1
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Yang S, Zhang Y, Li C, Tan X. Repurposing endogenous Type I-D CRISPR-Cas system for genome editing in Synechococcus sp. PCC7002. Microbiol Res 2024; 288:127884. [PMID: 39226667 DOI: 10.1016/j.micres.2024.127884] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2024] [Revised: 07/29/2024] [Accepted: 08/25/2024] [Indexed: 09/05/2024]
Abstract
Synechococcus sp. PCC7002 has been considered as a photosynthetic chassis for the conversion of CO2 into biochemicals through genetic modification. However, conventional genetic manipulation techniques prove inadequate for comprehensive genetic modifications in this strain. Here, we present the development of a genome editing tool tailored for S. PCC7002, leveraging its endogenous type I-D CRISPR-Cas system. Utilizing this novel tool, we successfully deleted the glgA1 gene and iteratively edited the genome to obtain a double mutant of glgA1 and glgA2 genes. Additionally, large DNA fragments encompassing the entire type I-A (∼14 kb) or III-B CRISPR-Cas (∼21 kb) systems were completely knocked-out in S. PCC7002 using our tool. Furthermore, the endogenous pAQ5 plasmid, approximately 38 kb in length, was successfully cured from S. PCC7002. Our work demonstrates the feasibility of harnessing the endogenous CRISPR-Cas system for genome editing in S. PCC7002, thereby enriching the genetic toolkit for this species and providing a foundation for future enhancements in its biosynthetic efficiency.
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Affiliation(s)
- Shuxiao Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yongjiu Zhang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Chunyan Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Xiaoming Tan
- State Key Laboratory of Biocatalysis and Enzyme Engineering, Environmental Microbial Technology Center of Hubei Province, and School of Life Sciences, Hubei University, Wuhan 430062, China.
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2
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Li XD, Liu LM, Xi YC, Sun QW, Luo Z, Huang HL, Wang XW, Jiang HB, Chen W. Development of a base editor for convenient and multiplex genome editing in cyanobacteria. Commun Biol 2024; 7:994. [PMID: 39143188 PMCID: PMC11324792 DOI: 10.1038/s42003-024-06696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
Cyanobacteria are important primary producers, contributing to 25% of the global carbon fixation through photosynthesis. They serve as model organisms to study the photosynthesis, and are important cell factories for synthetic biology. To enable efficient genetic dissection and metabolic engineering in cyanobacteria, effective and accurate genetic manipulation tools are required. However, genetic manipulation in cyanobacteria by the conventional homologous recombination-based method and the recently developed CRISPR-Cas gene editing system require complicated cloning steps, especially during multi-site editing and single base mutation. This restricts the extensive research on cyanobacteria and reduces its application potential. In this study, a highly efficient and convenient cytosine base editing system was developed which allows rapid and precise C → T point mutation and gene inactivation in the genomes of Synechocystis and Anabaena. This base editing system also enables efficient multiplex editing and can be easily cured after editing by sucrose counter-selection. This work will expand the knowledge base regarding the engineering of cyanobacteria. The findings of this study will encourage the biotechnological applications of cyanobacteria.
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Affiliation(s)
- Xing-Da Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling-Mei Liu
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yi-Cao Xi
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Qiao-Wei Sun
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Zhen Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Long Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xin-Wei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
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3
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Gao H, Wang Y, Huang Z, Yu F, Hu X, Ning D, Xu X. Development of Leptolyngbya sp. BL0902 into a model organism for synthetic biological research in filamentous cyanobacteria. Front Microbiol 2024; 15:1409771. [PMID: 39104590 PMCID: PMC11298460 DOI: 10.3389/fmicb.2024.1409771] [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: 04/01/2024] [Accepted: 07/10/2024] [Indexed: 08/07/2024] Open
Abstract
Cyanobacteria have great potential in CO2-based bio-manufacturing and synthetic biological studies. The filamentous cyanobacterium, Leptolyngbya sp. strain BL0902, is comparable to Arthrospira (Spirulina) platensis in commercial-scale cultivation while proving to be more genetically tractable. Here, we report the analyses of the whole genome sequence, gene inactivation/overexpression in the chromosome and deletion of non-essential chromosomal regions in this strain. The genetic manipulations were performed via homologous double recombination using either an antibiotic resistance marker or the CRISPR/Cpf1 editing system for positive selection. A desD-overexpressing strain produced γ-linolenic acid in an open raceway photobioreactor with the productivity of 0.36 g·m-2·d-1. Deletion mutants of predicted patX and hetR, two genes with opposite effects on cell differentiation in heterocyst-forming species, were used to demonstrate an analysis of the relationship between regulatory genes in the non-heterocystous species. Furthermore, a 50.8-kb chromosomal region was successfully deleted in BL0902 with the Cpf1 system. These results supported that BL0902 can be developed into a stable photosynthetic cell factory for synthesizing high value-added products, or used as a model strain for investigating the functions of genes that are unique to filamentous cyanobacteria, and could be systematically modified into a genome-streamlined chassis for synthetic biological purposes.
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Affiliation(s)
- Hong Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Yali Wang
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Ziling Huang
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Feiqi Yu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
| | - Xi Hu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Degang Ning
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
| | - Xudong Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
- School of Life Sciences, Central China Normal University, Wuhan, China
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4
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Mishra R, Kaur P, Soni R, Madan A, Agarwal P, Singh G. Decoding the photoprotection strategies and manipulating cyanobacterial photoprotective metabolites, mycosporine-like amino acids, for next-generation sunscreens. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 212:108744. [PMID: 38781638 DOI: 10.1016/j.plaphy.2024.108744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/02/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
The most recent evaluation of the impacts of UV-B radiation and depletion of stratospheric ozone points out the need for effective photoprotection strategies for both biological and nonbiological components. To mitigate the disruptive consequences of artificial sunscreens, photoprotective compounds synthesized from gram-negative, oxygenic, and photoautotrophic prokaryote, cyanobacteria have been studied. In a quest to counteract the harmful UV radiation, cyanobacterial species biosynthesize photoprotective metabolites named as mycosporine-like amino acids (MAAs). The investigation of MAAs as potential substitutes for commercial sunscreen compounds is motivated by their inherent characteristics, such as antioxidative properties, water solubility, low molecular weight, and high molar extinction coefficients. These attributes contribute to the stability of MAAs and make them promising candidates for natural alternatives in sunscreen formulations. They are effective at reducing direct damage caused by UV radiation and do not lead to the production of reactive oxygen radicals. In order to better understand the role, ecology, and its application at a commercial scale, tools like genome mining, heterologous expression, and synthetic biology have been explored in this review to develop next-generation sunscreens. Utilizing tactical concepts of bio-nanoconjugate formation for the development of an efficient MAA-nanoparticle conjugate structure would not only give the sunscreen complex stability but would also serve as a promising tool for the production of analogues. This review would provide insight on efforts to produce MAAs by diversifying the biosynthetic pathways, modulating the precursors and stress conditions, and comprehending the gene cluster arrangement for MAA biosynthesis and its application in developing effective sunscreen.
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Affiliation(s)
- Reema Mishra
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Pritam Kaur
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Renu Soni
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Akanksha Madan
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Preeti Agarwal
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
| | - Garvita Singh
- Department of Botany, Gargi College, University of Delhi, Siri Fort Road, New Delhi, 110049, India.
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5
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Bandyopadhyay A, Sengupta A, Elvitigala T, Pakrasi HB. Endogenous clock-mediated regulation of intracellular oxygen dynamics is essential for diazotrophic growth of unicellular cyanobacteria. Nat Commun 2024; 15:3712. [PMID: 38697963 PMCID: PMC11065991 DOI: 10.1038/s41467-024-48039-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/16/2024] [Indexed: 05/05/2024] Open
Abstract
The discovery of nitrogen fixation in unicellular cyanobacteria provided the first clues for the existence of a circadian clock in prokaryotes. However, recalcitrance to genetic manipulation barred their use as model systems for deciphering the clock function. Here, we explore the circadian clock in the now genetically amenable Cyanothece 51142, a unicellular, nitrogen-fixing cyanobacterium. Unlike non-diazotrophic clock models, Cyanothece 51142 exhibits conspicuous self-sustained rhythms in various discernable phenotypes, offering a platform to directly study the effects of the clock on the physiology of an organism. Deletion of kaiA, an essential clock component in the cyanobacterial system, impacted the regulation of oxygen cycling and hindered nitrogenase activity. Our findings imply a role for the KaiA component of the clock in regulating the intracellular oxygen dynamics in unicellular diazotrophic cyanobacteria and suggest that its addition to the KaiBC clock was likely an adaptive strategy that ensured optimal nitrogen fixation as microbes evolved from an anaerobic to an aerobic atmosphere under nitrogen constraints.
