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Li J, Wu S, Zhang K, Sun X, Lin W, Wang C, Lin S. Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-Associated Protein and Its Utility All at Sea: Status, Challenges, and Prospects. Microorganisms 2024; 12:118. [PMID: 38257946 PMCID: PMC10820777 DOI: 10.3390/microorganisms12010118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/02/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Initially discovered over 35 years ago in the bacterium Escherichia coli as a defense system against invasion of viral (or other exogenous) DNA into the genome, CRISPR/Cas has ushered in a new era of functional genetics and served as a versatile genetic tool in all branches of life science. CRISPR/Cas has revolutionized the methodology of gene knockout with simplicity and rapidity, but it is also powerful for gene knock-in and gene modification. In the field of marine biology and ecology, this tool has been instrumental in the functional characterization of 'dark' genes and the documentation of the functional differentiation of gene paralogs. Powerful as it is, challenges exist that have hindered the advances in functional genetics in some important lineages. This review examines the status of applications of CRISPR/Cas in marine research and assesses the prospect of quickly expanding the deployment of this powerful tool to address the myriad fundamental marine biology and biological oceanography questions.
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Affiliation(s)
- Jiashun Li
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Shuaishuai Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in the South China Sea, School of Marine Biology and Fisheries, Hainan University, Haikou 570203, China
| | - Xueqiong Sun
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Wenwen Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Cong Wang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
| | - Senjie Lin
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen 361101, China
- Department of Marine Sciences, University of Connecticut, Groton, CT 06340, USA
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2
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Chen H, Yang QL, Xu JX, Deng X, Zhang YJ, Liu T, Rots MG, Xu GL, Huang KY. Efficient methods for multiple types of precise gene-editing in Chlamydomonas. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023. [PMID: 37310200 DOI: 10.1111/tpj.16265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Revised: 04/20/2023] [Accepted: 04/26/2023] [Indexed: 06/14/2023]
Abstract
Precise gene-editing using CRISPR/Cas9 technology remains a long-standing challenge, especially for genes with low expression and no selectable phenotypes in Chlamydomonas reinhardtii, a classic model for photosynthesis and cilia research. Here, we developed a multi-type and precise genetic manipulation method in which a DNA break was generated by Cas9 nuclease and the repair was mediated using a homologous DNA template. The efficacy of this method was demonstrated for several types of gene editing, including inactivation of two low-expression genes (CrTET1 and CrKU80), the introduction of a FLAG-HA epitope tag into VIPP1, IFT46, CrTET1 and CrKU80 genes, and placing a YFP tag into VIPP1 and IFT46 for live-cell imaging. We also successfully performed a single amino acid substitution for the FLA3, FLA10 and FTSY genes, and documented the attainment of the anticipated phenotypes. Lastly, we demonstrated that precise fragment deletion from the 3'-UTR of MAA7 and VIPP1 resulted in a stable knock-down effect. Overall, our study has established efficient methods for multiple types of precise gene editing in Chlamydomonas, enabling substitution, insertion and deletion at the base resolution, thus improving the potential of this alga in both basic research and industrial applications.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Qing-Lin Yang
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
| | - Jia-Xi Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xuan Deng
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Yun-Jie Zhang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
| | - Ting Liu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Marianne G Rots
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, 9713 GZ, Groningen, The Netherlands
| | - Guo-Liang Xu
- State Key Laboratory of Molecular Biology, Shanghai Institute of Biochemistry and Cell Biology, Center for Excellence in Molecular Cell Science, Chinese Academy of Sciences, Shanghai, 200031, China
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
- Shanghai Key Laboratory of Medical Epigenetics, Laboratory of Cancer Epigenetics, Institutes of Biomedical Sciences, Medical College of Fudan University, Chinese Academy of Medical Sciences (RU069), Shanghai, China
| | - Kai-Yao Huang
- Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, 430072, China
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3
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Jeong BR, Jang J, Jin E. Genome engineering via gene editing technologies in microalgae. BIORESOURCE TECHNOLOGY 2023; 373:128701. [PMID: 36746216 DOI: 10.1016/j.biortech.2023.128701] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/27/2023] [Accepted: 02/01/2023] [Indexed: 06/18/2023]
Abstract
CRISPR-Cas has revolutionized genetic modification with its comparative simplicity and accuracy, and it can be used even at the genomic level. Microalgae are excellent feedstocks for biofuels and nutraceuticals because they contain high levels of fatty acids, carotenoids, and other metabolites; however, genome engineering for microalgae is not yet as developed as for other model organisms. Microalgal engineering at the genetic and metabolic levels is relatively well established, and a few genomic resources are available. Their genomic information was used for a "safe harbor" site for stable transgene expression in microalgae. This review proposes further genome engineering schemes including the construction of sgRNA libraries, pan-genomic and epigenomic resources, and mini-genomes, which can together be developed into synthetic biology for carbon-based engineering in microalgae. Acetyl-CoA is at the center of carbon metabolic pathways and is further reviewed for the production of molecules including terpenoids in microalgae.
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Affiliation(s)
- Byeong-Ryool Jeong
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - Junhwan Jang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea; Hanyang Institute of Bioscience and Biotechnology, Hanyang University, Seoul 04763, Korea.
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4
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Gotovtsev P. Microbial Cells as a Microrobots: From Drug Delivery to Advanced Biosensors. Biomimetics (Basel) 2023; 8:biomimetics8010109. [PMID: 36975339 PMCID: PMC10046805 DOI: 10.3390/biomimetics8010109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/01/2023] [Accepted: 03/06/2023] [Indexed: 03/29/2023] Open
Abstract
The presented review focused on the microbial cell based system. This approach is based on the application of microorganisms as the main part of a robot that is responsible for the motility, cargo shipping, and in some cases, the production of useful chemicals. Living cells in such microrobots have both advantages and disadvantages. Regarding the advantages, it is necessary to mention the motility of cells, which can be natural chemotaxis or phototaxis, depending on the organism. There are approaches to make cells magnetotactic by adding nanoparticles to their surface. Today, the results of the development of such microrobots have been widely discussed. It has been shown that there is a possibility of combining different types of taxis to enhance the control level of the microrobots based on the microorganisms' cells and the efficiency of the solving task. Another advantage is the possibility of applying the whole potential of synthetic biology to make the behavior of the cells more controllable and complex. Biosynthesis of the cargo, advanced sensing, on/off switches, and other promising approaches are discussed within the context of the application for the microrobots. Thus, a synthetic biology application offers significant perspectives on microbial cell based microrobot development. Disadvantages that follow from the nature of microbial cells such as the number of external factors influence the cells, potential immune reaction, etc. They provide several limitations in the application, but do not decrease the bright perspectives of microrobots based on the cells of the microorganisms.
