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Madhu S, Sengupta A, Sarnaik AP, Wangikar PP. Expanding the synthetic biology repertoire of a fast-growing cyanobacterium Synechococcus elongatus PCC 11801. Biotechnol Bioeng 2024; 121:2974-2980. [PMID: 38773863 DOI: 10.1002/bit.28740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 05/04/2024] [Accepted: 05/07/2024] [Indexed: 05/24/2024]
Abstract
Synechococcus elongatus PCC 11801 is a fast-growing cyanobacterium, exhibiting high tolerance to environmental stresses. We have earlier characterized its genome and analysed its transcriptome and proteome. However, to deploy it as a potential cell factory, it is necessary to expand its synthetic biology toolbox, including promoter elements and ribosome binding sites (RBSs). Here, based on the global transcriptome analysis, 48 native promoters of the genes with high transcript count were characterized using a fluorescent reporter system. The promoters PcpcB, PpsbA1, and P11770 exhibited consistently high fluorescence under all the cultivation conditions. Similarly, from the genome data and proteome analysis, 534 operons were identified. Fifteen intergenic regions exhibiting higher protein expression from the downstream gene were systematically characterized for identifying RBSs, using an operon construct comprising fluorescent protein genes eyfp and mTurq under PcpcB (PcpcB:eyfp:RBS:mTurq:TrrnB). Overall, the work presents promoter and RBS sequence libraries, with varying strengths, to expedite bioengineering of PCC 11801.
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Affiliation(s)
- Swati Madhu
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Annesha Sengupta
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Aditya P Sarnaik
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
| | - Pramod P Wangikar
- Department of Chemical Engineering, Indian Institute of Technology Bombay, Mumbai, India
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2
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Li Z, Li S, Chen L, Sun T, Zhang W. Fast-growing cyanobacterial chassis for synthetic biology application. Crit Rev Biotechnol 2024; 44:414-428. [PMID: 36842999 DOI: 10.1080/07388551.2023.2166455] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 11/19/2022] [Accepted: 12/28/2022] [Indexed: 02/28/2023]
Abstract
Carbon neutrality by 2050 has become one of the most urgent challenges the world faces today. To address the issue, it is necessary to develop and promote new technologies related with CO2 recycling. Cyanobacteria are the only prokaryotes performing oxygenic photosynthesis, capable of fixing CO2 into biomass under sunlight and serving as one of the most important primary producers on earth. Notably, recent progress on synthetic biology has led to utilizing model cyanobacteria such as Synechocystis sp. PCC 6803 and Synechococcus elongatus PCC 7942 as chassis for "light-driven autotrophic cell factories" to produce several dozens of biofuels and various fine chemicals directly from CO2. However, due to the slow growth rate and low biomass accumulation in the current chassis, the productivity for most products is still lower than the threshold necessary for large-scale commercial application, raising the importance of developing high-efficiency cyanobacterial chassis with fast growth and/or higher biomass accumulation capabilities. In this article, we critically reviewed recent progresses on identification, systems biology analysis, and engineering of fast-growing cyanobacterial chassis. Specifically, fast-growing cyanobacteria identified in recent years, such as S. elongatus UTEX 2973, S. elongatus PCC 11801, S. elongatus PCC 11802 and Synechococcus sp. PCC 11901 was comparatively analyzed. In addition, the progresses on their recent application in converting CO2 into chemicals, and genetic toolboxes developed for these new cyanobacterial chassis were discussed. Finally, the article provides insights into future challenges and perspectives on the synthetic biology application of cyanobacterial chassis.