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Affiliation(s)
| | - Annesha Sengupta
- Department of Biology, Washington University, St. Louis, MO, USA
- Department of Chemical Engineering, University of Toronto, Toronto, ON, Canada
| | - Thanura Elvitigala
- Department of Biology, Washington University, St. Louis, MO, USA
- General Motors Research and Development, Warren, MI, 48092, USA
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6
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Li Z, Li S, Chen L, Sun T, Zhang W. Fast-growing cyanobacterial chassis for synthetic biology application. Crit Rev Biotechnol 2024; 44:414-428. [PMID: 36842999 DOI: 10.1080/07388551.2023.2166455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/19/2022] [Accepted: 12/28/2022] [Indexed: 02/28/2023]
Abstract
Carbon neutrality by 2050 has become one of the most urgent challenges the world faces today. To address the issue, it is necessary to develop and promote new technologies related with CO2 recycling. Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis, capable of fixing CO2 into biomass under sunlight and serving as one of the most important primary producers on earth. Notably, recent progress on synthetic biology has led to utilizing model cyanobacteria such as Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 as chassis for "light-driven autotrophic cell factories" to produce several dozens of biofuels and various fine chemicals directly from CO2. However, due to the slow growth rate and low biomass accumulation in the current chassis, the productivity for most products is still lower than the threshold necessary for large-scale commercial application, raising the importance of developing high-efficiency cyanobacterial chassis with fast growth and/or higher biomass accumulation capabilities. In this article, we critically reviewed recent progresses on identification, systems biology analysis, and engineering of fast-growing cyanobacterial chassis. Specifically, fast-growing cyanobacteria identified in recent years, such as S. elongatus UTEX 2973, S. elongatus PCC 11801, S. elongatus PCC 11802 and Synechococcus sp. PCC 11901 was comparatively analyzed. In addition, the progresses on their recent application in converting CO2 into chemicals, and genetic toolboxes developed for these new cyanobacterial chassis were discussed. Finally, the article provides insights into future challenges and perspectives on the synthetic biology application of cyanobacterial chassis.
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Affiliation(s)
- Zhixiang Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
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7
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Grosjean N, Yee EF, Kumaran D, Chopra K, Abernathy M, Biswas S, Byrnes J, Kreitler DF, Cheng JF, Ghosh A, Almo SC, Iwai M, Niyogi KK, Pakrasi HB, Sarangi R, van Dam H, Yang L, Blaby IK, Blaby-Haas CE. A hemoprotein with a zinc-mirror heme site ties heme availability to carbon metabolism in cyanobacteria. Nat Commun 2024; 15:3167. [PMID: 38609367 PMCID: PMC11014987 DOI: 10.1038/s41467-024-47486-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Accepted: 04/02/2024] [Indexed: 04/14/2024] Open
Abstract
Heme has a critical role in the chemical framework of the cell as an essential protein cofactor and signaling molecule that controls diverse processes and molecular interactions. Using a phylogenomics-based approach and complementary structural techniques, we identify a family of dimeric hemoproteins comprising a domain of unknown function DUF2470. The heme iron is axially coordinated by two zinc-bound histidine residues, forming a distinct two-fold symmetric zinc-histidine-iron-histidine-zinc site. Together with structure-guided in vitro and in vivo experiments, we further demonstrate the existence of a functional link between heme binding by Dri1 (Domain related to iron 1, formerly ssr1698) and post-translational regulation of succinate dehydrogenase in the cyanobacterium Synechocystis, suggesting an iron-dependent regulatory link between photosynthesis and respiration. Given the ubiquity of proteins containing homologous domains and connections to heme metabolism across eukaryotes and prokaryotes, we propose that DRI (Domain Related to Iron; formerly DUF2470) functions at the molecular level as a heme-dependent regulatory domain.
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Affiliation(s)
- Nicolas Grosjean
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Estella F Yee
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Desigan Kumaran
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Kriti Chopra
- Computational Science Initiative, Brookhaven National Laboratory, Upton, NY, USA
| | - Macon Abernathy
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO, USA
| | - James Byrnes
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Dale F Kreitler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Jan-Fang Cheng
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Agnidipta Ghosh
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Steven C Almo
- Department of Biochemistry, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Masakazu Iwai
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Krishna K Niyogi
- Department of Plant and Microbial Biology, University of California, Berkeley, CA, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Howard Hughes Medical Institute, University of California, Berkeley, CA, USA
| | | | - Ritimukta Sarangi
- Stanford Synchrotron Radiation Lightsource, SLAC National Accelerator Laboratory, Menlo Park, CA, USA
| | - Hubertus van Dam
- Condensed Matter Physics and Materials Science Department, Brookhaven National Laboratory, Upton, NY, USA
| | - Lin Yang
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, NY, USA
| | - Ian K Blaby
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Crysten E Blaby-Haas
- Biology Department, Brookhaven National Laboratory, Upton, NY, USA.
- US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
- The Molecular Foundry, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
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8
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Webster LJ, Villa-Gomez D, Brown R, Clarke W, Schenk PM. A synthetic biology approach for the treatment of pollutants with microalgae. Front Bioeng Biotechnol 2024; 12:1379301. [PMID: 38646010 PMCID: PMC11032018 DOI: 10.3389/fbioe.2024.1379301] [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: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.
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Affiliation(s)
- Luke J. Webster
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Denys Villa-Gomez
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben Brown
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - William Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
- Algae Biotechnology, Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD, Australia
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9
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Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
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Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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10
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Sengupta A, Bandyopadhyay A, Sarkar D, Hendry JI, Schubert MG, Liu D, Church GM, Maranas CD, Pakrasi HB. Genome streamlining to improve performance of a fast-growing cyanobacterium Synechococcus elongatus UTEX 2973. mBio 2024; 15:e0353023. [PMID: 38358263 PMCID: PMC10936165 DOI: 10.1128/mbio.03530-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2024] [Accepted: 01/22/2024] [Indexed: 02/16/2024] Open
Abstract
Cyanobacteria are photosynthetic organisms that have garnered significant recognition as potential hosts for sustainable bioproduction. However, their complex regulatory networks pose significant challenges to major metabolic engineering efforts, thereby limiting their feasibility as production hosts. Genome streamlining has been demonstrated to be a successful approach for improving productivity and fitness in heterotrophs but is yet to be explored to its full potential in phototrophs. Here, we present the systematic reduction of the genome of the cyanobacterium exhibiting the fastest exponential growth, Synechococcus elongatus UTEX 2973. This work, the first of its kind in a photoautotroph, involved an iterative process using state-of-the-art genome-editing technology guided by experimental analysis and computational tools. CRISPR-Cas3 enabled large, progressive deletions of predicted dispensable regions and aided in the identification of essential genes. The large deletions were combined to obtain a strain with 55-kb genome reduction. The strains with streamlined genome showed improvement in growth (up to 23%) and productivity (by 22.7%) as compared to the wild type (WT). This streamlining strategy not only has the potential to develop cyanobacterial strains with improved growth and productivity traits but can also facilitate a better understanding of their genome-to-phenome relationships.IMPORTANCEGenome streamlining is an evolutionary strategy used by natural living systems to dispense unnecessary genes from their genome as a mechanism to adapt and evolve. While this strategy has been successfully borrowed to develop synthetic heterotrophic microbial systems with desired phenotype, it has not been extensively explored in photoautotrophs. Genome streamlining strategy incorporates both computational predictions to identify the dispensable regions and experimental validation using genome-editing tool, and in this study, we have employed a modified strategy with the goal to minimize the genome size to an extent that allows optimal cellular fitness under specified conditions. Our strategy has explored a novel genome-editing tool in photoautotrophs, which, unlike other existing tools, enables large, spontaneous optimal deletions from the genome. Our findings demonstrate the effectiveness of this modified strategy in obtaining strains with streamlined genome, exhibiting improved fitness and productivity.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Debolina Sarkar
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - John I. Hendry
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
| | - Max G. Schubert
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
| | - Deng Liu
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | - George M. Church
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, Massachusetts, USA
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
| | - Costas D. Maranas
- Department of Chemical Engineering, Pennsylvania State University, State College, Pennsylvania, USA
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11
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Tang Y, Qin D, Tian Z, Chen W, Ma Y, Wang J, Yang J, Yan D, Dixon R, Wang YP. Diurnal switches in diazotrophic lifestyle increase nitrogen contribution to cereals. Nat Commun 2023; 14:7516. [PMID: 37980355 PMCID: PMC10657418 DOI: 10.1038/s41467-023-43370-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2022] [Accepted: 11/07/2023] [Indexed: 11/20/2023] Open
Abstract
Uncoupling of biological nitrogen fixation from ammonia assimilation is a prerequisite step for engineering ammonia excretion and improvement of plant-associative nitrogen fixation. In this study, we have identified an amino acid substitution in glutamine synthetase, which provides temperature sensitive biosynthesis of glutamine, the intracellular metabolic signal of the nitrogen status. As a consequence, negative feedback regulation of genes and enzymes subject to nitrogen regulation, including nitrogenase is thermally controlled, enabling ammonia excretion in engineered Escherichia coli and the plant-associated diazotroph Klebsiella oxytoca at 23 °C, but not at 30 °C. We demonstrate that this temperature profile can be exploited to provide diurnal oscillation of ammonia excretion when variant bacteria are used to inoculate cereal crops. We provide evidence that diurnal temperature variation improves nitrogen donation to the plant because the inoculant bacteria have the ability to recover and proliferate at higher temperatures during the daytime.
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Affiliation(s)
- Yuqian Tang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Debin Qin
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Zhexian Tian
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Wenxi Chen
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Yuanxi Ma
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jilong Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Jianguo Yang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China
| | - Dalai Yan
- Department of Microbiology and Immunology, Indiana University School of Medicine, Indianapolis, IN, 46202, USA
| | - Ray Dixon
- Department of Molecular Microbiology, John Innes Centre, Norwich, NR4 7UH, UK.
| | - Yi-Ping Wang
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences & School of Advanced Agricultural Sciences, Peking University, Beijing, 100871, China.
