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Li X, Zhang Y, Wen X, Pan J. Utilizing codon degeneracy in the design of donor DNA for CRISPR/Cas9-mediated gene editing to streamline the screening process for single amino acid mutations. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024. [PMID: 38963727 DOI: 10.1111/tpj.16903] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Revised: 06/07/2024] [Accepted: 06/17/2024] [Indexed: 07/06/2024]
Abstract
Chlamydomonas reinhardtii, a unicellular green alga, has been widely used as a model organism for studies of algal, plant and ciliary biology. The generation of targeted amino acid mutations is often necessary, and this can be achieved using CRISPR/Cas9 induced homology-directed repair to install genomic modifications from exogenous donor DNA. Due to the low gene editing efficiency, the technical challenge lies in identifying the mutant cells. Direct sequencing is not practical, and pre-screening is required. Here, we report a strategy for generating and screening for amino acid point mutations using the CRISPR/Cas9 gene editing system. The strategy is based on designing donor DNA using codon degeneracy, which enables the design of specific primers to facilitate mutant screening by PCR. An in vitro assembled RNP complex, along with a dsDNA donor and an antibiotic resistance marker, was electroporated into wild-type cells, followed by PCR screening. To demonstrate this principle, we have generated the E102K mutation in centrin and the K40R mutation in α-tubulin. The editing efficiencies at the target sites for Centrin, TUA1, TUA2 were 4, 24 and 8% respectively, based on PCR screening. More than 80% of the mutants with the expected size of PCR products were precisely edited, as revealed by DNA sequencing. Subsequently, the precision-edited mutants were biochemically verified. The introduction of codon degeneracy did not affect the gene expression of centrin and α-tubulins. Thus, this approach can be used to facilitate the identification of point mutations, especially in genes with low editing rates.
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Affiliation(s)
- Xuecheng Li
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Yongli Zhang
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Xin Wen
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
| | - Junmin Pan
- MOE Key Laboratory of Protein Sciences, Tsinghua-Peking Center for Life Sciences, School of Life Sciences, Tsinghua University, Beijing, 100084, China
- Laboratory for Marine Biology and Biotechnology, Qingdao Marine Science and Technology Center, Qingdao, Shandong Province, 266000, China
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2
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Kneip JS, Kniepkamp N, Jang J, Mortaro MG, Jin E, Kruse O, Baier T. CRISPR/Cas9-Mediated Knockout of the Lycopene ε-Cyclase for Efficient Astaxanthin Production in the Green Microalga Chlamydomonas reinhardtii. PLANTS (BASEL, SWITZERLAND) 2024; 13:1393. [PMID: 38794462 PMCID: PMC11125023 DOI: 10.3390/plants13101393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/09/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024]
Abstract
Carotenoids are valuable pigments naturally occurring in all photosynthetic plants and microalgae as well as in selected fungi, bacteria, and archaea. Green microalgae developed a complex carotenoid profile suitable for efficient light harvesting and light protection and harbor great capacity for carotenoid production through the substantial power of the endogenous 2-C-methyl-D-erythritol 4-phosphate (MEP) pathway. Previous works established successful genome editing and induced significant changes in the cellular carotenoid content in Chlamydomonas reinhardtii. This study employs a tailored carotenoid pathway for engineered bioproduction of the valuable ketocarotenoid astaxanthin. Functional knockout of lycopene ε-cyclase (LCYE) and non-homologous end joining (NHEJ)-based integration of donor DNA at the target site inhibit the accumulation of α-carotene and consequently lutein and loroxanthin, abundant carotenoids in C. reinhardtii without changes in cellular fitness. PCR-based screening indicated that 4 of 96 regenerated candidate lines carried (partial) integrations of donor DNA and increased ß-carotene as well as derived carotenoid contents. Iterative overexpression of CrBKT, PacrtB, and CrCHYB resulted in a 2.3-fold increase in astaxanthin accumulation in mutant ΔLCYE#3 (1.8 mg/L) compared to the parental strain UVM4, which demonstrates the potential of genome editing for the design of a green cell factory for astaxanthin bioproduction.
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Affiliation(s)
- Jacob Sebastian Kneip
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Niklas Kniepkamp
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Junhwan Jang
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Maria Grazia Mortaro
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, Republic of Korea
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
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3
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Kumar V, Barwal A, Sharma N, Mir DS, Kumar P, Kumar V. Therapeutic proteins: developments, progress, challenges, and future perspectives. 3 Biotech 2024; 14:112. [PMID: 38510462 PMCID: PMC10948735 DOI: 10.1007/s13205-024-03958-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Accepted: 02/13/2024] [Indexed: 03/22/2024] Open
Abstract
Proteins are considered magic molecules due to their enormous applications in the health sector. Over the past few decades, therapeutic proteins have emerged as a promising treatment option for various diseases, particularly cancer, cardiovascular disease, diabetes, and others. The formulation of protein-based therapies is a major area of research, however, a few factors still hinder the large-scale production of these therapeutic products, such as stability, heterogenicity, immunogenicity, high cost of production, etc. This review provides comprehensive information on various sources and production of therapeutic proteins. The review also summarizes the challenges currently faced by scientists while developing protein-based therapeutics, along with possible solutions. It can be concluded that these proteins can be used in combination with small molecular drugs to give synergistic benefits in the future.
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Affiliation(s)
- Vimal Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Arti Barwal
- Department of Microbial Biotechnology, Panjab University, South Campus, Sector-25, Chandigarh, 160014 India
| | - Nitin Sharma
- Department of Biotechnology, Chandigarh Group of Colleges, Mohali, Punjab 140307 India
| | - Danish Shafi Mir
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
| | - Pradeep Kumar
- Faculty of Applied Sciences and Biotechnology, Shoolini University of Biotechnology and Management Sciences, Solan, 173229 India
| | - Vikas Kumar
- University Institute of Biotechnology, Chandigarh University, Gharuan, Mohali, Punjab 140413 India
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4
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Gupta A, Kang K, Pathania R, Saxton L, Saucedo B, Malik A, Torres-Tiji Y, Diaz CJ, Dutra Molino JV, Mayfield SP. Harnessing genetic engineering to drive economic bioproduct production in algae. Front Bioeng Biotechnol 2024; 12:1350722. [PMID: 38347913 PMCID: PMC10859422 DOI: 10.3389/fbioe.2024.1350722] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Accepted: 01/16/2024] [Indexed: 02/15/2024] Open
Abstract
Our reliance on agriculture for sustenance, healthcare, and resources has been essential since the dawn of civilization. However, traditional agricultural practices are no longer adequate to meet the demands of a burgeoning population amidst climate-driven agricultural challenges. Microalgae emerge as a beacon of hope, offering a sustainable and renewable source of food, animal feed, and energy. Their rapid growth rates, adaptability to non-arable land and non-potable water, and diverse bioproduct range, encompassing biofuels and nutraceuticals, position them as a cornerstone of future resource management. Furthermore, microalgae's ability to capture carbon aligns with environmental conservation goals. While microalgae offers significant benefits, obstacles in cost-effective biomass production persist, which curtails broader application. This review examines microalgae compared to other host platforms, highlighting current innovative approaches aimed at overcoming existing barriers. These approaches include a range of techniques, from gene editing, synthetic promoters, and mutagenesis to selective breeding and metabolic engineering through transcription factors.
