1
|
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.
Collapse
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
| |
Collapse
|
2
|
Jodlbauer J, Schmal M, Waltl C, Rohr T, Mach-Aigner AR, Mihovilovic MD, Rudroff F. Unlocking the potential of cyanobacteria: a high-throughput strategy for enhancing biocatalytic performance through genetic optimization. Trends Biotechnol 2024:S0167-7799(24)00189-6. [PMID: 39214789 DOI: 10.1016/j.tibtech.2024.07.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2024] [Revised: 07/15/2024] [Accepted: 07/19/2024] [Indexed: 09/04/2024]
Abstract
Cyanobacteria show promise as hosts for whole-cell biocatalysis. Their photoautotrophic metabolism can be leveraged for a sustainable production process. Despite advancements, performance still lags behind heterotrophic hosts. A key challenge is the limited ability to overexpress recombinant enzymes, which also hinders their biocatalytic efficiency. To address this, we generated large-scale expression libraries and developed a high-throughput method combining fluorescence-activated cell sorting (FACS) and deep sequencing in Synechocystis sp. PCC 6803 (Syn. 6803) to screen and optimize its genetic background. We apply this approach to enhance expression and biocatalyst performance for three enzymes: the ketoreductase LfSDR1M50, enoate reductase YqjM, and Baeyer-Villiger monooxygenase (BVMO) CHMOmut. Diverse genetic combinations yielded significant improvements: optimizing LfSDR1M50 expression showed a 17-fold increase to 39.2 U gcell dry weight (CDW)-1. In vivo activity of Syn. YqjM was improved 16-fold to 58.7 U gCDW-1 and, for Syn. CHMOmut, a 1.5-fold increase to 7.3 U gCDW-1 was achieved by tailored genetic design. Thus, this strategy offers a pathway to optimize cyanobacteria as expression hosts, paving the way for broader applications in other cyanobacteria strains and larger libraries.
Collapse
Affiliation(s)
- Julia Jodlbauer
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Matthias Schmal
- Institute of Chemical, Environmental, and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, 1060, Vienna, Austria
| | - Christian Waltl
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Thomas Rohr
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Astrid R Mach-Aigner
- Institute of Chemical, Environmental, and Bioscience Engineering, TU Wien, Gumpendorfer Str. 1a, 1060, Vienna, Austria
| | - Marko D Mihovilovic
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria
| | - Florian Rudroff
- Institute of Applied Synthetic Chemistry, TU Wien, Getreidemarkt 9, 1060, Vienna, Austria.
| |
Collapse
|
3
|
Li XD, Liu LM, Xi YC, Sun QW, Luo Z, Huang HL, Wang XW, Jiang HB, Chen W. Development of a base editor for convenient and multiplex genome editing in cyanobacteria. Commun Biol 2024; 7:994. [PMID: 39143188 PMCID: PMC11324792 DOI: 10.1038/s42003-024-06696-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
Cyanobacteria are important primary producers, contributing to 25% of the global carbon fixation through photosynthesis. They serve as model organisms to study the photosynthesis, and are important cell factories for synthetic biology. To enable efficient genetic dissection and metabolic engineering in cyanobacteria, effective and accurate genetic manipulation tools are required. However, genetic manipulation in cyanobacteria by the conventional homologous recombination-based method and the recently developed CRISPR-Cas gene editing system require complicated cloning steps, especially during multi-site editing and single base mutation. This restricts the extensive research on cyanobacteria and reduces its application potential. In this study, a highly efficient and convenient cytosine base editing system was developed which allows rapid and precise C → T point mutation and gene inactivation in the genomes of Synechocystis and Anabaena. This base editing system also enables efficient multiplex editing and can be easily cured after editing by sucrose counter-selection. This work will expand the knowledge base regarding the engineering of cyanobacteria. The findings of this study will encourage the biotechnological applications of cyanobacteria.
Collapse
Affiliation(s)
- Xing-Da Li
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Ling-Mei Liu
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
- School of Life Sciences, Central China Normal University, Wuhan, Hubei, 430079, China
| | - Yi-Cao Xi
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Qiao-Wei Sun
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Zhen Luo
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Long Huang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Xin-Wei Wang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China
| | - Hai-Bo Jiang
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
- Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, Guangdong, 519080, China.
| | - Weizhong Chen
- School of Marine Sciences, Ningbo University, Ningbo, Zhejiang, 315211, China.
| |
Collapse
|
4
|
Tiwari D, Kumar N, Bongirwar R, Shukla P. Nutraceutical prospects of genetically engineered cyanobacteria- technological updates and significance. World J Microbiol Biotechnol 2024; 40:263. [PMID: 38980547 DOI: 10.1007/s11274-024-04064-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2024] [Accepted: 06/23/2024] [Indexed: 07/10/2024]
Abstract
Genetically engineered cyanobacterial strains that have improved growth rate, biomass productivity, and metabolite productivity could be a better option for sustainable bio-metabolite production. The global demand for biobased metabolites with nutraceuticals and health benefits has increased due to their safety and plausible therapeutic and nutritional utility. Cyanobacteria are solar-powered green cellular factories that can be genetically tuned to produce metabolites with nutraceutical and pharmaceutical benefits. The present review discusses biotechnological endeavors for producing bioprospective compounds from genetically engineered cyanobacteria and discusses the challenges and troubleshooting faced during metabolite production. This review explores the cyanobacterial versatility, the use of engineered strains, and the techno-economic challenges associated with scaling up metabolite production from cyanobacteria. Challenges to produce cyanobacterial bioactive compounds with remarkable nutraceutical values have been discussed. Additionally, this review also summarises the challenges and future prospects of metabolite production from genetically engineered cyanobacteria as a sustainable approach.
Collapse
Affiliation(s)
- Deepali Tiwari
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Niwas Kumar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Riya Bongirwar
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India
| | - Pratyoosh Shukla
- Enzyme Technology and Protein Bioinformatics Laboratory, School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi, 221005, Uttar Pradesh, India.
| |
Collapse
|
5
|
Christi K, Hudson J, Egan S. Current approaches to genetic modification of marine bacteria and considerations for improved transformation efficiency. Microbiol Res 2024; 284:127729. [PMID: 38663232 DOI: 10.1016/j.micres.2024.127729] [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: 10/18/2023] [Revised: 02/25/2024] [Accepted: 04/15/2024] [Indexed: 05/26/2024]
Abstract
Marine bacteria play vital roles in symbiosis, biogeochemical cycles and produce novel bioactive compounds and enzymes of interest for the pharmaceutical, biofuel and biotechnology industries. At present, investigations into marine bacterial functions and their products are primarily based on phenotypic observations, -omic type approaches and heterologous gene expression. To advance our understanding of marine bacteria and harness their full potential for industry application, it is critical that we have the appropriate tools and resources to genetically manipulate them in situ. However, current genetic tools that are largely designed for model organisms such as E. coli, produce low transformation efficiencies or have no transfer ability in marine bacteria. To improve genetic manipulation applications for marine bacteria, we need to improve transformation methods such as conjugation and electroporation in addition to identifying more marine broad host range plasmids. In this review, we aim to outline the reported methods of transformation for marine bacteria and discuss the considerations for each approach in the context of improving efficiency. In addition, we further discuss marine plasmids and future research areas including CRISPR tools and their potential applications for marine bacteria.
Collapse
Affiliation(s)
- Katrina Christi
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Jennifer Hudson
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia
| | - Suhelen Egan
- Centre for Marine Science and Innovation, School of Biological, Earth and Environmental Sciences, Faculty of Science, The University of New South Wales, Kensington, NSW, Australia.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Hieronimus K, Donauer T, Klein J, Hinkel B, Spänle JV, Probst A, Niemeyer J, Kibrom S, Kiefer AM, Schneider L, Husemann B, Bischoff E, Möhring S, Bayer N, Klein D, Engels A, Ziehmer BG, Stieβ J, Moroka P, Schroda M, Deponte M. A Modular Cloning Toolkit for the production of recombinant proteins in Leishmania tarentolae. MICROBIAL CELL (GRAZ, AUSTRIA) 2024; 11:128-142. [PMID: 38799406 PMCID: PMC11121976 DOI: 10.15698/mic2024.04.821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 03/20/2024] [Accepted: 03/28/2024] [Indexed: 05/29/2024]
Abstract
Modular Cloning (MoClo) is based on libraries of standardized genetic parts that can be directionally assembled via Golden Gate cloning in one-pot reactions into transcription units and multigene constructs. Here, a team of bachelor students established a MoClo toolkit for the protist Leishmania tarentolae in the frame of the international Genetically Engineered Machine (iGEM) competition. Our modular toolkit is based on a domesticated version of a commercial LEXSY expression vector and comprises 34 genetic parts encoding various affinity tags, targeting signals as well as fluorescent and luminescent proteins. We demonstrated the utility of our kit by the successful production of 16 different tagged versions of the receptor binding domain (RBD) of the SARS-CoV-2 spike protein in L. tarentolae liquid cultures. While highest yields of secreted recombinant RBD were obtained for GST-tagged fusion proteins 48 h post induction, C-terminal peptide tags were often degraded and resulted in lower yields of secreted RBD. Fusing secreted RBD to a synthetic O-glycosylation SP20 module resulted in an apparent molecular mass shift around 10 kDa. No disadvantage regarding the production of RBD was detected when the three antibiotics of the LEXSY system were omitted during the 48-h induction phase. Furthermore, the successful purification of secreted RBD from the supernatant of L. tarentolae liquid cultures was demonstrated in pilot experiments. In summary, we established a MoClo toolkit and exemplified its application for the production of recombinant proteins in L. tarentolae.
