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Victoria AJ, Selão TT, Moreno-Cabezuelo JÁ, Mills LA, Gale GAR, Lea-Smith DJ, McCormick AJ. A toolbox to engineer the highly productive cyanobacterium Synechococcus sp. PCC 11901. PLANT PHYSIOLOGY 2024; 196:1674-1690. [PMID: 38713768 PMCID: PMC11444289 DOI: 10.1093/plphys/kiae261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/09/2024] [Revised: 04/09/2024] [Accepted: 04/14/2024] [Indexed: 05/09/2024]
Abstract
Synechococcus sp. PCC 11901 (PCC 11901) is a fast-growing marine cyanobacterial strain that has a capacity for sustained biomass accumulation to very high cell densities, comparable to that achieved by commercially relevant heterotrophic organisms. However, genetic tools to engineer PCC 11901 for biotechnology applications are limited. Here we describe a suite of tools based on the CyanoGate MoClo system to unlock the engineering potential of PCC 11901. First, we characterized neutral sites suitable for stable genomic integration that do not affect growth even at high cell densities. Second, we tested a suite of constitutive promoters, terminators, and inducible promoters including a 2,4-diacetylphloroglucinol (DAPG)-inducible PhlF repressor system, which has not previously been demonstrated in cyanobacteria and showed tight regulation and a 228-fold dynamic range of induction. Lastly, we developed a DAPG-inducible dCas9-based CRISPR interference (CRISPRi) system and a modular method to generate markerless mutants using CRISPR-Cas12a. Based on our findings, PCC 11901 is highly responsive to CRISPRi-based repression and showed high efficiencies for single insertion (31% to 81%) and multiplex double insertion (25%) genome editing with Cas12a. We envision that these tools will lay the foundations for the adoption of PCC 11901 as a robust model strain for engineering biology and green biotechnology.
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Affiliation(s)
- Angelo J Victoria
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK
| | | | - Lauren A Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
- Centre for Engineering Biology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
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2
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Santos-Merino M, Sakkos JK, Singh AK, Ducat DC. Coordination of carbon partitioning and photosynthesis by a two-component signaling network in Synechococcus elongatus PCC 7942. Metab Eng 2024; 81:38-52. [PMID: 37925065 DOI: 10.1016/j.ymben.2023.11.001] [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: 06/09/2023] [Revised: 10/26/2023] [Accepted: 11/02/2023] [Indexed: 11/06/2023]
Abstract
Photosynthetic organisms need to balance the rate of photosynthesis with the utilization of photosynthetic products by downstream reactions. While such "source/sink" pathways are well-interrogated in plants, analogous regulatory systems are unknown or poorly studied in single-celled algal and cyanobacterial species. Towards the identification of energy/sugar sensors in cyanobacteria, we utilized an engineered strain of Synechococcus elongatus PCC 7942 that allows experimental manipulation of carbon status. We conducted a screening of all two-component systems (TCS) and serine/threonine kinases (STKs) encoded in S. elongatus PCC 7942 by analyzing phenotypes consistent with sucrose-induced relaxation of sink inhibition. We narrowed the candidate sensor proteins by analyzing changes observed after sucrose feeding. We show that a clustered TCS network containing RpaA, CikB, ManS and NblS are involved in the regulation of genes related to photosynthesis, pigment synthesis, and Rubisco concentration in response to sucrose. Altogether, these results highlight a regulatory TCS group that may play under-appreciated functions in carbon partitioning and energy balancing in cyanobacteria.
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Affiliation(s)
- María Santos-Merino
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Jonathan K Sakkos
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Amit K Singh
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States
| | - Daniel C Ducat
- MSU-DOE Plant Research Laboratory, Michigan State University, East Lansing, MI, 48824, United States; Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, MI, 48824, United States.
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3
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Cao K, Wang X, Sun F, Zhang H, Cui Y, Cao Y, Yao Q, Zhu X, Yao T, Wang M, Meng C, Gao Z. Promoting Heme and Phycocyanin Biosynthesis in Synechocystis sp. PCC 6803 by Overexpression of Porphyrin Pathway Genes with Genetic Engineering. Mar Drugs 2023; 21:403. [PMID: 37504934 PMCID: PMC10382063 DOI: 10.3390/md21070403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/08/2023] [Accepted: 07/12/2023] [Indexed: 07/29/2023] Open
Abstract
Due to their unique biochemical and spectroscopic properties, both heme and phycocyanobilin are widely applied in the medical and food industries. Synechocystis sp. PCC 6803 contains both heme and phycocyanin, and is capable of synthesizing phycocyanin using heme as a precursor. The aim of this study was to uncover viable metabolic targets in the porphyrin pathway from Synechocystis sp. PCC 6803 to promote the accumulation of heme and phycocyanin in the recombinant strains of microalgae. A total of 10 genes related to heme synthesis pathway derived from Synechococcus elongatus PCC 7942 and 12 genes related to endogenous heme synthesis were individually overexpressed in strain PCC 6803. The growth rate and pigment content (heme, phycocyanin, chlorophyll a and carotenoids) of 22 recombinant algal strains were characterized. Quantitative real-time PCR technology was used to investigate the molecular mechanisms underlying the changes in physiological indicators in the recombinant algal strains. Among the 22 mutant strains, the mutant overexpressing the haemoglobin gene (glbN) of strain PCC 6803 had the highest heme content, which was 2.5 times higher than the wild type; the mutant overexpressing the gene of strain PCC 7942 (hemF) had the highest phycocyanin content, which was 4.57 times higher than the wild type. Overall, the results suggest that genes in the porphyrin pathway could significantly affect the heme and phycocyanin content in strain PCC 6803. Our study provides novel crucial targets for promoting the accumulation of heme and phycocyanin in cyanobacteria.
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Affiliation(s)
- Kai Cao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Xiaodong Wang
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Hao Zhang
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yulin Cui
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Yujiao Cao
- School of Foreign Languages, Shandong University of Technology, Zibo 255090, China
| | - Qingshou Yao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Xiangyu Zhu
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Ting Yao
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Meng Wang
- Yantai Hongyuan Bio-Fertilizer Co., Ltd., Yantai 264000, China
| | - Chunxiao Meng
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
| | - Zhengquan Gao
- School of Life Sciences and Medicine, Shandong University of Technology, Zibo 255049, China
- School of Pharmacy, Binzhou Medical University, Yantai 264003, China
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4
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Madhu S, Sengupta A, Sarnaik AP, Sahasrabuddhe D, Wangikar PP. Global Transcriptome-Guided Identification of Neutral Sites for Engineering Synechococcus elongatus PCC 11801. ACS Synth Biol 2023; 12:1677-1685. [PMID: 37252895 DOI: 10.1021/acssynbio.3c00019] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Engineered cyanobacteria are attractive hosts for the phototrophic conversion of CO2 to chemicals. Synechococcus elongatus PCC11801, a novel, fast-growing, and stress-tolerant cyanobacterium, has the potential to be a platform cell factory, and hence, it necessitates the development of a synthetic biology toolbox. Considering the widely followed cyanobacterial engineering strategy of chromosomal integration of heterologous DNA, it is of interest to discover and validate new chromosomal neutral sites (NSs) in this strain. To that end, global transcriptome analysis was performed using RNA Seq under the conditions of high temperature (HT), carbon (HC), and salt (HS) and ambient growth conditions. We found upregulation of 445, 138, and 87 genes and downregulation of 333, 125, and 132 genes, under HC, HT, and HS, respectively. Following nonhierarchical clustering, gene enrichment, and bioinformatics analysis, 27 putative NSs were predicted. Six of them were experimentally tested, and five showed confirmed neutrality, based on unaltered cell growth. Thus, global transcriptomic analysis was effectively exploited for NS annotation and would be advantageous for multiplexed genome editing.
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Affiliation(s)
- Swati Madhu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Aditya P Sarnaik
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Deepti Sahasrabuddhe
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076 India
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5
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Cheng J, Zhang K, Hou Y. The current situations and limitations of genetic engineering in cyanobacteria: a mini review. Mol Biol Rep 2023; 50:5481-5487. [PMID: 37119415 DOI: 10.1007/s11033-023-08456-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Accepted: 04/12/2023] [Indexed: 05/01/2023]
Abstract
Cyanobacteria are an ancient group of photoautotrophic prokaryotes, and play an essential role in the global carbon cycle. They are also model organisms for studying photosynthesis and circadian regulation, and metabolic engineering and synthetic biology strategies grants light-driven biotechnological applications to cyanobacteria, especially for engineering cyanobacteria cells to achieve an efficient light-driven system for synthesizing any product of interest from renewable feedstocks. However, lower yield limits the potential of industrial application of cyanobacterial synthetic biology, and some key limitations must be overcome to realize the full biotechnological potential of these versatile microorganisms. Although genetic engineering toolkits for cyanobacteria have made some progress, the tools available still lag behind conventional heterotrophic microorganism. Consequently, this study describes the current situations and limitations of genetic engineering in cyanobacteria, and further improvements are proposed to improve the output of targeted products. We believe that cyanobacteria-mediated light-driven platforms towards efficient synthesis of green chemicals could unlock a bright future by developing the tools for strain manipulation and novel chassis organisms with excellent performance for biotechnological applications, which could also accelerate the advancement of bio-manufacturing industries.
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Affiliation(s)
- Jie Cheng
- School of Life Sciences, Liaocheng University, Liaocheng, 252000, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Kaidian Zhang
- State Key Laboratory of Marine Resource Utilization in South China Sea, Hainan Aquaculture Breeding Engineering Research Center, Hainan University, Haikou, 570100, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
| | - Yuyong Hou
- Key Laboratory of Systems Microbial Biotechnology, Tianjin Institute of Industrial Biotechnology, Chinese Academy of Sciences, Tianjin, 300308, China.