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Affiliation(s)
- Zhixiang Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Shubin Li
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Lei Chen
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
| | - Tao Sun
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
| | - Weiwen Zhang
- Laboratory of Synthetic Microbiology, School of Chemical Engineering and Technology, Tianjin University, Tianjin, P.R. China
- Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering, Ministry of Education of China, Tianjin, P.R. China
- Center for Biosafety Research and Strategy, Tianjin University, Tianjin, P.R. China
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3
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Zhou H, Wang Z, Qian J. Engineering of the hypoxia-induced Pichia stipitis ADH2 promoter to construct a promoter library for Pichia pastoris. J Biotechnol 2023; 376:24-32. [PMID: 37690664 DOI: 10.1016/j.jbiotec.2023.09.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/05/2023] [Accepted: 09/07/2023] [Indexed: 09/12/2023]
Abstract
Hypoxia-inducible promoters of a wide range of activities are desirable for fine-tuning gene expression in response to oxygen limitation, especially for the Crabtree negative yeast Pichia pastoris (Komagataella phaffii) with a high oxygen consumption rate in large-scale fermentations. Here we constructed a hypoxia-inducible promoter library for P. pastoris through error-prone PCR of Pichia stipitis ADH2 promoter (PsADH2). The library of 30 selected promoters showing 0.4- to 5.5-fold of the PsADH2 activity was obtained through high-throughput screening in microplates using the reporter yeast-enhanced green fluorescent protein. Two strong promoters, AM23 and AM30, were further characterized in shake flask cultures at high and low dissolved oxygen levels. They responded more sensitively to the low dissolved oxygen level, achieving a 4.6-, 7.9-fold and 3.6-, 7.7-fold higher fluorescence intensity and transcript level, respectively, than the wild-type PsADH2. Their hypoxia-inducible properties were confirmed with two additional reporters: β-galactosidase and Vitreoscilla hemoglobin, to demonstrate the broad applicability of the promoter library. During the typical fermentation process in shake flasks, the promoter AM30 showed strong expression with cell growth and decreased oxygen levels, without any additional chemical inducers or operations. Since the potent industrial host P. pastoris is recognized as an easy to scale-up system, it is reasonable to expect that the obtained hypoxia-inducible promoter library may have great potential to enable convenient regulation of gene expression under industrial fermentations which are usually run under oxygen limitation due to high cell density cultivations.
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Affiliation(s)
- Hangcheng Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Zhipeng Wang
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Jiangchao Qian
- State Key Laboratory of Bioreactor Engineering, East China University of Science & Technology, 130 Meilong Road, Shanghai 200237, PR China.
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4
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Sengupta A, Bandyopadhyay A, Schubert MG, Church GM, Pakrasi HB. Antenna Modification in a Fast-Growing Cyanobacterium Synechococcus elongatus UTEX 2973 Leads to Improved Efficiency and Carbon-Neutral Productivity. Microbiol Spectr 2023; 11:e0050023. [PMID: 37318337 PMCID: PMC10433846 DOI: 10.1128/spectrum.00500-23] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 05/19/2023] [Indexed: 06/16/2023] Open
Abstract
Our planet is sustained by sunlight, the primary energy source made accessible to all life forms by photoautotrophs. Photoautotrophs are equipped with light-harvesting complexes (LHCs) that enable efficient capture of solar energy, particularly when light is limiting. However, under high light, LHCs can harvest photons in excess of the utilization capacity of cells, causing photodamage. This damaging effect is most evident when there is a disparity between the amount of light harvested and carbon available. Cells strive to circumvent this problem by dynamically adjusting the antenna structure in response to the changing light signals, a process known to be energetically expensive. Much emphasis has been laid on elucidating the relationship between antenna size and photosynthetic efficiency and identifying strategies to synthetically modify antennae for optimal light capture. Our study is an effort in this direction and investigates the possibility of modifying phycobilisomes, the LHCs present in cyanobacteria, the simplest of photoautotrophs. We systematically truncate the phycobilisomes of Synechococcus elongatus UTEX 2973, a widely studied, fast-growing model cyanobacterium and demonstrate that partial truncation of its antenna can lead to a growth advantage of up to 36% compared to the wild type and an increase in sucrose titer of up to 22%. In contrast, targeted deletion of the linker protein which connects the first phycocyanin rod to the core proved detrimental, indicating that the core alone is not enough, and it is essential to maintain a minimal rod-core structure for efficient light harvest and strain fitness. IMPORTANCE Light energy is essential for the existence of life on this planet, and only photosynthetic organisms, equipped with light-harvesting antenna protein complexes, can capture this energy, making it readily accessible to all other life forms. However, these light-harvesting antennae are not designed to function optimally under extreme high light, a condition which can cause photodamage and significantly reduce photosynthetic productivity. In this study, we attempt to assess the optimal antenna structure for a fast-growing, high-light tolerant photosynthetic microbe with the goal of improving its productivity. Our findings provide concrete evidence that although the antenna complex is essential, antenna modification is a viable strategy to maximize strain performance under controlled growth conditions. This understanding can also be translated into identifying avenues to improve light harvesting efficiency in higher photoautotrophs.