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Affiliation(s)
- Pavel Gotovtsev
- National Research Center "Kurchatov Institute", Biotechnology and Bioenergy Department, Akademika Kurchatova pl. 1, 123182 Moscow, Russia
- Moscow Institute of Physics and Technology, National Research University, 9 Institutskiy per., 141701 Moscow, Russia
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Patel VK, Das A, Kumari R, Kajla S. Recent progress and challenges in CRISPR-Cas9 engineered algae and cyanobacteria. ALGAL RES 2023. [DOI: 10.1016/j.algal.2023.103068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
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Kuo EY, Yang RY, Chin YY, Chien YL, Chen YC, Wei CY, Kao LJ, Chang YH, Li YJ, Chen TY, Lee TM. Multi-omics approaches and genetic engineering of metabolism for improved biorefinery and wastewater treatment in microalgae. Biotechnol J 2022; 17:e2100603. [PMID: 35467782 DOI: 10.1002/biot.202100603] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 03/12/2022] [Accepted: 04/01/2022] [Indexed: 11/06/2022]
Abstract
Microalgae, a group of photosynthetic microorganisms rich in diverse and novel bioactive metabolites, have been explored for the production of biofuels, high value-added compounds as food and feeds, and pharmaceutical chemicals as agents with therapeutic benefits. This article reviews the development of omics resources and genetic engineering techniques including gene transformation methodologies, mutagenesis, and genome-editing tools in microalgae biorefinery and wastewater treatment. The introduction of these enlisted techniques has simplified the understanding of complex metabolic pathways undergoing microalgal cells. The multiomics approach of the integrated omics datasets, big data analysis, and machine learning for the discovery of objective traits and genes responsible for metabolic pathways was reviewed. Recent advances and limitations of multiomics analysis and genetic bioengineering technology to facilitate the improvement of microalgae as the dual role of wastewater treatment and biorefinery feedstock production are discussed. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Eva YuHua Kuo
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Ru-Yin Yang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yuan Yu Chin
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Lin Chien
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu Chu Chen
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Cheng-Yu Wei
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Li-Jung Kao
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yi-Hua Chang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Yu-Jia Li
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Te-Yuan Chen
- Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
| | - Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Frontier Center for Ocean Science and Technology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan.,Doctoral Degree Program in Marine Biotechnology, National Sun Yat-sen University, Kaohsiung, 804, Taiwan
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Naduthodi MIS, Südfeld C, Avitzigiannis EK, Trevisan N, van Lith E, Alcaide Sancho J, D’Adamo S, Barbosa M, van der Oost J. Comprehensive Genome Engineering Toolbox for Microalgae Nannochloropsis oceanica Based on CRISPR-Cas Systems. ACS Synth Biol 2021; 10:3369-3378. [PMID: 34793143 PMCID: PMC8689688 DOI: 10.1021/acssynbio.1c00329] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Microalgae can produce
industrially relevant metabolites using
atmospheric CO2 and sunlight as carbon and energy sources,
respectively. Developing molecular tools for high-throughput genome
engineering could accelerate the generation of tailored strains with
improved traits. To this end, we developed a genome editing strategy
based on Cas12a ribonucleoproteins (RNPs) and homology-directed repair
(HDR) to generate scarless and markerless mutants of the microalga Nannochloropsis oceanica. We also developed an episomal
plasmid-based Cas12a system for efficiently introducing indels at
the target site. Additionally, we exploited the ability of Cas12a
to process an associated CRISPR array to perform multiplexed genome
engineering. We efficiently targeted three sites in the host genome
in a single transformation, thereby making a major step toward high-throughput
genome engineering in microalgae. Furthermore, a CRISPR interference
(CRISPRi) tool based on Cas9 and Cas12a was developed for effective
downregulation of target genes. We observed up to 85% reduction in
the transcript levels upon performing CRISPRi with dCas9 in N. oceanica. Overall, these developments substantially
accelerate genome engineering efforts in N. oceanica and potentially provide a general toolbox for improving other microalgal
strains.
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Affiliation(s)
- Mihris Ibnu Saleem Naduthodi
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, The Netherlands
- Bioprocess Engineering, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Christian Südfeld
- Bioprocess Engineering, Wageningen University, Wageningen 6708 PB, The Netherlands
| | | | - Nicola Trevisan
- Bioprocess Engineering, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Eduard van Lith
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Javier Alcaide Sancho
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, The Netherlands
| | - Sarah D’Adamo
- Bioprocess Engineering, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - Maria Barbosa
- Bioprocess Engineering, Wageningen University, Wageningen 6708 PB, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Wageningen 6708 WE, The Netherlands
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8
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Akella S, Ma X, Bacova R, Harmer ZP, Kolackova M, Wen X, Wright DA, Spalding MH, Weeks DP, Cerutti H. Co-targeting strategy for precise, scarless gene editing with CRISPR/Cas9 and donor ssODNs in Chlamydomonas. PLANT PHYSIOLOGY 2021; 187:2637-2655. [PMID: 34618092 PMCID: PMC8644747 DOI: 10.1093/plphys/kiab418] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 07/30/2021] [Indexed: 05/20/2023]
Abstract
Programmable site-specific nucleases, such as the clustered regularly interspaced short palindromic repeat (CRISPR)/ CRISPR-associated protein 9 (Cas9) ribonucleoproteins (RNPs), have allowed creation of valuable knockout mutations and targeted gene modifications in Chlamydomonas (Chlamydomonas reinhardtii). However, in walled strains, present methods for editing genes lacking a selectable phenotype involve co-transfection of RNPs and exogenous double-stranded DNA (dsDNA) encoding a selectable marker gene. Repair of the dsDNA breaks induced by the RNPs is usually accompanied by genomic insertion of exogenous dsDNA fragments, hindering the recovery of precise, scarless mutations in target genes of interest. Here, we tested whether co-targeting two genes by electroporation of pairs of CRISPR/Cas9 RNPs and single-stranded oligodeoxynucleotides (ssODNs) would facilitate the recovery of precise edits in a gene of interest (lacking a selectable phenotype) by selection for precise editing of another gene (creating a selectable marker)-in a process completely lacking exogenous dsDNA. We used PPX1 (encoding protoporphyrinogen IX oxidase) as the generated selectable marker, conferring resistance to oxyfluorfen, and identified precise edits in the homolog of bacterial ftsY or the WD and TetratriCopeptide repeats protein 1 genes in ∼1% of the oxyfluorfen resistant colonies. Analysis of the target site sequences in edited mutants suggested that ssODNs were used as templates for DNA synthesis during homology directed repair, a process prone to replicative errors. The Chlamydomonas acetolactate synthase gene could also be efficiently edited to serve as an alternative selectable marker. This transgene-free strategy may allow creation of individual strains containing precise mutations in multiple target genes, to study complex cellular processes, pathways, or structures.