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Affiliation(s)
- Abhishek Gupta
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ruchi Pathania
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Lisa Saxton
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Barbara Saucedo
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Ashleyn Malik
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Crisandra J. Diaz
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - João Vitor Dutra Molino
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Laboratory, Department of Molecular Biology, School of Biological Sciences, University of California San Diego, San Diego, CA, United States
- California Center for Algae Biotechnology, University of California San Diego, San Diego, CA, United States
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5
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Chaux F, Jarrige D, Rodrigues-Azevedo M, Bujaldon S, Caspari OD, Ozawa SI, Drapier D, Vallon O, Choquet Y, de Vitry C. Chloroplast ATP synthase biogenesis requires peripheral stalk subunits AtpF and ATPG and stabilization of atpE mRNA by OPR protein MDE1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 116:1582-1599. [PMID: 37824282 DOI: 10.1111/tpj.16448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 08/15/2023] [Accepted: 08/21/2023] [Indexed: 10/14/2023]
Abstract
Chloroplast ATP synthase contains subunits of plastid and nuclear genetic origin. To investigate the coordinated biogenesis of this complex, we isolated novel ATP synthase mutants in the green alga Chlamydomonas reinhardtii by screening for high light sensitivity. We report here the characterization of mutants affecting the two peripheral stalk subunits b and b', encoded respectively by the atpF and ATPG genes, and of three independent mutants which identify the nuclear factor MDE1, required to stabilize the chloroplast-encoded atpE mRNA. Whole-genome sequencing revealed a transposon insertion in the 3'UTR of ATPG while mass spectrometry shows a small accumulation of functional ATP synthase in this knock-down ATPG mutant. In contrast, knock-out ATPG mutants, obtained by CRISPR-Cas9 gene editing, fully prevent ATP synthase function and accumulation, as also observed in an atpF frame-shift mutant. Crossing ATP synthase mutants with the ftsh1-1 mutant of the major thylakoid protease identifies AtpH as an FTSH substrate, and shows that FTSH significantly contributes to the concerted accumulation of ATP synthase subunits. In mde1 mutants, the absence of atpE transcript fully prevents ATP synthase biogenesis and photosynthesis. Using chimeric atpE genes to rescue atpE transcript accumulation, we demonstrate that MDE1, a novel octotricopeptide repeat (OPR) protein, genetically targets the atpE 5'UTR. In the perspective of the primary endosymbiosis (~1.5 Gy), the recruitment of MDE1 to its atpE target exemplifies a nucleus/chloroplast interplay that evolved rather recently, in the ancestor of the CS clade of Chlorophyceae, ~300 My ago.
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Affiliation(s)
- Frédéric Chaux
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Domitille Jarrige
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Marcio Rodrigues-Azevedo
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Sandrine Bujaldon
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Oliver D Caspari
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Shin-Ichiro Ozawa
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Dominique Drapier
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Olivier Vallon
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Yves Choquet
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
| | - Catherine de Vitry
- Unité Mixte de Recherche (UMR) 7141, Centre National de la Recherche Scientifique (CNRS) and Sorbonne Université, Institut de Biologie Physico-Chimique, 13 rue Pierre et Marie Curie, F-75005, Paris, France
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6
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Feng S, Xie X, Liu J, Li A, Wang Q, Guo D, Li S, Li Y, Wang Z, Guo T, Zhou J, Tang DYY, Show PL. A potential paradigm in CRISPR/Cas systems delivery: at the crossroad of microalgal gene editing and algal-mediated nanoparticles. J Nanobiotechnology 2023; 21:370. [PMID: 37817254 PMCID: PMC10563294 DOI: 10.1186/s12951-023-02139-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2023] [Accepted: 10/03/2023] [Indexed: 10/12/2023] Open
Abstract
Microalgae as the photosynthetic organisms offer enormous promise in a variety of industries, such as the generation of high-value byproducts, biofuels, pharmaceuticals, environmental remediation, and others. With the rapid advancement of gene editing technology, CRISPR/Cas system has evolved into an effective tool that revolutionised the genetic engineering of microalgae due to its robustness, high target specificity, and programmability. However, due to the lack of robust delivery system, the efficacy of gene editing is significantly impaired, limiting its application in microalgae. Nanomaterials have become a potential delivery platform for CRISPR/Cas systems due to their advantages of precise targeting, high stability, safety, and improved immune system. Notably, algal-mediated nanoparticles (AMNPs), especially the microalgae-derived nanoparticles, are appealing as a sustainable delivery platform because of their biocompatibility and low toxicity in a homologous relationship. In addition, living microalgae demonstrated effective and regulated distribution into specified areas as the biohybrid microrobots. This review extensively summarised the uses of CRISPR/Cas systems in microalgae and the recent developments of nanoparticle-based CRISPR/Cas delivery systems. A systematic description of the properties and uses of AMNPs, microalgae-derived nanoparticles, and microalgae microrobots has also been discussed. Finally, this review highlights the challenges and future research directions for the development of gene-edited microalgae.
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Affiliation(s)
- Shuying Feng
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China.
| | - Xin Xie
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Junjie Liu
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Aifang Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Qianqian Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Dandan Guo
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Shuxuan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Yalan Li
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Zilong Wang
- Medical College, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China
| | - Tao Guo
- Department of Pharmacy, Henan University of Chinese Medicine, Zhengzhou, 450046, Henan, China.
| | - Jin Zhou
- Institute for Ocean Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen, 518055, Guangdong, China.
| | - Doris Ying Ying Tang
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, 43500, Semenyih, Malaysia
| | - Pau Loke Show
- Department of Chemical Engineering, Khalifa University, P.O. Box 127788, Abu Dhabi, United Arab Emirates.