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Affiliation(s)
- Annesha Sengupta
- Department of Biology, Washington University, St. Louis, Missouri, USA
| | | | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, Massachusetts, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, Massachusetts, USA
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:microorganisms11020455. [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
- Correspondence:
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6
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Bourgade B, Stensjö K. Synthetic biology in marine cyanobacteria: Advances and challenges. Front Microbiol 2022; 13:994365. [PMID: 36188008 PMCID: PMC9522894 DOI: 10.3389/fmicb.2022.994365] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 08/24/2022] [Indexed: 11/19/2022] Open
Abstract
The current economic and environmental context requests an accelerating development of sustainable alternatives for the production of various target compounds. Biological processes offer viable solutions and have gained renewed interest in the recent years. For example, photosynthetic chassis organisms are particularly promising for bioprocesses, as they do not require biomass-derived carbon sources and contribute to atmospheric CO2 fixation, therefore supporting climate change mitigation. Marine cyanobacteria are of particular interest for biotechnology applications, thanks to their rich diversity, their robustness to environmental changes, and their metabolic capabilities with potential for therapeutics and chemicals production without requiring freshwater. The additional cyanobacterial properties, such as efficient photosynthesis, are also highly beneficial for biotechnological processes. Due to their capabilities, research efforts have developed several genetic tools for direct metabolic engineering applications. While progress toward a robust genetic toolkit is continuously achieved, further work is still needed to routinely modify these species and unlock their full potential for industrial applications. In contrast to the understudied marine cyanobacteria, genetic engineering and synthetic biology in freshwater cyanobacteria are currently more advanced with a variety of tools already optimized. This mini-review will explore the opportunities provided by marine cyanobacteria for a greener future. A short discussion will cover the advances and challenges regarding genetic engineering and synthetic biology in marine cyanobacteria, followed by a parallel with freshwater cyanobacteria and their current genetic availability to guide the prospect for marine species.
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Affiliation(s)
- Barbara Bourgade
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
| | - Karin Stensjö
- Microbial Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Uppsala, Sweden
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7
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Song H, Yang Y, Li H, Du J, Hu Z, Chen Y, Yang N, Mei M, Xiong Z, Tang K, Yi L, Zhang Y, Yang S. Determination of Nucleotide Sequences within Promoter Regions Affecting Promoter Compatibility between Zymomonas mobilis and Escherichia coli. ACS Synth Biol 2022; 11:2811-2819. [PMID: 35771099 DOI: 10.1021/acssynbio.2c00187] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A promoter plays a crucial role in controlling the expression of the target gene in cells, thus being one of the key biological parts for synthetic biology practices. Although significant efforts have been made to identify and characterize promoters with different strengths in various microorganisms, the compatibility of promoters within different hosts still lacks investigation. In this study, we chose the native Pgap promoter of Zymomonas mobilis to investigate nucleotide sequences within promoter regions affecting promoter compatibility between Escherichia coli and Z. mobilis. Pgap is one of the strongest promotors in Z. mobilis that has many excellent characteristics to be developed as microbial cell factories. Using EGFP as a reporter, a Z. mobilis-derived Pgap mutant library was constructed and sorted in E. coli, with candidate promoters exhibiting high fluorescence intensity collected. A total of 53 variants were finally selected and sequenced by Sanger sequencing. The sequencing results grouped these variants into 12 different Pgap variant types, among which seven types presented higher promoter strength than native Pgap in E. coli. The next-generation sequencing technique was then employed to identify key mutations within the Pgap promoter region that affect the promoter compatibility. Finally, six important sites were identified and confirmed to help increase Pgap strength in E. coli while keeping similar strength of native Pgap in Z. mobilis. Compared to native Pgap, synthetic promoters combining these sites had enhanced strength; especially, Pgap-6M combining all six sites exhibited 20-fold greater strength than native Pgap in E. coli. This study thus not only determined six important sites affecting promoter compatibility but also confirmed a series of Pgap promoter variants with strong promoter activity in both E. coli and Z. mobilis. In addition, a strategy was established in this study to investigate and determine nucleotide sequences in promoter regions affecting promoter compatibility, which can be applied in other microorganisms to help reveal universal factors affecting promoter compatibility and design promoters with desired strengths among different microbial cell factories.
