced genes in the model diatom Phaeodactylum tricornutum. Mar Genomics 2018; 42:41-48. [PMID: 30509379 DOI: 10.1016/j.margen.2018.06.003] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 06/20/2018] [Accepted: 06/20/2018] [Indexed: 10/28/2022]
Abstract
The marine diatom Phaeodactylum tricornutum is attractive for basic and applied diatom research. We isolated putative endogenous gene promoters derived from genes that are highly expressed in P. tricornutum: the fucoxanthin chlorophyll a/c-binding protein (FCP) C gene, the vacuolar ATP synthase 16-kDa proteolipid subunit (V-ATPase C) gene, the clumping factor A gene and the solute carrier family 34 member 2 gene. Five putative promoter regions were isolated, linked to an antibiotic resistance gene (Sh ble) and transformed into P. tricornutum. Using quantitative RT-PCR, the promoter activities in the transformants were analyzed and compared to that of the diatom endogenous gene promoter, the FCP A gene promoter which has been used for the transformation of P. tricornutum. Among the five isolated potential promoters, the activity of the V-ATPase C gene promoter was approximately 2.73 times higher than that of the FCP A gene promoter. The V-ATPase C gene promoter drove the expression of Sh ble mRNA transcripts under both light and dark conditions at the stationary phase. These results suggest that the V-ATPase C gene promoter is a novel tool for the genetic engineering of P. tricornutum.
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Affiliation(s)
- Yumi Watanabe
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Takashi Kadono
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Nozomu Kira
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, Japan
| | - Kengo Suzuki
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Osamu Iwata
- Euglena Co., Ltd., 22F, Morinaga Plaza Building, Shiba-5-33-1, Minato-ku, Tokyo 108-0019, Japan
| | - Kouhei Ohnishi
- Research Institute of Molecular Genetics, Kochi University, Otsu-200, Nankoku, Kochi 783-8502, Japan
| | - Haruo Yamaguchi
- Laboratory of Aquatic Environmental Science, Faculty of Agriculture and Marine Science, Kochi University, Otsu-200, Monobe, Nankoku, Kochi 783-8502, 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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19
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Huang W, Daboussi F. Genetic and metabolic engineering in diatoms. Philos Trans R Soc Lond B Biol Sci 2018; 372:rstb.2016.0411. [PMID: 28717021 DOI: 10.1098/rstb.2016.0411] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/22/2017] [Indexed: 12/23/2022] Open
Abstract
Diatoms have attracted considerable attention due to their success in diverse environmental conditions, which probably is a consequence of their complex origins. Studies of their metabolism will provide insight into their adaptation capacity and are a prerequisite for metabolic engineering. Several years of investigation have led to the development of the genome engineering tools required for such studies, and a profusion of appropriate tools is now available for exploring and exploiting the metabolism of these organisms. Diatoms are highly prized in industrial biotechnology, due to both their richness in natural lipids and carotenoids and their ability to produce recombinant proteins, of considerable value in diverse markets. This review provides an overview of recent advances in genetic engineering methods for diatoms, from the development of gene expression cassettes and gene delivery methods, to cutting-edge genome-editing technologies. It also highlights the contributions of these rapid developments to both basic and applied research: they have improved our understanding of key physiological processes; and they have made it possible to modify the natural metabolism to favour the production of specific compounds or to produce new compounds for green chemistry and pharmaceutical applications.This article is part of the themed issue 'The peculiar carbon metabolism in diatoms'.
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Affiliation(s)
- Weichao Huang
- LISBP, Université de Toulouse, CNRS, INRA, INSA (LISBP-INSA Toulouse), 135 Avenue de Rangueil, 31077 Toulouse, France
| | - Fayza Daboussi
- LISBP, Université de Toulouse, CNRS, INRA, INSA (LISBP-INSA Toulouse), 135 Avenue de Rangueil, 31077 Toulouse, France
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20
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Zulu NN, Zienkiewicz K, Vollheyde K, Feussner I. Current trends to comprehend lipid metabolism in diatoms. Prog Lipid Res 2018. [DOI: 10.1016/j.plipres.2018.03.001] [Citation(s) in RCA: 104] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
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21
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Velmurugan N, Deka D. Transformation techniques for metabolic engineering of diatoms and haptophytes: current state and prospects. Appl Microbiol Biotechnol 2018; 102:4255-4267. [DOI: 10.1007/s00253-018-8925-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Revised: 03/08/2018] [Accepted: 03/10/2018] [Indexed: 12/11/2022]
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22
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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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23
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Zulu NN, Popko J, Zienkiewicz K, Tarazona P, Herrfurth C, Feussner I. Heterologous co-expression of a yeast diacylglycerol acyltransferase ( ScDGA1) and a plant oleosin ( AtOLEO3) as an efficient tool for enhancing triacylglycerol accumulation in the marine diatom Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:187. [PMID: 28725267 PMCID: PMC5514505 DOI: 10.1186/s13068-017-0874-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Accepted: 07/11/2017] [Indexed: 05/03/2023]
Abstract