Collapse
Affiliation(s)
- Katrin Hieronimus
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Tabea Donauer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Jonas Klein
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Bastian Hinkel
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Julia Vanessa Spänle
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Anna Probst
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Justus Niemeyer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Salina Kibrom
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Anna Maria Kiefer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Luzia Schneider
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Britta Husemann
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Eileen Bischoff
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Sophie Möhring
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Nicolas Bayer
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Dorothée Klein
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Adrian Engels
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Benjamin Gustav Ziehmer
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Julian Stieβ
- Faculty of Computer Science, RPTU Kaiserslautern, D-67663
Kaiserslautern, Germany
| | - Pavlo Moroka
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Michael Schroda
- Faculty of Biology, Molecular Biotechnology & Systems
Biology, RPTU Kaiserslautern, D-67663 Kaiserslautern, Germany
| | - Marcel Deponte
- Faculty of Chemistry, Comparative Biochemistry, RPTU
Kaiserslautern, D-67663 Kaiserslautern, Germany
| |
Collapse
|
8
|
Webster LJ, Villa-Gomez D, Brown R, Clarke W, Schenk PM. A synthetic biology approach for the treatment of pollutants with microalgae. Front Bioeng Biotechnol 2024; 12:1379301. [PMID: 38646010 PMCID: PMC11032018 DOI: 10.3389/fbioe.2024.1379301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Accepted: 03/11/2024] [Indexed: 04/23/2024] Open
Abstract
The increase in global population and industrial development has led to a significant release of organic and inorganic pollutants into water streams, threatening human health and ecosystems. Microalgae, encompassing eukaryotic protists and prokaryotic cyanobacteria, have emerged as a sustainable and cost-effective solution for removing these pollutants and mitigating carbon emissions. Various microalgae species, such as C. vulgaris, P. tricornutum, N. oceanica, A. platensis, and C. reinhardtii, have demonstrated their ability to eliminate heavy metals, salinity, plastics, and pesticides. Synthetic biology holds the potential to enhance microalgae-based technologies by broadening the scope of treatment targets and improving pollutant removal rates. This review provides an overview of the recent advances in the synthetic biology of microalgae, focusing on genetic engineering tools to facilitate the removal of inorganic (heavy metals and salinity) and organic (pesticides and plastics) compounds. The development of these tools is crucial for enhancing pollutant removal mechanisms through gene expression manipulation, DNA introduction into cells, and the generation of mutants with altered phenotypes. Additionally, the review discusses the principles of synthetic biology tools, emphasizing the significance of genetic engineering in targeting specific metabolic pathways and creating phenotypic changes. It also explores the use of precise engineering tools, such as CRISPR/Cas9 and TALENs, to adapt genetic engineering to various microalgae species. The review concludes that there is much potential for synthetic biology based approaches for pollutant removal using microalgae, but there is a need for expansion of the tools involved, including the development of universal cloning toolkits for the efficient and rapid assembly of mutants and transgenic expression strains, and the need for adaptation of genetic engineering tools to a wider range of microalgae species.
Collapse
Affiliation(s)
- Luke J. Webster
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
| | - Denys Villa-Gomez
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, Brisbane, QLD, Australia
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Reuben Brown
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
| | - William Clarke
- School of Civil Engineering, The University of Queensland, Brisbane, QLD, Australia
| | - Peer M. Schenk
- Algae Biotechnology Laboratory, School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD, Australia
- Algae Biotechnology, Sustainable Solutions Hub, Global Sustainable Solutions Pty Ltd, Brisbane, QLD, Australia
| |
Collapse
|
9
|
Arévalo S, Pérez Rico D, Abarca D, Dijkhuizen LW, Sarasa-Buisan C, Lindblad P, Flores E, Nierzwicki-Bauer S, Schluepmann H. Genome Engineering by RNA-Guided Transposition for Anabaena sp. PCC 7120. ACS Synth Biol 2024; 13:901-912. [PMID: 38445989 PMCID: PMC10949235 DOI: 10.1021/acssynbio.3c00583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Revised: 01/30/2024] [Accepted: 02/16/2024] [Indexed: 03/07/2024]
Abstract
In genome engineering, the integration of incoming DNA has been dependent on enzymes produced by dividing cells, which has been a bottleneck toward increasing DNA insertion frequencies and accuracy. Recently, RNA-guided transposition with CRISPR-associated transposase (CAST) was reported as highly effective and specific in Escherichia coli. Here, we developed Golden Gate vectors to test CAST in filamentous cyanobacteria and to show that it is effective in Anabaena sp. strain PCC 7120. The comparatively large plasmids containing CAST and the engineered transposon were successfully transferred into Anabaena via conjugation using either suicide or replicative plasmids. Single guide (sg) RNA encoding the leading but not the reverse complement strand of the target were effective with the protospacer-associated motif (PAM) sequence included in the sgRNA. In four out of six cases analyzed over two distinct target loci, the insertion site was exactly 63 bases after the PAM. CAST on a replicating plasmid was toxic, which could be used to cure the plasmid. In all six cases analyzed, only the transposon cargo defined by the sequence ranging from left and right elements was inserted at the target loci; therefore, RNA-guided transposition resulted from cut and paste. No endogenous transposons were remobilized by exposure to CAST enzymes. This work is foundational for genome editing by RNA-guided transposition in filamentous cyanobacteria, whether in culture or in complex communities.
Collapse
Affiliation(s)
- Sergio Arévalo
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Daniel Pérez Rico
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Dolores Abarca
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Laura W. Dijkhuizen
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Cristina Sarasa-Buisan
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Peter Lindblad
- Microbial
Chemistry, Department of Chemistry-Ångström Laboratory, Uppsala University, Lägerhyddsvägen 1, 751
20 Uppsala, Sweden
| | - Enrique Flores
- Instituto
de Bioquímica Vegetal y Fotosíntesis, CSIC and Universidad
de Sevilla, Avenida Americo Vespucio 49, Sevilla 41092, Spain
| | - Sandra Nierzwicki-Bauer
- Department
of Biological Sciences, Rensselaer Polytechnic
Institute, 110 Eighth
Street, Troy, New York 12180-3590, United
States
| | - Henriette Schluepmann
- Biology
Department, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| |
Collapse
|
10
|
Lee SY, Lee JS, Sim SJ. Cost-effective production of bioplastic polyhydroxybutyrate via introducing heterogeneous constitutive promoter and elevating acetyl-Coenzyme A pool of rapidly growing cyanobacteria. BIORESOURCE TECHNOLOGY 2024; 394:130297. [PMID: 38185449 DOI: 10.1016/j.biortech.2023.130297] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/31/2023] [Accepted: 12/31/2023] [Indexed: 01/09/2024]
Abstract
Bioplastic production using cyanobacteria can be an effective strategy to cope with environmental problems caused by using petroleum-based plastics. Synechococcus elongatus UTEX 2973 with heterogeneous phaCAB can produce bioplastic polyhydroxybutyrate (PHB) with a high CO2 uptake rate. For cost-effective production of PHB in S. elongatus UTEX 2973, phaCAB was expressed by the constitutive Pcpc560, resulting in the production of 226 mg/L of PHB by only photoautotrophic cultivation without the addition of inducer. Several culture conditions were applied to increase PHB productivity, and when acetate was supplied at a concentration of 1 g/L as an organic carbon source, productivity significantly increased resulting in 607.2 mg/L of PHB and additive cost reduction of more than 300 times was achieved compared to IPTG. Consequently, these results suggest the possibility of cyanobacteria as an agent that can economically produce PHB and as a solution to the problem of petroleum-based plastics.
Collapse
Affiliation(s)
- So Young Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Jeong Seop Lee
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea
| | - Sang Jun Sim
- Department of Chemical and Biological Engineering, Korea University, 145, Anam-ro, Seongbuk-gu, Seoul 02841, Republic of Korea.
| |
Collapse
|
11
|
Diankristanti PA, Lin YC, Yi YC, Ng IS. Polyhydroxyalkanoates bioproduction from bench to industry: Thirty years of development towards sustainability. BIORESOURCE TECHNOLOGY 2024; 393:130149. [PMID: 38049017 DOI: 10.1016/j.biortech.2023.130149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/06/2023]
Abstract
The pursuit of carbon neutrality goals has sparked considerable interest in expanding bioplastics production from microbial cell factories. One prominent class of bioplastics, polyhydroxyalkanoates (PHA), is generated by specific microorganisms, serving as carbon and energy storage materials. To begin with, a native PHA producer, Cupriavidus necator (formerly Ralstonia eutropha) is extensively studied, covering essential topics such as carbon source selection, cultivation techniques, and accumulation enhancement strategies. Recently, various hosts including archaea, bacteria, cyanobacteria, yeast, and plants have been explored, stretching the limit of microbial PHA production. This review provides a comprehensive overview of current advancements in PHA bioproduction, spanning from the native to diversified cell factories. Recovery and purification techniques are discussed, and the current status of industrial applications is assessed as a critical milestone for startups. Ultimately, it concludes by addressing contemporary challenges and future prospects, offering insights into the path towards reduced carbon emissions and sustainable development goals.
Collapse
Affiliation(s)
| | - Yu-Chieh Lin
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan
| | - Ying-Chen Yi
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan; Department of Energy, Environmental and Chemical Engineering, Washington University in St. Louis, USA
| | - I-Son Ng
- Department of Chemical Engineering, National Cheng Kung University, Tainan, Taiwan.
| |
Collapse
|
12
|
Rondthaler S, Sarker B, Howitz N, Shah I, Andrews LB. Toolbox of Characterized Genetic Parts for Staphylococcus aureus. ACS Synth Biol 2024; 13:103-118. [PMID: 38064657 PMCID: PMC10805105 DOI: 10.1021/acssynbio.3c00325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 10/06/2023] [Accepted: 10/10/2023] [Indexed: 01/23/2024]
Abstract
Staphylococcus aureus is an important clinical bacterium prevalent in human-associated microbiomes and the cause of many diseases. However, S. aureus has been intractable to synthetic biology approaches due to limited characterized genetic parts for this nonmodel Gram-positive bacterium. Moreover, genetic manipulation of S. aureus has relied on cumbersome and inefficient cloning strategies. Here, we report the first standardized genetic parts toolbox for S. aureus, which includes characterized promoters, ribosome binding sites, terminators, and plasmid replicons from a variety of bacteria for precise control of gene expression. We established a standard relative expression unit (REU) for S. aureus using a plasmid reference and characterized genetic parts in standardized REUs using S. aureus ATCC 12600. We constructed promoter and terminator part plasmids that are compatible with an efficient Type IIS DNA assembly strategy to effectively build multipart DNA constructs. A library of 24 constitutive promoters was built and characterized in S. aureus, which showed a 380-fold activity range. This promoter library was also assayed in Bacillus subtilis (122-fold activity range) to demonstrate the transferability of the constitutive promoters between these Gram-positive bacteria. By applying an iterative design-build-test-learn cycle, we demonstrated the use of our toolbox for the rational design and engineering of a tetracycline sensor in S. aureus using the PXyl-TetO aTc-inducible promoter that achieved 25.8-fold induction. This toolbox greatly expands the growing number of genetic parts for Gram-positive bacteria and will allow researchers to leverage synthetic biology approaches to study and engineer cellular processes in S. aureus.