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Affiliation(s)
- Haoyue Song
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yongfu Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Han Li
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Jun Du
- Beijing Tsingke Biotechnology Co., Ltd., Beijing 101111, China
| | - Zhousheng Hu
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yunhao Chen
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ning Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Meng Mei
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Zhiqiang Xiong
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Ke Tang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Li Yi
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
| | - Shihui Yang
- State Key Laboratory of Biocatalysis and Enzyme Engineering, and School of Life Sciences, Hubei University, Wuhan 430062, China
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Verma S, Thapa S, Siddiqui N, Chakdar H. Cyanobacterial secondary metabolites towards improved commercial significance through multiomics approaches. World J Microbiol Biotechnol 2022; 38:100. [PMID: 35486205 DOI: 10.1007/s11274-022-03285-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2022] [Accepted: 04/13/2022] [Indexed: 11/28/2022]
Abstract
Cyanobacteria are ubiquitous photosynthetic prokaryotes responsible for the oxygenation of the earth's reducing atmosphere. Apart from oxygen they are producers of a myriad of bioactive metabolites with diverse complex chemical structures and robust biological activities. These secondary metabolites are known to have a variety of medicinal and therapeutic applications ranging from anti-microbial, anti-viral, anti-inflammatory, anti-cancer, and immunomodulating properties. The present review discusses various aspects of secondary metabolites viz. biosynthesis, types and applications, which highlights the repertoire of bioactive constituents they harbor. Majority of these products have been produced from only a handful of genera. Moreover, with the onset of various OMICS approaches, cyanobacteria have become an attractive chassis for improved secondary metabolites production. Also the intervention of synthetic biology tools such as gene editing technologies and a variety of metabolomics and fluxomics approaches, used for engineering cyanobacteria, have significantly enhanced the production of secondary metabolites.
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Affiliation(s)
- Shaloo Verma
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.,Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Shobit Thapa
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India
| | - Nahid Siddiqui
- Amity Institute of Biotechnology (AIB), Amity University, Noida, Uttar Pradesh, 201313, India
| | - Hillol Chakdar
- ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Kushmaur, Mau, Uttar Pradesh, 275103, India.
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9
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Zhuang X, Zhang Y, Xiao AF, Zhang A, Fang B. Applications of Synthetic Biotechnology on Carbon Neutrality Research: A Review on Electrically Driven Microbial and Enzyme Engineering. Front Bioeng Biotechnol 2022; 10:826008. [PMID: 35145960 PMCID: PMC8822124 DOI: 10.3389/fbioe.2022.826008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Accepted: 01/04/2022] [Indexed: 12/26/2022] Open
Abstract
With the advancement of science, technology, and productivity, the rapid development of industrial production, transportation, and the exploitation of fossil fuels has gradually led to the accumulation of greenhouse gases and deterioration of global warming. Carbon neutrality is a balance between absorption and emissions achieved by minimizing carbon dioxide (CO2) emissions from human social productive activity through a series of initiatives, including energy substitution and energy efficiency improvement. Then CO2 was offset through forest carbon sequestration and captured at last. Therefore, efficiently reducing CO2 emissions and enhancing CO2 capture are a matter of great urgency. Because many species have the natural CO2 capture properties, more and more scientists focus their attention on developing the biological carbon sequestration technique and further combine with synthetic biotechnology and electricity. In this article, the advances of the synthetic biotechnology method for the most promising organisms were reviewed, such as cyanobacteria, Escherichia coli, and yeast, in which the metabolic pathways were reconstructed to enhance the efficiency of CO2 capture and product synthesis. Furthermore, the electrically driven microbial and enzyme engineering processes are also summarized, in which the critical role and principle of electricity in the process of CO2 capture are canvassed. This review provides detailed summary and analysis of CO2 capture through synthetic biotechnology, which also pave the way for implementing electrically driven combined strategies.