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6
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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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7
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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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8
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Kong S, Yu W, Gao N, Zhai X, Zhou YJ. Expanding the neutral sites for integrated gene expression in Saccharomyces cerevisiae. FEMS Microbiol Lett 2022; 369:6671531. [PMID: 35981819 DOI: 10.1093/femsle/fnac081] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/13/2022] [Accepted: 08/16/2022] [Indexed: 11/13/2022] Open
Abstract
Construction of efficient microbial cell factories always requires assembling biosynthetic pathways and rewiring cellular metabolism with overexpression of multiple genes. Genomic integration is considered to be helpful for stable gene expression in compared with the episomal plasmids. However, the limited availability of suitable loci hinders the extensive metabolic engineering. We here characterized 30 neutral sites in Saccharomyces cerevisiae genome that did not affect cellular fitness by using expression cassettes of green fluorescent protein (eGFP) and fatty acyl-CoA reductase (MaFAR1) with the aid of efficient CRISPR-Cas9 technique. We found that integration of gene expression cassettes to different genome loci resulted a varied GFP signal and fatty alcohol production, which showed that genomic loci could be used for tuning gene expression. The characterized set of neutral sites should be helpful for extensively metabolic engineering of S. cerevisiae for chemical production and other purposes.
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Affiliation(s)
- Sijia Kong
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Ning Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiaoxin Zhai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
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9
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Opel F, Siebert NA, Klatt S, Tüllinghoff A, Hantke JG, Toepel J, Bühler B, Nürnberg DJ, Klähn S. Generation of Synthetic Shuttle Vectors Enabling Modular Genetic Engineering of Cyanobacteria. ACS Synth Biol 2022; 11:1758-1771. [PMID: 35405070 DOI: 10.1021/acssynbio.1c00605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Cyanobacteria have raised great interest in biotechnology due to their potential for a sustainable, photosynthesis-driven production of fuels and value-added chemicals. This has led to a concomitant development of molecular tools to engineer the metabolism of those organisms. In this regard, however, even cyanobacterial model strains lag behind compared to their heterotrophic counterparts. For instance, replicative shuttle vectors that allow gene transfer independent of recombination into host DNA are still scarce. Here, we introduce the pSOMA shuttle vector series comprising 10 synthetic plasmids for comprehensive genetic engineering of Synechocystis sp. PCC 6803. The series is based on the small endogenous plasmids pCA2.4 and pCB2.4, each combined with a replicon from Escherichia coli, different selection markers as well as features facilitating molecular cloning and the insulated introduction of gene expression cassettes. We made use of genes encoding green fluorescent protein (GFP) and a Baeyer-Villiger monooxygenase (BVMO) to demonstrate functional gene expression from the pSOMA plasmids in vivo. Moreover, we demonstrate the expression of distinct heterologous genes from individual plasmids maintained in the same strain and thereby confirmed compatibility between the two pSOMA subseries as well as with derivatives of the broad-host-range plasmid RSF1010. We also show that gene transfer into the filamentous model strain Anabaena sp. PCC 7120 is generally possible, which is encouraging to further explore the range of cyanobacterial host species that could be engineered via pSOMA plasmids. Altogether, the pSOMA shuttle vector series displays an attractive alternative to existing plasmid series and thus meets the current demand for the introduction of complex genetic setups and to perform extensive metabolic engineering of cyanobacteria.
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Affiliation(s)
- Franz Opel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Nina A. Siebert
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Sabine Klatt
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Adrian Tüllinghoff
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Janis G. Hantke
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Jörg Toepel
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
| | - Dennis J. Nürnberg
- Institute of Experimental Physics, Biochemistry and Biophysics of Photosynthetic Organisms, Free University Berlin, Arnimallee 14, 14195 Berlin, Germany
| | - Stephan Klähn
- Department of Solar Materials (SOMA), Helmholtz Centre for Environmental Research─UFZ, Permoserstrasse 15, 04318 Leipzig, Germany
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10
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Bernhards CB, Liem AT, Berk KL, Roth PA, Gibbons HS, Lux MW. Putative Phenotypically Neutral Genomic Insertion Points in Prokaryotes. ACS Synth Biol 2022; 11:1681-1685. [PMID: 35271248 PMCID: PMC9016761 DOI: 10.1021/acssynbio.1c00531] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
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The barriers to effective
genome editing in diverse prokaryotic
organisms have been falling at an accelerated rate. As editing becomes
easier in more organisms, quickly identifying genomic locations to
insert new genetic functions without disrupting organism fitness becomes
increasingly useful. When the insertion is noncoding DNA for applications
such as information storage or barcoding, a neutral insertion point
can be especially important. Here we describe an approach to identify
putatively neutral insertion sites in prokaryotes. An algorithm (targetFinder)
finds convergently transcribed genes with gap sizes within a specified
range, and looks for annotations within the gaps. We report putative
editing targets for 10 common synthetic biology chassis organisms,
including coverage of available RNA-seq data, and provide software
to apply to others. We further experimentally evaluate the neutrality
of six identified targets in Escherichia coli through
insertion of a DNA barcode. We anticipate this information and the
accompanying tool will prove useful for synthetic biologists seeking
neutral insertion points for genome editing.
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Affiliation(s)
- Casey B. Bernhards
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- Excet, Inc., Springfield, Virginia 22150, United States
| | - Alvin T. Liem
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Kimberly L. Berk
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Pierce A. Roth
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
- DCS Corporation, Belcamp, Maryland 21017, United States
| | - Henry S. Gibbons
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
| | - Matthew W. Lux
- U.S. Army Combat Capabilities Development Command Chemical Biological Center, Aberdeen Proving Ground, Maryland 21010, United States
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Immethun CM, Kathol M, Changa T, Saha R. Synthetic Biology Tool Development Advances Predictable Gene Expression in the Metabolically Versatile Soil Bacterium Rhodopseudomonas palustris. Front Bioeng Biotechnol 2022; 10:800734. [PMID: 35372317 PMCID: PMC8966681 DOI: 10.3389/fbioe.2022.800734] [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: 10/23/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Abstract
Harnessing the unique biochemical capabilities of non-model microorganisms would expand the array of biomanufacturing substrates, process conditions, and products. There are non-model microorganisms that fix nitrogen and carbon dioxide, derive energy from light, catabolize methane and lignin-derived aromatics, are tolerant to physiochemical stresses and harsh environmental conditions, store lipids in large quantities, and produce hydrogen. Model microorganisms often only break down simple sugars and require low stress conditions, but they have been engineered for the sustainable manufacture of numerous products, such as fragrances, pharmaceuticals, cosmetics, surfactants, and specialty chemicals, often by using tools from synthetic biology. Transferring complex pathways has proven to be exceedingly difficult, as the cofactors, cellular conditions, and energy sources necessary for this pathway to function may not be present in the host organism. Utilization of unique biochemical capabilities could also be achieved by engineering the host; although, synthetic biology tools developed for model microbes often do not perform as designed in other microorganisms. The metabolically versatile Rhodopseudomonas palustris CGA009, a purple non-sulfur bacterium, catabolizes aromatic compounds derived from lignin in both aerobic and anaerobic conditions and can use light, inorganic, and organic compounds for its source of energy. R. palustris utilizes three nitrogenase isozymes to fulfill its nitrogen requirements while also generating hydrogen. Furthermore, the bacterium produces two forms of RuBisCo in response to carbon dioxide/bicarbonate availability. While this potential chassis harbors many beneficial traits, stable heterologous gene expression has been problematic due to its intrinsic resistance to many antibiotics and the lack of synthetic biology parts investigated in this microbe. To address these problems, we have characterized gene expression and plasmid maintenance for different selection markers, started a synthetic biology toolbox specifically for the photosynthetic R. palustris, including origins of replication, fluorescent reporters, terminators, and 5′ untranslated regions, and employed the microbe’s endogenous plasmid for exogenous protein production. This work provides essential synthetic biology tools for engineering R. palustris’ many unique biochemical processes and has helped define the principles for expressing heterologous genes in this promising microbe through a methodology that could be applied to other non-model microorganisms.
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12
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The Molecular Toolset and Techniques Required to Build Cyanobacterial Cell Factories. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2022. [DOI: 10.1007/10_2022_210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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13
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Mittermair S, Lakatos G, Nicoletti C, Ranglová K, Manoel JC, Grivalský T, Kozhan DM, Masojídek J, Richter J. Impact of glgA1, glgA2 or glgC overexpression on growth and glycogen production in Synechocystis sp. PCC 6803. J Biotechnol 2021; 340:47-56. [PMID: 34481001 DOI: 10.1016/j.jbiotec.2021.08.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 08/16/2021] [Accepted: 08/20/2021] [Indexed: 11/17/2022]
Abstract
Low production rates are still one limiting factor for the industrial climate-neutral production of biovaluable compounds in cyanobacteria. Next to optimized cultivation conditions, new production strategies are required. Hence, the use of established molecular tools could lead to increased product yields in the cyanobacterial model organism Synechocystis sp. PCC6803. Its main storage compound glycogen was chosen to be increased by the use of these tools. In this study, the three genes glgC, glgA1 and glgA2, which are part of the glycogen synthesis pathway, were combined with the Pcpc560 promoter and the neutral cloning site NSC1. The complete genome integration, protein formation, biomass production and glycogen accumulation were determined to select the most productive transformants. The overexpression of glgA2 did not increase the biomass or glycogen production in short-term trials compared to the other two genes but caused transformants death in long-term trials. The transformants glgA1_11 and glgC_2 showed significantly increased biomass (1.6-fold - 1.7-fold) and glycogen production (3.5-fold - 4-fold) compared to the wild type after 96 h making them a promising energy source for further applications. Those could include for example a two-stage production process, with first energy production (glycogen) and second increased product formation (e.g. ethanol).