Collapse
Affiliation(s)
- Stephen
N. Rondthaler
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Biprodev Sarker
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Nathaniel Howitz
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Ishita Shah
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| | - Lauren B. Andrews
- Department
of Chemical Engineering, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
- Molecular
and Cellular Biology Graduate Program, University
of Massachusetts Amherst, Amherst, Massachusetts 01003, United States
- Biotechnology
Training Program, University of Massachusetts
Amherst, Amherst, Massachusetts 01003, United States
| |
Collapse
|
13
|
Weber E. Setup and Applications of Modular Protein Expression Toolboxes (MoPET) for Mammalian Systems. Methods Mol Biol 2024; 2774:15-29. [PMID: 38441755 DOI: 10.1007/978-1-0716-3718-0_2] [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] [Indexed: 03/07/2024]
Abstract
The design and generation of an optimal protein expression construct is the first and essential step in the characterization of any protein of interest. However, the exchange and modification of the coding and/or noncoding elements to analyze their effect on protein function or generating the optimal result can be a tedious and time-consuming process using standard molecular biology cloning methods. To streamline the process to generate defined expression constructs or libraries of otherwise difficult to express proteins, the Modular Protein Expression Toolbox (MoPET) has been developed (Weber E, PloS One 12(5):e0176314, 2017). The system applies Golden Gate cloning as an assembly method and follows the standardized modular cloning (MoClo) principle (Weber E, PloS One 6(2):e16765, 2011). This cloning platform allows highly efficient DNA assembly of pre-defined, standardized functional DNA modules effecting protein expression with a focus on minimizing the cloning burden in coding regions. The original MoPET system consists of 53 defined DNA modules divided into eight functional main classes and can be flexibly expanded dependent on the need of the experimenter and expression host. However, already with a limited set of only 53 modules, 792,000 different constructs can be rationally designed or used to generate combinatorial expression optimization libraries. We provide here a detailed protocol for the (1) design and generation of level 0 basic parts, (2) generation of defined expressions constructs, and (3) generation of combinatorial expression libraries.
Collapse
Affiliation(s)
- Ernst Weber
- Molecular Design & Engineering, Biologics Research, Bayer AG, Wuppertal, Germany.
| |
Collapse
|
14
|
McNelly R, Vergara-Cruces Á, Lea-Smith D, Seung D, Webster M. Exploring the potential of plastid biology and biotechnology: Plastid Preview Meeting, Norwich, 1-2 September 2022. THE NEW PHYTOLOGIST 2023; 240:2187-2190. [PMID: 37787085 DOI: 10.1111/nph.19296] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/04/2023]
Affiliation(s)
- Rose McNelly
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | | | - David Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | - David Seung
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| | - Michael Webster
- John Innes Centre, Norwich Research Park, Norwich, NR4 7UH, UK
| |
Collapse
|
15
|
Blázquez B, León DS, Torres-Bacete J, Gómez-Luengo Á, Kniewel R, Martínez I, Sordon S, Wilczak A, Salgado S, Huszcza E, Popłoński J, Prieto A, Nogales J. Golden Standard: a complete standard, portable, and interoperative MoClo tool for model and non-model proteobacteria. Nucleic Acids Res 2023; 51:e98. [PMID: 37718823 PMCID: PMC10602866 DOI: 10.1093/nar/gkad758] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/06/2023] [Indexed: 09/19/2023] Open
Abstract
Modular cloning has become a benchmark technology in synthetic biology. However, a notable disparity exists between its remarkable development and the need for standardization to facilitate seamless interoperability among systems. The field is thus impeded by an overwhelming proliferation of organism-specific systems that frequently lack compatibility. To overcome these issues, we present Golden Standard (GS), a Type IIS assembly method underpinned by the Standard European Vector Architecture. GS unlocks modular cloning applications for most bacteria, and delivers combinatorial multi-part assembly to create genetic circuits of up to twenty transcription units (TUs). Reliance on MoClo syntax renders GS fully compatible with many existing tools and it sets the path towards efficient reusability of available part libraries and assembled TUs. GS was validated in terms of DNA assembly, portability, interoperability and phenotype engineering in α-, β-, γ- and δ-proteobacteria. Furthermore, we provide a computational pipeline for parts characterization that was used to assess the performance of GS parts. To promote community-driven development of GS, we provide a dedicated web-portal including a repository of parts, vectors, and Wizard and Setup tools that guide users in designing constructs. Overall, GS establishes an open, standardized framework propelling the progress of synthetic biology as a whole.
Collapse
Affiliation(s)
- Blas Blázquez
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - David San León
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Álvaro Gómez-Luengo
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| | - Ryan Kniewel
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Igor Martínez
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
| | - Sandra Sordon
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Aleksandra Wilczak
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Sergio Salgado
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Ewa Huszcza
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Jarosław Popłoński
- Wrocław University of Environmental and Life Sciences, Department of Food Chemistry and Biocatalysis, Norwida 25, 50-375, Wrocław, Poland
| | - Auxiliadora Prieto
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
- Microbial and Plant Biotechnology Department, Biological Research Center-Margarita Salas, CSIC, Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnología, CSIC, Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), Madrid, Spain
| |
Collapse
|
16
|
Tüllinghoff A, Djaya‐Mbissam H, Toepel J, Bühler B. Light-driven redox biocatalysis on gram-scale in Synechocystis sp. PCC 6803 via an in vivo cascade. PLANT BIOTECHNOLOGY JOURNAL 2023; 21:2074-2083. [PMID: 37439151 PMCID: PMC10502755 DOI: 10.1111/pbi.14113] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 06/08/2023] [Accepted: 06/18/2023] [Indexed: 07/14/2023]
Abstract
The photosynthetic light reaction in cyanobacteria constitutes a highly attractive tool for productive biocatalysis, as it can provide redox reactions with high-energy reduction equivalents using sunlight and water as sources of energy and electrons, respectively. Here, we describe the first artificial light-driven redox cascade in Synechocystis sp. PCC 6803 to convert cyclohexanone to the polymer building block 6-hydroxyhexanoic acid (6-HA). Co-expression of a Baeyer-Villiger monooxygenase (BVMO) and a lactonase, both from Acidovorax sp. CHX100, enabled this two-step conversion with an activity of up to 63.1 ± 1.0 U/gCDW without accumulating inhibitory ε-caprolactone. Thereby, one of the key limitations of biocatalytic reactions, that is, reactant inhibition or toxicity, was overcome. In 2 L stirred-tank-photobioreactors, the process could be stabilized for 48 h, forming 23.50 ± 0.84 mm (3.11 ± 0.12 g/L) 6-HA. The high specificity enabling a product yield (YP/S ) of 0.96 ± 0.01 mol/mol and the remarkable biocatalyst-related yield of 3.71 ± 0.21 g6-HA /gCDW illustrate the potential of producing this non-toxic product in a synthetic cascade. The fine-tuning of the energy burden on the catalyst was found to be crucial, which indicates a limitation by the metabolic capacity of the cells possibly being compromised by biocatalysis-related reductant withdrawal. Intriguingly, energy balancing revealed that the biotransformation could tap surplus electrons derived from the photosynthetic light reaction and thereby relieve photosynthetic sink limitation. This study shows the feasibility of light-driven biocatalytic cascade operation in cyanobacteria and highlights respective metabolic limitations and engineering targets to unleash the full potential of photosynthesis.
Collapse
Affiliation(s)
- Adrian Tüllinghoff
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| | | | - Jörg Toepel
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| | - Bruno Bühler
- Helmholtz‐Centre for Environmental Research – UFZ, PermoserstrLeipzigGermany
| |
Collapse
|
17
|
Zedler JAZ, Michel M, Pohnert G, Russo DA. Cell surface composition, released polysaccharides, and ionic strength mediate fast sedimentation in the cyanobacterium Synechococcus elongatus PCC 7942. Environ Microbiol 2023; 25:1955-1966. [PMID: 37259888 DOI: 10.1111/1462-2920.16426] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 05/09/2023] [Indexed: 06/02/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes of high ecological and biotechnological relevance that have been cultivated in laboratories around the world for more than 70 years. Prolonged laboratory culturing has led to multiple microevolutionary events and the appearance of a large number of 'domesticated' substrains among model cyanobacteria. Despite its widespread occurrence, strain domestication is still largely ignored. In this work we describe Synechococcus elongatus PCC 7942-KU, a novel domesticated substrain of the model cyanobacterium S. elongatus PCC 7942, which presents a fast-sedimenting phenotype. Under higher ionic strengths the sedimentation rate increased leading to complete sedimentation in just 12 h. Through whole genome sequencing and gene deletion, we demonstrated that the Group 3 alternative sigma factor F plays a key role in cell sedimentation. Further analysis showed that significant changes in cell surface structures and a three-fold increase in released polysaccharides lead to the appearance of a fast-sedimenting phenotype. This work sheds light on the determinants of the planktonic to benthic transitions and provides genetic targets to generate fast-sedimenting strains that could unlock cost-effective cyanobacterial harvesting at scale.