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Affiliation(s)
- Xiaoyan Zhuang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Yonghui Zhang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - An-Feng Xiao
- College of Food and Biology Engineering, Jimei University, Xiamen, China
| | - Aihui Zhang
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
| | - Baishan Fang
- College of Food and Biology Engineering, Jimei University, Xiamen, China
- Department of Chemical and Biochemical Engineering, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, China
- *Correspondence: Aihui Zhang, ; Baishan Fang,
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10
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Kato Y, Inabe K, Hidese R, Kondo A, Hasunuma T. Metabolomics-based engineering for biofuel and bio-based chemical production in microalgae and cyanobacteria: A review. BIORESOURCE TECHNOLOGY 2022; 344:126196. [PMID: 34710610 DOI: 10.1016/j.biortech.2021.126196] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/06/2021] [Revised: 10/18/2021] [Accepted: 10/19/2021] [Indexed: 06/13/2023]
Abstract
Metabolomics, an essential tool in modern synthetic biology based on the design-build-test-learn platform, is useful for obtaining a detailed understanding of cellular metabolic mechanisms through comprehensive analyses of the metabolite pool size and its dynamic changes. Metabolomics is critical to the design of a rational metabolic engineering strategy by determining the rate-limiting reaction and assimilated carbon distribution in a biosynthetic pathway of interest. Microalgae and cyanobacteria are promising photosynthetic producers of biofuels and bio-based chemicals, with high potential for developing a bioeconomic society through bio-based carbon neutral manufacturing. Metabolomics technologies optimized for photosynthetic organisms have been developed and utilized in various microalgal and cyanobacterial species. This review provides a concise overview of recent achievements in photosynthetic metabolomics, emphasizing the importance of microalgal and cyanobacterial cell factories that satisfy industrial requirements.
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Affiliation(s)
- Yuichi Kato
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Kosuke Inabe
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Ryota Hidese
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Akihiko Kondo
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Department of Chemical Science and Engineering, Graduate School of Engineering, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan
| | - Tomohisa Hasunuma
- Engineering Biology Research Center, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan; Graduate School of Science, Innovation and Technology, Kobe University, 1-1 Rokkodai, Nada, Kobe 657-8501, Japan.
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11
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Sengupta A, Liu D, Pakrasi HB. CRISPR-Cas mediated genome engineering of cyanobacteria. Methods Enzymol 2022; 676:403-432. [DOI: 10.1016/bs.mie.2022.07.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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Andrews F, Faulkner M, Toogood HS, Scrutton NS. Combinatorial use of environmental stresses and genetic engineering to increase ethanol titres in cyanobacteria. BIOTECHNOLOGY FOR BIOFUELS 2021; 14:240. [PMID: 34920731 PMCID: PMC8684110 DOI: 10.1186/s13068-021-02091-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 12/05/2021] [Indexed: 06/07/2023]
Abstract
Current industrial bioethanol production by yeast through fermentation generates carbon dioxide. Carbon neutral bioethanol production by cyanobacteria uses biological fixation (photosynthesis) of carbon dioxide or other waste inorganic carbon sources, whilst being sustainable and renewable. The first ethanologenic cyanobacterial process was developed over two decades ago using Synechococcus elongatus PCC 7942, by incorporating the recombinant pdc and adh genes from Zymomonas mobilis. Further engineering has increased bioethanol titres 24-fold, yet current levels are far below what is required for industrial application. At the heart of the problem is that the rate of carbon fixation cannot be drastically accelerated and carbon partitioning towards bioethanol production impacts on cell fitness. Key progress has been achieved by increasing the precursor pyruvate levels intracellularly, upregulating synthetic genes and knocking out pathways competing for pyruvate. Studies have shown that cyanobacteria accumulate high proportions of carbon reserves that are mobilised under specific environmental stresses or through pathway engineering to increase ethanol production. When used in conjunction with specific genetic knockouts, they supply significantly more carbon for ethanol production. This review will discuss the progress in generating ethanologenic cyanobacteria through chassis engineering, and exploring the impact of environmental stresses on increasing carbon flux towards ethanol production.
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Affiliation(s)
- Fraser Andrews
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Matthew Faulkner
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Helen S Toogood
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK
| | - Nigel S Scrutton
- EPSRC/BBSRC Future Biomanufacturing Research Hub, BBSRC/EPSRC Synthetic Biology Research Centre SYNBIOCHEM Manchester Institute of Biotechnology and School of Chemistry, The University of Manchester, Manchester, M1 7DN, UK.