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Cazzaniga S, Kim M, Pivato M, Perozeni F, Sardar S, D'Andrea C, Jin E, Ballottari M. Photosystem II monomeric antenna CP26 plays a key role in nonphotochemical quenching in Chlamydomonas. PLANT PHYSIOLOGY 2023; 193:1365-1380. [PMID: 37403662 DOI: 10.1093/plphys/kiad391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Revised: 05/17/2023] [Accepted: 06/06/2023] [Indexed: 07/06/2023]
Abstract
Thermal dissipation of excess excitation energy, called nonphotochemical quenching (NPQ), is 1 of the main photoprotective mechanisms in oxygenic photosynthetic organisms. Here, we investigated the function of the monomeric photosystem II (PSII) antenna protein CP26 in photoprotection and light harvesting in Chlamydomonas reinhardtii, a model organism for green algae. We used CRISPR/Cas9 genome editing and complementation to generate cp26 knockout mutants (named k6#) that did not negatively affect CP29 accumulation, which differed from previous cp26 mutants, allowing us to compare mutants specifically deprived of CP26, CP29, or both. The absence of CP26 partially affected PSII activity, causing reduced growth at low or medium light but not at high irradiances. However, the main phenotype observed in k6# mutants was a more than 70% reduction of NPQ compared to the wild type (Wt). This phenotype was fully rescued by genetic complementation and complemented strains accumulating different levels of CP26, demonstrating that ∼50% of CP26 content, compared to the Wt, was sufficient to restore the NPQ capacity. Our findings demonstrate a pivotal role for CP26 in NPQ induction, while CP29 is crucial for PSII activity. The genetic engineering of these 2 proteins could be a promising strategy to regulate the photosynthetic efficiency of microalgae under different light regimes.
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Affiliation(s)
- Stefano Cazzaniga
- Dipartimento di Biotecnologie, Università di Verona, Verona 37134, Italy
| | - Minjae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Matteo Pivato
- Dipartimento di Biotecnologie, Università di Verona, Verona 37134, Italy
| | - Federico Perozeni
- Dipartimento di Biotecnologie, Università di Verona, Verona 37134, Italy
| | - Samim Sardar
- Istituto Italiano di Tecnologia, Center for Nano Science and Technology, Milano 20134, Italy
| | - Cosimo D'Andrea
- Istituto Italiano di Tecnologia, Center for Nano Science and Technology, Milano 20134, Italy
- Dipartimento di Fisica, Politecnico di Milano, Milano 20133, Italy
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, Seoul 04763, South Korea
| | - Matteo Ballottari
- Dipartimento di Biotecnologie, Università di Verona, Verona 37134, Italy
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Gu X, Deng Y, Wang A, Gan Q, Xin Y, Paithoonrangsarid K, Lu Y. Engineering a marine microalga Chlorella sp. as the cell factory. BIOTECHNOLOGY FOR BIOFUELS AND BIOPRODUCTS 2023; 16:133. [PMID: 37679828 PMCID: PMC10485975 DOI: 10.1186/s13068-023-02384-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 08/19/2023] [Indexed: 09/09/2023]
Abstract
The use of marine microalgae in industrial systems is attractive for converting CO2 into value-added products using saline water and sunlight. The plant nature and demonstrated industrial potential facilitate Chlorella spp. as excellent model organisms for both basic research and commercial application. However, the transformation method has not been developed in marine Chlorella spp., thus genetic engineering is hindered in exploiting the industrial potentialities of these strains. In this study, we provided a transformation protocol for the marine Chlorella strain MEM25, which showed robust characteristics, including high production of proteins and polyunsaturated fatty acids in multiple cultivation systems over various spatial-temporal scales. We showed that transformants could be obtained in a dramatically time-saving manner (comparable to Saccharomyces cerevisiae) with four functional proteins expressed properly. The transgenes are integrated into the genome and can be successfully inherited for more than two years. The development of a marine Chlorella transformation method, in combination with the complete genome, will greatly facilitate more comprehensive mechanism studies and provide possibilities to use this species as chassis for synthetic biology to produce value-added compounds with mutual advantage in neutralization of CO2 in commercial scales.
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Affiliation(s)
- Xinping Gu
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China
| | - Ying Deng
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China
| | - Aoqi Wang
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China
| | - Qinhua Gan
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China
| | - Yi Xin
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China
| | - Kalyanee Paithoonrangsarid
- Biochemical Engineering and Systems Biology Research Group, National Center for Genetic Engineering and Biotechnology, National Science and Technology Development Agency at King Mongkut's University of Technology Thonburi, Bangkok, 10150, Thailand
| | - Yandu Lu
- Single-cell BioEngineering Group, State Key Laboratory of Marine Resource Utilization in South China Sea, School of Marine Life and Aquaculture, Hainan University, Haikou, 570228, China.
- Hainan Provincial Key Laboratory of Tropical Hydrobiotechnology, Hainan University, Haikou, China.
- Haikou Technology Innovation Center for Research and Utilization of Algal Bioresources, Hainan University, Haikou, China.
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9
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Boisset ND, Favoino G, Meloni M, Jomat L, Cassier-Chauvat C, Zaffagnini M, Lemaire SD, Crozet P. Phosphoribulokinase abundance is not limiting the Calvin-Benson-Bassham cycle in Chlamydomonas reinhardtii. FRONTIERS IN PLANT SCIENCE 2023; 14:1230723. [PMID: 37719215 PMCID: PMC10501310 DOI: 10.3389/fpls.2023.1230723] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Accepted: 07/21/2023] [Indexed: 09/19/2023]
Abstract
Improving photosynthetic efficiency in plants and microalgae is of utmost importance to support the growing world population and to enable the bioproduction of energy and chemicals. Limitations in photosynthetic light conversion efficiency can be directly attributed to kinetic bottlenecks within the Calvin-Benson-Bassham cycle (CBBC) responsible for carbon fixation. A better understanding of these bottlenecks in vivo is crucial to overcome these limiting factors through bio-engineering. The present study is focused on the analysis of phosphoribulokinase (PRK) in the unicellular green alga Chlamydomonas reinhardtii. We have characterized a PRK knock-out mutant strain and showed that in the absence of PRK, Chlamydomonas cannot grow photoautotrophically while functional complementation with a synthetic construct allowed restoration of photoautotrophy. Nevertheless, using standard genetic elements, the expression of PRK was limited to 40% of the reference level in complemented strains and could not restore normal growth in photoautotrophic conditions suggesting that the CBBC is limited. We were subsequently able to overcome this initial limitation by improving the design of the transcriptional unit expressing PRK using diverse combinations of DNA parts including PRK endogenous promoter and introns. This enabled us to obtain strains with PRK levels comparable to the reference strain and even overexpressing strains. A collection of strains with PRK levels between 16% and 250% of WT PRK levels was generated and characterized. Immunoblot and growth assays revealed that a PRK content of ≈86% is sufficient to fully restore photoautotrophic growth. This result suggests that PRK is present in moderate excess in Chlamydomonas. Consistently, the overexpression of PRK did not increase photosynthetic growth indicating that that the endogenous level of PRK in Chlamydomonas is not limiting the Calvin-Benson-Bassham cycle under optimal conditions.