Collapse
Affiliation(s)
- Julie A Z Zedler
- Friedrich Schiller University Jena, Matthias Schleiden Institute for Genetics, Bioinformatics and Molecular Botany, Synthetic Biology of Photosynthetic Organisms, Jena, Germany
| | - Marlene Michel
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
| | - Georg Pohnert
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
| | - David A Russo
- Friedrich Schiller University Jena, Institute for Inorganic and Analytical Chemistry, Bioorganic Analytics, Jena, Germany
| |
Collapse
|
18
|
Alker AT, Farrell MV, Aspiras AE, Dunbar TL, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine bacteria reveals functional insights during bacteria-stimulated metamorphosis. mBio 2023; 14:e0150223. [PMID: 37530556 PMCID: PMC10470607 DOI: 10.1128/mbio.01502-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2023] [Accepted: 06/17/2023] [Indexed: 08/03/2023] Open
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea, which stimulates the metamorphosis of the model tubeworm, Hydroides elegans. Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for testing the genetic tractability of marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts resulted in the successful conjugation of 12 marine strains from the Alphaproteobacteria and Gammaproteobacteria classes. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with potential implications for environmental restoration and biotechnology. IMPORTANCE Marine Proteobacteria are attractive targets for genetic engineering due to their ability to produce a diversity of bioactive metabolites and their involvement in host-microbe symbioses. Modular cloning toolkits have become a standard for engineering model microbes, such as Escherichia coli, because they enable innumerable mix-and-match DNA assembly and engineering options. However, such modular tools have not yet been applied to most marine bacterial species. In this work, we adapt a modular plasmid toolkit for use in a set of 12 marine bacteria from the Gammaproteobacteria and Alphaproteobacteria classes. We demonstrate the utility of this genetic toolkit by engineering a marine Pseudoalteromonas bacterium to study their association with its host animal Hydroides elegans. This work provides a proof of concept that modular genetic tools can be applied to diverse marine bacteria to address basic science questions and for biotechnology innovations.
Collapse
Affiliation(s)
- Amanda T. Alker
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Morgan V. Farrell
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Alpher E. Aspiras
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Tiffany L. Dunbar
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Andriy Fedoriouk
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Jeffrey E. Jones
- Department of Biology, San Diego State University, San Diego, California, USA
| | - Sama R. Mikhail
- Department of Biology, San Diego State University, San Diego, California, USA
| | | | - Bradley S. Moore
- Center for Marine Biotechnology and Biomedicine, Scripps Institution of Oceanography, University of California, San Diego, California, USA
| | - Nicholas J. Shikuma
- Department of Biology, San Diego State University, San Diego, California, USA
| |
Collapse
|
19
|
Perozeni F, Baier T. Current Nuclear Engineering Strategies in the Green Microalga Chlamydomonas reinhardtii. Life (Basel) 2023; 13:1566. [PMID: 37511941 PMCID: PMC10381326 DOI: 10.3390/life13071566] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Revised: 07/07/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The green model microalga Chlamydomonas reinhardtii recently emerged as a sustainable production chassis for the efficient biosynthesis of recombinant proteins and high-value metabolites. Its capacity for scalable, rapid and light-driven growth in minimal salt solutions, its simplicity for genetic manipulation and its "Generally Recognized As Safe" (GRAS) status are key features for its application in industrial biotechnology. Although nuclear transformation has typically resulted in limited transgene expression levels, recent developments now allow the design of powerful and innovative bioproduction concepts. In this review, we summarize the main obstacles to genetic engineering in C. reinhardtii and describe all essential aspects in sequence adaption and vector design to enable sufficient transgene expression from the nuclear genome. Several biotechnological examples of successful engineering serve as blueprints for the future establishment of C. reinhardtii as a green cell factory.
Collapse
Affiliation(s)
- Federico Perozeni
- Department of Biotechnology, University of Verona, 37134 Verona, Italy
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, 33615 Bielefeld, Germany
| |
Collapse
|
20
|
Mager M, Pineda Hernandez H, Brandenburg F, López-Maury L, McCormick AJ, Nürnberg DJ, Orthwein T, Russo DA, Victoria AJ, Wang X, Zedler JAZ, Branco dos Santos F, Schmelling NM. Interlaboratory Reproducibility in Growth and Reporter Expression in the Cyanobacterium Synechocystis sp. PCC 6803. ACS Synth Biol 2023; 12:1823-1835. [PMID: 37246820 PMCID: PMC10278186 DOI: 10.1021/acssynbio.3c00150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Indexed: 05/30/2023]
Abstract
In recent years, a plethora of new synthetic biology tools for use in cyanobacteria have been published; however, their reported characterizations often cannot be reproduced, greatly limiting the comparability of results and hindering their applicability. In this interlaboratory study, the reproducibility of a standard microbiological experiment for the cyanobacterial model organism Synechocystis sp. PCC 6803 was assessed. Participants from eight different laboratories quantified the fluorescence intensity of mVENUS as a proxy for the transcription activity of the three promoters PJ23100, PrhaBAD, and PpetE over time. In addition, growth rates were measured to compare growth conditions between laboratories. By establishing strict and standardized laboratory protocols, reflecting frequently reported methods, we aimed to identify issues with state-of-the-art procedures and assess their effect on reproducibility. Significant differences in spectrophotometer measurements across laboratories from identical samples were found, suggesting that commonly used reporting practices of optical density values need to be supplemented by cell count or biomass measurements. Further, despite standardized light intensity in the incubators, significantly different growth rates between incubators used in this study were observed, highlighting the need for additional reporting requirements of growth conditions for phototrophic organisms beyond the light intensity and CO2 supply. Despite the use of a regulatory system orthogonal to Synechocystis sp. PCC 6803, PrhaBAD, and a high level of protocol standardization, ∼32% variation in promoter activity under induced conditions was found across laboratories, suggesting that the reproducibility of other data in the field of cyanobacteria might be affected similarly.
Collapse
Affiliation(s)
- Maurice Mager
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| | - Hugo Pineda Hernandez
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Fabian Brandenburg
- Helmholtz
Centre for Environmental Research (UFZ), Permoserstrasse 15, 04318 Leipzig, Germany
| | - Luis López-Maury
- Instituto
de Bioquímica Vegetal y Fotosíntesis, University of Seville − CSIC, Américo Vespucio 49, 41092 Sevilla, Spain
- Departamento
de Bioquímica Vegetal y Biología Molecular, Facultad
de Biología, University of Seville, Avenida Reina Mercedes, 41012 Sevilla, Spain
| | - Alistair J. McCormick
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Dennis J. Nürnberg
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
- Dahlem
Centre of Plant Sciences, Freie Universität
Berlin, Albrecht-Thaer-Weg 6, 14195 Berlin, Germany
| | - Tim Orthwein
- Interfaculty
Institute of Microbiology and Infection Medicine, University of Tuebingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany
| | - David A. Russo
- Institute
for Inorganic and Analytical Chemistry, Bioorganic Analytics, Friedrich Schiller University Jena, Lessingstrasse 8, 07743 Jena, Germany
| | - Angelo Joshua Victoria
- Institute
of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, 1.04 Daniel Rutherford Building, King’s
Buildings, EH9 3BF Edinburgh, U.K.
| | - Xiaoran Wang
- Department
of Physics, Experimental Biophysics, Freie
University Berlin, Arnimallee
14, 14195 Berlin, Germany
| | - Julie A. Z. Zedler
- Matthias
Schleiden Institute for Genetics, Bioinformatics and Molecular Botany,
Synthetic Biology of Photosynthetic Organisms, Friedrich Schiller University Jena, Dornburgerstrasse 159, 07743 Jena, Germany
| | - Filipe Branco dos Santos
- Molecular
Microbial Physiology Group, Swammerdam Institute for Life Sciences,
Faculty of Science, University of Amsterdam, Science Park 904, Amsterdam 1098 XH, The Netherlands
| | - Nicolas M. Schmelling
- Institute
for Synthetic Microbiology, Heinrich Heine
University Duesseldorf, Universitaetsstrasse 1, 40225 Duesseldorf, Germany
| |
Collapse
|
21
|
Mo J, Han L, Lv R, Chiang MWL, Fan R, Guo J. Triclosan toxicity in a model cyanobacterium (Anabaena flos-aquae): Growth, photosynthesis and transcriptomic response. J Environ Sci (China) 2023; 127:82-90. [PMID: 36522109 DOI: 10.1016/j.jes.2022.03.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 03/24/2022] [Accepted: 03/25/2022] [Indexed: 06/17/2023]
Abstract
Exposure to triclosan (TCS) has been reported to reduce photosynthetic pigments, suppress photosynthesis, and inhibit growth in both prokaryotic and eukaryotic algae including Anabaena flos-aquae (a model cyanobacterium). In particular, cyanobacteria are more sensitive to TCS toxicity compared to eukaryotic algae possibly due to the structural similarity to bacteria (target organisms); however, whether TCS exerts its toxicity to cyanobacteria by targeting signaling pathways of fatty acid biosynthesis as in bacteria remains virtually unknown, particularly at environmental exposure levels. With the complete genome sequence of A. flos-aquae presented in this study, the transcriptomic alterations and potential toxic mechanisms in A. flos-aquae under TCS stress were revealed. The growth, pigments and photosynthetic activity of A. flos-aquae were markedly suppressed following a 7-day TCS exposure at 0.5 µg/L but not 0.1 µg/L (both concentrations applied are environmentally relevant). The transcriptomic sequencing analysis showed that signaling pathways, such as biofilm formation - Pseudomonas aeruginosa, two-component system, starch and sucrose metabolism, and photosynthesis were closely related to the TCS-induced growth inhibition in the 0.5 µg/L TCS treatment. Photosynthesis systems and potentially two-component system were identified to be sensitive targets of TCS toxicity in A. flos-aquae. The present study provides novel insights on TCS toxicity at the transcriptomic level in A. flos-aquae.
Collapse
Affiliation(s)
- Jiezhang Mo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China; State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Linrong Han
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Runnan Lv
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Michael W L Chiang
- State Key Laboratory of Marine Pollution and Department of Chemistry, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Rong Fan
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China
| | - Jiahua Guo
- Shaanxi Key Laboratory of Earth Surface System and Environmental Carrying Capacity, College of Urban and Environmental Sciences, Northwest University, Xi'an 710127, China.
| |
Collapse
|
22
|
Goodchild-Michelman IM, Church GM, Schubert MG, Tang TC. Light and carbon: Synthetic biology toward new cyanobacteria-based living biomaterials. Mater Today Bio 2023; 19:100583. [PMID: 36846306 PMCID: PMC9945787 DOI: 10.1016/j.mtbio.2023.100583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 01/30/2023] [Accepted: 02/10/2023] [Indexed: 02/13/2023] Open
Abstract
Cyanobacteria are ideal candidates to use in developing carbon neutral and carbon negative technologies; they are efficient photosynthesizers and amenable to genetic manipulation. Over the past two decades, researchers have demonstrated that cyanobacteria can make sustainable, useful biomaterials, many of which are engineered living materials. However, we are only beginning to see such technologies applied at an industrial scale. In this review, we explore the ways in which synthetic biology tools enable the development of cyanobacteria-based biomaterials. First we give an overview of the ecological and biogeochemical importance of cyanobacteria and the work that has been done using cyanobacteria to create biomaterials so far. This is followed by a discussion of commonly used cyanobacteria strains and synthetic biology tools that exist to engineer cyanobacteria. Then, three case studies-bioconcrete, biocomposites, and biophotovoltaics-are explored as potential applications of synthetic biology in cyanobacteria-based materials. Finally, challenges and future directions of cyanobacterial biomaterials are discussed.