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Affiliation(s)
- Sandra Mittermair
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria
| | - Gergely Lakatos
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Cecilia Nicoletti
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria
| | - Karolína Ranglová
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - João Câmara Manoel
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Tomáš Grivalský
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Daniyar Malikuly Kozhan
- Al-Farabi Kazakh National University, Faculty of Biology and Biotechnology, 71 Al-Farabi Ave., Almaty 050040, Kazakhstan
| | - Jiří Masojídek
- Institute of Microbiology of the Czech Academy of Sciences, Centre Algatech, Laboratory of Algal Biotechnology, Novohradská 237 - Opatovický mlýn, 37901 Třeboň, Czech Republic
| | - Juliane Richter
- Department of Biology and Chemistry, AG Biosciences, University of Applied Sciences Upper Austria, Roseggerstraße 15, 4600 Wels, Austria.
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Yadav I, Rautela A, Kumar S. Approaches in the photosynthetic production of sustainable fuels by cyanobacteria using tools of synthetic biology. World J Microbiol Biotechnol 2021; 37:201. [PMID: 34664124 DOI: 10.1007/s11274-021-03157-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 09/29/2021] [Indexed: 10/20/2022]
Abstract
Cyanobacteria, photosynthetic prokaryotic microorganisms having a simple genetic composition are the prospective photoautotrophic cell factories for the production of a wide range of biofuel molecules. The simple genetic composition of cyanobacteria allows effortless genetic manipulation which leads to increased research endeavors from the synthetic biology approach. Various unicellular model cyanobacterial strains like Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 have been successfully engineered for biofuels generation. Improved development of synthetic biology tools, genetic modification methods and advancement in transformation techniques to construct a strain that can contain multiple foreign genes in a single operon have vastly expanded the functions that can be used for engineering photosynthetic cyanobacteria for the generation of various biofuel molecules. In this review, recent advancements and approaches in synthetic biology tools used for cyanobacterial genome editing have been discussed. Apart from this, cyanobacterial productions of various fuel molecules like isoprene, limonene, α-farnesene, squalene, alkanes, butanol, and fatty acids, which can be a substitute for petroleum and fossil fuels in the future, have been elaborated.
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Affiliation(s)
- Indrajeet Yadav
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh, 221005, India
| | - Akhil Rautela
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh, 221005, India
| | - Sanjay Kumar
- School of Biochemical Engineering, IIT (BHU) Varanasi, Varanasi, Uttar Pradesh, 221005, India.
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15
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Dhakal D, Chen M, Luesch H, Ding Y. Heterologous production of cyanobacterial compounds. J Ind Microbiol Biotechnol 2021; 48:6119914. [PMID: 33928376 PMCID: PMC8210676 DOI: 10.1093/jimb/kuab003] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Accepted: 11/17/2020] [Indexed: 12/29/2022]
Abstract
Cyanobacteria produce a plethora of compounds with unique chemical structures and diverse biological activities. Importantly, the increasing availability of cyanobacterial genome sequences and the rapid development of bioinformatics tools have unraveled the tremendous potential of cyanobacteria in producing new natural products. However, the discovery of these compounds based on cyanobacterial genomes has progressed slowly as the majority of their corresponding biosynthetic gene clusters (BGCs) are silent. In addition, cyanobacterial strains are often slow-growing, difficult for genetic engineering, or cannot be cultivated yet, limiting the use of host genetic engineering approaches for discovery. On the other hand, genetically tractable hosts such as Escherichia coli, Actinobacteria, and yeast have been developed for the heterologous expression of cyanobacterial BGCs. More recently, there have been increased interests in developing model cyanobacterial strains as heterologous production platforms. Herein, we present recent advances in the heterologous production of cyanobacterial compounds in both cyanobacterial and noncyanobacterial hosts. Emerging strategies for BGC assembly, host engineering, and optimization of BGC expression are included for fostering the broader applications of synthetic biology tools in the discovery of new cyanobacterial natural products.
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Affiliation(s)
- Dipesh Dhakal
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Manyun Chen
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Hendrik Luesch
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
| | - Yousong Ding
- Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 31610, USA
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16
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Nagy C, Thiel K, Mulaku E, Mustila H, Tamagnini P, Aro EM, Pacheco CC, Kallio P. Comparison of alternative integration sites in the chromosome and the native plasmids of the cyanobacterium Synechocystis sp. PCC 6803 in respect to expression efficiency and copy number. Microb Cell Fact 2021; 20:130. [PMID: 34246263 PMCID: PMC8272380 DOI: 10.1186/s12934-021-01622-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 06/29/2021] [Indexed: 11/10/2022] Open
Abstract
Background Synechocystis sp. PCC 6803 provides a well-established reference point to cyanobacterial metabolic engineering as part of basic photosynthesis research, as well as in the development of next-generation biotechnological production systems. This study focused on expanding the current knowledge on genomic integration of expression constructs in Synechocystis, targeting a range of novel sites in the chromosome and in the native plasmids, together with established loci used in literature. The key objective was to obtain quantitative information on site-specific expression in reference to replicon copy numbers, which has been speculated but never compared side by side in this host. Results An optimized sYFP2 expression cassette was successfully integrated in two novel sites in Synechocystis chromosome (slr0944; sll0058) and in all four endogenous megaplasmids (pSYSM/slr5037-slr5038; pSYSX/slr6037; pSYSA/slr7023; pSYSG/slr8030) that have not been previously evaluated for the purpose. Fluorescent analysis of the segregated strains revealed that the expression levels between the megaplasmids and chromosomal constructs were very similar, and reinforced the view that highest expression in Synechocystis can be obtained using RSF1010-derived replicative vectors or the native small plasmid pCA2.4 evaluated in comparison. Parallel replicon copy number analysis by RT-qPCR showed that the expression from the alternative loci is largely determined by the gene dosage in Synechocystis, thereby confirming the dependence formerly proposed based on literature. Conclusions This study brings together nine different integrative loci in the genome of Synechocystis to demonstrate quantitative differences between target sites in the chromosome, the native plasmids, and a RSF1010-based replicative expression vector. To date, this is the most comprehensive comparison of alternative integrative sites in Synechocystis, and provides the first direct reference between expression efficiency and replicon gene dosage in the context. In the light of existing literature, the findings support the view that the small native plasmids can be notably more difficult to target than the chromosome or the megaplasmids, and that the RSF1010-derived vectors may be surprisingly well maintained under non-selective culture conditions in this cyanobacterial host. Altogether, the work broadens our views on genomic integration and the rational use of different integrative loci versus replicative plasmids, when aiming at expressing heterologous genes in Synechocystis. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-021-01622-2.
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Affiliation(s)
- Csaba Nagy
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Kati Thiel
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Edita Mulaku
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Henna Mustila
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Paula Tamagnini
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,Departamento de Biologia, Faculdade de Ciências, Universidade do Porto, Rua do Campo Alegre, Edifício FC4, 4169-007, Porto, Portugal
| | - Eva-Mari Aro
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland
| | - Catarina C Pacheco
- i3S-Instituto de Investigação e Inovação em Saúde, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal.,IBMC-Instituto de Biologia Molecular e Celular, Universidade do Porto, Rua Alfredo Allen, 208, 4200-135, Porto, Portugal
| | - Pauli Kallio
- Molecular Plant Biology, Department of Life Technologies, University of Turku, Itäinen Pitkäkatu 4 C, 20520, Turku, Finland.
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17
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Yu W, Gao J, Zhai X, Zhou YJ. Screening neutral sites for metabolic engineering of methylotrophic yeast Ogataea polymorpha. Synth Syst Biotechnol 2021; 6:63-68. [PMID: 33869812 PMCID: PMC8040119 DOI: 10.1016/j.synbio.2021.03.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Revised: 02/19/2021] [Accepted: 03/10/2021] [Indexed: 12/13/2022] Open
Abstract
Methylotrophic yeast Ogataea polymorpha is capable to utilize multiple carbon feedstocks especially methanol as sole carbon source and energy, making it an ideal host for bio-manufacturing. However, the lack of gene integration sites limits its systems metabolic engineering, in particular construction of genome-integrated pathway. We here screened the genomic neutral sites for gene integration without affecting cellular fitness, by genomic integration of an enhanced green fluorescent protein (eGFP) gene via CRISPR-Cas9 technique. After profiling the growth and fluorescent intensity in various media, 17 genome positions were finally identified as potential neutral sites. Finally, integration of fatty alcohol synthetic pathway genes into neutral sites NS2 and NS3, enabled the production of 4.5 mg/L fatty alcohols, indicating that these neutral sites can be used for streamline metabolic engineering in O. polymorpha. We can anticipate that the neutral sites screening method described here can be easily adopted to other eukaryotes.
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Affiliation(s)
- Wei Yu
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,University of Chinese Academy of Sciences, Beijing, 100049, PR China
| | - Jiaoqi Gao
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Xiaoxin Zhai
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
| | - Yongjin J Zhou
- Division of Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, 457 Zhongshan Road, Dalian, 116023, PR China.,CAS Key Laboratory of Separation Science for Analytical Chemistry, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China.,Dalian Key Laboratory of Energy Biotechnology, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, 116023, PR China
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18
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Genetic, Genomics, and Responses to Stresses in Cyanobacteria: Biotechnological Implications. Genes (Basel) 2021; 12:genes12040500. [PMID: 33805386 PMCID: PMC8066212 DOI: 10.3390/genes12040500] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 03/25/2021] [Accepted: 03/25/2021] [Indexed: 02/07/2023] Open
Abstract
Cyanobacteria are widely-diverse, environmentally crucial photosynthetic prokaryotes of great interests for basic and applied science. Work to date has focused mostly on the three non-nitrogen fixing unicellular species Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002, which have been selected for their genetic and physiological interests summarized in this review. Extensive "omics" data sets have been generated, and genome-scale models (GSM) have been developed for the rational engineering of these cyanobacteria for biotechnological purposes. We presently discuss what should be done to improve our understanding of the genotype-phenotype relationships of these models and generate robust and predictive models of their metabolism. Furthermore, we also emphasize that because Synechocystis PCC 6803, Synechococcus PCC 7942, and Synechococcus PCC 7002 represent only a limited part of the wide biodiversity of cyanobacteria, other species distantly related to these three models, should be studied. Finally, we highlight the need to strengthen the communication between academic researchers, who know well cyanobacteria and can engineer them for biotechnological purposes, but have a limited access to large photobioreactors, and industrial partners who attempt to use natural or engineered cyanobacteria to produce interesting chemicals at reasonable costs, but may lack knowledge on cyanobacterial physiology and metabolism.