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12
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Capovilla G, Castro KG, Collani S, Kearney SM, Kehoe DM, Chisholm SW. Chitin degradation by Synechococcus WH7803. Sci Rep 2023; 13:19944. [PMID: 37968300 PMCID: PMC10651935 DOI: 10.1038/s41598-023-47332-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/12/2023] [Indexed: 11/17/2023] Open
Abstract
Chitin is an abundant, carbon-rich polymer in the marine environment. Chitinase activity has been detected in spent media of Synechococcus WH7803 cultures-yet it was unclear which specific enzymes were involved. Here we delivered a CRISPR tool into the cells via electroporation to generate loss-of-function mutants of putative candidates and identified ChiA as the enzyme required for the activity detected in the wild type.
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Affiliation(s)
- Giovanna Capovilla
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Kurt G Castro
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Silvio Collani
- Department of Fysiologisk Botanik, Umeå Plant Science Centre (UPSC), Umeå University, Umeå, Sweden
| | - Sean M Kearney
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - David M Kehoe
- Department of Biology, Indiana University, Bloomington, IN, USA
| | - Sallie W Chisholm
- Department of Civil and Environmental Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
- Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
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13
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Taton A, Gilderman TS, Ernst DC, Omaga CA, Cohen LA, Rey-Bedon C, Golden JW, Golden SS. Synechococcus elongatus Argonaute reduces natural transformation efficiency and provides immunity against exogenous plasmids. mBio 2023; 14:e0184323. [PMID: 37791787 PMCID: PMC10653904 DOI: 10.1128/mbio.01843-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Accepted: 08/11/2023] [Indexed: 10/05/2023] Open
Abstract
IMPORTANCE S. elongatus is an important cyanobacterial model organism for the study of its prokaryotic circadian clock, photosynthesis, and other biological processes. It is also widely used for genetic engineering to produce renewable biochemicals. Our findings reveal an SeAgo-based defense mechanism in S. elongatus against the horizontal transfer of genetic material. We demonstrate that deletion of the ago gene facilitates genetic studies and genetic engineering of S. elongatus.
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Affiliation(s)
- Arnaud Taton
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Tami S. Gilderman
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Dustin C. Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Carla A. Omaga
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
| | - Lucas A. Cohen
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Camilo Rey-Bedon
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - James W. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
| | - Susan S. Golden
- School of Biological Sciences, University of California, San Diego, La Jolla, California, USA
- Center for Circadian Biology, University of California, San Diego, La Jolla, California, USA
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14
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Feng Q, Ning X, Qin L, Li J, Li C. Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae. Front Bioeng Biotechnol 2023; 11:1218832. [PMID: 38026848 PMCID: PMC10666755 DOI: 10.3389/fbioe.2023.1218832] [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: 05/08/2023] [Accepted: 10/05/2023] [Indexed: 12/01/2023] Open
Abstract
Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs. Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP64-p65-Rta) and inhibiting effector proteins (KRAB, MeCP2, and KRAB-MeCP2), along with RNA scaffolds of MS2, PP7 and crRNA arrays were implemented in different combinations to investigate quantitative promoter strength. In the CRISPR/dCas9 system, the regulation rate ranged from 81.9% suppression to 627% activation in the mCherry gene reporter system. Studies on crRNA point mutations and crRNA arrays were conducted in the CRISPR/dCpf1 system, with the highest transcriptional inhibitory rate reaching up to 530% higher than the control. Furthermore, the orthogonal CRISPR/dCas9-dCpf1 inhibition system displayed distinct dual functions, simultaneously regulating the mCherry gene by dCas9/gRNA (54.6% efficiency) and eGFP gene by dCpf1/crRNA (62.4% efficiency) without signal crosstalk. Results and discussion: Finally, we established an engineered yeast cell factory for β-carotene production using the CRISPR/dCas9-dCpf1 bifunctional system to achieve targeted modulation of both heterologous and endogenous metabolic pathways in Saccharomyces cerevisiae. The system includes an activation module of CRISPRa/dCas9 corresponding to a gRNA-protein complex library of 136 plasmids, and an inhibition module of CRISPRi/dCpf1 corresponding to a small crRNA array library. Results show that this CRISPR/dCas9-dCpf1 bifunctional orthogonal system is more quantitatively effective and expandable for simultaneous CRISPRa/i network control compared to single-guide edition, demonstrating higher potential of future application in yeast biotechnology.
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Affiliation(s)
- Qing Feng
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Xiaoyu Ning
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Lei Qin
- Key Lab for Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
| | - Jun Li
- Key Laboratory of Medical Molecule Science and Pharmaceutics Engineering, School of Chemistry and Chemical Engineering, Ministry of Industry and Information Technology, Beijing Institute of Technology, Beijing, China
| | - Chun Li
- Key Lab for Industrial Biocatalysis, Department of Chemical Engineering, Ministry of Education, Tsinghua University, Beijing, China
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15
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Gonzales JN, Treece TR, Mayfield SP, Simkovsky R, Atsumi S. Utilization of lignocellulosic hydrolysates for photomixotrophic chemical production in Synechococcus elongatus PCC 7942. Commun Biol 2023; 6:1022. [PMID: 37813969 PMCID: PMC10562401 DOI: 10.1038/s42003-023-05394-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 09/27/2023] [Indexed: 10/11/2023] Open
Abstract
To meet the need for environmentally friendly commodity chemicals, feedstocks for biological chemical production must be diversified. Lignocellulosic biomass are an carbon source with the potential for effective use in a large scale and cost-effective production systems. Although the use of lignocellulosic biomass lysates for heterotrophic chemical production has been advancing, there are challenges to overcome. Here we aim to investigate the obligate photoautotroph cyanobacterium Synechococcus elongatus PCC 7942 as a chassis organism for lignocellulosic chemical production. When modified to import monosaccharides, this cyanobacterium is an excellent candidate for lysates-based chemical production as it grows well at high lysate concentrations and can fix CO2 to enhance carbon efficiency. This study is an important step forward in enabling the simultaneous use of two sugars as well as lignocellulosic lysate. Incremental genetic modifications enable catabolism of both sugars concurrently without experiencing carbon catabolite repression. Production of 2,3-butanediol is demonstrated to characterize chemical production from the sugars in lignocellulosic hydrolysates. The engineered strain achieves a titer of 13.5 g L-1 of 2,3-butanediol over 12 days under shake-flask conditions. This study can be used as a foundation for industrial scale production of commodity chemicals from a combination of sunlight, CO2, and lignocellulosic sugars.
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Affiliation(s)
- Jake N Gonzales
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA
| | - Tanner R Treece
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA
| | - Stephen P Mayfield
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Ryan Simkovsky
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA, 92093, USA
- California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, 92093, USA
| | - Shota Atsumi
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, 95616, USA.
- Department of Chemistry, University of California, Davis, Davis, CA, 95616, USA.
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16
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Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB. Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr 2023; 11:e0050023. [PMID: 37318337 PMCID: PMC10433846 DOI: 10.1128/spectrum.00500-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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17
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Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2023; 12:1823-1835. [PMID: 37246820 PMCID: PMC10278186 DOI: 10.1021/acssynbio.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 05/30/2023]
Abstract
In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters PJ23100, PrhaBAD, and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD, and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly.
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Affiliation(s)
- Maurice Mager
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Hugo Pineda Hernandez
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Fabian Brandenburg
- Helmholtz
Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Luis López-Maury
- Instituto
de Bioquímica Vegetal y Fotosíntesis, University of Seville − CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento
de Bioquímica Vegetal y Biología Molecular, Facultad
de Biología, University of Seville, Avenida Reina Mercedes, 41012 Sevilla, Spain
| | - Alistair J. McCormick
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Dennis J. Nürnberg
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
- Dahlem
Centre of Plant Sciences, Freie Universität
Berlin, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
| | - Tim Orthwein
- Interfaculty
Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - David A. Russo
- Institute
for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena, Germany
| | - Angelo Joshua Victoria
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Xiaoran Wang
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
| | - Julie A. Z. Zedler
- Matthias
Schleiden Institute for Genetics, Bioinformatics and Molecular Botany,
Synthetic Biology of Photosynthetic Organisms, Friedrich Schiller University Jena, Dornburgerstrasse 159, 07743 Jena, Germany
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Nicolas M. Schmelling
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
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18
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Wang ZQ, Yang Y, Zhang JY, Zeng X, Zhang CC. Global translational control by the transcriptional repressor TrcR in the filamentous cyanobacterium Anabaena sp. PCC 7120. Commun Biol 2023; 6:643. [PMID: 37322092 PMCID: PMC10272220 DOI: 10.1038/s42003-023-05012-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 06/02/2023] [Indexed: 06/17/2023] Open
Abstract
Transcriptional and translational regulations are important mechanisms for cell adaptation to environmental conditions. In addition to house-keeping tRNAs, the genome of the filamentous cyanobacterium Anabaena sp. strain PCC 7120 (Anabaena) has a long tRNA operon (trn operon) consisting of 26 genes present on a megaplasmid. The trn operon is repressed under standard culture conditions, but is activated under translational stress in the presence of antibiotics targeting translation. Using the toxic amino acid analog β-N-methylamino-L-alanine (BMAA) as a tool, we isolated and characterized several BMAA-resistance mutants from Anabaena, and identified one gene of unknown function, all0854, named as trcR, encoding a transcription factor belonging to the ribbon-helix-helix (RHH) family. We provide evidence that TrcR represses the expression of the trn operon and is thus the missing link between the trn operon and translational stress response. TrcR represses the expression of several other genes involved in translational control, and is required for maintaining translational fidelity. TrcR, as well as its binding sites, are highly conserved in cyanobacteria, and its functions represent an important mechanism for the coupling of the transcriptional and translational regulations in cyanobacteria.