Collapse
Affiliation(s)
- Isabella M. Goodchild-Michelman
- Department of Molecular and Cellular Biology, Harvard University, Cambridge, MA, USA
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - George M. Church
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Max G. Schubert
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| | - Tzu-Chieh Tang
- Department of Genetics, Harvard Medical School, Boston, MA, USA
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, USA
| |
Collapse
|
23
|
Yan P, Tuo D, Shen W, Deng H, Zhou P, Gao X. A Nimble Cloning-compatible vector system for high-throughput gene functional analysis in plants. PLANT COMMUNICATIONS 2023; 4:100471. [PMID: 36352791 PMCID: PMC10030367 DOI: 10.1016/j.xplc.2022.100471] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 11/01/2022] [Accepted: 11/02/2022] [Indexed: 05/04/2023]
Abstract
Plant expression vectors are essential tools for gene functional analysis and molecular plant breeding. The gene of interest is transferred to the vector by molecular cloning technology. Nimble Cloning is a newly developed molecular cloning method with the advantages of simplicity, efficiency, and standardization. In this study, we developed a "pNC" vector system that contains 55 Nimble Cloning-compatible vectors for functional analysis of genes in plants. These vectors contain the NC frame flanked by unique adapters for one-step and standardized Nimble Cloning. We demonstrate that the pNC vectors are convenient and effective for the functional analysis of plant genes, including the study of gene ectopic expression, protein subcellular localization, protein-protein interaction, gene silencing (RNAi), virus-induced gene silencing, promoter activity, and CRISPR-Cas9-mediated genome editing. The "pNC" vector system represents a high-throughput toolkit that can facilitate the large-scale analysis of plant functional genomics.
Collapse
Affiliation(s)
- Pu Yan
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China.
| | - Decai Tuo
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Wentao Shen
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Haida Deng
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China
| | - Peng Zhou
- Key Laboratory of Biology and Genetic Resources of Tropical Crops, Sanya Research Institute, Institute of Tropical Biosciences and Biotechnology, Chinese Academy of Tropical Agricultural Science & Key Laboratory for Biology and Genetic Resources of Tropical Crops of Hainan Province, Hainan Institute of Tropical Agricultural Resources, Haikou 571101, China.
| | - Xinzheng Gao
- Department of Biology, Hainan Medical University, Haikou, China.
| |
Collapse
|
24
|
Chamness JC, Kumar J, Cruz AJ, Rhuby E, Holum MJ, Cody JP, Tibebu R, Gamo ME, Starker CG, Zhang F, Voytas DF. An extensible vector toolkit and parts library for advanced engineering of plant genomes. THE PLANT GENOME 2023:e20312. [PMID: 36896468 DOI: 10.1002/tpg2.20312] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 01/15/2023] [Indexed: 06/18/2023]
Abstract
Plant biotechnology is rife with new advances in transformation and genome engineering techniques. A common requirement for delivery and coordinated expression in plant cells, however, places the design and assembly of transformation constructs at a crucial juncture as desired reagent suites grow more complex. Modular cloning principles have simplified some aspects of vector design, yet many important components remain unavailable or poorly adapted for rapid implementation in biotechnology research. Here, we describe a universal Golden Gate cloning toolkit for vector construction. The toolkit chassis is compatible with the widely accepted Phytobrick standard for genetic parts, and supports assembly of arbitrarily complex T-DNAs through improved capacity, positional flexibility, and extensibility in comparison to extant kits. We also provision a substantial library of newly adapted Phytobricks, including regulatory elements for monocot and dicot gene expression, and coding sequences for genes of interest such as reporters, developmental regulators, and site-specific recombinases. Finally, we use a series of dual-luciferase assays to measure contributions to expression from promoters, terminators, and from cross-cassette interactions attributable to enhancer elements in certain promoters. Taken together, these publicly available cloning resources can greatly accelerate the testing and deployment of new tools for plant engineering.
Collapse
Affiliation(s)
- James C Chamness
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Jitesh Kumar
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Anna J Cruz
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Elissa Rhuby
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Mason J Holum
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
| | - Jon P Cody
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Redeat Tibebu
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Maria Elena Gamo
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Colby G Starker
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
| | - Feng Zhang
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| | - Daniel F Voytas
- Department of Genetics, Cell Biology and Development, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
- Center for Precision Plant Genomics, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Department of Plant and Microbial Biology, College of Biological Sciences, University of Minnesota, Minneapolis, MN, USA
| |
Collapse
|
25
|
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]
|
26
|
Vamsi Bharadwaj S, Tiwari DS, Ghosh T, Mishra S. Construction of pSM201v: A broad host range replicative vector based on shortening of RSF1010. Heliyon 2023; 9:e14637. [PMID: 37025788 PMCID: PMC10070531 DOI: 10.1016/j.heliyon.2023.e14637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/06/2023] [Accepted: 03/14/2023] [Indexed: 03/19/2023] Open
Abstract
Despite possessing attractive features such as autotrophic growth on minimal media, industrial applications of cyanobacteria are hindered by a lack of genetic manipulative tools. There are two important features that are important for an effective manipulation: a vector which can carry the gene, and an induction system activated through external stimuli, giving us control over the expression. In this study, we describe the construction of an improved RSF1010-based vector as well as a temperature-inducible RNA thermometer. RSF1010 is a well-studied incompatibility group Q (IncQ) vector, capable of replication in most Gram negative, and some Gram positive bacteria. Our designed vector, named pSM201v, can be used as an expression vector in some Gram positive and a wide range of Gram negative bacteria including cyanobacteria. An induction system activated via physical external stimuli such as temperature, allows precise control of overexpression. pSM201v addresses several drawbacks of the RSF1010 plasmid; it has a reduced backbone size of 5189 bp compared to 8684 bp of the original plasmid, which provides more space for cloning and transfer of cargo DNA into the host organism. The mobilization function, required for plasmid transfer into several cyanobacterial strains, is reduced to a 99 bp region, as a result that mobilization of this plasmid is no longer linked to the plasmid replication. The RNA thermometer, named DTT1, is based on a RNA hairpin strategy that prevents expression of downstream genes at temperatures below 30 °C. Such RNA elements are expected to find applications in biotechnology to economically control gene expression in a scalable manner.
Collapse
|
27
|
Kumar K, Shinde A, Aeron V, Verma A, Arif NS. Genetic engineering of plants for phytoremediation: advances and challenges. JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY 2023; 32:12-30. [PMID: 0 DOI: 10.1007/s13562-022-00776-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 02/22/2022] [Indexed: 05/27/2023]
|
28
|
Alker AT, Aspiras AE, Dunbar TL, Farrell MV, Fedoriouk A, Jones JE, Mikhail SR, Salcedo GY, Moore BS, Shikuma NJ. A modular plasmid toolkit applied in marine Proteobacteria reveals functional insights during bacteria-stimulated metamorphosis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.31.526474. [PMID: 36778221 PMCID: PMC9915575 DOI: 10.1101/2023.01.31.526474] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A conspicuous roadblock to studying marine bacteria for fundamental research and biotechnology is a lack of modular synthetic biology tools for their genetic manipulation. Here, we applied, and generated new parts for, a modular plasmid toolkit to study marine bacteria in the context of symbioses and host-microbe interactions. To demonstrate the utility of this plasmid system, we genetically manipulated the marine bacterium Pseudoalteromonas luteoviolacea , which stimulates the metamorphosis of the model tubeworm, Hydroides elegans . Using these tools, we quantified constitutive and native promoter expression, developed reporter strains that enable the imaging of host-bacteria interactions, and used CRISPR interference (CRISPRi) to knock down a secondary metabolite and a host-associated gene. We demonstrate the broader utility of this modular system for rapidly creating and iteratively testing genetic tractability by modifying marine bacteria that are known to be associated with diverse host-microbe symbioses. These efforts enabled the successful transformation of twelve marine strains across two Proteobacteria classes, four orders and ten genera. Altogether, the present study demonstrates how synthetic biology strategies enable the investigation of marine microbes and marine host-microbe symbioses with broader implications for environmental restoration and biotechnology.
Collapse
|
29
|
Baldanta S, Arnal R, Blanco-Rivero A, Guevara G, Navarro Llorens JM. First characterization of cultivable extremophile Chroococcidiopsis isolates from a solar panel. Front Microbiol 2023; 14:982422. [PMID: 36876112 PMCID: PMC9982165 DOI: 10.3389/fmicb.2023.982422] [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: 06/30/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Introduction Microorganisms colonize a wide range of natural and artificial environments. Even though most of them are unculturable in laboratory conditions, some ecosystems are ideal niches for bioprospecting extremophiles with unique properties. Up today, there are few reports concerning microbial communities found on solar panels, a widespread, artificial, extreme habitat. Microorganisms found in this habitat belong to drought-, heat- and radiation-adapted genera, including fungi, bacteria, and cyanobacteria. Methods Here we isolated and identified several cyanobacteria from a solar panel. Then, some strains isolated were characterizated for their resistance to desiccation, UV-C exposition, and their growth on a range of temperature, pH, NaCl concentration or diverse carbon and nitrogen sources. Finally, gene transfer to these isolates was evaluated using several SEVA plasmids with different replicons to assess their potential in biotechnological applications. Results and discussion This study presents the first identification and characterization of cultivable extremophile cyanobacteria from a solar panel in Valencia, Spain. The isolates are members of the genera Chroococcidiopsis, Leptolyngbya, Myxacorys, and Oculatella all genera with species commonly isolated from deserts and arid regions. Four of the isolates were selected, all of them Chroococcidiopsis, and characterized. Our results showed that all Chroococcidiopsis isolates chosen were resistant up to a year of desiccation, viable after exposition to high doses of UV-C, and capable of being transformed. Our findings revealed that a solar panel is a useful ecological niche in searching for extremophilic cyanobacteria to further study the desiccation and UV-tolerance mechanisms. We conclude that these cyanobacteria can be modified and exploited as candidates for biotechnological purposes, including astrobiology applications.