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19
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20
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Metabolic Engineering and Synthetic Biology of Cyanobacteria for Carbon Capture and Utilization. BIOTECHNOL BIOPROC E 2020. [DOI: 10.1007/s12257-019-0447-1] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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21
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Abstract
Continual increases in the human population and growing concerns related to the energy crisis, food security, disease outbreaks, global warming, and other environmental issues require a sustainable solution from nature. One of the promising resources is cyanobacteria, also known as blue-green algae. They require simple ingredients to grow and possess a relatively simple genome. Cyanobacteria are known to produce a wide variety of bioactive compounds. In addition, cyanobacteria’s remarkable growth rate enables its potential use in a wide range of applications in the fields of bioenergy, biotechnology, natural products, medicine, agriculture, and the environment. In this review, we have summarized the potential applications of cyanobacteria in different areas of science and development, especially related to their use in producing biofuels and other valuable co-products. We have also discussed the challenges that hinder such development at an industrial level and ways to overcome such obstacles.
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22
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Sakaki K, Ohishi K, Shimizu T, Kobayashi I, Mori N, Matsuda K, Tomita T, Watanabe H, Tanaka K, Kuzuyama T, Nishiyama M. A suicide enzyme catalyzes multiple reactions for biotin biosynthesis in cyanobacteria. Nat Chem Biol 2020; 16:415-422. [DOI: 10.1038/s41589-019-0461-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 12/20/2019] [Indexed: 11/09/2022]
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23
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Hitchcock A, Hunter CN, Canniffe DP. Progress and challenges in engineering cyanobacteria as chassis for light-driven biotechnology. Microb Biotechnol 2019; 13:363-367. [PMID: 31880868 PMCID: PMC7017823 DOI: 10.1111/1751-7915.13526] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 11/29/2019] [Accepted: 12/01/2019] [Indexed: 11/26/2022] Open
Abstract
Cyanobacteria are prokaryotic phototrophs that, in addition to being excellent model organisms for studying photosynthesis, have tremendous potential for light‐driven synthetic biology and biotechnology. These versatile and resilient microorganisms harness the energy of sunlight to oxidise water, generating chemical energy (ATP) and reductant (NADPH) that can be used to drive sustainable synthesis of high‐value natural products in genetically modified strains. In this commentary article for the Synthetic Microbiology Caucus we discuss the great progress that has been made in engineering cyanobacterial hosts as microbial cell factories for solar‐powered biosynthesis. We focus on some of the main areas where the synthetic biology and metabolic engineering tools in cyanobacteria are not as advanced as those in more widely used heterotrophic chassis, and go on to highlight key improvements that we feel are required to unlock the full power of cyanobacteria for future green biotechnology.
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Affiliation(s)
- Andrew Hitchcock
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - C Neil Hunter
- Department of Molecular Biology and Biotechnology, University of Sheffield, Sheffield, UK
| | - Daniel P Canniffe
- Institute of Integrative Biology, University of Liverpool, Liverpool, UK
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24
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Evaluation of New Genetic Toolkits and Their Role for Ethanol Production in Cyanobacteria. ENERGIES 2019. [DOI: 10.3390/en12183515] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Since the public awareness for climate change has risen, increasing scientific effort has been made to find and develop alternative resources and production processes to reduce the dependency on petrol-based fuels and chemicals of our society. Among others, the biotechnological fuel production, as for example fermenting sugar-rich crops to ethanol, is one of the main strategies. For this purpose, various classical production systems like Escherichia coli or Saccharomyces cerevisiae are used and have been optimized via genetic modifications. Despite the progress made, this strategy competes for nutritional resources and agricultural land. To overcome this problem, various attempts were made for direct photosynthetic driven ethanol synthesis with different microalgal species including cyanobacteria. However, compared to existing platforms, the development of cyanobacteria as photoautotrophic cell factories has just started, and accordingly, the ethanol yield of established production systems is still unreached. This is mainly attributed to low ethanol tolerance levels of cyanobacteria and there is still potential for optimizing the cyanobacteria towards alternative gene expression systems. Meanwhile, several improvements were made by establishing new toolboxes for synthetic biology offering new possibilities for advanced genetic modifications of cyanobacteria. Here, current achievements and innovations of those new molecular tools are discussed.
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25
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Vavitsas K, Crozet P, Vinde MH, Davies F, Lemaire SD, Vickers CE. The Synthetic Biology Toolkit for Photosynthetic Microorganisms. PLANT PHYSIOLOGY 2019; 181:14-27. [PMID: 31262955 PMCID: PMC6716251 DOI: 10.1104/pp.19.00345] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Accepted: 06/09/2019] [Indexed: 05/10/2023]
Abstract
Photosynthetic microorganisms offer novel characteristics as synthetic biology chassis, and the toolbox of components and techniques for cyanobacteria and algae is rapidly increasing.
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Affiliation(s)
- Konstantinos Vavitsas
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Pierre Crozet
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Marcos Hamborg Vinde
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
| | - Fiona Davies
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401
| | - Stéphane D Lemaire
- Institut de Biologie Physico-Chimique, Unité Mixte de Recherche 8226, Centre National de la Recherche Scientifique, Sorbonne Université, 75005 Paris, France
| | - Claudia E Vickers
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, Queensland 4072, Australia
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Synthetic Biology Future Science Platform, CSIRO Land & Water, Brisbane, Queensland 4001, Australia
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26
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Khan AZ, Bilal M, Mehmood S, Sharma A, Iqbal HMN. State-of-the-Art Genetic Modalities to Engineer Cyanobacteria for Sustainable Biosynthesis of Biofuel and Fine-Chemicals to Meet Bio-Economy Challenges. Life (Basel) 2019; 9:life9030054. [PMID: 31252652 PMCID: PMC6789541 DOI: 10.3390/life9030054] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 06/15/2019] [Accepted: 06/26/2019] [Indexed: 02/07/2023] Open
Abstract
In recent years, metabolic engineering of microorganisms has attained much research interest to produce biofuels and industrially pertinent chemicals. Owing to the relatively fast growth rate, genetic malleability, and carbon neutral production process, cyanobacteria has been recognized as a specialized microorganism with a significant biotechnological perspective. Metabolically engineering cyanobacterial strains have shown great potential for the photosynthetic production of an array of valuable native or non-native chemicals and metabolites with profound agricultural and pharmaceutical significance using CO2 as a building block. In recent years, substantial improvements in developing and introducing novel and efficient genetic tools such as genome-scale modeling, high throughput omics analyses, synthetic/system biology tools, metabolic flux analysis and clustered regularly interspaced short palindromic repeats (CRISPR)-associated nuclease (CRISPR/cas) systems have been made for engineering cyanobacterial strains. Use of these tools and technologies has led to a greater understanding of the host metabolism, as well as endogenous and heterologous carbon regulation mechanisms which consequently results in the expansion of maximum productive ability and biochemical diversity. This review summarizes recent advances in engineering cyanobacteria to produce biofuel and industrially relevant fine chemicals of high interest. Moreover, the development and applications of cutting-edge toolboxes such as the CRISPR-cas9 system, synthetic biology, high-throughput "omics", and metabolic flux analysis to engineer cyanobacteria for large-scale cultivation are also discussed.
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Affiliation(s)
- Aqib Zafar Khan
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
| | - Muhammad Bilal
- School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huaian 223003, China.
| | - Shahid Mehmood
- Bio-X Institute, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders (Ministry of Education), Shanghai Jiao Tong University, Shanghai 200030, China
| | - Ashutosh Sharma
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Queretaro, Epigmenio Gonzalez 500, Queretaro CP 76130, Mexico
| | - Hafiz M N Iqbal
- Tecnologico de Monterrey, School of Engineering and Sciences, Campus Monterrey, Ave. Eugenio Garza Sada 2501, Monterrey CP 64849, N.L., Mexico.
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27
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Sengupta A, Sunder AV, Sohoni SV, Wangikar PP. Fine-Tuning Native Promoters of Synechococcus elongatus PCC 7942 To Develop a Synthetic Toolbox for Heterologous Protein Expression. ACS Synth Biol 2019; 8:1219-1223. [PMID: 30973704 DOI: 10.1021/acssynbio.9b00066] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The cyanobacterium Synechococcus elongatus PCC 7942 is a potential photosynthetic cell-factory. In this study, two native promoters from S. elongatus PCC 7942 driving the expression of abundant cyanobacterial proteins phycocyanin (P cpcB7942) and RuBisCO (P rbc7942) were characterized in relation to their sequence features, expression levels, diurnal behavior, and regulation by light and CO2, major abiotic factors important for cyanobacterial growth. P cpcB7942 was repressed under high light intensity, but cultivation at higher CO2 concentration was able to recover promoter activity. On the other hand, P rbc7942 was repressed by elevated CO2 with a negative regulatory region between 300 and 225 bp. Removal of this region flipped the effect of CO2 with Rbc225 being activated only at high CO2 concentration, besides leading to the loss of circadian rhythm. The results from this study on promoter features and regulation will help expand the repertoire of tools for pathway engineering in cyanobacteria.