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Affiliation(s)
- Nicolas D. Boisset
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Doctoral School of Plant Sciences, Université Paris-Saclay, Saint-Aubin, France
| | - Giusi Favoino
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Maria Meloni
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Lucile Jomat
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
| | - Corinne Cassier-Chauvat
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), UMR 9198, Gif-sur-Yvette, France
| | - Mirko Zaffagnini
- Department of Pharmacy and Biotechnologies, University of Bologna, Bologna, Italy
| | - Stéphane D. Lemaire
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
| | - Pierre Crozet
- Laboratoire de Biologie Computationnelle et Quantitative, Institut de Biologie Parie-Seine, Sorbonne Université, CNRS, UMR 7238, Paris, France
- Laboratoire de Biologie Moléculaire et Cellulaire des Eucaryotes, Institut de Biologie Physico-Chimique, Sorbonne Université, CNRS, UMR 8226, Paris, France
- Polytech-Sorbonne, Sorbonne Université, Paris, France
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10
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Chini Zittelli G, Lauceri R, Faraloni C, Silva Benavides AM, Torzillo G. Valuable pigments from microalgae: phycobiliproteins, primary carotenoids, and fucoxanthin. Photochem Photobiol Sci 2023; 22:1733-1789. [PMID: 37036620 DOI: 10.1007/s43630-023-00407-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Accepted: 03/03/2023] [Indexed: 04/11/2023]
Abstract
Phycobiliproteins, carotenoids and fucoxanthin are photosynthetic pigments extracted from microalgae and cyanobacteria with great potential biotechnological applications, as healthy food colorants and cosmetics. Phycocyanin possesses a brilliant blue color, with fluorescent properties making it useful as a reagent for immunological essays. The most important source of phycocyanin is the cyanobacterium Arthrospira platensis, however, recently, the Rhodophyta Galdieria sulphuraria has also been identified as such. The main obstacle to the commercialization of phycocyanin is represented by its chemical instability, strongly reducing its shelf-life. Moreover, the high level of purity needed for pharmaceutical applications requires several steps which increase both the production time and cost. Microalgae (Chlorella, Dunaliella, Nannochloropsis, Scenedesmus) produce several light harvesting carotenoids, and are able to manage with oxidative stress, due to their free radical scavenging properties, which makes them suitable for use as source of natural antioxidants. Many studies focused on the selection of the most promising strains producing valuable carotenoids and on their extraction and purification. Among carotenoids produced by marine microalgae, fucoxanthin is the most abundant, representing more than 10% of total carotenoids. Despite the abundance and diversity of fucoxanthin producing microalgae only a few species have been studied for commercial production, the most relevant being Phaeodactylum tricornutum. Due to its antioxidant activity, fucoxanthin can bring various potential benefits to the prevention and treatment of lifestyle-related diseases. In this review, we update the main results achieved in the production, extraction, purification, and commercialization of these important pigments, motivating the cultivation of microalgae as a source of natural pigments.
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Affiliation(s)
- Graziella Chini Zittelli
- Istituto per la Bioeconomia, CNR, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Florence, Italy
| | - Rosaria Lauceri
- Istituto di Ricerca sulle Acque, CNR, Sede Di Verbania, Largo Tonolli 50, 28922, Verbania, Italy
| | - Cecilia Faraloni
- Istituto per la Bioeconomia, CNR, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Florence, Italy
| | - Ana Margarita Silva Benavides
- Centro de Investigación en Ciencias del Mar Y Limnologίa, Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica
- Escuela de Biologia, Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica
| | - Giuseppe Torzillo
- Istituto per la Bioeconomia, CNR, Via Madonna del Piano 10, 50019, Sesto Fiorentino, Florence, Italy.
- Centro de Investigación en Ciencias del Mar Y Limnologίa, Universidad de Costa Rica, San Pedro, San José, 2060, Costa Rica.
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11
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Zadabbas Shahabadi H, Akbarzadeh A, Ofoghi H, Kadkhodaei S. Site-specific gene knock-in and bacterial phytase gene expression in Chlamydomonas reinhardtii via Cas9 RNP-mediated HDR. FRONTIERS IN PLANT SCIENCE 2023; 14:1150436. [PMID: 37275253 PMCID: PMC10235511 DOI: 10.3389/fpls.2023.1150436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Accepted: 03/28/2023] [Indexed: 06/07/2023]
Abstract
In the present study, we applied the HDR (homology-directed DNA repair) CRISPR-Cas9-mediated knock-in system to accurately insert an optimized foreign bacterial phytase gene at a specific site of the nitrate reductase (NR) gene (exon 2) to achieve homologous recombination with the stability of the transgene and reduce insertion site effects or gene silencing. To this end, we successfully knocked-in the targeted NR gene of Chlamydomonas reinhardtii using the bacterial phytase gene cassette through direct delivery of the CRISPR/Cas9 system as the ribonucleoprotein (RNP) complex consisting of Cas9 protein and the specific single guide RNAs (sgRNAs). The NR insertion site editing was confirmed by PCR and sequencing of the transgene positive clones. Moreover, 24 clones with correct editing were obtained, where the phytase gene cassette was located in exon 2 of the NR gene, and the editing efficiency was determined to be 14.81%. Additionally, site-specific gene expression was analyzed and confirmed using RT-qPCR. Cultivation of the positive knocked-in colonies on the selective media during 10 generations indicated the stability of the correct editing without gene silencing or negative insertion site effects. Our results demonstrated that CRISPR-Cas9-mediated knock-in could be applied for nuclear expression of the heterologous gene of interest, and also confirmed its efficacy as an effective tool for site-specific gene knock-in, avoiding nuclear positional effects and gene silencing in C. reinhardtii. These findings could also provide a new perspective on the advantageous application of RNP-CRISPR/Cas9 gene-editing to accelerate the commercial production of complex recombinant proteins in the food-grade organism "C. reinhardtii".