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Affiliation(s)
- Soujanya Akella
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Xinrong Ma
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Romana Bacova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Zachary P Harmer
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - Martina Kolackova
- Department of Chemistry and Biochemistry, Mendel University in Brno, Zemedelska 1, CZ-613 00, Brno, Czech Republic
| | - Xiaoxue Wen
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
| | - David A Wright
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Martin H Spalding
- Department of Genetics, Development and Cell Biology, Iowa State University, Ames, Iowa 50011, USA
| | - Donald P Weeks
- Department of Biochemistry, University of Nebraska-Lincoln, Lincoln, Nebraska 68588, USA
| | - Heriberto Cerutti
- School of Biological Sciences and Center for Plant Science Innovation, University of Nebraska–Lincoln, Lincoln, Nebraska 68588, USA
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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: 6] [Impact Index Per Article: 2.0] [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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10
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Rau EM, Ertesvåg H. Method Development Progress in Genetic Engineering of Thraustochytrids. Mar Drugs 2021; 19:515. [PMID: 34564177 PMCID: PMC8467673 DOI: 10.3390/md19090515] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 01/29/2023] Open
Abstract
Thraustochytrids are unicellular, heterotrophic marine eukaryotes. Some species are known to store surplus carbon as intracellular lipids, and these also contain the long-chain polyunsaturated fatty acid docosahexaenoic acid (DHA). Most vertebrates are unable to synthesize sufficient amounts of DHA, and this fatty acid is essential for, e.g., marine fish, domesticated animals, and humans. Thraustochytrids may also produce other commercially valuable fatty acids and isoprenoids. Due to the great potential of thraustochytrids as producers of DHA and other lipid-related molecules, a need for more knowledge on this group of organisms is needed. This necessitates the ability to do genetic manipulation of the different strains. Thus far, this has been obtained for a few strains, while it has failed for other strains. Here, we systematically review the genetic transformation methods used for different thraustochytrid strains, with the aim of aiding studies on strains not yet successfully transformed. The designs of transformation cassettes are also described and compared. Moreover, the potential problems when trying to establish transformation protocols in new thraustochytrid species/strains are discussed, along with suggestions utilized in other organisms to overcome similar challenges. The approaches discussed in this review could be a starting point when designing protocols for other non-model organisms.
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Affiliation(s)
| | - Helga Ertesvåg
- Department of Biotechnology and Food Science, NTNU Norwegian University of Science and Technology, N7491 Trondheim, Norway;
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11
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Sizova I, Kelterborn S, Verbenko V, Kateriya S, Hegemann P. Chlamydomonas POLQ is necessary for CRISPR/Cas9-mediated gene targeting. G3 (BETHESDA, MD.) 2021; 11:jkab114. [PMID: 33836052 PMCID: PMC8495919 DOI: 10.1093/g3journal/jkab114] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Accepted: 03/18/2021] [Indexed: 02/06/2023]
Abstract
The use of CRISPR/Cas endonucleases has revolutionized gene editing techniques for research on Chlamydomonas reinhardtii. To better utilize the CRISPR/Cas system, it is essential to develop a more comprehensive understanding of the DNA repair pathways involved in genome editing. In this study, we have analyzed contributions from canonical KU80/KU70-dependent nonhomologous end-joining (cNHEJ) and DNA polymerase theta (POLQ)-mediated end joining on SpCas9-mediated untemplated mutagenesis and homology-directed repair (HDR)/gene inactivation in Chlamydomonas. Using CRISPR/SpCas9 technology, we generated DNA repair-defective mutants ku80, ku70, polQ for gene targeting experiments. Our results show that untemplated repair of SpCas9-induced double strand breaks results in mutation spectra consistent with an involvement of both KU80/KU70 and POLQ. In addition, the inactivation of POLQ was found to negatively affect HDR of the inactivated paromomycin-resistant mut-aphVIII gene when donor single-stranded oligos were used. Nevertheless, mut-aphVIII was still repaired by homologous recombination in these mutants. POLQ inactivation suppressed random integration of transgenes co-transformed with the donor ssDNA. KU80 deficiency did not affect these events but instead was surprisingly found to stimulate HDR/gene inactivation. Our data suggest that in Chlamydomonas, POLQ is the main contributor to CRISPR/Cas-induced HDR and random integration of transgenes, whereas KU80/KU70 potentially plays a secondary role. We expect our results will lead to improvement of genome editing in C. reinhardtii and can be used for future development of algal biotechnology.
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Affiliation(s)
- Irina Sizova
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Simon Kelterborn
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
| | - Valeriy Verbenko
- Petersburg Nuclear Physics Institute named by B.P. Konstantinov of National Research Centre “Kurchatov Institute”, Gatchina 188300, Russia
- Kurchatov Genome Center - PNPI, Gatchina 188300, Russia
| | - Suneel Kateriya
- Laboratory of Optobiology School of Biotechnology, Jawaharlal Nehru University, New Delhi 110067, India
| | - Peter Hegemann
- Experimental Biophysics, Institute of Biology, Humboldt University of Berlin, Berlin D-10099, Germany
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Kim J, Chang KS, Lee S, Jin E. Establishment of a Genome Editing Tool Using CRISPR-Cas9 in Chlorella vulgaris UTEX395. Int J Mol Sci 2021; 22:E480. [PMID: 33418923 PMCID: PMC7825080 DOI: 10.3390/ijms22020480] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 12/30/2020] [Accepted: 01/03/2021] [Indexed: 12/12/2022] Open
Abstract
To date, Chlorella vulgaris is the most used species of microalgae in the food and feed additive industries, and also considered as a feasible cell factory for bioproducts. However, the lack of an efficient genetic engineering tool makes it difficult to improve the physiological characteristics of this species. Therefore, the development of new strategic approaches such as genome editing is trying to overcome this hurdle in many research groups. In this study, the possibility of editing the genome of C. vulgaris UTEX395 using clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) has been proven to target nitrate reductase (NR) and adenine phosphoribosyltransferase (APT). Genome-edited mutants, nr and apt, were generated by a DNA-mediated and/or ribonucleoprotein (RNP)-mediated CRISPR-Cas9 system, and isolated based on the negative selection against potassium chlorate or 2-fluoroadenine in place of antibiotics. The null mutation of edited genes was demonstrated by the expression level of the correspondent proteins or the mutation of transcripts, and through growth analysis under specific nutrient conditions. In conclusion, this study offers relevant empirical evidence of the possibility of genome editing in C. vulgaris UTEX395 by CRISPR-Cas9 and the practical methods. Additionally, among the generated mutants, nr can provide an easier screening strategy during DNA transformation than the use of antibiotics owing to their auxotrophic characteristics. These results will be a cornerstone for further advancement of the genetics of C. vulgaris.
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Affiliation(s)
| | | | | | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Korea; (J.K.); (K.S.C.); (S.L.)
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14
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Kang S, Jeon S, Kim S, Chang YK, Kim YC. Development of a pVEC peptide-based ribonucleoprotein (RNP) delivery system for genome editing using CRISPR/Cas9 in Chlamydomonas reinhardtii. Sci Rep 2020; 10:22158. [PMID: 33335164 PMCID: PMC7747696 DOI: 10.1038/s41598-020-78968-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2019] [Accepted: 11/19/2020] [Indexed: 12/13/2022] Open
Abstract
Recent technical advances related to the CRISPR/Cas9-based genome editing system have enabled sophisticated genome editing in microalgae. Although the demand for research on genome editing in microalgae has increased over time, methodological research has not been established to date for the delivery of a ribonucleoprotein (Cas9/sgRNA complex) using a cell penetrating peptide into microalgal cell lines. Here, we present a ribonucleoprotein delivery system for Chlamydomonas reinhardtii mediated by the cell penetrating peptide pVEC (LLIILRRRIRKQAHAHSK) which is in a non-covalent form. Using this technically simple method, the ribonucleoprotein was successfully delivered into C. reinhardtii. Gene Maa7 and FKB12 were disrupted, and their distinguishing patterns of Indel mutations were analyzed with the observation of several insertions of sequences not originating from the genome DNA, such as chloroplast DNA, into the expected loci. In addition, the cytotoxicity of Cas9 and the ribonucleoprotein was investigated according to the concentration and time in the algal cells. It was observed that Cas9 alone without the sgRNA induces a more severe cytotoxicity compared to the ribonucleoprotein. Our study will not only contribute to algal cell biology and its genetic engineering for further applications involving various organisms but will also provide a deeper understating of the basic science of the CRISPR/Cas9 system.