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28
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Vasudevan R, Gale GAR, Schiavon AA, Puzorjov A, Malin J, Gillespie MD, Vavitsas K, Zulkower V, Wang B, Howe CJ, Lea-Smith DJ, McCormick AJ. CyanoGate: A Modular Cloning Suite for Engineering Cyanobacteria Based on the Plant MoClo Syntax. PLANT PHYSIOLOGY 2019; 180:39-55. [PMID: 30819783 PMCID: PMC6501082 DOI: 10.1104/pp.18.01401] [Citation(s) in RCA: 87] [Impact Index Per Article: 17.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/16/2019] [Indexed: 05/10/2023]
Abstract
Recent advances in synthetic biology research have been underpinned by an exponential increase in available genomic information and a proliferation of advanced DNA assembly tools. The adoption of plasmid vector assembly standards and parts libraries has greatly enhanced the reproducibility of research and the exchange of parts between different labs and biological systems. However, a standardized modular cloning (MoClo) system is not yet available for cyanobacteria, which lag behind other prokaryotes in synthetic biology despite their huge potential regarding biotechnological applications. By building on the assembly library and syntax of the Plant Golden Gate MoClo kit, we have developed a versatile system called CyanoGate that unites cyanobacteria with plant and algal systems. Here, we describe the generation of a suite of parts and acceptor vectors for making (1) marked/unmarked knock-outs or integrations using an integrative acceptor vector, and (2) transient multigene expression and repression systems using known and previously undescribed replicative vectors. We tested and compared the CyanoGate system in the established model cyanobacterium Synechocystis sp. PCC 6803 and the more recently described fast-growing strain Synechococcus elongatus UTEX 2973. The UTEX 2973 fast-growth phenotype was only evident under specific growth conditions; however, UTEX 2973 accumulated high levels of proteins with strong native or synthetic promoters. The system is publicly available and can be readily expanded to accommodate other standardized MoClo parts to accelerate the development of reliable synthetic biology tools for the cyanobacterial community.
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Affiliation(s)
- Ravendran Vasudevan
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Grant A R Gale
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Alejandra A Schiavon
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Anton Puzorjov
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - John Malin
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Michael D Gillespie
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Konstantinos Vavitsas
- Australian Institute of Bioengineering and Nanotechnology, The University of Queensland, Brisbane, Queensland 4072, Australia
- CSIRO, Synthetic Biology Future Science Platform, Brisbane, Queensland 4001, Australia
| | - Valentin Zulkower
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
| | - Baojun Wang
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Institute of Quantitative Biology, Biochemistry and Biotechnology, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3FF, United Kingdom
| | - Christopher J Howe
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, United Kingdom
| | - David J Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich NR4 7TJ, United Kingdom
| | - Alistair J McCormick
- Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
- Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh EH9 3BF, United Kingdom
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Machida S, Suzuki I. Characterization of cyanobacterial cells synthesizing 10-methyl stearic acid. PHOTOSYNTHESIS RESEARCH 2019; 139:173-183. [PMID: 29943360 DOI: 10.1007/s11120-018-0537-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2018] [Accepted: 06/15/2018] [Indexed: 06/08/2023]
Abstract
Recently, microalgae have attracted attention as sources of biomass energy. However, fatty acids from the microalgae are mainly unsaturated and show low stability in oxygenated environments, due to oxidation of the double bonds. The branched-chain fatty acid, 10-methyl stearic acid, is synthesized from oleic acid in certain bacteria; the fatty acid is saturated, but melting point is low. Thus, it is stable in the presence of oxygen and is highly fluid. We previously demonstrated that BfaA and BfaB in Mycobacterium chlorophenolicum are involved in the synthesis of 10-methyl stearic acid from oleic acid. In this study, as a consequence of the introduction of bfaA and bfaB into the cyanobacterium, Synechocystis sp. PCC 6803, we succeeded in producing 10-methyl stearic acid, with yields up to 4.1% of the total fatty acid content. The synthesis of 10-methyl stearic acid in Synechocystis cells did not show a significant effect on photosynthetic activity, but the growth of the cells was retarded at 34 °C. We observed that the synthesis of 10-methylene stearic acid, a precursor of 10-methyl stearic acid, had an inhibitory effect on the growth of the transformants, which was mitigated under microoxic conditions. Eventually, the amount of 10-methyl stearic acid present in the sulfoquinovosyl diacylglycerol and phosphatidylglycerol of the transformants was remarkably higher than that in the monogalactosyldiacylglycerol and digalactosyldiacylglycerol. Overall, we successfully synthesized 10-methyl stearic acid in the phototroph, Synechocystis, demonstrating that it is possible to synthesize unique modified fatty acids via photosynthesis that are not naturally produced in photosynthetic organisms.
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Affiliation(s)
- Shuntaro Machida
- Graduate School of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan
- Food Research Institute, National Agriculture and Food Research Organization, Kannondai 2-1-12, Tsukuba, Ibaraki, 305-8642, Japan
| | - Iwane Suzuki
- Faculty of Life and Environmental Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba, Ibaraki, 305-8572, Japan.
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30
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Metabolic engineering tools in model cyanobacteria. Metab Eng 2018; 50:47-56. [DOI: 10.1016/j.ymben.2018.03.014] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2018] [Revised: 03/15/2018] [Accepted: 03/15/2018] [Indexed: 12/27/2022]
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31
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Yao R, Liu D, Jia X, Zheng Y, Liu W, Xiao Y. CRISPR-Cas9/Cas12a biotechnology and application in bacteria. Synth Syst Biotechnol 2018; 3:135-149. [PMID: 30345399 PMCID: PMC6190536 DOI: 10.1016/j.synbio.2018.09.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 09/24/2018] [Accepted: 09/25/2018] [Indexed: 12/26/2022] Open
Abstract
CRISPR-Cas technologies have greatly reshaped the biology field. In this review, we discuss the CRISPR-Cas with a particular focus on the associated technologies and applications of CRISPR-Cas9 and CRISPR-Cas12a, which have been most widely studied and used. We discuss the biological mechanisms of CRISPR-Cas as immune defense systems, recently-discovered anti-CRISPR-Cas systems, and the emerging Cas variants (such as xCas9 and Cas13) with unique characteristics. Then, we highlight various CRISPR-Cas biotechnologies, including nuclease-dependent genome editing, CRISPR gene regulation (including CRISPR interference/activation), DNA/RNA base editing, and nucleic acid detection. Last, we summarize up-to-date applications of the biotechnologies for synthetic biology and metabolic engineering in various bacterial species.
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Affiliation(s)
- Ruilian Yao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Di Liu
- Department of Biomass Science and Conversion Technology, Sandia National Laboratories, Livermore, CA 94551, USA
| | - Xiao Jia
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yuan Zheng
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Wei Liu
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
| | - Yi Xiao
- State Key Laboratory of Microbial Metabolism, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240, China
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32
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Ferreira EA, Pacheco CC, Pinto F, Pereira J, Lamosa P, Oliveira P, Kirov B, Jaramillo A, Tamagnini P. Expanding the toolbox for Synechocystis sp. PCC 6803: validation of replicative vectors and characterization of a novel set of promoters. Synth Biol (Oxf) 2018; 3:ysy014. [PMID: 32995522 PMCID: PMC7445879 DOI: 10.1093/synbio/ysy014] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 11/14/2022] Open
Abstract
Cyanobacteria are promising 'low-cost' cell factories since they have minimal nutritional requirements, high metabolic plasticity and can use sunlight and CO2 as energy and carbon sources. The unicellular Synechocystis sp. PCC 6803, already considered the 'green' Escherichia coli, is the best studied cyanobacterium but to be used as an efficient and robust photoautotrophic chassis it requires a customized and well-characterized toolbox. In this context, we evaluated the possibility of using three self-replicative vectors from the Standard European Vector Architecture (SEVA) repository to transform Synechocystis. Our results demonstrated that the presence of the plasmid does not lead to an evident phenotype or hindered Synechocystis growth, being the vast majority of the cells able to retain the replicative plasmid even in the absence of selective pressure. In addition, a set of heterologous and redesigned promoters were characterized exhibiting a wide range of activities compared to the reference P rnpB , three of which could be efficiently repressed. As a proof-of-concept, from the expanded toolbox, one promoter was selected and assembled with the ggpS gene [encoding one of the proteins involved in the synthesis of the native compatible solute glucosylglycerol (GG)] and the synthetic device was introduced into Synechocystis using one of the SEVA plasmids. The presence of this device restored the production of the GG in a ggpS deficient mutant validating the functionality of the tools/device developed in this study.