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Affiliation(s)
- Hassan Zadabbas Shahabadi
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
- Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
| | - Arash Akbarzadeh
- Department of Fisheries, Faculty of Marine Science and Technology, University of Hormozgan, Bandar Abbas, Iran
| | - Hamideh Ofoghi
- Department of Biotechnology, Iranian Research Organization for Science and Technology (IROST), Tehran, Iran
| | - Saeid Kadkhodaei
- Agricultural Biotechnology Research Institute of Iran (ABRII), Isfahan Branch, Agricultural Research, Education and Extension Organization (AREEO), Isfahan, Iran
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12
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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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13
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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: 12] [Impact Index Per Article: 12.0] [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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14
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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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15
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Verma V, Kumar A, Partap M, Thakur M, Bhargava B. CRISPR-Cas: A robust technology for enhancing consumer-preferred commercial traits in crops. FRONTIERS IN PLANT SCIENCE 2023; 14:1122940. [PMID: 36824195 PMCID: PMC9941649 DOI: 10.3389/fpls.2023.1122940] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Accepted: 01/16/2023] [Indexed: 06/18/2023]
Abstract
The acceptance of new crop varieties by consumers is contingent on the presence of consumer-preferred traits, which include sensory attributes, nutritional value, industrial products and bioactive compounds production. Recent developments in genome editing technologies provide novel insight to identify gene functions and improve the various qualitative and quantitative traits of commercial importance in plants. Various conventional as well as advanced gene-mutagenesis techniques such as physical and chemical mutagenesis, CRISPR-Cas9, Cas12 and base editors are used for the trait improvement in crops. To meet consumer demand, breakthrough biotechnologies, especially CRISPR-Cas have received a fair share of scientific and industrial interest, particularly in plant genome editing. CRISPR-Cas is a versatile tool that can be used to knock out, replace and knock-in the desired gene fragments at targeted locations in the genome, resulting in heritable mutations of interest. This review highlights the existing literature and recent developments in CRISPR-Cas technologies (base editing, prime editing, multiplex gene editing, epigenome editing, gene delivery methods) for reliable and precise gene editing in plants. This review also discusses the potential of gene editing exhibited in crops for the improvement of consumer-demanded traits such as higher nutritional value, colour, texture, aroma/flavour, and production of industrial products such as biofuel, fibre, rubber and pharmaceuticals. In addition, the bottlenecks and challenges associated with gene editing system, such as off targeting, ploidy level and the ability to edit organelle genome have also been discussed.
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Affiliation(s)
- Vipasha Verma
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Akhil Kumar
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Mahinder Partap
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
| | - Meenakshi Thakur
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
| | - Bhavya Bhargava
- Floriculture Laboratory, Agrotechnology Division, Council of Scientific and Industrial Research (CSIR) –Institute of Himalayan Bioresource Technology (IHBT), Palampur, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, India
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16
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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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17
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Sex-linked deubiquitinase establishes uniparental transmission of chloroplast DNA. Nat Commun 2022; 13:1133. [PMID: 35241655 PMCID: PMC8894339 DOI: 10.1038/s41467-022-28807-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Accepted: 02/09/2022] [Indexed: 12/26/2022] Open
Abstract
Most sexual organisms inherit organelles from one parent, commonly by excluding organelles from the smaller gametes. However, post-mating elimination of organelles derived from one gamete ensures uniparental inheritance, where the underlying mechanisms to distinguish organelles by their origin remain obscure. Mating in Chlamydomonas reinhardtii combines isomorphic plus and minus gametes, but chloroplast DNA from minus gametes is selectively degraded in zygotes. Here, we identify OTU2p (otubain protein 2), encoded in the plus mating-type locus MT+, as the protector of plus chloroplast. Otu2p is an otubain-like deubiquitinase, which prevents proteasome-mediated degradation of the preprotein translocase of the outer chloroplast membrane (TOC) during gametogenesis. Using OTU2p-knockouts and proteasome inhibitor treatment, we successfully redirect selective DNA degradation in chloroplasts with reduced TOC levels regardless of mating type, demonstrating that plus-specific Otu2p establishes uniparental chloroplast DNA inheritance. Our work documents that a sex-linked organelle quality control mechanism drives the uniparental organelle inheritance without dimorphic gametes. Most sexual organisms ensure that organelles are inherited from a single parent. Here, the authors describe OTU2p, a Chlamydomonas deubiquitinase that drives uniparental organelle inheritance without gametic dimorphism by preventing proteasome-mediated degradation exclusively in gametes of the plus mating type.
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18
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The Spermidine Synthase Gene SPD1: A Novel Auxotrophic Marker for Chlamydomonas reinhardtii Designed by Enhanced CRISPR/Cas9 Gene Editing. Cells 2022; 11:cells11050837. [PMID: 35269459 PMCID: PMC8909627 DOI: 10.3390/cells11050837] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Revised: 02/15/2022] [Accepted: 02/24/2022] [Indexed: 01/09/2023] Open
Abstract
Biotechnological application of the green microalga Chlamydomonas reinhardtii hinges on the availability of selectable markers for effective expression of multiple transgenes. However, biological safety concerns limit the establishment of new antibiotic resistance genes and until today, only a few auxotrophic markers exist for C. reinhardtii. The recent improvements in gene editing via CRISPR/Cas allow directed exploration of new endogenous selectable markers. Since editing frequencies remain comparably low, a Cas9-sgRNA ribonucleoprotein (RNP) delivery protocol was strategically optimized by applying nitrogen starvation to the pre-culture, which improved successful gene edits from 10% to 66% after pre-selection. Probing the essential polyamine biosynthesis pathway, the spermidine synthase gene (SPD1) is shown to be a potent selectable marker with versatile biotechnological applicability. Very low levels of spermidine (0.75 mg/L) were required to maintain normal mixotrophic and phototrophic growth in newly designed spermidine auxotrophic strains. Complementation of these strains with a synthetic SPD1 gene was achieved when the mature protein was expressed in the cytosol or targeted to the chloroplast. This work highlights the potential of new selectable markers for biotechnology as well as basic research and proposes an effective pipeline for the identification of new auxotrophies in C. reinhardtii.
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19
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Kselíková V, Singh A, Bialevich V, Čížková M, Bišová K. Improving microalgae for biotechnology - From genetics to synthetic biology - Moving forward but not there yet. Biotechnol Adv 2021; 58:107885. [PMID: 34906670 DOI: 10.1016/j.biotechadv.2021.107885] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Revised: 11/28/2021] [Accepted: 12/07/2021] [Indexed: 12/28/2022]
Abstract
Microalgae are a diverse group of photosynthetic organisms that can be exploited for the production of different compounds, ranging from crude biomass and biofuels to high value-added biochemicals and synthetic proteins. Traditionally, algal biotechnology relies on bioprospecting to identify new highly productive strains and more recently, on forward genetics to further enhance productivity. However, it has become clear that further improvements in algal productivity for biotechnology is impossible without combining traditional tools with the arising molecular genetics toolkit. We review recent advantages in developing high throughput screening methods, preparing genome-wide mutant libraries, and establishing genome editing techniques. We discuss how algae can be improved in terms of photosynthetic efficiency, biofuel and high value-added compound production. Finally, we critically evaluate developments over recent years and explore future potential in the field.