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Affiliation(s)
- Seongsu Kang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Seungjib Jeon
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Seungcheol Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Yong Keun Chang
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea
| | - Yeu-Chun Kim
- Department of Chemical and Biomolecular Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 305-701, Republic of Korea.
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15
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Ghribi M, Nouemssi SB, Meddeb-Mouelhi F, Desgagné-Penix I. Genome Editing by CRISPR-Cas: A Game Change in the Genetic Manipulation of Chlamydomonas. Life (Basel) 2020; 10:E295. [PMID: 33233548 PMCID: PMC7699682 DOI: 10.3390/life10110295] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 11/18/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Microalgae are promising photosynthetic unicellular eukaryotes among the most abundant on the planet and are considered as alternative sustainable resources for various industrial applications. Chlamydomonas is an emerging model for microalgae to be manipulated by multiple biotechnological tools in order to produce high-value bioproducts such as biofuels, bioactive peptides, pigments, nutraceuticals, and medicines. Specifically, Chlamydomonas reinhardtii has become a subject of different genetic-editing techniques adapted to modulate the production of microalgal metabolites. The main nuclear genome-editing tools available today include zinc finger nucleases (ZFNs), transcriptional activator-like effector nucleases (TALENs), and more recently discovered the clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR associated protein (Cas) nuclease system. The latter, shown to have an interesting editing capacity, has become an essential tool for genome editing. In this review, we highlight the available literature on the methods and the applications of CRISPR-Cas for C. reinhardtii genetic engineering, including recent transformation methods, most used bioinformatic tools, best strategies for the expression of Cas protein and sgRNA, the CRISPR-Cas mediated gene knock-in/knock-out strategies, and finally the literature related to CRISPR expression and modification approaches.
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Affiliation(s)
- Manel Ghribi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
| | - Serge Basile Nouemssi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
| | - Fatma Meddeb-Mouelhi
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
- Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
| | - Isabel Desgagné-Penix
- Department of Chemistry, Biochemistry and Physics, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada; (M.G.); (S.B.N.); (F.M.-M.)
- Groupe de Recherche en Biologie Végétale, Université du Québec à Trois-Rivières, 3351, Boulevard des Forges, C.P. 500, Trois-Rivières, QC G9A 5H7, Canada
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16
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Dhokane D, Bhadra B, Dasgupta S. CRISPR based targeted genome editing of Chlamydomonas reinhardtii using programmed Cas9-gRNA ribonucleoprotein. Mol Biol Rep 2020; 47:8747-8755. [PMID: 33074412 DOI: 10.1007/s11033-020-05922-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2020] [Accepted: 10/13/2020] [Indexed: 11/26/2022]
Abstract
The clustered regularly interspaced short palindromic repeats (CRISPR) - Cas associated protein 9 (Cas9) system is very precise, efficient and relatively simple in creating genetic modifications at a predetermined locus in the genome. Genome editing with Cas9 ribonucleoproteins (RNPs) has reduced cytotoxic effects, off-target cleavage and increased on-target activity and the editing efficiencies. The unicellular alga Chlamydomonas reinhardtii is an emerging model for studying the production of high-value products for industrial applications. Development of C. reinhardtii as an industrial biotechnology host can be achieved more efficiently through genetic modifications using genome editing tools. We made an attempt to target MAA7 gene that encodes the tryptophan synthase β-Subunit using CRISPR-Cas9 RNPs to demonstrate knock-out and knock-in through homology-dependent repair template at the target site. In this study, we have demonstrated targeted gene knock-out in C. reinhardtii using programmed RNPs. Targeted editing of MAA7 gene was confirmed by sequencing the clones that were resistant to 5-Fluoroindole (5-FI). Non-homologous end joining (NHEJ) repair mechanism led to insertion, deletion, and/or base substitution in the Cas9 cleavage vicinity, encoding non-functional MAA7 protein product (knock-out), conferring resistance to 5-FI. Here, we report an efficient protocol for developing knock-out mutants in Chlamydomonas using CRISPR-Cas9 RNPs. The high potential efficiency of editing may also eliminate the need to select mutants by phenotype. These research findings would be more likely applied to other green algae for developing green cell factories to produce high-value molecules.
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Affiliation(s)
- Dhananjay Dhokane
- Synthetic Biology Group, Reliance Corporate Park, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India
| | - Bhaskar Bhadra
- Synthetic Biology Group, Reliance Corporate Park, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India.
| | - Santanu Dasgupta
- Synthetic Biology Group, Reliance Corporate Park, Reliance Industries Ltd, Ghansoli, Navi Mumbai, 400701, India
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17
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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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18
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Achievements and challenges of genetic engineering of the model green alga Chlamydomonas reinhardtii. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101986] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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19
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Lin YL, Chung CL, Huang PJ, Chen CH, Fang SC. Revised annotation and extended characterizations of components of the Chlamydomonas reinhardtii SUMOylation system. PLANT DIRECT 2020; 4:e00266. [PMID: 33015534 PMCID: PMC7522501 DOI: 10.1002/pld3.266] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 05/16/2023]
Abstract
Small ubiquitin-like modifier (SUMO) conjugation, or SUMOylation, is a reversible post-translational modification that is important for regulation of many cellular processes including cell division cycle in the eukaryotic kingdom. However, only a portion of the components of the Chlamydomonas SUMOylation system are known and their functions and regulation investigated. The present studies are aimed at extending discovery and characterization of new components and improving the annotation and nomenclature of all known proteins and genes involved in the system. Even though only one copy of the heterodimerized SUMO-activating enzyme, SAE1 and SAE2, was identified, the number of SUMO-conjugating enzymes (SCEs) and SUMO proteases/isopeptidase was expanded in Chlamydomonas. Using the reconstituted SUMOylation system, we showed that SCE1, SCE2, and SCE3 have SUMO-conjugating activity. In addition to SUMOylation, components required for other post-translational modifications such as NEDDylation, URMylation, and UFMylation, were confirmed to be present in Chlamydomonas. Our data also showed that besides isopeptidase activity, the SUMO protease domain of SUPPRESSOR OF MAT3 7/SENTRIN-SPECIFIC PROTEASE 1 (SMT7/SENP1) has endopeptidase activity that is capable of processing SUMO precursors. Moreover, the key cell cycle regulators of Chlamydomonas E2F1, DP1, CDKG1, CYCD2, and CYCD3 were SUMOylated in vitro, suggesting SUMOylation may be part of regulatory pathway modulating cell cycle regulators.