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Affiliation(s)
- Eunice A Ferreira
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal.,ICBAS - Instituto de Ciências Biomédicas Abel Salazar Universidade do Porto, Porto, Portugal
| | - Catarina C Pacheco
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Filipe Pinto
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal.,School of Biological Sciences, University of Edinburgh, Edinburgh, UK.,Centre for Synthetic and Systems Biology, University of Edinburgh, Edinburgh, UK
| | - José Pereira
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Pedro Lamosa
- Instituto de Tecnologia Química e Biológica António Xavier, ITQB NOVA, Oeiras, Portugal
| | - Paulo Oliveira
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal
| | - Boris Kirov
- CNRS-UMR8030 Laboratoire iSSB and Université Paris-Saclay and Université d'Évry and CEA DRF, IG, Genoscope, Évry, France.,ANP - Faculty of Automatics, TU - Sofia, Sofia, Bulgaria.,BioInfoTech Lab - RDIC, Sofia Tech Park, Sofia, Bulgaria
| | - Alfonso Jaramillo
- CNRS-UMR8030 Laboratoire iSSB and Université Paris-Saclay and Université d'Évry and CEA DRF, IG, Genoscope, Évry, France.,Warwick Integrative Synthetic Biology Centre and School of Life Sciences, University of Warwick, Coventry, UK.,Institute for Integrative Systems Biology (I2SysBio) University of Valencia-CSIC, Paterna, Spain
| | - Paula Tamagnini
- i3S - Instituto de Investigação e Inovação em Saúde Universidade do Porto, Porto, Portugal.,IBMC - Instituto de Biologia Molecular e Celular Universidade do Porto, Porto, Portugal.,Faculdade de Ciências, Departamento de Biologia, Universidade do Porto, Porto, Portugal
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Sun T, Li S, Song X, Diao J, Chen L, Zhang W. Toolboxes for cyanobacteria: Recent advances and future direction. Biotechnol Adv 2018; 36:1293-1307. [DOI: 10.1016/j.biotechadv.2018.04.007] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 04/09/2018] [Accepted: 04/26/2018] [Indexed: 12/20/2022]
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34
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Xiao Y, Wang S, Rommelfanger S, Balassy A, Barba-Ostria C, Gu P, Galazka JM, Zhang F. Developing a Cas9-based tool to engineer native plasmids in Synechocystis sp. PCC 6803. Biotechnol Bioeng 2018; 115:2305-2314. [PMID: 29896914 DOI: 10.1002/bit.26747] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2018] [Revised: 05/06/2018] [Accepted: 06/05/2018] [Indexed: 01/05/2023]
Abstract
The oxygenic photosynthetic bacterium Synechocystis sp. PCC 6803 (S6803) is a model cyanobacterium widely used for fundamental research and biotechnology applications. Due to its polyploidy, existing methods for genome engineering of S6803 require multiple rounds of selection to modify all genome copies, which is time-consuming and inefficient. In this study, we engineered the Cas9 tool for one-step, segregation-free genome engineering. We further used our Cas9 tool to delete three of seven S6803 native plasmids. Our results show that all three small-size native plasmids, but not the large-size native plasmids, can be deleted with this tool. To further facilitate heterologous gene expression in S6803, a shuttle vector based on the native plasmid pCC5.2 was created. The shuttle vector can be introduced into Cas9-containing S6803 in one step without requiring segregation and can be stably maintained without antibiotic pressure for at least 30 days. Moreover, genes encoded on the shuttle vector remain functional after 30 days of continuous cultivation without selective pressure. Thus, this study provides a set of new tools for rapid modification of the S6803 genome and for stable expression of heterologous genes, potentially facilitating both fundamental research and biotechnology applications using S6803.
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Affiliation(s)
- Yi Xiao
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: State Key Laboratory for Microbial Metabolism, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Shaojie Wang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Sarah Rommelfanger
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
| | - Andrea Balassy
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Carlos Barba-Ostria
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Present address: Department of Health Sciences, Ambato Technical University, Ambato, Ecuador
| | - Pengfei Gu
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
| | - Jonathan M Galazka
- Space Biosciences Division, Ames Research Center, National Aeronautics and Space Administration, Mountain View, California
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, Saint Louis, Missori
- Division of Biological & Biomedical Sciences, Washington University in St. Louis, Saint Louis, Missori
- Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Misssori
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35
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Abstract
Biological nitrogen fixation is catalyzed by nitrogenase, a complex metalloenzyme found only in prokaryotes. N2 fixation is energetically highly expensive, and an energy-generating process such as photosynthesis can meet the energy demand of N2 fixation. However, synthesis and expression of nitrogenase are exquisitely sensitive to the presence of oxygen. Thus, engineering nitrogen fixation activity in photosynthetic organisms that produce oxygen is challenging. Cyanobacteria are oxygenic photosynthetic prokaryotes, and some of them also fix N2. Here, we demonstrate a feasible way to engineer nitrogenase activity in the nondiazotrophic cyanobacterium Synechocystis sp. PCC 6803 through the transfer of 35 nitrogen fixation (nif) genes from the diazotrophic cyanobacterium Cyanothece sp. ATCC 51142. In addition, we have identified the minimal nif cluster required for such activity in Synechocystis 6803. Moreover, nitrogenase activity was significantly improved by increasing the expression levels of nif genes. Importantly, the O2 tolerance of nitrogenase was enhanced by introduction of uptake hydrogenase genes, showing this to be a functional way to improve nitrogenase enzyme activity under micro-oxic conditions. To date, our efforts have resulted in engineered Synechocystis 6803 strains that, remarkably, have more than 30% of the N2 fixation activity of Cyanothece 51142, the highest such activity established in any nondiazotrophic oxygenic photosynthetic organism. This report establishes a baseline for the ultimate goal of engineering nitrogen fixation ability in crop plants. Application of chemically synthesized nitrogen fertilizers has revolutionized agriculture. However, the energetic costs of such production processes and the widespread application of fertilizers have raised serious environmental issues. A sustainable alternative is to endow to crop plants the ability to fix atmospheric N2in situ. One long-term approach is to transfer all nif genes from a prokaryote to plant cells and to express nitrogenase in an energy-producing organelle, chloroplast, or mitochondrion. In this context, Synechocystis 6803, the nondiazotrophic cyanobacterium utilized in this study, provides a model chassis for rapid investigation of the necessary requirements to establish diazotrophy in an oxygenic phototroph.
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36
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Sengupta A, Pakrasi HB, Wangikar PP. Recent advances in synthetic biology of cyanobacteria. Appl Microbiol Biotechnol 2018; 102:5457-5471. [PMID: 29744631 DOI: 10.1007/s00253-018-9046-x] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2018] [Revised: 04/23/2018] [Accepted: 04/24/2018] [Indexed: 12/11/2022]
Abstract
Cyanobacteria are attractive hosts that can be engineered for the photosynthetic production of fuels, fine chemicals, and proteins from CO2. Moreover, the responsiveness of these photoautotrophs towards different environmental signals, such as light, CO2, diurnal cycle, and metals make them potential hosts for the development of biosensors. However, engineering these hosts proves to be a challenging and lengthy process. Synthetic biology can make the process of biological engineering more predictable through the use of standardized biological parts that are well characterized and tools to assemble them. While significant progress has been made with model heterotrophic organisms, many of the parts and tools are not portable in cyanobacteria. Therefore, efforts are underway to develop and characterize parts derived from cyanobacteria. In this review, we discuss the reported parts and tools with the objective to develop cyanobacteria as cell factories or biosensors. We also discuss the issues related to characterization, tunability, portability, and the need to develop enabling technologies to engineer this "green" chassis.
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Affiliation(s)
- Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India
| | - Himadri B Pakrasi
- Department of Biology, Washington University, St. Louis, MO, USA.,Department of Energy, Environmental and Chemical Engineering, Washington University, St. Louis, MO, USA
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,DBT-Pan IIT Center for Bioenergy, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India. .,Wadhwani Research Center for Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai, 400076, India.
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37
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Liu D, Pakrasi HB. Exploring native genetic elements as plug-in tools for synthetic biology in the cyanobacterium Synechocystis sp. PCC 6803. Microb Cell Fact 2018; 17:48. [PMID: 29580240 PMCID: PMC5868059 DOI: 10.1186/s12934-018-0897-8] [Citation(s) in RCA: 59] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 03/21/2018] [Indexed: 11/24/2022] Open
Abstract
Background The unicellular cyanobacterium Synechocystis sp. PCC 6803 has been widely used as a photoautotrophic host for synthetic biology studies. However, as a green chassis to capture CO2 for biotechnological applications, the genetic toolbox for Synechocystis 6803 is still a limited factor. Results We systematically characterized endogenous genetic elements of Synechocystis 6803, including promoters, ribosome binding sites, transcription terminators, and plasmids. Expression from twelve native promoters was compared by measuring fluorescence from the reporter protein EYFP in an identical setup, exhibiting an 8000-fold range of promoter activities. Moreover, we measured the strength of twenty native ribosome binding sites and eight native terminators, indicating their influence on the expression of the reporter genes. In addition, two shuttle vectors, pCA-UC118 and pCB-SC101, capable of replication in both Synechocystis 6803 and E. coli were constructed. Expression of reporter proteins were significantly enhanced in cells containing these new plasmids, thus providing superior gene expression platforms in this cyanobacterium. Conclusions The results of this study provide useful and well characterized native tools for bioengineering work in the model cyanobacterium Synechocystis 6803. Electronic supplementary material The online version of this article (10.1186/s12934-018-0897-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Deng Liu
- Department of Biology, Washington University, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA
| | - Himadri B Pakrasi
- Department of Biology, Washington University, Campus Box 1137, One Brookings Drive, St. Louis, MO, 63130, USA.
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38
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Liang F, Englund E, Lindberg P, Lindblad P. Engineered cyanobacteria with enhanced growth show increased ethanol production and higher biofuel to biomass ratio. Metab Eng 2018; 46:51-59. [DOI: 10.1016/j.ymben.2018.02.006] [Citation(s) in RCA: 67] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2017] [Revised: 12/14/2017] [Accepted: 02/18/2018] [Indexed: 01/02/2023]
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39
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DeLorenzo DM, Rottinghaus AG, Henson WR, Moon TS. Molecular Toolkit for Gene Expression Control and Genome Modification in Rhodococcus opacus PD630. ACS Synth Biol 2018; 7:727-738. [PMID: 29366319 DOI: 10.1021/acssynbio.7b00416] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Rhodococcus opacus PD630 is a non-model Gram-positive bacterium that possesses desirable traits for lignocellulosic biomass conversion. In particular, it has a relatively rapid growth rate, exhibits genetic tractability, produces high quantities of lipids, and can tolerate and consume toxic lignin-derived aromatic compounds. Despite these unique, industrially relevant characteristics, R. opacus has been underutilized because of a lack of reliable genetic parts and engineering tools. In this work, we developed a molecular toolbox for reliable gene expression control and genome modification in R. opacus. To facilitate predictable gene expression, a constitutive promoter library spanning ∼45-fold in output was constructed. To improve the characterization of available plasmids, the copy numbers of four heterologous and nine endogenous plasmids were determined using quantitative PCR. The molecular toolbox was further expanded by screening a previously unreported antibiotic resistance marker (HygR) and constructing a curable plasmid backbone for temporary gene expression (pB264). Furthermore, a system for genome modification was devised, and three neutral integration sites were identified using a novel combination of transcriptomic data, genomic architecture, and growth rate analysis. Finally, the first reported system for targeted, tunable gene repression in Rhodococcus was developed by utilizing CRISPR interference (CRISPRi). Overall, this work greatly expands the ability to manipulate and engineer R. opacus, making it a viable new chassis for bioproduction from renewable feedstocks.