Collapse
Affiliation(s)
- Sara Baldanta
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Raquel Arnal
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Amaya Blanco-Rivero
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Govinda Guevara
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| | - Juana María Navarro Llorens
- Metabolic Engineering Group, Department of Biochemistry and Molecular Biology, Universidad Complutense de Madrid, Madrid, Spain
| |
Collapse
|
30
|
Bird J, Marles-Wright J, Giachino A. A User's Guide to Golden Gate Cloning Methods and Standards. ACS Synth Biol 2022; 11:3551-3563. [PMID: 36322003 PMCID: PMC9680027 DOI: 10.1021/acssynbio.2c00355] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2022] [Indexed: 11/06/2022]
Abstract
The continual demand for specialized molecular cloning techniques that suit a broad range of applications has driven the development of many different cloning strategies. One method that has gained significant traction is Golden Gate assembly, which achieves hierarchical assembly of DNA parts by utilizing Type IIS restriction enzymes to produce user-specified sticky ends on cut DNA fragments. This technique has been modularized and standardized, and includes different subfamilies of methods, the most widely adopted of which are the MoClo and Golden Braid standards. Moreover, specialized toolboxes tailored to specific applications or organisms are also available. Still, the quantity and range of assembly methods can constitute a barrier to adoption for new users, and even experienced scientists might find it difficult to discern which tools are best suited toward their goals. In this review, we provide a beginner-friendly guide to Golden Gate assembly, compare the different available standards, and detail the specific features and quirks of commonly used toolboxes. We also provide an update on the state-of-the-art in Golden Gate technology, discussing recent advances and challenges to inform existing users and promote standard practices.
Collapse
Affiliation(s)
- Jasmine
E. Bird
- School
of Computing, Faculty of Science Agriculture and Engineering, Newcastle University, Newcastle upon Tyne, NE1 7RU, United Kingdom
| | - Jon Marles-Wright
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom
| | - Andrea Giachino
- Biosciences
Institute, Faculty of Medical Sciences, Newcastle University, Newcastle
upon Tyne, NE2 4HH, United
Kingdom
- School
of Science, Engineering & Environment, University of Salford, Salford, M5 4NT, United Kingdom
| |
Collapse
|
31
|
Usai G, Cordara A, Re A, Polli MF, Mannino G, Bertea CM, Fino D, Pirri CF, Menin B. Combining metabolite doping and metabolic engineering to improve 2-phenylethanol production by engineered cyanobacteria. Front Bioeng Biotechnol 2022; 10:1005960. [PMID: 36204466 PMCID: PMC9530348 DOI: 10.3389/fbioe.2022.1005960] [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: 07/28/2022] [Accepted: 08/25/2022] [Indexed: 11/13/2022] Open
Abstract
2-Phenylethanol (2-PE) is a rose-scented aromatic compound, with broad application in cosmetic, pharmaceutical, food and beverage industries. Many plants naturally synthesize 2-PE via Shikimate Pathway, but its extraction is expensive and low-yielding. Consequently, most 2-PE derives from chemical synthesis, which employs petroleum as feedstock and generates unwanted by products and health issues. The need for "green" processes and the increasing public demand for natural products are pushing biotechnological production systems as promising alternatives. So far, several microorganisms have been investigated and engineered for 2-PE biosynthesis, but a few studies have focused on autotrophic microorganisms. Among them, the prokaryotic cyanobacteria can represent ideal microbial factories thanks to their ability to photosynthetically convert CO2 into valuable compounds, their minimal nutritional requirements, high photosynthetic rate and the availability of genetic and bioinformatics tools. An engineered strain of Synechococcus elongatus PCC 7942 for 2-PE production, i.e., p120, was previously published elsewhere. The strain p120 expresses four heterologous genes for the complete 2-PE synthesis pathway. Here, we developed a combined approach of metabolite doping and metabolic engineering to improve the 2-PE production kinetics of the Synechococcus elongatus PCC 7942 p120 strain. Firstly, the growth and 2-PE productivity performances of the p120 recombinant strain were analyzed to highlight potential metabolic constraints. By implementing a BG11 medium doped with L-phenylalanine, we covered the metabolic burden to which the p120 strain is strongly subjected, when the 2-PE pathway expression is induced. Additionally, we further boosted the carbon flow into the Shikimate Pathway by overexpressing the native Shikimate Kinase in the Synechococcus elongatus PCC 7942 p120 strain (i.e., 2PE_aroK). The combination of these different approaches led to a 2-PE yield of 300 mg/gDW and a maximum 2-PE titer of 285 mg/L, 2.4-fold higher than that reported in literature for the p120 recombinant strain and, to our knowledge, the highest recorded for photosynthetic microorganisms, in photoautotrophic growth condition. Finally, this work provides the basis for further optimization of the process aimed at increasing 2-PE productivity and concentration, and could offer new insights about the use of cyanobacteria as appealing microbial cell factories for the synthesis of aromatic compounds.
Collapse
Affiliation(s)
- Giulia Usai
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Alessandro Cordara
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Angela Re
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| | - Maria Francesca Polli
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Agricultural, Forest and Food Sciences—DISAFA, University of Turin, Grugliasco, Italy
| | - Giuseppe Mannino
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Cinzia Margherita Bertea
- Plant Physiology Unit, Department of Life Sciences and Systems Biology, University of Turin, Turin, Italy
| | - Debora Fino
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Candido Fabrizio Pirri
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
- Department of Applied Science and Technology—DISAT, Politecnico di Torino, Turin, Italy
| | - Barbara Menin
- Centre for Sustainable Future Technologies, Fondazione Istituto Italiano di Tecnologia, Turin, Italy
| |
Collapse
|
32
|
Cengic I, Cañadas IC, Minton NP, Hudson EP. Inducible CRISPR/Cas9 Allows for Multiplexed and Rapidly Segregated Single-Target Genome Editing in Synechocystis Sp. PCC 6803. ACS Synth Biol 2022; 11:3100-3113. [PMID: 35969224 PMCID: PMC9486961 DOI: 10.1021/acssynbio.2c00375] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Establishing various synthetic biology tools is crucial for the development of cyanobacteria for biotechnology use, especially tools that allow for precise and markerless genome editing in a time-efficient manner. Here, we describe a riboswitch-inducible CRISPR/Cas9 system, contained on a single replicative vector, for the model cyanobacterium Synechocystis sp. PCC 6803. A theophylline-responsive riboswitch allowed tight control of Cas9 expression, which enabled reliable transformation of the CRISPR/Cas9 vector intoSynechocystis. Induction of the CRISPR/Cas9 mediated various types of genomic edits, specifically deletions and insertions of varying size. The editing efficiency varied depending on the target and intended edit; smaller edits performed better, reaching, e.g., 100% for insertion of a FLAG-tag onto rbcL. Importantly, the single-vector CRISPR/Cas9 system mediated multiplexed editing of up to three targets in parallel inSynechocystis. All single-target and several double-target mutants were also fully segregated after the first round of induction. Lastly, a vector curing system based on the nickel-inducible expression of the toxic mazF (from Escherichia coli) was added to the CRISPR/Cas9 vector. This inducible system allowed for curing of the vector in 25-75% of screened colonies, enabling edited mutants to become markerless.
Collapse
Affiliation(s)
- Ivana Cengic
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden
| | - Inés C. Cañadas
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Nigel P. Minton
- BBSRC/EPSRC
Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham NG7 2RD, U.K.
| | - Elton P. Hudson
- School
of Engineering Sciences in Chemistry, Biotechnology and Health, Science
for Life Laboratory, KTH Royal Institute
of Technology, Stockholm 17121, Sweden,
| |
Collapse
|
33
|
Mills LA, Moreno-Cabezuelo JÁ, Włodarczyk A, Victoria AJ, Mejías R, Nenninger A, Moxon S, Bombelli P, Selão TT, McCormick AJ, Lea-Smith DJ. Development of a Biotechnology Platform for the Fast-Growing Cyanobacterium Synechococcus sp. PCC 11901. Biomolecules 2022; 12:biom12070872. [PMID: 35883428 PMCID: PMC9313322 DOI: 10.3390/biom12070872] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 06/21/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
Synechococcus sp. PCC 11901 reportedly demonstrates the highest, most sustained growth of any known cyanobacterium under optimized conditions. Due to its recent discovery, our knowledge of its biology, including the factors underlying sustained, fast growth, is limited. Furthermore, tools specific for genetic manipulation of PCC 11901 are not established. Here, we demonstrate that PCC 11901 shows faster growth than other model cyanobacteria, including the fast-growing species Synechococcuselongatus UTEX 2973, under optimal growth conditions for UTEX 2973. Comparative genomics between PCC 11901 and Synechocystis sp. PCC 6803 reveal conservation of most metabolic pathways but PCC 11901 has a simplified electron transport chain and reduced light harvesting complex. This may underlie its superior light use, reduced photoinhibition, and higher photosynthetic and respiratory rates. To aid biotechnology applications, we developed a vitamin B12 auxotrophic mutant but were unable to generate unmarked knockouts using two negative selectable markers, suggesting that recombinase- or CRISPR-based approaches may be required for repeated genetic manipulation. Overall, this study establishes PCC 11901 as one of the most promising species currently available for cyanobacterial biotechnology and provides a useful set of bioinformatics tools and strains for advancing this field, in addition to insights into the factors underlying its fast growth phenotype.
Collapse
Affiliation(s)
- Lauren A. Mills
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - José Ángel Moreno-Cabezuelo
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Artur Włodarczyk
- Bondi Bio Pty Ltd., c/o Climate Change Cluster, University of Technology Sydney, 745 Harris Street, Ultimo, NSW 2007, Australia;
| | - Angelo J. Victoria
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Rebeca Mejías
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Anja Nenninger
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - Simon Moxon
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
| | - Paolo Bombelli
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1QW, UK;
| | - Tiago T. Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, Nottingham NG7 2RD, UK;
| | - Alistair J. McCormick
- SynthSys and Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK; (A.J.V.); (A.N.); (A.J.M.)
| | - David J. Lea-Smith
- School of Biological Sciences, University of East Anglia, Norwich Research Park, Norwich NR4 7TJ, UK; (L.A.M.); (J.Á.M.-C.); (R.M.); (S.M.)