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Affiliation(s)
- Veronika Kselíková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic; Faculty of Science, University of South Bohemia, 37005 České Budějovice, Czech Republic
| | - Anjali Singh
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Vitali Bialevich
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Mária Čížková
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic
| | - Kateřina Bišová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Cell Cycles of Algae, 379 81 Třeboň, Czech Republic.
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20
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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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Ferenczi A, Chew YP, Kroll E, von Koppenfels C, Hudson A, Molnar A. Mechanistic and genetic basis of single-strand templated repair at Cas12a-induced DNA breaks in Chlamydomonas reinhardtii. Nat Commun 2021; 12:6751. [PMID: 34799578 PMCID: PMC8604939 DOI: 10.1038/s41467-021-27004-1] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Accepted: 10/26/2021] [Indexed: 12/12/2022] Open
Abstract
Single-stranded oligodeoxynucleotides (ssODNs) are widely used as DNA repair templates in CRISPR/Cas precision genome editing. However, the underlying mechanisms of single-strand templated DNA repair (SSTR) are inadequately understood, constraining rational improvements to precision editing. Here we study SSTR at CRISPR/Cas12a-induced DNA double-strand breaks (DSBs) in the eukaryotic model green microalga Chlamydomonas reinhardtii. We demonstrate that ssODNs physically incorporate into the genome during SSTR at Cas12a-induced DSBs. This process is genetically independent of the Rad51-dependent homologous recombination and Fanconi anemia pathways, is strongly antagonized by non-homologous end-joining, and is mediated almost entirely by the alternative end-joining enzyme polymerase θ. These findings suggest differences in SSTR between C. reinhardtii and animals. Our work illustrates the promising potentially of C. reinhardtii as a model organism for studying nuclear DNA repair.
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Affiliation(s)
- Aron Ferenczi
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Yen Peng Chew
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Erika Kroll
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
- Department of Biointeractions and Crop Protection, Rothamsted Research, Harpenden, AL5 2JQ, UK
| | | | - Andrew Hudson
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Attila Molnar
- Institute of Molecular Plant Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK.
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22
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Microalgae Xanthophylls: From Biosynthesis Pathway and Production Techniques to Encapsulation Development. Foods 2021; 10:foods10112835. [PMID: 34829118 PMCID: PMC8623138 DOI: 10.3390/foods10112835] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Revised: 11/01/2021] [Accepted: 11/10/2021] [Indexed: 12/28/2022] Open
Abstract
In the last 20 years, xanthophylls from microalgae have gained increased scientific and industrial interests. This review highlights the essential issues that concern this class of high value compounds. Firstly, their chemical diversity as the producer microorganisms was detailed. Then, the use of conventional and innovative extraction techniques was discussed. Upgraded knowledge on the biosynthetic pathway of the main xanthophylls produced by photosynthetic microorganisms was reviewed in depth, providing new insightful ideas, clarifying the function of these active biomolecules. In addition, the recent advances in encapsulation techniques of astaxanthin and fucoxanthin, such as spray and freeze drying, gelation, emulsification and coacervation were updated. Providing information about these topics and their applications and advances could be a help to students and young researchers who are interested in chemical and metabolic engineering, chemistry and natural products communities to approach the complex thematic of xanthophylls.
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Ahmad S, Tang L, Shahzad R, Mawia AM, Rao GS, Jamil S, Wei C, Sheng Z, Shao G, Wei X, Hu P, Mahfouz MM, Hu S, Tang S. CRISPR-Based Crop Improvements: A Way Forward to Achieve Zero Hunger. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2021; 69:8307-8323. [PMID: 34288688 DOI: 10.1021/acs.jafc.1c02653] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/14/2023]
Abstract
Zero hunger is one of the sustainable development goals set by the United Nations in 2015 to achieve global food security by 2030. The current harvest of crops is insufficient; feeding the world's population and meeting the goal of zero hunger by 2030 will require larger and more consistent crop production. Clustered regularly interspaced short palindromic repeats-associated protein (CRISPR-Cas) technology is widely used for the plant genome editing. In this review, we consider this technology as a potential tool for achieving zero hunger. We provide a comprehensive overview of CRISPR-Cas technology and its most important applications for food crops' improvement. We also conferred current and potential technological breakthroughs that will help in breeding future crops to end global hunger. The regulatory aspects of deploying this technology in commercial sectors, bioethics, and the production of transgene-free plants are also discussed. We hope that the CRISPR-Cas system will accelerate the breeding of improved crop cultivars compared with conventional breeding and pave the way toward the zero hunger goal.
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Affiliation(s)
- Shakeel Ahmad
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
- Maize Research Station, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Liqun Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Rahil Shahzad
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Amos Musyoki Mawia
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gundra Sivakrishna Rao
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shakra Jamil
- Agricultural Biotechnology Research Institute, Ayub Agricultural Research Institute, Faisalabad 38000, Pakistan
| | - Chen Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Zhonghua Sheng
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Gaoneng Shao
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Xiangjin Wei
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Peisong Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Magdy M Mahfouz
- Laboratory for Genome Engineering and Synthetic Biology, Division of Biological Sciences, 4700 King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia
| | - Shikai Hu
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
| | - Shaoqing Tang
- State Key Laboratory of Rice Biology, China National Center for Rice Improvement, China National Rice Research Institute, Hangzhou 310006, China
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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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25
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Mubarik MS, Khan SH, Sajjad M, Raza A, Hafeez MB, Yasmeen T, Rizwan M, Ali S, Arif MS. A manipulative interplay between positive and negative regulators of phytohormones: A way forward for improving drought tolerance in plants. PHYSIOLOGIA PLANTARUM 2021; 172:1269-1290. [PMID: 33421147 DOI: 10.1111/ppl.13325] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 11/20/2020] [Accepted: 12/23/2020] [Indexed: 05/28/2023]
Abstract
Among different abiotic stresses, drought stress is the leading cause of impaired plant growth and low productivity worldwide. It is therefore essential to understand the process of drought tolerance in plants and thus to enhance drought resistance. Accumulating evidence indicates that phytohormones are essential signaling molecules that regulate diverse processes of plant growth and development under drought stress. Plants can often respond to drought stress through a cascade of phytohormones signaling as a means of plant growth regulation. Understanding biosynthesis pathways and regulatory crosstalk involved in these vital compounds could pave the way for improving plant drought tolerance while maintaining overall plant health. In recent years, the identification of phytohormones related key regulatory genes and their manipulation through state-of-the-art genome engineering tools have helped to improve drought tolerance plants. To date, several genes linked to phytohormones signaling networks, biosynthesis, and metabolism have been described as a promising contender for engineering drought tolerance. Recent advances in functional genomics have shown that enhanced expression of positive regulators involved in hormone biosynthesis could better equip plants against drought stress. Similarly, knocking down negative regulators of phytohormone biosynthesis can also be very effective to negate the negative effects of drought on plants. This review explained how manipulating positive and negative regulators of phytohormone signaling could be improvised to develop future crop varieties exhibiting higher drought tolerance. In addition, we also discuss the role of a promising genome editing tool, CRISPR/Cas9, on phytohormone mediated plant growth regulation for tackling drought stress.