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Affiliation(s)
- Zi-Qian Wang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- University of Chinese Academy of Sciences, Beijing, 100049, People's Republic of China.
- State Key Laboratory of Microbial Resources, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China.
| | - Yiling Yang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Ju-Yuan Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Xiaoli Zeng
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China
| | - Cheng-Cai Zhang
- State Key Laboratory of Freshwater Ecology and Biotechnology and Key Laboratory of Algal Biology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, Hubei, 430072, People's Republic of China.
- Institute AMU-WUT, Aix-Marseille Université and Wuhan University of Technology, Wuhan, Hubei, People's Republic of China.
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19
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Hou F, Ke Z, Xu Y, Wang Y, Zhu G, Gao H, Ji S, Xu X. Systematic Large Fragment Deletions in the Genome of Synechococcus elongatus and the Consequent Changes in Transcriptomic Profiles. Genes (Basel) 2023; 14:genes14051091. [PMID: 37239451 DOI: 10.3390/genes14051091] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Revised: 05/12/2023] [Accepted: 05/12/2023] [Indexed: 05/28/2023] Open
Abstract
Genome streamlining, as a natural process in the evolution of microbes, has become a common approach for generating ideal chassis cells for synthetic biology studies and industrial applications. However, systematic genome reduction remains a bottleneck in the generation of such chassis cells with cyanobacteria, due to very time-consuming genetic manipulations. Synechococcus elongatus PCC 7942, a unicellular cyanobacterium, is a candidate for systematic genome reduction, as its essential and nonessential genes have been experimentally identified. Here, we report that at least 20 of the 23 over 10 kb nonessential gene regions could be deleted and that stepwise deletions of these regions could be achieved. A septuple-deletion mutant (genome reduced by 3.8%) was generated, and the effects of genome reduction on the growth and genome-wide transcription were investigated. In the ancestral triple to sextuple mutants (b, c, d, e1), an increasingly large number of genes (up to 998) were upregulated relative to the wild type, while slightly fewer genes (831) were upregulated in the septuple mutant (f). In a different sextuple mutant (e2) derived from the quintuple mutant d, much fewer genes (232) were upregulated. Under the standard conditions in this study, the mutant e2 showed a higher growth rate than the wild type, e1 and f. Our results indicate that it is feasible to extensively reduce the genomes of cyanobacteria for generation of chassis cells and for experimental evolutionary studies.
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Affiliation(s)
- Feifei Hou
- College of Fisheries and Life Science, Dalian Ocean University, Dalian 116000, China
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Zhufang Ke
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yi Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Yali Wang
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Geqian Zhu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Hong Gao
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
| | - Shuiling Ji
- Hubei Key Laboratory of Genetic Regulation and Integrative Biology, School of Life Sciences, Central China Normal University, Wuhan 430079, China
| | - Xudong Xu
- Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan 430072, China
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20
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Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC. Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio 2023; 19:100583. [PMID: 36846306 PMCID: PMC9945787 DOI: 10.1016/j.mtbio.2023.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.
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Affiliation(s)
- Isabella M. Goodchild-Michelman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
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21
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Barone GD, Cernava T, Ullmann J, Liu J, Lio E, Germann AT, Nakielski A, Russo DA, Chavkin T, Knufmann K, Tripodi F, Coccetti P, Secundo F, Fu P, Pfleger B, Axmann IM, Lindblad P. Recent developments in the production and utilization of photosynthetic microorganisms for food applications. Heliyon 2023; 9:e14708. [PMID: 37151658 PMCID: PMC10161259 DOI: 10.1016/j.heliyon.2023.e14708] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/08/2023] [Accepted: 03/15/2023] [Indexed: 05/09/2023] Open
Abstract
The growing use of photosynthetic microorganisms for food and food-related applications is driving related biotechnology research forward. Increasing consumer acceptance, high sustainability, demand of eco-friendly sources for food, and considerable global economic concern are among the main factors to enhance the focus on the novel foods. In the cases of not toxic strains, photosynthetic microorganisms not only provide a source of sustainable nutrients but are also potentially healthy. Several published studies showed that microalgae are sources of accessible protein and fatty acids. More than 400 manuscripts were published per year in the last 4 years. Furthermore, industrial approaches utilizing these microorganisms are resulting in new jobs and services. This is in line with the global strategy for bioeconomy that aims to support sustainable development of bio-based sectors. Despite the recognized potential of the microalgal biomass value chain, significant knowledge gaps still exist especially regarding their optimized production and utilization. This review highlights the potential of microalgae and cyanobacteria for food and food-related applications as well as their market size. The chosen topics also include advanced production as mixed microbial communities, production of high-value biomolecules, photoproduction of terpenoid flavoring compounds, their utilization for sustainable agriculture, application as source of nutrients in space, and a comparison with heterotrophic microorganisms like yeast to better evaluate their advantages over existing nutrient sources. This comprehensive assessment should stimulate further interest in this highly relevant research topic.
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Affiliation(s)
- Giovanni D. Barone
- Institute of Molecular Biotechnology, Graz University of Technology, Petersgasse 14, 8010, Graz, Austria
- Corresponding author.
| | - Tomislav Cernava
- Institute of Environmental Biotechnology, Graz University of Technology, Petersgasse 12/I, 8010, Graz, Austria
| | - Jörg Ullmann
- Roquette Klötze GmbH & Co. KG, Lockstedter Chaussee 1, D-38486, Klötze, Germany
| | - Jing Liu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Elia Lio
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Anna T. Germann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - Andreas Nakielski
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
| | - David A. Russo
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Lessingstr. 8, D-07743, Jena, Germany
| | - Ted Chavkin
- Department of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI, USA
| | | | - Farida Tripodi
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Paola Coccetti
- Department of Biotechnology and Biosciences, University of Milano-Bicocca, 20126, Milano, Italy
| | - Francesco Secundo
- Institute of Chemical Sciences and Technologies (SCITEC) “Giulio Natta” Italian National Research Council (CNR), via Mario Bianco 9, 20131, Milan, Italy
| | - Pengcheng Fu
- State Key Laboratory of Marine Resource Utilization in South China Sea Hainan University, 58 Renmin Avenue, Meilan District, Haikou, Hainan Province, 570228, PR China
| | - Brian Pfleger
- Knufmann GmbH, Bergstraße 23, D-38486, Klötze, Germany
| | - Ilka M. Axmann
- Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany
- Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University Düsseldorf, D-40001, Düsseldorf, Germany
- Corresponding author. Synthetic Microbiology, Department of Biology, Heinrich Heine University Düsseldorf, 40225, Düsseldorf, Germany.
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry–Ångström, Uppsala University, Box 523, SE-75120, Uppsala, Sweden
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22
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Yang Y, Wang D, Lü P, Ma S, Chen K. Research progress on nucleic acid detection and genome editing of CRISPR/Cas12 system. Mol Biol Rep 2023; 50:3723-3738. [PMID: 36648696 PMCID: PMC9843688 DOI: 10.1007/s11033-023-08240-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 01/03/2023] [Indexed: 01/18/2023]
Abstract
PURPOSE This work characterizes the applications of CRISPR/Cas12 system, including nucleic acid detection, animal, plant and microbial genome editing. METHODS The literature on CRISPR/Cas12 system was collected and reviewed. RESULTS CRISPR/Cas system is an acquired immune system derived from bacteria and archaea, which has become the most popular technology around the world because of its outstanding contribution in genome editing. Type V CRISPR/Cas systems are distinguished by a single RNA-guided RuvC nuclease domain with single effector molecule. Cas12a, the first reported type V CRISPR/Cas system, targets double-stranded DNA (dsDNA) adjacent to PAM sequences and trans-cleaves single-stranded DNA (ssDNA). We present the applications of CRISPR/Cas12 system for nucleic acid detection and genome editing in animals, plants and microorganisms. Furthermore, this review also summarizes the applications of other Cas12 proteins, such as Cas12b, Cas12c, Cas12d, and so on, which further widen the application prospects of CRISPR/Cas12 system. CONCLUSIONS Knowledge of the applications of CRISPR/Cas12 system is necessary for improving the understanding of the functional diversity of CRISPR/Cas12 system and also provides significant references for further research and utilization of CRISPR/Cas12 in other new fields.
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Affiliation(s)
- Yanhua Yang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China.
| | - Dandan Wang
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Peng Lü
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Shangshang Ma
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
| | - Keping Chen
- School of Life Sciences, Jiangsu University, 301 Xuefu Road, Zhenjiang, 212013, Jiangsu Province, People's Republic of China
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23
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Dallo T, Krishnakumar R, Kolker SD, Ruffing AM. High-Density Guide RNA Tiling and Machine Learning for Designing CRISPR Interference in Synechococcus sp. PCC 7002. ACS Synth Biol 2023; 12:1175-1186. [PMID: 36893454 DOI: 10.1021/acssynbio.2c00653] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/11/2023]
Abstract
While CRISPRi was previously established in Synechococcus sp. PCC 7002 (hereafter 7002), the design principles for guide RNA (gRNA) effectiveness remain largely unknown. Here, 76 strains of 7002 were constructed with gRNAs targeting three reporter systems to evaluate features that impact gRNA efficiency. Correlation analysis of the data revealed that important features of gRNA design include the position relative to the start codon, GC content, protospacer adjacent motif (PAM) site, minimum free energy, and targeted DNA strand. Unexpectedly, some gRNAs targeting upstream of the promoter region showed small but significant increases in reporter expression, and gRNAs targeting the terminator region showed greater repression than gRNAs targeting the 3' end of the coding sequence. Machine learning algorithms enabled prediction of gRNA effectiveness, with Random Forest having the best performance across all training sets. This study demonstrates that high-density gRNA data and machine learning can improve gRNA design for tuning gene expression in 7002.