- C3 Biotechnologies Ltd, 20 Mannin Way, Lancaster Business Park, Caton Road, Lancaster, LA1 3SW, Lancashire, UK.
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14
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Jaiswal D, Sahasrabuddhe D, Wangikar PP. Cyanobacteria as cell factories: the roles of host and pathway engineering and translational research. Curr Opin Biotechnol 2021; 73:314-322. [PMID: 34695729 DOI: 10.1016/j.copbio.2021.09.010] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/02/2021] [Accepted: 09/20/2021] [Indexed: 11/03/2022]
Abstract
Cyanobacteria, a group of photoautotrophic prokaryotes, are attractive hosts for the sustainable production of chemicals from carbon dioxide and sunlight. However, the rates, yields, and titers have remained well below those needed for commercial deployment. We argue that the following areas will be central to the development of cyanobacterial cell factories: engineered and well-characterized host strains, model-guided pathway design, and advanced synthetic biology tools. Although several foundational studies report improved strain properties, translational research will be needed to develop engineered hosts and deploy them for metabolic engineering. Further, the recent developments in metabolic modeling and synthetic biology of cyanobacteria will enable nimble strategies for strain improvement with the complete cycle of design, build, test, and learn.
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Affiliation(s)
- Damini Jaiswal
- 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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15
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Gupta JK, Srivastava S. The Effect of Promoter and RBS Combination on the Growth and Glycogen Productivity of Sodium-Dependent Bicarbonate Transporter (SbtA) Overexpressing Synechococcus sp. PCC 7002 Cells. Front Microbiol 2021; 12:607411. [PMID: 33927699 PMCID: PMC8076525 DOI: 10.3389/fmicb.2021.607411] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 03/22/2021] [Indexed: 12/20/2022] Open
Abstract
Sodium dependent bicarbonate transporter, SbtA is a high-affinity, inducible bicarbonate transporter in cyanobacterial cells. Our previous work has shown that overexpression of this transporter can significantly increase growth and glycogen accumulation in Synechococcus sp. PCC 7002 cells. In this work, we have tested the effect of two different RBS sequences (RBS1: GGAGGA and RBS2: AGGAGA) and three different promoters (PcpcB, PcpcB560, and PrbcL2) on the growth and glycogen production in SbtA-overexpressing Synechococcus sp. PCC 7002 cells. Our results show that PcpcB or PcpcB560 were more effective than PrbcL2 in increasing the growth and glycogen content. The choice of RBS sequence had relatively minor effect, though RBS2 was more effective than RBS1. The transformant E, with PcpcB560 and RBS2, showed the highest growth. The biomass after 5 days of growth on air or 1% CO2 was increased by about 90% in the strain E compared to PCC 7002 cells. All transformants overexpressing SbtA had higher glycogen content. However, growing the cells with bubbling of 1% CO2 did not increase cellular glycogen content any further. The strain E had about 80% higher glycogen content compared to WT PCC 7002 cells. Therefore, the glycogen productivity of the strain E grown with air-bubbling was about 2.5-fold that of the WT PCC 7002 cells grown similarly. Additionally, some of the transformants had higher chlorophyll content while all the transformants had higher carotenoid content compared to the PCC 7002 cells, suggesting interaction between carbon transport and pigment levels. Thus, this work shows that the choice of photosynthetic promoters and RBSs sequences can impact growth and glycogen accumulation in SbtA-overexpressing cells.