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Affiliation(s)
- Drew M. DeLorenzo
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Austin G. Rottinghaus
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - William R. Henson
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
| | - Tae Seok Moon
- Department of Energy, Environmental
and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri 63130, United States
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40
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Stensjö K, Vavitsas K, Tyystjärvi T. Harnessing transcription for bioproduction in cyanobacteria. PHYSIOLOGIA PLANTARUM 2018; 162:148-155. [PMID: 28762505 DOI: 10.1111/ppl.12606] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Revised: 07/04/2017] [Accepted: 07/10/2017] [Indexed: 06/07/2023]
Abstract
Sustainable production of biofuels and other valuable compounds is one of our future challenges. One tempting possibility is to use photosynthetic cyanobacteria as production factories. Currently, tools for genetic engineering of cyanobacteria are not good enough to exploit the full potential of cyanobacteria. A wide variety of expression systems will be required to adjust both the expression of heterologous enzyme(s) and metabolic routes to the best possible balance, allowing the optimal production of a particular substance. In bacteria, transcription, especially the initiation of transcription, has a central role in adjusting gene expression and thus also metabolic fluxes of cells according to environmental cues. Here we summarize the recent progress in developing tools for efficient cyanofactories, focusing especially on transcriptional regulation.
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Affiliation(s)
- Karin Stensjö
- Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, 75120 Uppsala, Sweden
| | - Konstantinos Vavitsas
- Copenhagen Plant Science Centre, Department of Plant and Environmental Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Taina Tyystjärvi
- Molecular Plant Biology, Department of Biochemistry, University of Turku, FI-20014 Turku, Finland
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41
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Wang B, Eckert C, Maness PC, Yu J. A Genetic Toolbox for Modulating the Expression of Heterologous Genes in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2018; 7:276-286. [PMID: 29232504 DOI: 10.1021/acssynbio.7b00297] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Cyanobacteria, genetic models for photosynthesis research for decades, have recently become attractive hosts for producing renewable fuels and chemicals, owing to their genetic tractability, relatively fast growth, and their ability to utilize sunlight, fix carbon dioxide, and in some cases, fix nitrogen. Despite significant advances, there is still an urgent demand for synthetic biology tools in order to effectively manipulate genetic circuits in cyanobacteria. In this study, we have compared a total of 17 natural and chimeric promoters, focusing on expression of the ethylene-forming enzyme (EFE) in the cyanobacterium Synechocystis sp. PCC 6803. We report the finding that the E. coli σ70 promoter Ptrc is superior compared to the previously reported strong promoters, such as PcpcB and PpsbA, for the expression of EFE. In addition, we found that the EFE expression level was very sensitive to the 5'-untranslated region upstream of the open reading frame. A library of ribosome binding sites (RBSs) was rationally designed and was built and systematically characterized. We demonstrate a strategy complementary to the RBS prediction software to facilitate the rational design of an RBS library to optimize the gene expression in cyanobacteria. Our results show that the EFE expression level is dramatically enhanced through these synthetic biology tools and is no longer the rate-limiting step for cyanobacterial ethylene production. These systematically characterized promoters and the RBS design strategy can serve as useful tools to tune gene expression levels and to identify and mitigate metabolic bottlenecks in cyanobacteria.
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Affiliation(s)
- Bo Wang
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Carrie Eckert
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
- Renewable
and Sustainable Energy Institute, University of Colorado, Boulder, 4001 Discovery Drive, Boulder, Colorado 80303, United States
| | - Pin-Ching Maness
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
| | - Jianping Yu
- Biosciences
Center, National Renewable Energy Laboratory, 15013 Denver West Parkway, Golden, Colorado 80401, United States
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42
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Metabolic engineering of the pentose phosphate pathway for enhanced limonene production in the cyanobacterium Synechocysti s sp. PCC 6803. Sci Rep 2017; 7:17503. [PMID: 29235513 PMCID: PMC5727528 DOI: 10.1038/s41598-017-17831-y] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2017] [Accepted: 11/30/2017] [Indexed: 11/08/2022] Open
Abstract
Isoprenoids are diverse natural compounds, which have various applications as pharmaceuticals, fragrances, and solvents. The low yield of isoprenoids in plants makes them difficult for cost-effective production, and chemical synthesis of complex isoprenoids is impractical. Microbial production of isoprenoids has been considered as a promising approach to increase the yield. In this study, we engineered the model cyanobacterium Synechocystis sp. PCC 6803 for sustainable production of a commercially valuable isoprenoid, limonene. Limonene synthases from the plants Mentha spicata and Citrus limon were expressed in cyanobacteria for limonene production. Production of limonene was two-fold higher with limonene synthase from M. spicata than that from C. limon. To enhance isoprenoid production, computational strain design was conducted by applying the OptForce strain design algorithm on Synechocystis 6803. Based on the metabolic interventions suggested by this algorithm, genes (ribose 5-phosphate isomerase and ribulose 5-phosphate 3-epimerase) in the pentose phosphate pathway were overexpressed, and a geranyl diphosphate synthase from the plant Abies grandis was expressed to optimize the limonene biosynthetic pathway. The optimized strain produced 6.7 mg/L of limonene, a 2.3-fold improvement in productivity. Thus, this study presents a feasible strategy to engineer cyanobacteria for photosynthetic production of isoprenoids.
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Miao R, Liu X, Englund E, Lindberg P, Lindblad P. Isobutanol production in Synechocystis PCC 6803 using heterologous and endogenous alcohol dehydrogenases. Metab Eng Commun 2017; 5:45-53. [PMID: 29188183 PMCID: PMC5699533 DOI: 10.1016/j.meteno.2017.07.003] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2017] [Revised: 07/18/2017] [Accepted: 07/27/2017] [Indexed: 12/24/2022] Open
Abstract
Isobutanol is a flammable compound that can be used as a biofuel due to its high energy density and suitable physical and chemical properties. In this study, we examined the capacity of engineered strains of Synechocystis PCC 6803 containing the α-ketoisovalerate decarboxylase from Lactococcus lactis and different heterologous and endogenous alcohol dehydrogenases (ADH) for isobutanol production. A strain expressing an introduced kivd without any additional copy of ADH produced 3 mg L-1 OD750-1 isobutanol in 6 days. After the cultures were supplemented with external addition of isobutyraldehyde, the substrate for ADH, 60.8 mg L-1 isobutanol was produced after 24 h when OD750 was 0.8. The in vivo activities of four different ADHs, two heterologous and two putative endogenous in Synechocystis, were examined and the Synechocystis endogenous ADH encoded by slr1192 showed the highest efficiency for isobutanol production. Furthermore, the strain overexpressing the isobutanol pathway on a self-replicating vector with the strong Ptrc promoter showed significantly higher gene expression and isobutanol production compared to the corresponding strains expressing the same operon introduced on the genome. Hence, this study demonstrates that Synechocystis endogenous AHDs have a high capacity for isobutanol production, and identifies kivd encoded α-ketoisovalerate decarboxylase as one of the likely bottlenecks for further isobutanol production.
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Affiliation(s)
| | | | | | | | - Peter Lindblad
- Microbial chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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Xiao Y, Jiang W, Zhang F. Developing a Genetically Encoded, Cross-Species Biosensor for Detecting Ammonium and Regulating Biosynthesis of Cyanophycin. ACS Synth Biol 2017; 6:1807-1815. [PMID: 28683543 DOI: 10.1021/acssynbio.7b00069] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Responding to nitrogen status is essential for all living organisms. Bacteria have evolved various complex and exquisite regulatory systems to control nitrogen metabolism. However, natural nitrogen regulatory systems, owing to their complexity, often function only in their original hosts and do not respond properly when transferred to another species. By harnessing the Lactococcus GlnRA system, we developed a genetically encoded, cross-species ammonium biosensor that displays a dynamic range up to 9-fold upon detection of ammonium ion. We demonstrated applications of this ammonium biosensor in three different species (Escherichia coli, Pseudomonas putida, and Synechocystis sp.) to detect different nitrogen sources. This ammonium sensor was further used to regulate the biosynthesis of a nitrogen-rich polymer, cyanophycin, based on ammonium concentration. Given the importance of nitrogen responses, the developed biosensor should be broadly applicable to synthetic biology and bioengineering.