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Affiliation(s)
- Tessa Dallo
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, P.O. Box 969, MS 9292, Livermore, California 94551, United States
| | - Stephanie D Kolker
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
| | - Anne M Ruffing
- Molecular and Microbiology, Sandia National Laboratories, P.O. Box 5800, MS 1413, Albuquerque, New Mexico 87185, United States
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24
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An update on CRISPR-Cas12 as a versatile tool in genome editing. Mol Biol Rep 2023; 50:2865-2881. [PMID: 36641494 DOI: 10.1007/s11033-023-08239-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 01/03/2023] [Indexed: 01/16/2023]
Abstract
Gene editing techniques, which help in modification of any DNA sequence at ease, have revolutionized the world of Genetic engineering. Although there are other gene-editing techniques, CRISPR has emerged as the chief and most preferred tool due to its simplicity and capacity to execute effective gene editing in a wide range of organisms. Although Cas9 has widely been employed for genetic modification over the years, Cas12 systems have lately emerged as a viable option. This review primarily focuses on assessing Cas12-mediated mutagenesis and elucidating the editing efficacy of both Cpf1 (Cas12a) and C2c1 (Cas12b) systems in microbes, plants, and other species. Also, we reviewed several genetic alterations that have been performed with these Cas12 systems to improve editing efficiency. Furthermore, the experimental benefits and applications of Cas12 systems are highlighted in this study.
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25
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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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26
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [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: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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27
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Lee M, Heo YB, Woo HM. Cytosine base editing in cyanobacteria by repressing archaic Type IV uracil-DNA glycosylase. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2023; 113:610-625. [PMID: 36565011 DOI: 10.1111/tpj.16074] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 12/19/2022] [Indexed: 06/17/2023]
Abstract
Base editing enables precise gene editing without requiring donor DNA or double-stranded breaks. To facilitate base editing tools, a uracil DNA glycosylase inhibitor (UGI) was fused to cytidine deaminase-Cas nickase to inhibit uracil DNA glycosylase (UDG). Herein, we revealed that the bacteriophage PBS2-derived UGI of the cytosine base editor (CBE) could not inhibit archaic Type IV UDG in oligoploid cyanobacteria. To overcome the limitation of the CBE, dCas12a-assisted gene repression of the udg allowed base editing at the desired targets with up to 100% mutation frequencies, and yielded correct phenotypes of desired mutants in cyanobacteria. Compared with the original CBE (BE3), base editing was analyzed within a broader C4-C16 window with a strong TC-motif preference. Using multiplexed CyanoCBE, while udg was repressed, simultaneous base editing at two different sites was achieved with lower mutation frequencies than single CBE. Our discovery of a Type IV UDG that is not inhibited by the UGI of the CBE in cyanobacteria and the development of dCas12a-mediated base editing should facilitate the application of base editing not only in cyanobacteria, but also in archaea and green algae that possess Type IV UDGs. We revealed the bacteriophage-derived UGI of the base editor did not repress Type IV UDG in cyanobacteria. To overcome the limitation, orthogonal dCas12a interference was successfully applied to repress the UDG gene expression in cyanobacteria during base editing occurred, yielding a premature translational termination at desired targets. This study will open a new opportunity to perform base editing with Type IV UDGs in archaea and green algae.
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Affiliation(s)
- Mieun Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
- BioFoundry Research Center, Institute of Biotechnology and Bioengineering, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon, 16419, Republic of Korea
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28
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Lee TM, Lin JY, Tsai TH, Yang RY, Ng IS. Clustered regularly interspaced short palindromic repeats (CRISPR) technology and genetic engineering strategies for microalgae towards carbon neutrality: A critical review. BIORESOURCE TECHNOLOGY 2023; 368:128350. [PMID: 36414139 DOI: 10.1016/j.biortech.2022.128350] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 11/14/2022] [Accepted: 11/15/2022] [Indexed: 06/16/2023]
Abstract
Carbon dioxide is the major greenhouse gas and regards as the critical issue of global warming and climate changes. The inconspicuous microalgae are responsible for 40% of carbon fixation among all photosynthetic plants along with a higher photosynthetic efficiency and convert the carbon into lipids, protein, pigments, and bioactive compounds. Genetic approach and metabolic engineering are applied to accelerate the growth rate and biomass of microalgae, hence achieve the mission of carbon neutrality. Meanwhile, CRISPR/Cas9 is efficiently to enhance the productivity of high-value compounds in microalgae for it is easier operation, more affordable and is able to regulate multiple genes simultaneously. The genetic engineering strategies provide the multidisciplinary concept to evolute and increase the CO2 fixation rate through Calvin-Benson-Bassham cycle. Therefore, the technologies, bioinformatics tools, systematic engineering approaches for carbon neutrality and circular economy are summarized and leading one step closer to the decarbonization society in this review.
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Affiliation(s)
- Tse-Min Lee
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - Jia-Yi Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Tsung-Han Tsai
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan
| | - Ru-Yin Yang
- Department of Marine Biotechnology and Resources, National Sun Yat-sen University, Kaohsiung 80424, Taiwan
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 70101, Taiwan.
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29
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Ajeng AA, Rosli NSM, Abdullah R, Yaacob JS, Qi NC, Loke SP. Resource recovery from hydroponic wastewaters using microalgae-based biorefineries: A circular bioeconomy perspective. J Biotechnol 2022; 360:11-22. [PMID: 36272573 DOI: 10.1016/j.jbiotec.2022.10.011] [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: 05/13/2022] [Revised: 10/09/2022] [Accepted: 10/17/2022] [Indexed: 11/07/2022]
Abstract
As the world's population grows, it is necessary to rethink how countries throughout the world produce food in order to replace the conventional and unsustainable agricultural techniques. Microalgae cultivation using a nutrient-rich solution from hydroponic systems not only presents a novel approach to solving problems pertaining to the impact of the discharges on the natural environment but also provides a plethora of other biotechnological applications particularly in the productions of high value-added products and plants growth stimulants, which can be potentially assimilated into the circular bioeconomy (CBE) in the hydroponic sector. In this review, the potential and practicability of microalgae to be merged into hydroponics CBE are reviewed. Overall, the integration of microalgal biorefineries in hydroponics systems can be realized after considering their Technology Readiness Level and System Readiness Level beforehand. Several suggestions on strains and hydroponics system improvement using existing biotechnological tools, Artificial Intelligence (AI) and nanobiotechnology in support of the CBE will be covered.
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Affiliation(s)
- Aaronn Avit Ajeng
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Noor Sharina Mohd Rosli
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Rosazlin Abdullah
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Jamilah Syafawati Yaacob
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia; Centre for Research in Biotechnology for Agriculture (CEBAR), Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Ng Cai Qi
- Institute of Biological Sciences, Faculty of Science, Universiti Malaya, 50603 Kuala Lumpur, Malaysia.
| | - Show Pau Loke
- Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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30
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Ma Z, Cheah WY, Ng IS, Chang JS, Zhao M, Show PL. Microalgae-based biotechnological sequestration of carbon dioxide for net zero emissions. Trends Biotechnol 2022; 40:1439-1453. [PMID: 36216714 DOI: 10.1016/j.tibtech.2022.09.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Revised: 08/26/2022] [Accepted: 09/06/2022] [Indexed: 11/05/2022]
Abstract
Excessive carbon dioxide (CO2) emissions into the atmosphere have become a dire threat to the human race and environmental sustainability. The ultimate goal of net zero emissions requires combined efforts on CO2 sequestration (natural sinks, biomass fixation, engineered approaches) and reduction in CO2 emissions while delivering economic growth (CO2 valorization for a circular carbon bioeconomy, CCE). We discuss microalgae-based CO2 biosequestration, including flue gas cultivation, biotechnological approaches for enhanced CO2 biosequestration, technological innovations for microalgal cultivation, and CO2 valorization/biofuel productions. We highlight challenges to current practices and future perspectives with the goal of contributing to environmental sustainability, net zero emissions, and the CCE.
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Affiliation(s)
- Zengling Ma
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China
| | - Wai Yan Cheah
- Centre of Research in Development, Social and Environment (SEEDS), Faculty of Social Sciences and Humanities, Universiti Kebangsaan Malaysia, 43600 UKM Bangi, Selangor Darul Ehsan, Malaysia
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan
| | - Jo-Shu Chang
- Department of Chemical Engineering, National Cheng Kung University, Tainan 701, Taiwan; Department of Chemical and Materials Engineering, Tunghai University, Taichung 407, Taiwan; Research Center for Smart Sustainable Circular Economy, Tunghai University, Taichung 407, Taiwan.
| | - Min Zhao
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China.
| | - Pau Loke Show
- Zhejiang Provincial Key Laboratory for Subtropical Water Environment and Marine Biological Resources Protection, Wenzhou University, Wenzhou 325035, China; Department of Sustainable Engineering, Saveetha School of Engineering, SIMATS, Chennai 602105, India; Department of Chemical and Environmental Engineering, Faculty of Science and Engineering, University of Nottingham Malaysia, Jalan Broga, 43500 Semenyih, Selangor Darul Ehsan, Malaysia.