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Affiliation(s)
- Jai Kumar Gupta
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India
| | - Shireesh Srivastava
- Systems Biology for Biofuels Group, International Centre for Genetic Engineering and Biotechnology (ICGEB), New Delhi, India.,Department of Biotechnology-International Centre for Genetic Engineering and Biotechnology (DBT-ICGEB), Centre for Advanced Bioenergy Research, New Delhi, India
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16
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Jeong Y, Cho SH, Lee H, Choi HK, Kim DM, Lee CG, Cho S, Cho BK. Current Status and Future Strategies to Increase Secondary Metabolite Production from Cyanobacteria. Microorganisms 2020; 8:E1849. [PMID: 33255283 PMCID: PMC7761380 DOI: 10.3390/microorganisms8121849] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2020] [Revised: 11/15/2020] [Accepted: 11/23/2020] [Indexed: 12/16/2022] Open
Abstract
Cyanobacteria, given their ability to produce various secondary metabolites utilizing solar energy and carbon dioxide, are a potential platform for sustainable production of biochemicals. Until now, conventional metabolic engineering approaches have been applied to various cyanobacterial species for enhanced production of industrially valued compounds, including secondary metabolites and non-natural biochemicals. However, the shortage of understanding of cyanobacterial metabolic and regulatory networks for atmospheric carbon fixation to biochemical production and the lack of available engineering tools limit the potential of cyanobacteria for industrial applications. Recently, to overcome the limitations, synthetic biology tools and systems biology approaches such as genome-scale modeling based on diverse omics data have been applied to cyanobacteria. This review covers the synthetic and systems biology approaches for advanced metabolic engineering of cyanobacteria.
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Affiliation(s)
- Yujin Jeong
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Sang-Hyeok Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Hookeun Lee
- Institute of Pharmaceutical Research, College of Pharmacy, Gachon University, Incheon 21999, Korea;
| | | | - Dong-Myung Kim
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Korea;
| | - Choul-Gyun Lee
- Department of Biological Engineering, Inha University, Incheon 22212, Korea;
| | - Suhyung Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
| | - Byung-Kwan Cho
- Department of Biological Sciences and KAIST Institutes for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea; (Y.J.); (S.-H.C.)
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17
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Wang F, Gao Y, Yang G. Recent advances in synthetic biology of cyanobacteria for improved chemicals production. Bioengineered 2020; 11:1208-1220. [PMID: 33124500 PMCID: PMC8291842 DOI: 10.1080/21655979.2020.1837458] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cyanobacteria are Gram-negative photoautotrophic prokaryotes and have shown great importance to the Earth’s ecology. Based on their capability in oxygenic photosynthesis and genetic merits, they can be engineered as microbial chassis for direct conversion of carbon dioxide to value-added biofuels and chemicals. In the last decades, attempts have given to the application of synthetic biology tools and approaches in the development of cyanobacterial cell factories. Despite the successful proof-of-principle studies, large-scale application is still a technical challenge due to low yields of bioproducts. Therefore, recent efforts are underway to characterize and develop genetic regulatory parts and strategies for the synthetic biology applications in cyanobacteria. In this review, we present the recent advancements and application in cyanobacterial synthetic biology toolboxes. We also discuss the limitations and future perspectives for using such novel tools in cyanobacterial biotechnology.
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Affiliation(s)
- Fen Wang
- Department of Surgery, College of Medicine, University of Florida , Gainesville, FL, USA
| | - Yuanyuan Gao
- Jining Academy of Agricultural Science , Jining, Shandong, China
| | - Guang Yang
- Department of Aging and Geriatric Research, Institute on Aging, University of Florida , Gainesville, FL, USA
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18
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Caicedo-Burbano P, Smit T, Pineda Hernández H, Du W, Branco dos Santos F. Construction of Fully Segregated Genomic Libraries in Polyploid Organisms Such as Synechocystis sp. PCC 6803. ACS Synth Biol 2020; 9:2632-2638. [PMID: 33017143 PMCID: PMC7573980 DOI: 10.1021/acssynbio.0c00353] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Indexed: 12/11/2022]
Abstract
Several microbes are polyploid, meaning they contain several copies of their chromosome. Cyanobacteria, while holding great potential as photosynthetic cell factories of various products, are found among them. In these clades the diversity of genetic elements that serve within the basic molecular toolbox is often limiting. To assist mining for the latter, we present here a method for the generation of fully segregated genomic libraries, specifically designed for polyploids. We provide proof-of-principle for this method by generating a fully segregated genomic promoter library in the cyanobacterium Synechocystis sp. PCC 6803. This new tool was first analyzed through fluorescence activated cell sorting (FACS) and then a fraction was further characterized regarding promoter sequence. The location of libraries on the chromosome provides a better reflection of the behavior of its elements. Our work presents the first method for constructing fully segregated genomic libraries in polyploids, which may facilitate their usage in synthetic biology applications.
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Affiliation(s)
- Patricia Caicedo-Burbano
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Tycho Smit
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Hugo Pineda Hernández
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Wei Du
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH,The Netherlands
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