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Affiliation(s)
- Muhammad Salman Mubarik
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Sultan Habibullah Khan
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
- Center for Advanced Studies in Agriculture and Food Security (CAS-AFS), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Sajjad
- Department of Biosciences, COMSATS University Islamabad (CUI), Islamabad, Pakistan
| | - Ali Raza
- Key Laboratory of Biology and Genetic Improvement of Oil Crops, Oil Crops Research Institute, Chinese Academy of Agricultural Sciences (CAAS), Wuhan, China
| | | | - Tahira Yasmeen
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Rizwan
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Shafaqat Ali
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
| | - Muhammad Saleem Arif
- Department of Environmental Sciences and Engineering, Government College University Faisalabad, Faisalabad, Pakistan
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26
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Einhaus A, Baier T, Rosenstengel M, Freudenberg RA, Kruse O. Rational Promoter Engineering Enables Robust Terpene Production in Microalgae. ACS Synth Biol 2021; 10:847-856. [PMID: 33764741 DOI: 10.1021/acssynbio.0c00632] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Microalgal biotechnology promises sustainable light-driven production of valuable bioproducts and addresses urgent demands to attain a sustainable economy. However, to unfold its full potential as a platform for biotechnology, new and powerful tools for nuclear engineering need to be established. Chlamydomonas reinhardtii, the model for microalgal synthetic biology and genetic engineering has already been used to produce various bioproducts. Nevertheless, low transgene titers, the lack of potent expression elements, and sparse comparative evaluation prevents further development of C. reinhardtii as a biotechnological host. By systematically evaluating existing expression elements combined with rational promoter engineering, we established novel synthetic expression elements, improved the standardized application of synthetic biology tools, and unveiled an existing synergism between the PSAD 5' UTR and its corresponding chloroplast targeting peptide. Promoter engineering strategies, implemented in a newly designed synthetic algal promoter, increased the production of the sesquiterpene (E)-α-bisabolene by 18-fold compared to its native version and 4-fold to commonly used expression elements. Our results improve the application of synthetic biology in microalgae and display a significant step toward establishing C. reinhardtii as a sustainable green cell-factory.
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Affiliation(s)
- Alexander Einhaus
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Thomas Baier
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Marian Rosenstengel
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Robert A. Freudenberg
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
| | - Olaf Kruse
- Bielefeld University, Faculty of Biology, Center for Biotechnology (CeBiTec), Universitaetsstrasse 27, 33615 Bielefeld, Germany
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27
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Zhang D, Zhang Z, Unver T, Zhang B. CRISPR/Cas: A powerful tool for gene function study and crop improvement. J Adv Res 2021; 29:207-221. [PMID: 33842017 PMCID: PMC8020163 DOI: 10.1016/j.jare.2020.10.003] [Citation(s) in RCA: 85] [Impact Index Per Article: 28.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Revised: 09/29/2020] [Accepted: 10/15/2020] [Indexed: 12/26/2022] Open
Abstract
Background It is a long-standing goal of scientists and breeders to precisely control a gene for studying its function as well as improving crop yield, quality, and tolerance to various environmental stresses. The discovery and modification of CRISPR/Cas system, a nature-occurred gene editing tool, opens an era for studying gene function and precision crop breeding. Aim of Review In this review, we first introduce the brief history of CRISPR/Cas discovery followed the mechanism and application of CRISPR/Cas system on gene function study and crop improvement. Currently, CRISPR/Cas genome editing has been becoming a mature cutting-edge biotechnological tool for crop improvement that already used in many different traits in crops, including pathogen resistance, abiotic tolerance, plant development and morphology and even secondary metabolism and fiber development. Finally, we point out the major issues associating with CRISPR/Cas system and the future research directions.Key Scientific Concepts of Review: CRISPR/Cas9 system is a robust and powerful biotechnological tool for targeting an individual DNA and RNA sequence in the genome. It can be used to target a sequence for gene knockin, knockout and replacement as well as monitoring and regulating gene expression at the genome and epigenome levels by binding a specific sequence. Agrobacterium-mediated method is still the major and efficient method for delivering CRISPR/Cas regents into targeted plant cells. However, other delivery methods, such as virus-mediated method, have been developed and enhanced the application potentials of CRISPR/Cas9-based crop improvement. PAM requirement offers the CRISPR/Cas9-targted genetic loci and also limits the application of CRISPR/Cas9. Discovering new Cas proteins and modifying current Cas enzymes play an important role in CRISPR/Cas9-based genome editing. Developing a better CRISPR/Cas9 system, including the delivery system and the methods eliminating off-target effects, and finding key/master genes for controlling crop growth and development is two major directions for CRISPR/Cas9-based crop improvement.
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Affiliation(s)
- Dangquan Zhang
- Henan Province Engineering Research Center for Forest Biomass Value-Added Products, College of Forestry, Henan Agricultural University, Zhengzhou, Henan 450002, China
| | - Zhiyong Zhang
- Henan Collaborative Innovation Center of Modern Biological Breeding and Henan Key Laboratory for Molecular Ecology and Germplasm Innovation of Cotton and Wheat, Henan Institute of Science and Technology, Xinxiang, Henan 453003, China
| | - Turgay Unver
- Ficus Biotechnology, Ostim Teknopark, No: 1/1/76, 06378, Yenimahalle, Ankara, Turkey
| | - Baohong Zhang
- Department of Biology, East Carolina University, Greenville, NC 27858, USA
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28
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Zhang S, Shen J, Li D, Cheng Y. Strategies in the delivery of Cas9 ribonucleoprotein for CRISPR/Cas9 genome editing. Theranostics 2021; 11:614-648. [PMID: 33391496 PMCID: PMC7738854 DOI: 10.7150/thno.47007] [Citation(s) in RCA: 168] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Accepted: 08/31/2020] [Indexed: 12/26/2022] Open
Abstract
CRISPR/Cas9 genome editing has gained rapidly increasing attentions in recent years, however, the translation of this biotechnology into therapy has been hindered by efficient delivery of CRISPR/Cas9 materials into target cells. Direct delivery of CRISPR/Cas9 system as a ribonucleoprotein (RNP) complex consisting of Cas9 protein and single guide RNA (sgRNA) has emerged as a powerful and widespread method for genome editing due to its advantages of transient genome editing and reduced off-target effects. In this review, we summarized the current Cas9 RNP delivery systems including physical approaches and synthetic carriers. The mechanisms and beneficial roles of these strategies in intracellular Cas9 RNP delivery were reviewed. Examples in the development of stimuli-responsive and targeted carriers for RNP delivery are highlighted. Finally, the challenges of current Cas9 RNP delivery systems and perspectives in rational design of next generation materials for this promising field will be discussed.