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31
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Kumar N, Kar S, Shukla P. Role of regulatory pathways and multi-omics approaches for carbon capture and mitigation in cyanobacteria. BIORESOURCE TECHNOLOGY 2022; 366:128104. [PMID: 36257524 DOI: 10.1016/j.biortech.2022.128104] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/05/2022] [Accepted: 10/07/2022] [Indexed: 06/16/2023]
Abstract
Cyanobacteria are known for their metabolic potential and carbon capture and sequestration capabilities. These cyanobacteria are not only an effective source for carbon minimization and resource mobilization into value-added products for biotechnological gains. The present review focuses on the detailed description of carbon capture mechanisms exerted by the various cyanobacterial strains, the role of important regulatory pathways, and their subsequent genes responsible for such mechanisms. Moreover, this review will also describe effectual mechanisms of central carbon metabolism like isoprene synthesis, ethylene production, MEP pathway, and the role of Glyoxylate shunt in the carbon sequestration mechanisms. This review also describes some interesting facets of using carbon assimilation mechanisms for valuable bio-products. The role of regulatory pathways and multi-omics approaches in cyanobacteria will not only be crucial towards improving carbon utilization but also will give new insights into utilizing cyanobacterial bioresource for carbon neutrality.
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Affiliation(s)
- Niwas Kumar
- Society for Research and Initiatives for Sustainable Technologies and Institutions, Navrangapura, Ahmedabad 380009, India
| | - Srabani Kar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, India.
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32
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Saravanan A, Deivayanai VC, Senthil Kumar P, Rangasamy G, Varjani S. CO 2 bio-mitigation using genetically modified algae and biofuel production towards a carbon net-zero society. BIORESOURCE TECHNOLOGY 2022; 363:127982. [PMID: 36126842 DOI: 10.1016/j.biortech.2022.127982] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 09/10/2022] [Accepted: 09/12/2022] [Indexed: 06/15/2023]
Abstract
CO2 sequestration carried by biological methodologies shows enhanced potential and has the advantage that biomass produced from the captured CO2 can be used for different applications. Bio-mitigation of carbons through a micro-algal system addresses a promising and feasible option. This review mostly focused on the role of algae, particular mechanisms, bioreactors in algae cultivation, and genetically modified algae in CO2 fixation and energy generation systems. A combination of CO2 bio-mitigation and biofuel production might deliver an extremely promising alternative to current CO2 mitigation systems. Bio mitigation in which the excess carbon is captured and bio fixation which the carbon is captured by algae or autotrophs and used for producing biofuel. This review revealed that steps for biofuel production from algae include factors affecting, harvesting techniques, oil extraction and transesterification. This review helps environmentalists and researchers to assess the effect of algae-based biorefinery on the green environment.
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Affiliation(s)
- A Saravanan
- Department of Sustainable Engineering, Institute of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai 602105, India
| | - V C Deivayanai
- Department of Sustainable Engineering, Institute of Biotechnology, Saveetha School of Engineering, SIMATS, Chennai 602105, India
| | - P Senthil Kumar
- Department of Chemical Engineering, Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India; Centre of Excellence in Water Research (CEWAR), Sri Sivasubramaniya Nadar College of Engineering, Chennai 603110, India.
| | - Gayathri Rangasamy
- University Centre for Research and Development & Department of Civil Engineering, Chandigarh University, Gharuan, Mohali, Punjab 140413, India
| | - Sunita Varjani
- Gujarat Pollution Control Board, Gandhinagar 382 010, Gujarat, India
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33
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Light-Driven Synthetic Biology: Progress in Research and Industrialization of Cyanobacterial Cell Factory. LIFE (BASEL, SWITZERLAND) 2022; 12:life12101537. [PMID: 36294972 PMCID: PMC9605453 DOI: 10.3390/life12101537] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Revised: 09/21/2022] [Accepted: 09/29/2022] [Indexed: 11/07/2022]
Abstract
Light-driven synthetic biology refers to an autotrophic microorganisms-based research platform that remodels microbial metabolism through synthetic biology and directly converts light energy into bio-based chemicals. This technology can help achieve the goal of carbon neutrality while promoting green production. Cyanobacteria are photosynthetic microorganisms that use light and CO2 for growth and production. They thus possess unique advantages as "autotrophic cell factories". Various fuels and chemicals have been synthesized by cyanobacteria, indicating their important roles in research and industrial application. This review summarized the progresses and remaining challenges in light-driven cyanobacterial cell factory. The choice of chassis cells, strategies used in metabolic engineering, and the methods for high-value CO2 utilization will be discussed.
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34
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Biswas S, Niedzwiedzki DM, Pakrasi HB. Introduction of cysteine-mediated quenching in the CP43 protein of photosystem II builds resilience to high-light stress in a cyanobacterium. BIOCHIMICA ET BIOPHYSICA ACTA. BIOENERGETICS 2022; 1863:148580. [PMID: 35654167 DOI: 10.1016/j.bbabio.2022.148580] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Revised: 05/16/2022] [Accepted: 05/25/2022] [Indexed: 06/15/2023]
Abstract
Photosystem (PS) II is prone to photodamage both as a direct consequence of light, and indirectly by producing reactive oxygen species. Engineering high-light tolerance in cyanobacteria with minimal impact on PSII function is desirable in synthetic biology. IsiA, a CP43 homolog found exclusively in cyanobacteria, can dissipate excess light energy. We have recently determined that the sole cysteine residue of IsiA in Synechocystis sp. PCC 6803 has a critical role in non-photochemical quenching. Similar cysteine-mediated energy quenching has also been observed in green‑sulfur bacteria. Sequence analysis of IsiA and CP43 aligns cysteine 260 of IsiA with valine 277 of CP43 in Synechocystis sp. PCC 6803. In the current study, we explore the impact of replacing valine 277 of CP43 to a cysteine on growth, PSII activity and high-light tolerance. Our results imply a decline in the PSII output for the mutant (CP43V277C) presumably due to the dissipation of absorbed light energy by cysteine. Spectroscopic analysis of isolated PSII from this mutant strain also suggests a delayed transfer of excitation energy from CP43-associated chlorophyll a to PSII reaction center. The mutation makes the PSII high-light tolerant and provides a small advantage in growth under high-light conditions. This previously unexplored strategy to engineer high-light tolerance could be a step further towards developing cyanobacterial cells as biofactories.
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Affiliation(s)
- Sandeep Biswas
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
| | - Dariusz M Niedzwiedzki
- Center for Solar Energy and Energy Storage, Washington University, St. Louis, MO 63130, USA; Department of Energy, Environmental & Chemical Engineering, Washington University, St. Louis, MO 63130, USA.
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO 63130, USA.
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35
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Wang Z, Wang Y, Wang Y, Chen W, Ji Q. CRISPR/Cpf1-Mediated Multiplex and Large-Fragment Gene Editing in Staphylococcus aureus. ACS Synth Biol 2022; 11:3049-3057. [PMID: 36001082 DOI: 10.1021/acssynbio.2c00248] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Staphylococcus aureus is a major human pathogen that causes a variety of infections, including life-threatening diseases. Research on S. aureus is constrained by complex and limited genetic manipulation methods. Here, we report a CRISPR/Cpf1-mediated system, pCpfSA, for rapid and versatile genome editing in S. aureus. In direct comparison with the existing CRISPR/Cas9-mediated genome-editing system, the pCpfSA system exhibits enhanced colony-forming units (CFUs) after editing and an expanded targetable range with comparable editing efficiency. Given the precursor crRNA (pre-crRNA) processing activity of Cpf1, the pCpfSA system also allows multiplex gene editing and large-fragment DNA knockout simply by introducing two crRNAs and the corresponding donor templates, which is difficult to achieve using the CRISPR/Cas9 system, thereby greatly expanding the genome editor toolbox for S. aureus.
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Affiliation(s)
- Zhipeng Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Yu Wang
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, Jiangxi 330045, China
| | - Yujue Wang
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.,University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weizhong Chen
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China
| | - Quanjiang Ji
- School of Physical Science and Technology, ShanghaiTech University, Shanghai 201210, China.,Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai 201210, China
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36
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Bourgade B, Stensjö K. Synthetic biology in marine cyanobacteria: Advances and challenges. Front Microbiol 2022; 13:994365. [PMID: 36188008 PMCID: PMC9522894 DOI: 10.3389/fmicb.2022.994365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
The current economic and environmental context requests an accelerating development of sustainable alternatives for the production of various target compounds. Biological processes offer viable solutions and have gained renewed interest in the recent years. For example, photosynthetic chassis organisms are particularly promising for bioprocesses, as they do not require biomass-derived carbon sources and contribute to atmospheric CO2 fixation, therefore supporting climate change mitigation. Marine cyanobacteria are of particular interest for biotechnology applications, thanks to their rich diversity, their robustness to environmental changes, and their metabolic capabilities with potential for therapeutics and chemicals production without requiring freshwater. The additional cyanobacterial properties, such as efficient photosynthesis, are also highly beneficial for biotechnological processes. Due to their capabilities, research efforts have developed several genetic tools for direct metabolic engineering applications. While progress toward a robust genetic toolkit is continuously achieved, further work is still needed to routinely modify these species and unlock their full potential for industrial applications. In contrast to the understudied marine cyanobacteria, genetic engineering and synthetic biology in freshwater cyanobacteria are currently more advanced with a variety of tools already optimized. This mini-review will explore the opportunities provided by marine cyanobacteria for a greener future. A short discussion will cover the advances and challenges regarding genetic engineering and synthetic biology in marine cyanobacteria, followed by a parallel with freshwater cyanobacteria and their current genetic availability to guide the prospect for marine species.