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Affiliation(s)
- Yen-Ling Lin
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
| | - Chin-Lin Chung
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Pin-Jui Huang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Chun-Han Chen
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
| | - Su-Chiung Fang
- Biotechnology Center in Southern Taiwan Academia Sinica Tainan Taiwan
- Agricultural Biotechnology Research Center Academia Sinica Taipei Taiwan
- Ph.D. Program in Microbial Genomics National Chung Hsing University and Academia Sinica Taichung Taiwan
- Institute of Tropical Plant Sciences and Microbiology National Cheng Kung University Tainan Taiwan
- National Cheng Kung University-Academia Sinica Graduate Program in Translational Agricultural Sciences Tainan Taiwan
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20
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Krishnan A, Cano M, Burch TA, Weissman JC, Posewitz MC. Genome editing using Cas9-RNA ribonucleoprotein complexes in the high-productivity marine alga Picochlorum celeri. ALGAL RES 2020. [DOI: 10.1016/j.algal.2020.101944] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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21
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Kim J, Lee S, Baek K, Jin E. Site-Specific Gene Knock-Out and On-Site Heterologous Gene Overexpression in Chlamydomonas reinhardtii via a CRISPR-Cas9-Mediated Knock-in Method. FRONTIERS IN PLANT SCIENCE 2020; 11:306. [PMID: 32265959 PMCID: PMC7099044 DOI: 10.3389/fpls.2020.00306] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 03/03/2020] [Indexed: 05/27/2023]
Abstract
Chlamydomonas reinhardtii is being transformed from a model organism to an industrial organism for the production of pigments, fatty acids, and pharmaceuticals. Genetic modification has been used to increase the economic value of C. reinhardtii. However, low gene-editing efficiency and position-effects hinder the genetic improvement of this microorganism. Recently, site-specific double-stranded DNA cleavage using CRISPR-Cas9 system has been applied to regulate a metabolic pathway in C. reinhardtii. In this study, we proved that site-specific gene expression can be induced by CRISPR-Cas9-mediated double-strand cleavage and non-homologous end joining (NHEJ) mechanism. The CRISPR-Cas9-mediated knock-in method was adopted to improve gene-editing efficiency and express the reporter gene on the intended site. Knock-in was performed using a combination of ribonucleoprotein (RNP) complex and DNA fragment (antibiotics resistance gene). Gene-editing efficiency was improved via optimization of a component of RNP complex. We found that when the gene CrFTSY was targeted, the efficiency of obtaining the desired mutant by the knock-in method combined with antibiotic resistance was nearly 37%; 2.5 times higher than the previous reports. Additionally, insertion of a long DNA fragment (3.2 and 6.4 kb) and site-specific gene expression were analyzed. We demonstrated the knock-out phenotype of CrFTSY and on-site inserted gene expression of luciferase and mVenus at the same time. This result showed that CRISPR-Cas9-mediated knock-in can be used to express the gene of interest avoiding position-effects in C. reinhardtii. This report could provide a new perspective to the use of gene-editing. Furthermore, the technical improvements in genetic modification may accelerate the commercialization of C. reinhardtii.
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Affiliation(s)
| | | | | | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Science, Hanyang University, Seoul, South Korea
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22
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Ng I, Keskin BB, Tan S. A Critical Review of Genome Editing and Synthetic Biology Applications in Metabolic Engineering of Microalgae and Cyanobacteria. Biotechnol J 2020; 15:e1900228. [DOI: 10.1002/biot.201900228] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 02/07/2020] [Indexed: 12/13/2022]
Affiliation(s)
- I‐Son Ng
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Batuhan Birol Keskin
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
| | - Shih‐I Tan
- Department of Chemical EngineeringNational Cheng Kung University Tainan 701 Taiwan
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23
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Zhong Z, Liu S, Liu X, Liu B, Tang X, Ren Q, Zhou J, Zheng X, Qi Y, Zhang Y. Intron-Based Single Transcript Unit CRISPR Systems for Plant Genome Editing. RICE (NEW YORK, N.Y.) 2020; 13:8. [PMID: 32016614 PMCID: PMC6997322 DOI: 10.1186/s12284-020-0369-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/20/2020] [Indexed: 05/08/2023]
Abstract
BACKGROUND Expression of either Cas9 or Cas12a and guide RNAs by a single Polymerase II (Pol II) promoter represents a compact CRISPR expression system and has many advantages for different applications. In order to make this system routine in plant biology, engineering efforts are needed for developing and optimizing such single transcript unit (STU) systems for plant genome editing. RESULTS To develop novel intron-based STU (iSTU) CRISPR system (STU CRISPR 3.0), we first evaluated three introns from three plant species for carrying guide RNAs by using an enhanced green fluorescence protein (eGFP) system in rice. After validation of proper intron slicing, we inserted these gRNA-containing introns into the open reading frames (ORFs) of Cas9 and Cas12a for testing their genome editing capability. Different guide RNA processing strategies have been tested for Cas9 and Cas12a. We demonstrated singular genome editing and multiplexed genome editing with these iSTU-Cas9 and iSTU-Cas12a systems. CONCLUSION We developed multiple iSTU-CRISPR/Cas9 and Cas12a systems for plant genome editing. Our results shed light on potential directions for further improvement of the iSTU systems.
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Affiliation(s)
- Zhaohui Zhong
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Shishi Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xiaopei Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Binglin Liu
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xu Tang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Qiurong Ren
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Jianping Zhou
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Xuelian Zheng
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China
| | - Yiping Qi
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, MD, 20742, USA.
- Institute for Bioscience and Biotechnology Research, University of Maryland, Rockville, MD, 20850, USA.
| | - Yong Zhang
- Department of Biotechnology, School of Life Sciences and Technology, Center for Informational Biology, University of Electronic Science and Technology of China, Room 216, Main Building, No. 4, Section 2, North Jianshe Road, Chengdu, 610054, People's Republic of China.
- Jiangsu Key Laboratory of Crop Genomics and Molecular Breeding, Agricultural College, Yangzhou University, Yangzhou, 225009, China.
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Tang X, Ren Q, Yang L, Bao Y, Zhong Z, He Y, Liu S, Qi C, Liu B, Wang Y, Sretenovic S, Zhang Y, Zheng X, Zhang T, Qi Y, Zhang Y. Single transcript unit CRISPR 2.0 systems for robust Cas9 and Cas12a mediated plant genome editing. PLANT BIOTECHNOLOGY JOURNAL 2019; 17:1431-1445. [PMID: 30582653 PMCID: PMC6576101 DOI: 10.1111/pbi.13068] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Revised: 12/16/2018] [Accepted: 12/18/2018] [Indexed: 05/03/2023]
Abstract
CRISPR-Cas9 and Cas12a are two powerful genome editing systems. Expression of CRISPR in plants is typically achieved with a mixed dual promoter system, in which Cas protein is expressed by a Pol II promoter and a guide RNA is expressed by a species-specific Pol III promoter such as U6 or U3. To achieve coordinated expression and compact vector packaging, it is desirable to express both CRISPR components under a single Pol II promoter. Previously, we demonstrated a first-generation single transcript unit (STU)-Cas9 system, STU-Cas9-RZ, which is based on hammerhead ribozyme for processing single guide RNAs (sgRNAs). In this study, we developed two new STU-Cas9 systems and one STU-Cas12a system for applications in plants, collectively called the STU CRISPR 2.0 systems. We demonstrated these systems for genome editing in rice with both transient expression and stable transgenesis. The two STU-Cas9 2.0 systems process the sgRNAs with Csy4 ribonuclease and endogenous tRNA processing system respectively. Both STU-Cas9-Csy4 and STU-Cas9-tRNA systems showed more robust genome editing efficiencies than our first-generation STU-Cas9-RZ system and the conventional mixed dual promoter system. We further applied the STU-Cas9-tRNA system to compare two C to T base editing systems based on rAPOBEC1 and PmCDA1 cytidine deaminases. The results suggest STU-based PmCDA1 base editor system is highly efficient in rice. The STU-Cas12a system, based on Cas12a' self-processing of a CRISPR RNA (crRNA) array, was also developed and demonstrated for expression of a single crRNA and four crRNAs. Altogether, our STU CRISPR 2.0 systems further expanded the CRISPR toolbox for plant genome editing and other applications.