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Affiliation(s)
- Yi Xiao
- Department of Energy, Environmental and Chemical Engineering, ‡Division of Biological & Biomedical Sciences, §Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Wen Jiang
- Department of Energy, Environmental and Chemical Engineering, ‡Division of Biological & Biomedical Sciences, §Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
| | - Fuzhong Zhang
- Department of Energy, Environmental and Chemical Engineering, ‡Division of Biological & Biomedical Sciences, §Institute of Materials Science & Engineering, Washington University in St. Louis, Saint Louis, Missouri 63130, United States
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45
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Immethun CM, DeLorenzo DM, Focht CM, Gupta D, Johnson CB, Moon TS. Physical, chemical, and metabolic state sensors expand the synthetic biology toolbox for Synechocystis sp. PCC 6803. Biotechnol Bioeng 2017; 114:1561-1569. [PMID: 28244586 DOI: 10.1002/bit.26275] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2016] [Revised: 01/19/2017] [Accepted: 02/19/2017] [Indexed: 02/04/2023]
Abstract
Many under-developed organisms possess important traits that can boost the effectiveness and sustainability of microbial biotechnology. Photoautotrophic cyanobacteria can utilize the energy captured from light to fix carbon dioxide for their metabolic needs while living in environments not suited for growing crops. Various value-added compounds have been produced by cyanobacteria in the laboratory; yet, the products' titers and yields are often not industrially relevant and lag behind what have been accomplished in heterotrophic microbes. Genetic tools for biological process control are needed to take advantage of cyanobacteria's beneficial qualities, as tool development also lags behind what has been created in common heterotrophic hosts. To address this problem, we developed a suite of sensors that regulate transcription in the model cyanobacterium Synechocystis sp. PCC 6803 in response to metabolically relevant signals, including light and the cell's nitrogen status, and a family of sensors that respond to the inexpensive chemical, l-arabinose. Increasing the number of available tools enables more complex and precise control of gene expression. Expanding the synthetic biology toolbox for this cyanobacterium also improves our ability to utilize this important under-developed organism in biotechnology. Biotechnol. Bioeng. 2017;114: 1561-1569. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Cheryl M Immethun
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Drew M DeLorenzo
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Caroline M Focht
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Dinesh Gupta
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Charles B Johnson
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
| | - Tae Seok Moon
- Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, St. Louis, Missouri
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46
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Kim WJ, Lee SM, Um Y, Sim SJ, Woo HM. Development of SyneBrick Vectors As a Synthetic Biology Platform for Gene Expression in Synechococcus elongatus PCC 7942. FRONTIERS IN PLANT SCIENCE 2017; 8:293. [PMID: 28303150 PMCID: PMC5332412 DOI: 10.3389/fpls.2017.00293] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2016] [Accepted: 02/17/2017] [Indexed: 05/20/2023]
Abstract
Cyanobacteria are oxygenic photosynthetic prokaryotes that are able to assimilate CO2 using solar energy and water. Metabolic engineering of cyanobacteria has suggested the possibility of direct CO2 conversion to value-added chemicals. However, engineering of cyanobacteria has been limited due to the lack of various genetic tools for expression and control of multiple genes to reconstruct metabolic pathways for biochemicals from CO2. Thus, we developed SyneBrick vectors as a synthetic biology platform for gene expression in Synechococcus elongatus PCC 7942 as a model cyanobacterium. The SyneBrick chromosomal integration vectors provide three inducible expression systems to control gene expression and three neutral sites for chromosomal integrations. Using a SyneBrick vector, LacI-regulated gene expression led to 24-fold induction of the eYFP reporter gene with 1 mM isopropyl β-D-1-thiogalactopyranoside (IPTG) inducer in S. elongatus PCC 7942 under 5% (v/v) CO2. TetR-regulated gene expression led to 19-fold induction of the GFP gene when 100 nM anhydrotetracycline (aTc) inducer was used. Gene expression decreased after 48 h due to degradation of aTc under light. T7 RNA polymerase-based gene expression resulted in efficient expression with a lower IPTG concentration than a previously developed pTrc promoter. A library of T7 promoters can be used for tunable gene expression. In summary, SyneBrick vectors were developed as a synthetic biology platform for gene expression in S. elongatus PCC 7942. These results will accelerate metabolic engineering of biosolar cell factories through expressing and controlling multiple genes of interest.
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Affiliation(s)
- Wook Jin Kim
- Clean Energy Research Center, Korea Institute of Science and TechnologySeoul, South Korea
- Green School (Graduate School of Energy and Environment), Korea UniversitySeoul, South Korea
| | - Sun-Mi Lee
- Clean Energy Research Center, Korea Institute of Science and TechnologySeoul, South Korea
- Green School (Graduate School of Energy and Environment), Korea UniversitySeoul, South Korea
| | - Youngsoon Um
- Clean Energy Research Center, Korea Institute of Science and TechnologySeoul, South Korea
| | - Sang Jun Sim
- Green School (Graduate School of Energy and Environment), Korea UniversitySeoul, South Korea
- Department of Chemical and Biological Engineering, Korea UniversitySeoul, South Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan UniversitySuwon, South Korea
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Liang F, Lindblad P. Synechocystis PCC 6803 overexpressing RuBisCO grow faster with increased photosynthesis. Metab Eng Commun 2017; 4:29-36. [PMID: 29468130 PMCID: PMC5779733 DOI: 10.1016/j.meteno.2017.02.002] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2016] [Revised: 11/28/2016] [Accepted: 02/17/2017] [Indexed: 12/21/2022] Open
Abstract
The ribulose-1,5-bisphosphate (RuBP) oxygenation reaction catalyzed by Ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO) is competing with carboxylation, being negative for both energy and carbon balances in photoautotrophic organisms. This makes RuBisCO one of the bottlenecks for oxygenic photosynthesis and carbon fixation. In this study, RuBisCO was overexpressed in the unicellular cyanobacterium Synechocystis PCC 6803. Relative RuBisCO levels in the engineered strains FL50 and FL52 increased 2.1 times and 1.4 times, respectively, and both strains showed increased growth, photosynthesis and in vitro RuBisCO activity. The oxygen evolution rate increased by 54% and 42% on per chlorophyll basis, while the in vitro RuBisCO activity increased by 52% and 8.6%, respectively. The overexpressed RuBisCO were tagged with a FLAG tag, in strain FL50 on the N terminus of the large subunit while in strain FL52 on the C terminus of the small subunit. The presence of a FLAG tag enhanced transcription of the genes encoding RuBisCO, and, with high possibility, also enhanced the initiation of translation or stability of the enzyme. However, when using a streptavidin-binding tag II (strep-tag II), we did not observe a similar effect. Tagged RuBisCO offers an opportunity for further studying RuBisCO expression and stability. Increased levels of RuBisCO can further improve photosynthesis and growth in the cyanobacterium Synechocystis PCC 6803 under certain growth conditions.
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Affiliation(s)
- Feiyan Liang
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
| | - Peter Lindblad
- Microbial Chemistry, Department of Chemistry-Ångström, Uppsala University, Box 523, SE-751 20 Uppsala, Sweden
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48
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Cyanobacterial metabolic engineering for biofuel and chemical production. Curr Opin Chem Biol 2016; 35:43-50. [DOI: 10.1016/j.cbpa.2016.08.023] [Citation(s) in RCA: 120] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 11/21/2022]
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Rasmussen RE, Erstad SM, Ramos-Martinez EM, Fimognari L, De Porcellinis AJ, Sakuragi Y. An easy and efficient permeabilization protocol for in vivo enzyme activity assays in cyanobacteria. Microb Cell Fact 2016; 15:186. [PMID: 27825349 PMCID: PMC5101802 DOI: 10.1186/s12934-016-0587-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Accepted: 10/29/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Cyanobacteria are photosynthetic bacteria that thrive in diverse ecosystems and play major roles in the global carbon cycle. The abilities of cyanobacteria to fix atmospheric CO2 and to allocate the fixed carbons to chemicals and biofuels have attracted growing attentions as sustainable microbial cell factories. Better understanding of the activities of enzymes involved in the central carbon metabolism would lead to increasing product yields. Currently cell-free lysates are the most widely used method for determination of intracellular enzyme activities. However, due to thick cell walls, lysis of cyanobacterial cells is inefficient and often laborious. In some cases radioisotope-labeled substrates can be fed directly to intact cells; however, label-free assays are often favored due to safety and practical reasons. RESULTS Here we show an easy and highly efficient method for permeabilization of the cyanobacteria Synechococcus sp. PCC 7002 and Synechocystis sp. PCC 6803, and determination of two intracellular enzymes, ribulose-1,5-bisphosphate carboxylase/decarboxylase (Rubisco) and glucose-6-phosphate dehydrogenase (G6PDH), that play pivotal roles in the central carbon metabolism in cyanobacteria. Incubation of the cyanobacterial cells in the commercially available B-PER reagent for 10 min permeabilized the cells, as confirmed by the SYTOX Green staining. There was no significant change in the cell shape and no major loss of intracellular proteins was observed during the treatment. When used directly in the assays, the permeabilized cells exhibited the enzyme activities that are comparable or even higher than those detected for cell-free lysates. Moreover, the permeabilized cells could be stored at -20 °C without losing the enzyme activities. The permeabilization process and subsequent activity assays were successfully adapted to the 96-well plate system. CONCLUSIONS An easy, efficient and scalable permeabilization protocol was established for cyanobacteria. The permeabilized cells can be directly applied for measurement of G6PDH and Rubisco activities without using radioisotopes and the protocol may be readily adapted to studies of other cyanobacterial species and other intracellular enzymes. The permeabilization and enzyme assays can be performed in 96-well plates in a high-throughput manner.
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Affiliation(s)
- Randi Engelberth Rasmussen
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Simon Matthé Erstad
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Erick Miguel Ramos-Martinez
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Lorenzo Fimognari
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Alice Jara De Porcellinis
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark
| | - Yumiko Sakuragi
- Department of Plant and Environmental Sciences, Copenhagen Plant Science Center, University of Copenhagen, Frederiksberg, Denmark.
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50
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Case AE, Atsumi S. Cyanobacterial chemical production. J Biotechnol 2016; 231:106-114. [DOI: 10.1016/j.jbiotec.2016.05.023] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2016] [Accepted: 05/19/2016] [Indexed: 01/03/2023]
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