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Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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37
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Cengic I, Cañadas IC, Minton NP, Hudson EP. Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803. ACS Synth Biol 2022; 11:3100-3113. [PMID: 35969224 PMCID: PMC9486961 DOI: 10.1021/acssynbio.2c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here, we describe a riboswitch-inducible CRISPR/Cas9 system, contained on a single replicative vector, for the model cyanobacterium Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector intoSynechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits performed better, reaching, e.g., 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system mediated multiplexed editing of up to three targets in parallel inSynechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction. Lastly, a vector curing system based on the nickel-inducible expression of the toxic mazF (from Escherichia coli) was added to the CRISPR/Cas9 vector. This inducible system allowed for curing of the vector in 25-75% of screened colonies, enabling edited mutants to become markerless.
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Affiliation(s)
- Ivana Cengic
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden
| | - Inés C. Cañadas
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Elton P. Hudson
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden,
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38
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Allophycocyanin A is a carbon dioxide receptor in the cyanobacterial phycobilisome. Nat Commun 2022; 13:5289. [PMID: 36075935 PMCID: PMC9458709 DOI: 10.1038/s41467-022-32925-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 08/24/2022] [Indexed: 11/10/2022] Open
Abstract
Light harvesting is fundamental for production of ATP and reducing equivalents for CO2 fixation during photosynthesis. However, electronic energy transfer (EET) through a photosystem can harm the photosynthetic apparatus when not balanced with CO2. Here, we show that CO2 binding to the light-harvesting complex modulates EET in photosynthetic cyanobacteria. More specifically, CO2 binding to the allophycocyanin alpha subunit of the light-harvesting complex regulates EET and its fluorescence quantum yield in the cyanobacterium Synechocystis sp. PCC 6803. CO2 binding decreases the inter-chromophore distance in the allophycocyanin trimer. The result is enhanced EET in vitro and in live cells. Our work identifies a direct target for CO2 in the cyanobacterial light-harvesting apparatus and provides insights into photosynthesis regulation. The transfer of electronic energy through a photosystem can harm the photosynthetic apparatus when not balanced with CO2 fixation. Here, the authors show that CO2 modulates electronic energy transfer in cyanobacteria by binding to and enhancing the activity of the light-harvesting complex.
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39
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Zhao M, Li Y, Wang F, Ren Y, Wei D. A CRISPRi mediated self-inducible system for dynamic regulation of TCA cycle and improvement of itaconic acid production in Escherichia coli. Synth Syst Biotechnol 2022; 7:982-988. [PMID: 35782485 PMCID: PMC9213231 DOI: 10.1016/j.synbio.2022.05.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/26/2022] [Accepted: 05/27/2022] [Indexed: 11/17/2022] Open
Abstract
Itaconic acid (ITA), an effective alternative fossil fuel, derives from the bypass pathway of the tricarboxylic acid (TCA) cycle. Therefore, the imbalance of metabolic flux between TCA cycle and ITA biosynthetic pathway seriously limits the production of ITA. The optimization of flux distribution between biomass and production has the potential to the productivity of ITA. Based on the previously constructed strain Escherichia coli MG1655 Δ1-SAS-3 (ITA titer: 1.87 g/L), a CRISPRi-mediated self-inducible system (CiMS), which contained a responsive module based on the ITA biosensor YpItcR/P ccl and a regulative CRISPRi-mediated interferential module, was developed to regulate the flux of the TCA cycle and to enhance the capacity of the strain to produce ITA. First, a higher ITA-yielding strain, Δ4-P rmd -SAS-3 (ITA titer: 3.20 g/L), derived from Δ1-SAS-3, was constructed by replacing the promoter P J23100 , for the expression of ITA synthesis genes, with P rmd and knocking out the three bypass genes poxB, pflB, and ldhA. Subsequently, the CiMS was used to inhibit the expression of key genes icd, pykA, and sucCD to dynamically balance the metabolic flux between TCA cycle and ITA biosynthetic pathway during the ITA production stage. The constructed strain Δ4-P rmd -SAS-3 under the dynamic regulation of the CiMS, showed a 23% increase in the ITA titer, which reached 3.93 g/L. This study indicated that CiMS was a practical strategy to dynamically and precisely regulated the metabolic flux in microbial cell factories.
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Affiliation(s)
- Ming Zhao
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
- Anhui Engineering Laboratory for Industrial Microbiology Molecular Breeding, College of Biology and Food Engineering, Anhui Polytechnic University, Wuhu, 241000, China
| | - Yuting Li
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Fengqing Wang
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Yuhong Ren
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
| | - Dongzhi Wei
- State Key Lab of Bioreactor Engineering, Newworld Institute of Biotechnology, East China University of Science and Technology, Shanghai, 200237, China
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40
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Li W, Huang C, Chen J. The application of CRISPR /Cas mediated gene editing in synthetic biology: Challenges and optimizations. Front Bioeng Biotechnol 2022; 10:890155. [PMID: 36091445 PMCID: PMC9452635 DOI: 10.3389/fbioe.2022.890155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2022] [Accepted: 07/28/2022] [Indexed: 11/13/2022] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR) and its associated enzymes (Cas) is a simple and convenient genome editing tool that has been used in various cell factories and emerging synthetic biology in the recent past. However, several problems, including off-target effects, cytotoxicity, and low efficiency of multi-gene editing, are associated with the CRISPR/Cas system, which have limited its application in new species. In this review, we briefly describe the mechanisms of CRISPR/Cas engineering and propose strategies to optimize the system based on its defects, including, but not limited to, enhancing targeted specificity, reducing toxicity related to Cas protein, and improving multi-point editing efficiency. In addition, some examples of improvements in synthetic biology are also highlighted. Finally, future perspectives of system optimization are discussed, providing a reference for developing safe genome-editing tools for new species.
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Affiliation(s)
- Wenqian Li
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Can Huang
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
| | - Jingyu Chen
- MOE Key Laboratory of Precision Nutrition and Food Quality, College of Food Science and Nutritional Engineering, China Agricultural University, Beijing, China
- Key Laboratory of Food Bioengineering (China National Light Industry), College of Food Science and Nutritional Engineering, China Agricultural University, Beijing,China
- *Correspondence: Jingyu Chen,
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41
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Swan JA, Sandate CR, Chavan AG, Freeberg AM, Etwaru D, Ernst DC, Palacios JG, Golden SS, LiWang A, Lander GC, Partch CL. Coupling of distant ATPase domains in the circadian clock protein KaiC. Nat Struct Mol Biol 2022; 29:759-766. [PMID: 35864165 DOI: 10.1038/s41594-022-00803-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 06/06/2022] [Indexed: 11/09/2022]
Abstract
The AAA+ family member KaiC is the central pacemaker for circadian rhythms in the cyanobacterium Synechococcus elongatus. Composed of two hexameric rings of adenosine triphosphatase (ATPase) domains with tightly coupled activities, KaiC undergoes a cycle of autophosphorylation and autodephosphorylation on its C-terminal (CII) domain that restricts binding of clock proteins on its N-terminal (CI) domain to the evening. Here, we use cryogenic-electron microscopy to investigate how daytime and nighttime states of CII regulate KaiB binding on CI. We find that the CII hexamer is destabilized during the day but takes on a rigidified C2-symmetric state at night, concomitant with ring-ring compression. Residues at the CI-CII interface are required for phospho-dependent KaiB association, coupling ATPase activity on CI to cooperative KaiB recruitment. Together, these studies clarify a key step in the regulation of cyanobacterial circadian rhythms by KaiC phosphorylation.
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Affiliation(s)
- Jeffrey A Swan
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Colby R Sandate
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA
| | - Archana G Chavan
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA
| | - Alfred M Freeberg
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Diana Etwaru
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Dustin C Ernst
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA
| | - Joseph G Palacios
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA
| | - Susan S Golden
- Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA
| | - Andy LiWang
- Department of Chemistry and Biochemistry, University of California, Merced, CA, USA.,Center for Circadian Biology, University of California, San Diego, La Jolla, CA, USA.,Center for Cellular and Biomolecular Machines, University of California, Merced, CA, USA
| | - Gabriel C Lander
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Carrie L Partch
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, CA, USA. .,Division of Biological Sciences, University of California, San Diego, La Jolla, CA, USA.
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42
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Yu HY, Wang SG, Xia PF. Reprogramming Microbial CO 2-Metabolizing Chassis With CRISPR-Cas Systems. Front Bioeng Biotechnol 2022; 10:897204. [PMID: 35814004 PMCID: PMC9260013 DOI: 10.3389/fbioe.2022.897204] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 06/07/2022] [Indexed: 02/03/2023] Open
Abstract
Global warming is approaching an alarming level due to the anthropogenic emission of carbon dioxide (CO2). To overcome the challenge, the reliance on fossil fuels needs to be alleviated, and a significant amount of CO2 needs to be sequestrated from the atmosphere. In this endeavor, carbon-neutral and carbon-negative biotechnologies are promising ways. Especially, carbon-negative bioprocesses, based on the microbial CO2-metabolizing chassis, possess unique advantages in fixing CO2 directly for the production of fuels and value-added chemicals. In order to fully uncover the potential of CO2-metabolizing chassis, synthetic biology tools, such as CRISPR-Cas systems, have been developed and applied to engineer these microorganisms, revolutionizing carbon-negative biotechnology. Herein, we review the recent advances in the adaption of CRISPR-Cas systems, including CRISPR-Cas based genome editing and CRISPR interference/activation, in cyanobacteria, acetogens, and methanogens. We also envision future innovations via the implementation of rising CRISPR-Cas systems, such as base editing, prime editing, and transposon-mediated genome editing.