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Affiliation(s)
- Xu Tang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Qiurong Ren
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Lijia Yang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yu Bao
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Zhaohui Zhong
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yao He
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Shishi Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Caiyan Qi
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Binglin Liu
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Yan Wang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Simon Sretenovic
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Yingxiao Zhang
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
| | - Xuelian Zheng
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
| | - Tao Zhang
- Jiangsu Key Laboratory of Crop Genetics and PhysiologyJiangsu Co‐Innovation Center for Modern Production Technology of Grain CropsJiangsu Key Laboratory of Crop Genomics and Molecular BreedingCollege of AgricultureYangzhou UniversityYangzhouChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
| | - Yiping Qi
- Department of Plant Science and Landscape ArchitectureUniversity of MarylandCollege ParkMDUSA
- Institute for Bioscience and Biotechnology ResearchUniversity of MarylandRockvilleMDUSA
| | - Yong Zhang
- Department of BiotechnologyCenter for Informational BiologySchool of Life Sciences and TechnologyUniversity of Electronic Science and Technology of ChinaChengduChina
- Key Laboratory of Plant Functional Genomics of the Ministry of EducationJoint International Research Laboratory of Agriculture and Agri‐Product Safety of the Ministry of EducationYangzhou UniversityYangzhouChina
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Kong F, Yamaoka Y, Ohama T, Lee Y, Li-Beisson Y. Molecular Genetic Tools and Emerging Synthetic Biology Strategies to Increase Cellular Oil Content in Chlamydomonas reinhardtii. PLANT & CELL PHYSIOLOGY 2019; 60:1184-1196. [PMID: 30715500 DOI: 10.1093/pcp/pcz022] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 01/18/2019] [Indexed: 05/26/2023]
Abstract
Microalgae constitute a highly diverse group of eukaryotic and photosynthetic microorganisms that have developed extremely efficient systems for harvesting and transforming solar energy into energy-rich molecules such as lipids. Although microalgae are considered to be one of the most promising platforms for the sustainable production of liquid oil, the oil content of these organisms is naturally low, and algal oil production is currently not economically viable. Chlamydomonas reinhardtii (Chlamydomonas) is an established algal model due to its fast growth, high transformation efficiency, and well-understood physiology and to the availability of detailed genome information and versatile molecular tools for this organism. In this review, we summarize recent advances in the development of genetic manipulation tools for Chlamydomonas, from gene delivery methods to state-of-the-art genome-editing technologies and fluorescent dye-based high-throughput mutant screening approaches. Furthermore, we discuss practical strategies and toolkits that enhance transgene expression, such as choice of expression vector and background strain. We then provide examples of how advanced genetic tools have been used to increase oil content in Chlamydomonas. Collectively, the current literature indicates that microalgal oil content can be increased by overexpressing key enzymes that catalyze lipid biosynthesis, blocking lipid degradation, silencing metabolic pathways that compete with lipid biosynthesis and modulating redox state. The tools and knowledge generated through metabolic engineering studies should pave the way for developing a synthetic biological approach to enhance lipid productivity in microalgae.
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Affiliation(s)
- Fantao Kong
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- School of Life Science and Biotechnology, Dalian University of Technology, Dalian, China
| | - Yasuyo Yamaoka
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
| | - Takeshi Ohama
- School of Environmental Science and Engineering, Kochi University of Technology (KUT), Tosayamada, Kochi, Japan
| | - Youngsook Lee
- Department of Integrative Bioscience & Biotechnology, Pohang University of Science and Technology, Pohang, Korea
- Department of Life Science, Pohang University of Science and Technology, Pohang, Korea
| | - Yonghua Li-Beisson
- Aix-Marseille Univ., CEA, CNRS, BIAM, UMR7265, CEA Cadarache, Saint-Paul-lez Durance F, France
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27
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Naduthodi MIS, Mohanraju P, Südfeld C, D’Adamo S, Barbosa MJ, van der Oost J. CRISPR-Cas ribonucleoprotein mediated homology-directed repair for efficient targeted genome editing in microalgae Nannochloropsis oceanica IMET1. BIOTECHNOLOGY FOR BIOFUELS 2019; 12:66. [PMID: 30962821 PMCID: PMC6432748 DOI: 10.1186/s13068-019-1401-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Accepted: 03/09/2019] [Indexed: 06/07/2023]
Abstract
BACKGROUND Microalgae are considered as a sustainable feedstock for the production of biofuels and other value-added compounds. In particular, Nannochloropsis spp. stand out from other microalgal species due to their capabilities to accumulate both triacylglycerol (TAG) and polyunsaturated fatty acids (PUFAs). However, the commercialization of microalgae-derived products is primarily hindered by the high production costs compared to less sustainable alternatives. Efficient genome editing techniques leading to effective metabolic engineering could result in strains with enhanced productivities of interesting metabolites and thereby reduce the production costs. Competent CRISPR-based genome editing techniques have been reported in several microalgal species, and only very recently in Nannochloropsis spp. (2017). All the reported CRISPR-Cas-based systems in Nannochloropsis spp. rely on plasmid-borne constitutive expression of Cas9 and a specific guide, combined with repair of double-stranded breaks (DSB) by non-homologous end joining (NHEJ) for the target gene knockout. RESULTS In this study, we report for the first time an alternative approach for CRISPR-Cas-mediated genome editing in Nannochloropsis sp.; the Cas ribonucleoproteins (RNP) and an editing template were directly delivered into microalgal cells via electroporation, making Cas expression dispensable and homology-directed repair (HDR) possible with high efficiency. Apart from widely used SpCas9, Cas12a variants from three different bacterium were used for this approach. We observed that FnCas12a from Francisella novicida generated HDR-based targeted mutants with highest efficiency (up to 93% mutants among transformants) while AsCas12a from Acidaminococcus sp. resulted in the lowest efficiency. We initially show that the native homologous recombination (HR) system in N. oceanica IMET1 is not efficient for easy isolation of targeted mutants by HR. Cas9/sgRNA RNP delivery greatly enhanced HR at the target site, generating around 70% of positive mutant lines. CONCLUSION We show that the delivery of Cas RNP by electroporation can be an alternative approach to the presently reported plasmid-based Cas9 method for generating mutants of N. oceanica. The co-delivery of Cas-RNPs along with a dsDNA repair template efficiently enhanced HR at the target site, resulting in a remarkable higher percentage of positive mutant lines. Therefore, this approach can be used for efficient generation of targeted mutants in Nannochloropsis sp. In addition, we here report the activity of several Cas12a homologs in N. oceanica IMET1, identifying FnCas12a as the best performer for high efficiency targeted genome editing.