- Correspondence:
| |
Collapse
|
34
|
Baldanta S, Guevara G, Navarro-Llorens JM. SEVA-Cpf1, a CRISPR-Cas12a vector for genome editing in cyanobacteria. Microb Cell Fact 2022; 21:103. [PMID: 35643551 PMCID: PMC9148489 DOI: 10.1186/s12934-022-01830-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cyanobacteria are photosynthetic autotrophs that have tremendous potential for fundamental research and industrial applications due to their high metabolic plasticity and ability to grow using CO2 and sunlight. CRISPR technology using Cas9 and Cpf1 has been applied to different cyanobacteria for genome manipulations and metabolic engineering. Despite significant advances with genome editing in several cyanobacteria strains, the lack of proper genetic toolboxes is still a limiting factor compared to other model laboratory species. Among the limitations, it is essential to have versatile plasmids that could ease the benchwork when using CRISPR technology. Results In the present study, several CRISPR-Cpf1 vectors were developed for genetic manipulations in cyanobacteria using SEVA plasmids. SEVA collection is based on modular vectors that enable the exchangeability of diverse elements (e.g. origins of replication and antibiotic selection markers) and the combination with many cargo sequences for varied end-applications. Firstly, using SEVA vectors containing the broad host range RSF1010 origin we demonstrated that these vectors are replicative not only in model cyanobacteria but also in a new cyanobacterium specie, Chroococcidiopsis sp., which is different from those previously published. Then, we constructed SEVA vectors by harbouring CRISPR elements and showed that they can be easily assimilated not only by conjugation, but also by natural transformation. Finally, we used our SEVA-Cpf1 tools to delete the nblA gene in Synechocystis sp. PCC 6803, demonstrating that our plasmids can be applied for CRISPR-based genome editing technology. Conclusions The results of this study provide new CRISPR-based vectors based on the SEVA (Standard European Vector Architecture) collection that can improve editing processes using the Cpf1 nuclease in cyanobacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01830-4.
Collapse
|
35
|
Selão TT. Exploring cyanobacterial diversity for sustainable biotechnology. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:3057-3071. [PMID: 35467729 DOI: 10.1093/jxb/erac053] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 04/22/2022] [Indexed: 06/14/2023]
Abstract
Cyanobacteria are an evolutionarily ancient and diverse group of microorganisms. Their genetic diversity has
allowed them to occupy and play vital roles in a wide range of ecological niches, from desert soil crusts to tropical oceans. Owing to bioprospecting efforts and the development of new platform technologies enabling their study and manipulation, our knowledge of cyanobacterial metabolism is rapidly expanding. This review explores our current understanding of the genetic and metabolic features of cyanobacteria, from the more established cyanobacterial model strains to the newly isolated/described species, particularly the fast-growing, highly productive, and genetically amenable strains, as promising chassis for renewable biotechnology. It also discusses emerging technologies for their study and manipulation, enabling researchers to harness the astounding diversity of the cyanobacterial genomic and metabolic treasure trove towards the establishment of a sustainable bioeconomy.
Collapse
Affiliation(s)
- Tiago Toscano Selão
- Department of Chemical and Environmental Engineering, University of Nottingham, University Park Campus, Nottingham NG7 2RD, UK
| |
Collapse
|
36
|
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.
Collapse
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
| |
Collapse
|
37
|
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.
Collapse
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.
| |
Collapse
|
38
|
Kang DH, Ko SC, Heo YB, Lee HJ, Woo HM. RoboMoClo: A Robotics-Assisted Modular Cloning Framework for Multiple Gene Assembly in Biofoundry. ACS Synth Biol 2022; 11:1336-1348. [PMID: 35167276 DOI: 10.1021/acssynbio.1c00628] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Efficient and versatile DNA assembly frameworks have had an impact on promoting synthetic biology to build complex biological systems. To accelerate system development, laboratory automation (or biofoundry) provides an opportunity to construct organisms and DNA assemblies via computer-aided design. However, a modular cloning (MoClo) system for multiple DNA assemblies limits the biofoundry workflow in terms of simplicity and feasibility by preparing the number of cloning materials such as destination vectors prior to the automation process. Herein, we propose robot-assisted MoClo (RoboMoClo) to accelerate a synthetic biology project with multiple gene expressions at the biofoundry. The architecture of the RoboMoClo framework provides a hybrid strategy of hierarchical gene assembly and iterative gene assembly, and fewer destination vectors compared with other MoClo systems. An industrial bacterium, Corynebacterium glutamicum, was used as a model host for RoboMoClo. After building a biopart library (promoter and terminator; level 0) and evaluating its features (level 1), various transcriptional directions in multiple gene assemblies (level 2) were studied using the RoboMoClo vectors. Among the constructs, the convergent construct exhibited potential transcriptional interference through the collision of RNA polymerases. To study design of experiment-guided lycopene biosynthesis in C. glutamicum (levels 1, 2, and 3), the biofoundry-assisted multiple gene assembly was demonstrated as a proof-of-concept by constructing various sub-pathway units (level 2) and pathway units (level 3) for C. glutamicum. The RoboMoClo framework provides an improved MoClo toolkit for laboratory automation in a synthetic biology application.
Collapse
Affiliation(s)
- Dong Hun Kang
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Sung Cheon Ko
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Yu Been Heo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Hyun Jeong Lee
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| | - Han Min Woo
- Department of Food Science and Biotechnology, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
- Biofoundry Research Center, Sungkyunkwan University (SKKU), 2066 Seobu-ro, Jangan-gu, Suwon 16419, Republic of Korea
| |
Collapse
|
39
|
Mapstone LJ, Leite MN, Purton S, Crawford IA, Dartnell L. Cyanobacteria and microalgae in supporting human habitation on Mars. Biotechnol Adv 2022; 59:107946. [DOI: 10.1016/j.biotechadv.2022.107946] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 02/21/2022] [Accepted: 03/15/2022] [Indexed: 12/16/2022]
|
40
|
Han P, Teo WZ, Yew WS. Biologically engineered microbes for bioremediation of electronic waste: Wayposts, challenges and future directions. ENGINEERING BIOLOGY 2022; 6:23-34. [PMID: 36968558 PMCID: PMC9995160 DOI: 10.1049/enb2.12020] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2021] [Revised: 01/17/2022] [Accepted: 02/21/2022] [Indexed: 12/25/2022] Open
Abstract
In the face of a burgeoning stream of e-waste globally, e-waste recycling becomes increasingly imperative, not only to mitigate the environmental and health risks it poses but also as an urban mining strategy for resource recovery of precious metals, rare Earth elements, and even plastics. As part of the continual efforts to develop greener alternatives to conventional approaches of e-waste recycling, biologically assisted degradation of e-waste offers a promising recourse by capitalising on certain microorganisms' innate ability to interact with metals or degrade plastics. By harnessing emerging genetic tools in synthetic biology, the evolution of novel or enhanced capabilities needed to advance bioremediation and resource recovery could be potentially accelerated by improving enzyme catalytic abilities, modifying substrate specificities, and increasing toxicity tolerance. Yet, the management of e-waste presents formidable challenges due to its massive volume, high component complexity, and associated toxicity. Several limitations will need to be addressed before nascent laboratory-scale achievements in bioremediation can be translated to viable industrial applications. Nonetheless, vested groups, involving both start-up and established companies, have taken visionary steps towards deploying microbes for commercial implementation in e-waste recycling.
Collapse
Affiliation(s)
- Ping Han
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wei Zhe Teo
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| | - Wen Shan Yew
- Synthetic Biology for Clinical and Technological InnovationNational University of SingaporeSingaporeSingapore
- Synthetic Biology Translational Research ProgrammeYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
- Department of BiochemistryYong Loo Lin School of MedicineNational University of SingaporeSingaporeSingapore
| |
Collapse
|
41
|
Chen H, Wang Q. Microalgae-Based Green Bio-Manufacturing—How Far From Us. Front Microbiol 2022; 13:832097. [PMID: 35250947 PMCID: PMC8891535 DOI: 10.3389/fmicb.2022.832097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/26/2022] [Indexed: 02/04/2023] Open
Affiliation(s)
- Hui Chen
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
| | - Qiang Wang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Academy for Advanced Interdisciplinary Studies, Henan University, Kaifeng, China
- *Correspondence: Qiang Wang
| |
Collapse
|
42
|
Chakdar H, Thapa S, Srivastava A, Shukla P. Genomic and proteomic insights into the heavy metal bioremediation by cyanobacteria. JOURNAL OF HAZARDOUS MATERIALS 2022; 424:127609. [PMID: 34772552 DOI: 10.1016/j.jhazmat.2021.127609] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 10/16/2021] [Accepted: 10/24/2021] [Indexed: 06/13/2023]
Abstract
Heavy metals (HMs) pose a global ecological threat due to their toxic effects on aquatic and terrestrial life. Effective remediation of HMs from the environment can help to restore soil's fertility and ecological vigor, one of the key Sustainable Development Goals (SDG) set by the United Nations. The cyanobacteria have emerged as a potential option for bioremediation of HMs due to their unique adaptations and robust metabolic machineries. Generally, cyanobacteria deploy multifarious mechanisms such as biosorption, bioaccumulation, activation of metal transporters, biotransformation and induction of detoxifying enzymes to sequester and minimize the toxic effects of heavy metals. Therefore, understanding the physiological responses and regulation of adaptation mechanisms at molecular level is necessary to unravel the candidate genes and proteins which can be manipulated to improve the bioremediation efficiency of cyanobacteria. Chaperons, cellular metabolites (extracellular polymers, biosurfactants), transcriptional regulators, metal transporters, phytochelatins and metallothioneins are some of the potential targets for strain engineering. In the present review, we have discussed the potential of cyanobacteria for HM bioremediation and provided a deeper insight into their genomic and proteomic regulation of various tolerance mechanisms. These approaches might pave new possibilities of implementing genetic engineering strategies for improving bioremediation efficiency with a future perspective.