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Affiliation(s)
- Hai-Yan Yu
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Shu-Guang Wang
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
- Sino-French Research Institute for Ecology and Environment, Shandong University, Qingdao, China
| | - Peng-Fei Xia
- School of Environmental Science and Engineering, Shandong University, Qingdao, China
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43
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Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
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Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
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44
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A Ubiquitously Conserved Cyanobacterial Protein Phosphatase Essential for High Light Tolerance in a Fast-Growing Cyanobacterium. Microbiol Spectr 2022; 10:e0100822. [PMID: 35727069 PMCID: PMC9430166 DOI: 10.1128/spectrum.01008-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Synechococcus elongatus UTEX 2973, the fastest-growing cyanobacterial strain known, optimally grows under extreme high light (HL) intensities of 1,500-2,500 μmol photons m-2 s-1, which is lethal to most other photosynthetic microbes. We leveraged the few genetic differences between Synechococcus 2973 and the HL sensitive strain Synechococcus elongatus PCC 7942 to unravel factors essential for the high light tolerance. We identified a novel protein in Synechococcus 2973 that we have termed HltA for High light tolerance protein A. Using bioinformatic tools, we determined that HltA contains a functional PP2C-type protein phosphatase domain. Phylogenetic analysis showed that the PP2C domain belongs to the bacterial-specific Group II family and is closely related to the environmental stress response phosphatase RsbU. Additionally, we showed that unlike any previously described phosphatases, HltA contains a single N-terminal regulatory GAF domain. We found hltA to be ubiquitous throughout cyanobacteria, indicative of its potentially important role in the photosynthetic lifestyle of these oxygenic phototrophs. Mutations in the hltA gene resulted in severe defects specific to high light growth. These results provide evidence that hltA is a key factor in the tolerance of Synechococcus 2973 to high light and will open new insights into the mechanisms of cyanobacterial light stress response. IMPORTANCE Cyanobacteria are a diverse group of photosynthetic prokaryotes. The cyanobacterium Synechococcus 2973 is a high light tolerant strain with industrial promise due to its fast growth under high light conditions and the availability of genetic modification tools. Currently, little is known about the high light tolerance mechanisms of Synechococcus 2973, and there are many unknowns overall regarding high light tolerance of cyanobacteria. In this study, a comparative genomic analysis of Synechococcus 2973 identified a single nucleotide polymorphism in a locus encoding a serine phosphatase as a key factor for high light tolerance. This novel GAF-containing phosphatase was found to be the sole Group II metal-dependent protein phosphatase that is evolutionarily conserved throughout cyanobacteria. These results shed new light on the light response mechanisms of Synechococcus 2973, improving our understanding of environmental stress response. Additionally, this work will help facilitate the development of Synechococcus 2973 as an industrially useful organism.
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Baldanta S, Guevara G, Navarro-Llorens JM. SEVA-Cpf1, a CRISPR-Cas12a vector for genome editing in cyanobacteria. Microb Cell Fact 2022; 21:103. [PMID: 35643551 PMCID: PMC9148489 DOI: 10.1186/s12934-022-01830-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cyanobacteria are photosynthetic autotrophs that have tremendous potential for fundamental research and industrial applications due to their high metabolic plasticity and ability to grow using CO2 and sunlight. CRISPR technology using Cas9 and Cpf1 has been applied to different cyanobacteria for genome manipulations and metabolic engineering. Despite significant advances with genome editing in several cyanobacteria strains, the lack of proper genetic toolboxes is still a limiting factor compared to other model laboratory species. Among the limitations, it is essential to have versatile plasmids that could ease the benchwork when using CRISPR technology. Results In the present study, several CRISPR-Cpf1 vectors were developed for genetic manipulations in cyanobacteria using SEVA plasmids. SEVA collection is based on modular vectors that enable the exchangeability of diverse elements (e.g. origins of replication and antibiotic selection markers) and the combination with many cargo sequences for varied end-applications. Firstly, using SEVA vectors containing the broad host range RSF1010 origin we demonstrated that these vectors are replicative not only in model cyanobacteria but also in a new cyanobacterium specie, Chroococcidiopsis sp., which is different from those previously published. Then, we constructed SEVA vectors by harbouring CRISPR elements and showed that they can be easily assimilated not only by conjugation, but also by natural transformation. Finally, we used our SEVA-Cpf1 tools to delete the nblA gene in Synechocystis sp. PCC 6803, demonstrating that our plasmids can be applied for CRISPR-based genome editing technology. Conclusions The results of this study provide new CRISPR-based vectors based on the SEVA (Standard European Vector Architecture) collection that can improve editing processes using the Cpf1 nuclease in cyanobacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01830-4.
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Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
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Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
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Verma S, Thapa S, Siddiqui N, Chakdar H. Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches. World J Microbiol Biotechnol 2022; 38:100. [PMID: 35486205 DOI: 10.1007/s11274-022-03285-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.
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Affiliation(s)
- Shaloo Verma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.,Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India
| | - Nahid Siddiqui
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.
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Abstract
Strains of the freshwater cyanobacterium Synechococcus elongatus were first isolated approximately 60 years ago, and PCC 7942 is well established as a model for photosynthesis, circadian biology, and biotechnology research. The recent isolation of UTEX 3055 and subsequent discoveries in biofilm and phototaxis phenotypes suggest that lab strains of S. elongatus are highly domesticated. We performed a comprehensive genome comparison among the available genomes of S. elongatus and sequenced two additional laboratory strains to trace the loss of native phenotypes from the standard lab strains and determine the genetic basis of useful phenotypes. The genome comparison analysis provides a pangenome description of S. elongatus, as well as correction of extensive errors in the published sequence for the type strain PCC 6301. The comparison of gene sets and single nucleotide polymorphisms (SNPs) among strains clarifies strain isolation histories and, together with large-scale genome differences, supports a hypothesis of laboratory domestication. Prophage genes in laboratory strains, but not UTEX 3055, affect pigmentation, while unique genes in UTEX 3055 are necessary for phototaxis. The genomic differences identified in this study include previously reported SNPs that are, in reality, sequencing errors, as well as SNPs and genome differences that have phenotypic consequences. One SNP in the circadian response regulator rpaA that has caused confusion is clarified here as belonging to an aberrant clone of PCC 7942, used for the published genome sequence, that has confounded the interpretation of circadian fitness research.
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Advances in the Understanding of the Lifecycle of Photosystem II. Microorganisms 2022; 10:microorganisms10050836. [PMID: 35630282 PMCID: PMC9145668 DOI: 10.3390/microorganisms10050836] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 04/14/2022] [Accepted: 04/16/2022] [Indexed: 02/04/2023] Open
Abstract
Photosystem II is a light-driven water-plastoquinone oxidoreductase present in cyanobacteria, algae and plants. It produces molecular oxygen and protons to drive ATP synthesis, fueling life on Earth. As a multi-subunit membrane-protein-pigment complex, Photosystem II undergoes a dynamic cycle of synthesis, damage, and repair known as the Photosystem II lifecycle, to maintain a high level of photosynthetic activity at the cellular level. Cyanobacteria, oxygenic photosynthetic bacteria, are frequently used as model organisms to study oxygenic photosynthetic processes due to their ease of growth and genetic manipulation. The cyanobacterial PSII structure and function have been well-characterized, but its lifecycle is under active investigation. In this review, advances in studying the lifecycle of Photosystem II in cyanobacteria will be discussed, with a particular emphasis on new structural findings enabled by cryo-electron microscopy. These structural findings complement a rich and growing body of biochemical and molecular biology research into Photosystem II assembly and repair.
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Treece TR, Gonzales JN, Pressley JR, Atsumi S. Synthetic Biology Approaches for Improving Chemical Production in Cyanobacteria. Front Bioeng Biotechnol 2022; 10:869195. [PMID: 35372310 PMCID: PMC8965691 DOI: 10.3389/fbioe.2022.869195] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2022] [Accepted: 02/25/2022] [Indexed: 11/15/2022] Open
Abstract
Biological chemical production has gained traction in recent years as a promising renewable alternative to traditional petrochemical based synthesis. Of particular interest in the field of metabolic engineering are photosynthetic microorganisms capable of sequestering atmospheric carbon dioxide. CO2 levels have continued to rise at alarming rates leading to an increasingly uncertain climate. CO2 can be sequestered by engineered photosynthetic microorganisms and used for chemical production, representing a renewable production method for valuable chemical commodities such as biofuels, plastics, and food additives. The main challenges in using photosynthetic microorganisms for chemical production stem from the seemingly inherent limitations of carbon fixation and photosynthesis resulting in slower growth and lower average product titers compared to heterotrophic organisms. Recently, there has been an increase in research around improving photosynthetic microorganisms as renewable chemical production hosts. This review will discuss the various efforts to overcome the intrinsic inefficiencies of carbon fixation and photosynthesis, including rewiring carbon fixation and photosynthesis, investigating alternative carbon fixation pathways, installing sugar catabolism to supplement carbon fixation, investigating newly discovered fast growing photosynthetic species, and using new synthetic biology tools such as CRISPR to radically alter metabolism.
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Affiliation(s)
- Tanner R. Treece
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Jake N. Gonzales
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
| | - Joseph R. Pressley
- Department of Chemistry, University of California, Davis, Davis, CA, United States
| | - Shota Atsumi
- Department of Chemistry, University of California, Davis, Davis, CA, United States
- Plant Biology Graduate Group, University of California, Davis, Davis, CA, United States
- *Correspondence: Shota Atsumi,
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