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Affiliation(s)
- Song Zhang
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
| | - Jiangtao Shen
- The Second People's Hospital of Taizhou affiliated to Yangzhou University, Taizhou, 225500, China
| | - Dali Li
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, Shanghai 200241, China
| | - Yiyun Cheng
- South China Advanced Institute for Soft Matter Science and Technology, School of Molecular Science and Engineering, South China University of Technology, Guangzhou 510640, China
- Shanghai Key Laboratory of Regulatory Biology, East China Normal University, Shanghai 200241, China
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29
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Song I, Kim J, Baek K, Choi Y, Shin B, Jin E. The generation of metabolic changes for the production of high-purity zeaxanthin mediated by CRISPR-Cas9 in Chlamydomonas reinhardtii. Microb Cell Fact 2020; 19:220. [PMID: 33256757 PMCID: PMC7708255 DOI: 10.1186/s12934-020-01480-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 11/20/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND Zeaxanthin, a major xanthophyll pigment, has a significant role as a retinal pigment and antioxidant. Because zeaxanthin helps to prevent age-related macular degeneration, its commercial use in personalized nutritional and pharmaceutical applications has expanded. To meet the quantitative requirements for personalized treatment and pharmaceutical applications, it is necessary to produce highly purified zeaxanthin. RESULTS In this study, to meet the quantitative requirements for industrial applications, we generated a double knockout mutant which is gene-edited by the CRISPR-Cas9 ribonucleoprotein-mediated knock-in system. The lycopene epsilon cyclase (LCYE) was edited to the elimination of α-branch of xanthophyll biosynthesis in a knockout mutant of the zeaxanthin epoxidase gene (ZEP). The double knockout mutant (dzl) had a 60% higher zeaxanthin yield (5.24 mg L- 1) and content (7.28 mg g- 1) than that of the parental line after 3 days of cultivation. Furthermore, medium optimization improved the 3-day yield of zeaxanthin from the dzl mutant to 6.84 mg L- 1. CONCLUSIONS A Chlamydomonas strain with the elimination of lutein production by gene editing using CRISPR-Cas9 has been successfully developed. This research presents a solution to overcome the difficulties of the downstream-process for the production of high-purity zeaxanthin.
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Affiliation(s)
- Inhwa Song
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Jongrae Kim
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Kwangryul Baek
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea
| | - Young Choi
- Arca Eir, C-323, Daedeok Biz Center, 17 Techno4-ro, Yuseong-gu, Daejeon, 34013, Republic of Korea
| | - ByongCheol Shin
- Arca Eir, C-323, Daedeok Biz Center, 17 Techno4-ro, Yuseong-gu, Daejeon, 34013, Republic of Korea
| | - EonSeon Jin
- Department of Life Science, Research Institute for Natural Sciences, Hanyang University, 222, Wangsimni-ro, Seongdong-gu, Seoul, 04763, Republic of Korea.
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30
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Zhang MP, Wang M, Wang C. Nuclear transformation of Chlamydomonas reinhardtii: A review. Biochimie 2020; 181:1-11. [PMID: 33227342 DOI: 10.1016/j.biochi.2020.11.016] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2020] [Revised: 06/14/2020] [Accepted: 11/17/2020] [Indexed: 10/22/2022]
Abstract
Chlamydomonas reinhardtii is a model organism with three sequenced genomes capable of genetic transformation. C. reinhardtii has the advantages of being low cost, non-toxic, and having a post-translational modification system that ensures the recombinant proteins have the same activity as natural proteins, thus making it a great platform for application in molecular biology and other fields. In this review, we summarize the existing methods for nuclear transformation of C. reinhardtii, genes for selection, examples of foreign protein expression, and factors affecting transformation efficiency, to provide insights into effective strategies for the nuclear transformation of C. reinhardtii.
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Affiliation(s)
- Meng-Ping Zhang
- College of Biotechnology, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan province, China
| | - Mou Wang
- College of Biotechnology, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan province, China
| | - Chuan Wang
- College of Biotechnology, Sichuan University of Science and Engineering, Zigong, 643000, Sichuan province, China.
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31
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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: 11] [Impact Index Per Article: 2.8] [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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32
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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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Angstenberger M, de Signori F, Vecchi V, Dall’Osto L, Bassi R. Cell Synchronization Enhances Nuclear Transformation and Genome Editing via Cas9 Enabling Homologous Recombination in Chlamydomonas reinhardtii. ACS Synth Biol 2020; 9:2840-2850. [PMID: 32916053 PMCID: PMC8011982 DOI: 10.1021/acssynbio.0c00390] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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In Chlamydomonas reinhardtii, the model organism
for eukaryotic green algae and plants, the processes of nuclear transformation
and genome editing in particular are still marked by a low level of
efficiency, and so intensive work is required in order to create and
identify mutants for the investigation of basic physiological processes,
as well as the implementation of biotechnological applications. In
this work, we show that cell synchronization during the stages of
the cell cycle, obtained from long-term cultivation under specific
growth conditions, greatly enhances the efficiency of transformation
and allows the identification of DNA repair mechanisms that occur
preferentially at different stages of the cell cycle. We demonstrate
that the transformation of synchronized cells at different times was
differentially associated with nonhomologous end joining (NHEJ) and/or
homologous recombination (HR), and makes it possible to knock-in specific
foreign DNA at the genomic nuclear location desired by exploiting
HR. This optimization greatly reduces the overall complexity of the
genome editing procedure and creates new opportunities for altering
genes and their products.
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Affiliation(s)
- Max Angstenberger
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Francesco de Signori
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Valeria Vecchi
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Luca Dall’Osto
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
| | - Roberto Bassi
- Department of Biotechnology, University of Verona, Cà Vignal 1, Strada le Grazie 15, 31734 Verona, Italy
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