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Affiliation(s)
- Mihris Ibnu Saleem Naduthodi
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Prarthana Mohanraju
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
| | - Christian Südfeld
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Sarah D’Adamo
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - Maria J. Barbosa
- Bioprocess Engineering Department, Wageningen University, Droevendaalsesteeg 1, 6708 PB Wageningen, The Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University, Stippeneng 4, 6708 PD Wageningen, The Netherlands
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Guzmán-Zapata D, Sandoval-Vargas JM, Macedo-Osorio KS, Salgado-Manjarrez E, Castrejón-Flores JL, Oliver-Salvador MDC, Durán-Figueroa NV, Nogué F, Badillo-Corona JA. Efficient Editing of the Nuclear APT Reporter Gene in Chlamydomonas reinhardtii via Expression of a CRISPR-Cas9 Module. Int J Mol Sci 2019; 20:E1247. [PMID: 30871076 PMCID: PMC6429146 DOI: 10.3390/ijms20051247] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2019] [Revised: 03/04/2019] [Accepted: 03/07/2019] [Indexed: 12/20/2022] Open
Abstract
The clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) technology is a versatile and useful tool to perform genome editing in different organisms ranging from bacteria and yeast to plants and mammalian cells. For a couple of years, it was believed that the system was inefficient and toxic in the alga Chlamydomonas reinhardtii. However, recently the system has been successfully implemented in this model organism, albeit relying mostly on the electroporation of ribonucleoproteins (RNPs) into cell wall deficient strains. This requires a constant source of RNPs and limits the application of the technology to strains that are not necessarily the most relevant from a biotechnological point of view. Here, we show that transient expression of the Streptococcus pyogenes Cas9 gene and sgRNAs, targeted to the single-copy nuclear apt9 gene, encoding an adenine phosphoribosyl transferase (APT), results in efficient disruption at the expected locus. Introduction of indels to the apt9 locus results in cell insensitivity to the otherwise toxic compound 2-fluoroadenine (2-FA). We have used agitation with glass beads and particle bombardment to introduce the plasmids carrying the coding sequences for Cas9 and the sgRNAs in a cell-walled strain of C. reinhardtii (CC-125). Using sgRNAs targeting exons 1 and 3 of apt9, we obtained disruption efficiencies of 3 and 30% on preselected 2-FA resistant colonies, respectively. Our results show that transient expression of Cas9 and a sgRNA can be used for editing of the nuclear genome inexpensively and at high efficiency. Targeting of the APT gene could potentially be used as a pre-selection marker for multiplexed editing or disruption of genes of interest.
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Affiliation(s)
- Daniel Guzmán-Zapata
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José M Sandoval-Vargas
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Karla S Macedo-Osorio
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Edgar Salgado-Manjarrez
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - José L Castrejón-Flores
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - María Del Carmen Oliver-Salvador
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Noé V Durán-Figueroa
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
| | - Fabien Nogué
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Université Paris-Saclay, 78000 Versailles, France.
| | - Jesús A Badillo-Corona
- Instituto Politécnico Nacional, Unidad Profesional Interdisciplinaria de Biotecnología. Av. Acueducto S/N., Col. Barrio La Laguna Ticomán, 07340 Mexico City, Mexico.
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Ortega-Escalante JA, Jasper R, Miller SM. CRISPR/Cas9 mutagenesis in Volvox carteri. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2019; 97:661-672. [PMID: 30406958 DOI: 10.1111/tpj.14149] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/18/2018] [Accepted: 10/23/2018] [Indexed: 06/08/2023]
Abstract
Volvox carteri and other volvocine green algae comprise an excellent model for investigating developmental complexity and its origins. Here we describe a method for targeted mutagenesis in V. carteri using CRISPR/Cas9 components expressed from transgenes. We used V. carteri nitrate reductase gene (nitA) regulatory sequences to conditionally express Streptococcus pyogenes Cas9, and V. carteri U6 RNA gene regulatory sequences to constitutively express single-guide RNA (sgRNA) transcripts. Volvox carteri was bombarded with both Cas9 vector and one of several sgRNA vectors programmed to target different test genes (glsA, regA and invA), and transformants were selected for expression of a hygromycin-resistance marker present on the sgRNA vector. Hygromycin-resistant transformants grown with nitrate as sole nitrogen source (inducing for nitA) were tested for Cas9 and sgRNA expression, and for the ability to generate progeny with expected mutant phenotypes. Some transformants of a somatic regenerator (Reg) mutant strain receiving sgRNA plasmid with glsA protospacer sequence yielded progeny (at a rate of ~0.01%) with a gonidialess (Gls) phenotype similar to that observed for previously described glsA mutants, and sequencing of the glsA gene in independent mutants revealed short deletions within the targeted region of glsA, indicative of Cas9-directed non-homologous end joining. Similarly, bombardment of a morphologically wild-type strain with the Cas9 plasmid and sgRNA plasmids targeting regA or invA yielded regA and invA mutant transformants/progeny, respectively (at rates of 0.1-100%). The capacity to make precisely directed frameshift mutations should greatly accelerate the molecular genetic analysis of development in V. carteri, and of developmental novelty in the volvocine algae.
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Affiliation(s)
- José A Ortega-Escalante
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Robyn Jasper
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
| | - Stephen M Miller
- Department of Biological Sciences, University of Maryland, Baltimore County, 1000 Hilltop Circle, Baltimore, MD, 21250, USA
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Baier T, Wichmann J, Kruse O, Lauersen KJ. Intron-containing algal transgenes mediate efficient recombinant gene expression in the green microalga Chlamydomonas reinhardtii. Nucleic Acids Res 2018; 46:6909-6919. [PMID: 30053227 PMCID: PMC6061784 DOI: 10.1093/nar/gky532] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Revised: 05/16/2018] [Accepted: 06/08/2018] [Indexed: 12/27/2022] Open
Abstract
Among green freshwater microalgae, Chlamydomonas reinhardtii has the most comprehensive and developed molecular toolkit, however, advanced genetic and metabolic engineering driven from the nuclear genome is generally hindered by inherently low transgene expression levels. Progressive strain development and synthetic promoters have improved the capacity of transgene expression; however, the responsible regulatory mechanisms are still not fully understood. Here, we elucidate the sequence specific dynamics of native regulatory element insertion into nuclear transgenes. Systematic insertions of the first intron of the ribulose-1,5-bisphosphate carboxylase/oxygenase small subunit 2 (rbcS2i1) throughout codon-optimized coding sequences (CDS) generates optimized algal transgenes which express reliably in C. reinhardtii. The optimal rbcS2i1 insertion site for efficient splicing was systematically determined and improved gene expression rates were shown using a codon-optimized sesquiterpene synthase CDS. Sequential insertions of rbcS2i1 were found to have a step-wise additive effect on all levels of transgene expression, which is likely correlated to a synergy of transcriptional machinery recruitment and mimicking the short average exon lengths natively found in the C. reinhardtii genome. We further demonstrate the value of this optimization with five representative transgene examples and provide guidelines for the design of any desired sequence with this strategy.