BACKGROUND Microalgae are promising alternate and renewable sources for producing valuable products such as biofuel and essential fatty acids. Although this is the case, there are still challenges impeding on the effective commercial production of microalgal products. For instance, their product yield is still too low. Therefore, this study was oriented towards enhancing triacylglycerol (TAG) accumulation in the diatom Phaeodactylum tricornutum (strain Pt4). To achieve this, a type 2 acyl-CoA:diacylglycerol acyltransferase from yeast (ScDGA1) and the lipid droplet (LD) stabilizing oleosin protein 3 from Arabidopsis thaliana (AtOLEO3) were expressed in Pt4. RESULTS The individual expression of ScDGA1 and AtOLEO3 in Pt4 resulted in a 2.3- and 1.4-fold increase in TAG levels, respectively, in comparison to the wild type. The co-expression of both, ScDGA1 and AtOLEO3, was accompanied by a 3.6-fold increase in TAG content. On the cellular level, the lines co-expressing ScDGA1 and AtOLEO3 showed the presence of the larger and increased numbers of lipid droplets when compared to transformants expressing single genes and an empty vector. Under nitrogen stress, TAG productivity was further increased twofold in comparison to nitrogen-replete conditions. While TAG accumulation was enhanced in the analyzed transformants, the fatty acid composition remained unchanged neither in the total lipid nor in the TAG profile. CONCLUSIONS The co-expression of two genes was shown to be a more effective strategy for enhancing TAG accumulation in P. tricornutum strain Pt4 than a single gene strategy. For the first time in a diatom, a LD protein from a vascular plant, oleosin, was shown to have an impact on TAG accumulation and on LD organization.
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Affiliation(s)
- Nodumo Nokulunga Zulu
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
- Novagreen Projektmanagement GmbH, 49377 Vechta, Germany
| | - Jennifer Popko
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, 37077 Goettingen, Germany
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Alkaline phosphatase promoter as an efficient driving element for exogenic recombinant in the marine diatom Phaeodactylum tricornutum. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.01.007] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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25
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A fast and reliable strategy to generate TALEN-mediated gene knockouts in the diatom Phaeodactylum tricornutum. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.02.005] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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26
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Zulu NN, Popko J, Zienkiewicz K, Tarazona P, Herrfurth C, Feussner I. Heterologous co-expression of a yeast diacylglycerol acyltransferase ( ScDGA1) and a plant oleosin ( AtOLEO3) as an efficient tool for enhancing triacylglycerol accumulation in the marine diatom Phaeodactylum tricornutum. BIOTECHNOLOGY FOR BIOFUELS 2017. [PMID: 28725267 DOI: 10.1186/s13068-017-0874] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
BACKGROUND Microalgae are promising alternate and renewable sources for producing valuable products such as biofuel and essential fatty acids. Although this is the case, there are still challenges impeding on the effective commercial production of microalgal products. For instance, their product yield is still too low. Therefore, this study was oriented towards enhancing triacylglycerol (TAG) accumulation in the diatom Phaeodactylum tricornutum (strain Pt4). To achieve this, a type 2 acyl-CoA:diacylglycerol acyltransferase from yeast (ScDGA1) and the lipid droplet (LD) stabilizing oleosin protein 3 from Arabidopsis thaliana (AtOLEO3) were expressed in Pt4. RESULTS The individual expression of ScDGA1 and AtOLEO3 in Pt4 resulted in a 2.3- and 1.4-fold increase in TAG levels, respectively, in comparison to the wild type. The co-expression of both, ScDGA1 and AtOLEO3, was accompanied by a 3.6-fold increase in TAG content. On the cellular level, the lines co-expressing ScDGA1 and AtOLEO3 showed the presence of the larger and increased numbers of lipid droplets when compared to transformants expressing single genes and an empty vector. Under nitrogen stress, TAG productivity was further increased twofold in comparison to nitrogen-replete conditions. While TAG accumulation was enhanced in the analyzed transformants, the fatty acid composition remained unchanged neither in the total lipid nor in the TAG profile. CONCLUSIONS The co-expression of two genes was shown to be a more effective strategy for enhancing TAG accumulation in P. tricornutum strain Pt4 than a single gene strategy. For the first time in a diatom, a LD protein from a vascular plant, oleosin, was shown to have an impact on TAG accumulation and on LD organization.
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Affiliation(s)
- Nodumo Nokulunga Zulu
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
- Novagreen Projektmanagement GmbH, 49377 Vechta, Germany
| | - Jennifer Popko
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Krzysztof Zienkiewicz
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Pablo Tarazona
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Cornelia Herrfurth
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
| | - Ivo Feussner
- Department of Plant Biochemistry, Albrecht-von-Haller-Institute for Plant Sciences, University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, Goettingen Center for Molecular Biosciences (GZMB), University of Goettingen, 37077 Goettingen, Germany
- Department of Plant Biochemistry, International Center for Advanced Studies of Energy Conversion (ICASEC), University of Goettingen, 37077 Goettingen, Germany
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