Collapse
Affiliation(s)
- Hillol Chakdar
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Shobit Thapa
- Microbial Technology Unit II, ICAR-National Bureau of Agriculturally Important Microorganisms (NBAIM), Mau 275103, Uttar Pradesh, India
| | - Amit Srivastava
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, ID 47907-2048, United States
| | - Pratyoosh Shukla
- School of Biotechnology, Institute of Science, Banaras Hindu University, Varanasi 221005, Uttar Pradesh, India; Enzyme Technology and Protein Bioinformatics Laboratory, Department of Microbiology, Maharshi Dayanand University, Rohtak 124001, Haryana, India.
| |
Collapse
|
43
|
Santos-Aberturas J, Vior NM. Beyond Soil-Dwelling Actinobacteria: Fantastic Antibiotics and Where to Find Them. Antibiotics (Basel) 2022; 11:195. [PMID: 35203798 PMCID: PMC8868522 DOI: 10.3390/antibiotics11020195] [Citation(s) in RCA: 6] [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: 12/31/2021] [Revised: 01/27/2022] [Accepted: 01/29/2022] [Indexed: 12/10/2022] Open
Abstract
Bacterial secondary metabolites represent an invaluable source of bioactive molecules for the pharmaceutical and agrochemical industries. Although screening campaigns for the discovery of new compounds have traditionally been strongly biased towards the study of soil-dwelling Actinobacteria, the current antibiotic resistance and discovery crisis has brought a considerable amount of attention to the study of previously neglected bacterial sources of secondary metabolites. The development and application of new screening, sequencing, genetic manipulation, cultivation and bioinformatic techniques have revealed several other groups of bacteria as producers of striking chemical novelty. Biosynthetic machineries evolved from independent taxonomic origins and under completely different ecological requirements and selective pressures are responsible for these structural innovations. In this review, we summarize the most important discoveries related to secondary metabolites from alternative bacterial sources, trying to provide the reader with a broad perspective on how technical novelties have facilitated the access to the bacterial metabolic dark matter.
Collapse
Affiliation(s)
| | - Natalia M. Vior
- Department of Molecular Microbiology, John Innes Centre, Norwich NR7 4UH, UK
| |
Collapse
|
44
|
Puzorjov A, Mert Unal S, Wear MA, McCormick AJ. Pilot scale production, extraction and purification of a thermostable phycocyanin from Synechocystis sp. PCC 6803. BIORESOURCE TECHNOLOGY 2022; 345:126459. [PMID: 34863843 PMCID: PMC8811538 DOI: 10.1016/j.biortech.2021.126459] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Revised: 11/25/2021] [Accepted: 11/26/2021] [Indexed: 06/09/2023]
Abstract
Phycocyanin (PC) is a soluble blue pigment-protein primarily harvested from the cyanobacterium Arthrospira platensis. PC is in high demand from several industries, but its narrow stability range limits potential applications. Here, a pilot scale (120 L total) batch production, extraction and purification process for thermostable PC (Te-PC) from a Synechocystis sp. PCC 6803 'Olive' strain expressing the PC operon cpcBACD from Thermosynechococcus elongatus BP-1 on a self-replicating vector is presented. Batch cultivation without antibiotics had no impact on growth or Te-PC production and optimisation of growth conditions resulted in Te-PC contents of 75.3 ± 1.7 mg g DW-1. Wet biomass was harvested following chitosan-based flocculation with a 97 ± 2% efficiency, and Te-PC was extracted by high pressure homogenisation. Subsequent purification by heat-treatment and two-step ammonium sulfate precipitation removed chlorophyll and allophycocyanin contamination, resulting in Te-PC purities of 2.9 ± 0.7 and a mean Te-PC recovery of 84 ± 12%.
Collapse
Affiliation(s)
- Anton Puzorjov
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Suleyman Mert Unal
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK
| | - Martin A Wear
- The Edinburgh Protein Purification Facility, University of Edinburgh, Edinburgh EH9 3JR, UK
| | - Alistair J McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh EH9 3BF, UK.
| |
Collapse
|
45
|
Zieliński T, Hay J, Romanowski A, Nenninger A, McCormick A, Millar AJ. SynBio2Easy-a biologist-friendly tool for batch operations on SBOL designs with Excel inputs. SYNTHETIC BIOLOGY (OXFORD, ENGLAND) 2022; 7:ysac002. [PMID: 35350192 PMCID: PMC8944294 DOI: 10.1093/synbio/ysac002] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 11/26/2021] [Accepted: 01/25/2022] [Indexed: 01/09/2023]
Abstract
Practical delivery of Findable, Accessible, Reusable and Interoperable principles for research data management requires expertise, time resource, (meta)data standards and formats, software tools and public repositories. The Synthetic Biology Open Language (SBOL2) metadata standard enables FAIR sharing of the designs of synthetic biology constructs, notably in the repository of the SynBioHub platform. Large libraries of such constructs are increasingly easy to produce in practice, for example, in DNA foundries. However, manual curation of the equivalent libraries of designs remains cumbersome for a typical lab researcher, creating a barrier to data sharing. Here, we present a simple tool SynBio2Easy, which streamlines and automates operations on multiple Synthetic Biology Open Language (SBOL) designs using Microsoft Excel® tables as metadata inputs. The tool provides several utilities for manipulation of SBOL documents and interaction with SynBioHub: for example, generation of a library of plasmids based on an original design template, bulk deposition into SynBioHub, or annotation of existing SBOL component definitions with notes and authorship information. The tool was used to generate and deposit a collection of 3661 cyanobacterium Synechocystis plasmids into the public SynBioHub repository. In the process of developing the software and uploading these data, we evaluated some aspects of the SynBioHub platform and SBOL ecosystem, and we discuss proposals for improvement that could benefit the user community. With software such as SynBio2Easy, we aim to deliver a user-driven tooling to make FAIR a reality at all stages of the project lifecycle in synthetic biology research. Graphical Abstract.
Collapse
Affiliation(s)
- Tomasz Zieliński
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Johnny Hay
- EPCC, University of Edinburgh, Edinburgh, UK
| | - Andrew Romanowski
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Anja Nenninger
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Alistair McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | |
Collapse
|
46
|
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]
|
47
|
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]
|
48
|
Goosens VJ, Walker KT, Aragon SM, Singh A, Senthivel VR, Dekker L, Caro-Astorga J, Buat MLA, Song W, Lee KY, Ellis T. Komagataeibacter Tool Kit (KTK): A Modular Cloning System for Multigene Constructs and Programmed Protein Secretion from Cellulose Producing Bacteria. ACS Synth Biol 2021; 10:3422-3434. [PMID: 34767345 DOI: 10.1021/acssynbio.1c00358] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Bacteria proficient at producing cellulose are an attractive synthetic biology host for the emerging field of Engineered Living Materials (ELMs). Species from the Komagataeibacter genus produce high yields of pure cellulose materials in a short time with minimal resources, and pioneering work has shown that genetic engineering in these strains is possible and can be used to modify the material and its production. To accelerate synthetic biology progress in these bacteria, we introduce here the Komagataeibacter tool kit (KTK), a standardized modular cloning system based on Golden Gate DNA assembly that allows DNA parts to be combined to build complex multigene constructs expressed in bacteria from plasmids. Working in Komagataeibacter rhaeticus, we describe basic parts for this system, including promoters, fusion tags, and reporter proteins, before showcasing how the assembly system enables more complex designs. Specifically, we use KTK cloning to reformat the Escherichia coli curli amyloid fiber system for functional expression in K. rhaeticus, and go on to modify it as a system for programming protein secretion from the cellulose producing bacteria. With this toolkit, we aim to accelerate modular synthetic biology in these bacteria, and enable more rapid progress in the emerging ELMs community.
Collapse
Affiliation(s)
- Vivianne J. Goosens
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Kenneth T. Walker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Silvia M. Aragon
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Amritpal Singh
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Vivek R. Senthivel
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | - Linda Dekker
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Life Sciences, Imperial College London, London SW7 2AZ, U.K
| | - Joaquin Caro-Astorga
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| | | | - Wenzhe Song
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Koon-Yang Lee
- Department of Aeronautics, Imperial College London, London SW7 2AZ, U.K
| | - Tom Ellis
- Imperial College Centre for Synthetic Biology, Imperial College London, London SW7 2AZ, U.K
- Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
| |
Collapse
|
49
|
Puzorjov A, Dunn KE, McCormick AJ. Production of thermostable phycocyanin in a mesophilic cyanobacterium. Metab Eng Commun 2021; 13:e00175. [PMID: 34168957 PMCID: PMC8209669 DOI: 10.1016/j.mec.2021.e00175] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 05/12/2021] [Accepted: 05/28/2021] [Indexed: 11/01/2022] Open
Abstract
Phycocyanin (PC) is a soluble phycobiliprotein found within the light-harvesting phycobilisome complex of cyanobacteria and red algae, and is considered a high-value product due to its brilliant blue colour and fluorescent properties. However, commercially available PC has a relatively low temperature stability. Thermophilic species produce more thermostable variants of PC, but are challenging and energetically expensive to cultivate. Here, we show that the PC operon from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 (cpcBACD) is functional in the mesophile Synechocystis sp. PCC 6803. Expression of cpcBACD in an 'Olive' mutant strain of Synechocystis lacking endogenous PC resulted in high yields of thermostable PC (112 ± 1 mg g-1 DW) comparable to that of endogenous PC in wild-type cells. Heterologous PC also improved the growth of the Olive mutant, which was further supported by evidence of a functional interaction with the endogenous allophycocyanin core of the phycobilisome complex. The thermostability properties of the heterologous PC were comparable to those of PC from T. elongatus, and could be purified from the Olive mutant using a low-cost heat treatment method. Finally, we developed a scalable model to calculate the energetic benefits of producing PC from T. elongatus in Synechocystis cultures. Our model showed that the higher yields and lower cultivation temperatures of Synechocystis resulted in a 3.5-fold increase in energy efficiency compared to T. elongatus, indicating that producing thermostable PC in non-native hosts is a cost-effective strategy for scaling to commercial production.
Collapse
Affiliation(s)
- Anton Puzorjov
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Katherine E. Dunn
- Institute for Bioengineering, School of Engineering, University of Edinburgh, Edinburgh, EH9 3DW, UK
| | - Alistair J. McCormick
- SynthSys & Institute of Molecular Plant Sciences, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3BF, UK
| |
Collapse
|
50
|
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.
Collapse
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.
| |
Collapse
|