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MESH Headings
- Abies/enzymology
- Abies/genetics
- Chlamydomonas reinhardtii/genetics
- Codon/genetics
- DNA, Plant/genetics
- DNA, Recombinant/genetics
- Gene Expression Regulation, Plant
- Genes, Plant
- Genes, Synthetic
- Introns
- Isomerases/biosynthesis
- Isomerases/genetics
- Mutagenesis, Insertional
- Plant Proteins/biosynthesis
- Plant Proteins/genetics
- Pogostemon/enzymology
- Pogostemon/genetics
- Protein Engineering
- RNA Splicing
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Plant/genetics
- RNA, Plant/metabolism
- Recombinant Proteins/biosynthesis
- Ribulose-Bisphosphate Carboxylase/genetics
- Transgenes
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Affiliation(s)
- Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Julian Wichmann
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
| | - Kyle J Lauersen
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitätsstrasse 27, 33615 Bielefeld, Germany
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31
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Ding D, Chen K, Chen Y, Li H, Xie K. Engineering Introns to Express RNA Guides for Cas9- and Cpf1-Mediated Multiplex Genome Editing. MOLECULAR PLANT 2018; 11:542-552. [PMID: 29462720 DOI: 10.1016/j.molp.2018.02.005] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/23/2017] [Revised: 01/27/2018] [Accepted: 02/13/2018] [Indexed: 05/19/2023]
Abstract
The clustered regularly interspaced short palindromic repeat (CRISPR) system has emerged as the revolutionary platform for DNA targeting. This system uses a site-specific RNA guide to direct a CRISPR effector (e.g., Cas9 and Cpf1) to a DNA target. Here, we elaborate a general strategy to simultaneously express multiple guide RNAs (gRNA) and CRISPR RNAs (crRNA) from introns of Cas9 and Cpf1. This method utilizes the endogenous tRNA processing system or crRNA processing activity of Cpf1 to cleave the spliced intron that contains tRNA-gRNA polycistron or crRNA-crRNA array. We demonstrated that the tRNA-gRNA intron is able to fuse with Cas9 as one gene. Such a hybrid gene could be expressed using one polymerase II promoter, and exhibited high efficiency and robustness in simultaneously targeting multiple sites. We also implemented this strategy in Cpf1-mediated genome editing using intronic tRNA-crRNA and crRNA-crRNA arrays. Interestingly, hybrid genes containing Cpf1 and intronic crRNA array exhibited remarkably increased efficiency compared with the conventional Cpf1 vectors. Taken together, this study presents a method to express CRISPR reagents from one hybrid gene to increase genome-editing efficiency and capacity. Owing to its simplicity and versatility, this method could be broadly used to develop sophisticated CRISPR tools in eukaryotes.
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Affiliation(s)
- Dan Ding
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaiyuan Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuedan Chen
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hong Li
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kabin Xie
- National Key Laboratory of Crop Genetic Improvement and National Centre of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan 430070, China; Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China.
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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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Naduthodi MIS, Barbosa MJ, van der Oost J. Progress of CRISPR-Cas Based Genome Editing in Photosynthetic Microbes. Biotechnol J 2018; 13:e1700591. [PMID: 29396999 DOI: 10.1002/biot.201700591] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2017] [Revised: 01/20/2018] [Indexed: 12/29/2022]
Abstract
The carbon footprint caused by unsustainable development and its environmental and economic impact has become a major concern in the past few decades. Photosynthetic microbes such as microalgae and cyanobacteria are capable of accumulating value-added compounds from carbon dioxide, and have been regarded as environmentally friendly alternatives to reduce the usage of fossil fuels, thereby contributing to reducing the carbon footprint. This light-driven generation of green chemicals and biofuels has triggered the research for metabolic engineering of these photosynthetic microbes. CRISPR-Cas systems are successfully implemented across a wide range of prokaryotic and eukaryotic species for efficient genome editing. However, the inception of this genome editing tool in microalgal and cyanobacterial species took off rather slowly due to various complications. In this review, we elaborate on the established CRISPR-Cas based genome editing in various microalgal and cyanobacterial species. The complications associated with CRISPR-Cas based genome editing in these species are addressed along with possible strategies to overcome these issues. It is anticipated that in the near future this will result in improving and expanding the microalgal and cyanobacterial genome engineering toolbox.
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Affiliation(s)
- Mihris Ibnu Saleem Naduthodi
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands.,Bioprocess Engineering, AlgaePARC, Wageningen University and Research, Wageningen, Netherlands
| | - Maria J Barbosa
- Bioprocess Engineering, AlgaePARC, Wageningen University and Research, Wageningen, Netherlands
| | - John van der Oost
- Laboratory of Microbiology, Wageningen University and Research, Wageningen, Netherlands
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Greiner A, Kelterborn S, Evers H, Kreimer G, Sizova I, Hegemann P. Targeting of Photoreceptor Genes in Chlamydomonas reinhardtii via Zinc-Finger Nucleases and CRISPR/Cas9. THE PLANT CELL 2017; 29:2498-2518. [PMID: 28978758 PMCID: PMC5774583 DOI: 10.1105/tpc.17.00659] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/19/2017] [Accepted: 10/04/2017] [Indexed: 05/18/2023]
Abstract
The fast-growing biflagellated single-celled chlorophyte Chlamydomonas reinhardtii is the most widely used alga in basic research. The physiological functions of the 18 sensory photoreceptors are of particular interest with respect to Chlamydomonas development and behavior. Despite the demonstration of gene editing in Chlamydomonas in 1995, the isolation of mutants lacking easily ascertained newly acquired phenotypes remains problematic due to low DNA recombination efficiency. We optimized gene-editing protocols for several Chlamydomonas strains (including wild-type CC-125) using zinc-finger nucleases (ZFNs), genetically encoded CRISPR/associated protein 9 (Cas9) from Staphylococcus aureus and Streptococcus pyogenes, and recombinant Cas9 and developed protocols for rapidly isolating nonselectable gene mutants. Using this technique, we disrupted the photoreceptor genes COP1/2, COP3 (encoding channelrhodopsin 1 [ChR1]), COP4 (encoding ChR2), COP5, PHOT, UVR8, VGCC, MAT3, and aCRY and created the chr1 chr2 and uvr8 phot double mutants. Characterization of the chr1, chr2, and mat3 mutants confirmed the value of photoreceptor mutants for physiological studies. Genes of interest were disrupted in 5 to 15% of preselected clones (∼1 out of 4000 initial cells). Using ZFNs, genes were edited in a reliable, predictable manner via homologous recombination, whereas Cas9 primarily caused gene disruption via the insertion of cotransformed DNA. These methods should be widely applicable to research involving green algae.
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Affiliation(s)
- Andre Greiner
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Simon Kelterborn
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Heide Evers
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Georg Kreimer
- Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Irina Sizova
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
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