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Einhaus A, Baier T, Kruse O. Molecular design of microalgae as sustainable cell factories. Trends Biotechnol 2024; 42:728-738. [PMID: 38092627 DOI: 10.1016/j.tibtech.2023.11.010] [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: 09/28/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 06/09/2024]
Abstract
Microalgae are regarded as sustainable and potent chassis for biotechnology. Their capacity for efficient photosynthesis fuels dynamic growth independent from organic carbon sources and converts atmospheric CO2 directly into various valuable hydrocarbon-based metabolites. However, approaches to gene expression and metabolic regulation have been inferior to those in more established heterotrophs (e.g., prokaryotes or yeast) since the genetic tools and insights in expression regulation have been distinctly less advanced. In recent years, however, these tools and their efficiency have dramatically improved. Various examples have demonstrated new trends in microalgal biotechnology and the potential of microalgae for the transition towards a sustainable bioeconomy.
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Affiliation(s)
- Alexander Einhaus
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Thomas Baier
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany
| | - Olaf Kruse
- Algae Biotechnology and Bioenergy, Faculty of Biology, Center for Biotechnology (CeBiTec), Bielefeld University, Bielefeld, Germany.
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2
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Trujillo E, Monreal-Escalante E, Angulo C. Microalgae-made human vaccines and therapeutics: A decade of advances. Biotechnol J 2024; 19:e2400091. [PMID: 38719615 DOI: 10.1002/biot.202400091] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 04/05/2024] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
Microalgal emergence is a promising platform with two-decade historical background for producing vaccines and biopharmaceuticals. During that period, microalgal-based vaccines have reported successful production for various diseases. Thus, species selection is important for genetic transformation and delivery methods that have been developed. Although many vaccine prototypes have been produced for infectious and non-infectious diseases, fewer studies have reached immunological and immunoprotective evaluations. Microalgae-made vaccines for Staphylococcus aureus, malaria, influenza, human papilloma, and Zika viruses have been explored in their capacity to induce humoral or cellular immune responses and protective efficacies against experimental challenges. Therefore, specific pathogen antigens and immune system role are important and addressed in controlling these infections. Regarding non-communicable diseases, these vaccines have been investigated for breast cancer; microalgal-produced therapeutic molecules and microalgal-made interferon-α have been explored for hypertension and potential applications in treating viral infections and cancer, respectively. Thus, conducting immunological trials is emphasized, discussing the promising results observed in terms of immunogenicity, desired immune response for controlling affections, and challenges for achieving the desired protection levels. The potential advantages and hurdles associated with this innovative approach are highlighted, underlining the relevance of assessing immune responses in preclinical and clinical trials to validate the efficacy of these biopharmaceuticals. The promising future of this healthcare technology is also envisaged.
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Affiliation(s)
- Edgar Trujillo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S., México
| | - Elizabeth Monreal-Escalante
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S., México
- CONAHCYT-Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S., México
| | - Carlos Angulo
- Immunology & Vaccinology Group, Centro de Investigaciones Biológicas del Noroeste, S.C. (CIBNOR), Instituto Politécnico Nacional 195, Playa Palo de Santa Rita Sur, La Paz, B.C.S., México
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3
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Agustinus B, Gillam EMJ. Solar-powered P450 catalysis: Engineering electron transfer pathways from photosynthesis to P450s. J Inorg Biochem 2023; 245:112242. [PMID: 37187017 DOI: 10.1016/j.jinorgbio.2023.112242] [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: 02/02/2023] [Revised: 04/17/2023] [Accepted: 04/27/2023] [Indexed: 05/17/2023]
Abstract
With the increasing focus on green chemistry, biocatalysis is becoming more widely used in the pharmaceutical and other chemical industries for sustainable production of high value and structurally complex chemicals. Cytochrome P450 monooxygenases (P450s) are attractive biocatalysts for industrial application due to their ability to transform a huge range of substrates in a stereo- and regiospecific manner. However, despite their appeal, the industrial application of P450s is limited by their dependence on costly reduced nicotinamide adenine dinucleotide phosphate (NADPH) and one or more auxiliary redox partner proteins. Coupling P450s to the photosynthetic machinery of a plant allows photosynthetically-generated electrons to be used to drive catalysis, overcoming this cofactor dependency. Thus, photosynthetic organisms could serve as photobioreactors with the capability to produce value-added chemicals using only light, water, CO2 and an appropriate chemical as substrate for the reaction/s of choice, yielding new opportunities for producing commodity and high-value chemicals in a carbon-negative and sustainable manner. This review will discuss recent progress in using photosynthesis for light-driven P450 biocatalysis and explore the potential for further development of such systems.
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Affiliation(s)
- Bernadius Agustinus
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia
| | - Elizabeth M J Gillam
- School of Chemistry and Molecular Biosciences, The University of Queensland, St. Lucia, Brisbane 4072, Australia.
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4
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Santos-Merino M, Gargantilla-Becerra Á, de la Cruz F, Nogales J. Highlighting the potential of Synechococcus elongatus PCC 7942 as platform to produce α-linolenic acid through an updated genome-scale metabolic modeling. Front Microbiol 2023; 14:1126030. [PMID: 36998399 PMCID: PMC10043229 DOI: 10.3389/fmicb.2023.1126030] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/22/2023] [Indexed: 03/15/2023] Open
Abstract
Cyanobacteria are prokaryotic organisms that capture energy from sunlight using oxygenic photosynthesis and transform CO2 into products of interest such as fatty acids. Synechococcus elongatus PCC 7942 is a model cyanobacterium efficiently engineered to accumulate high levels of omega-3 fatty acids. However, its exploitation as a microbial cell factory requires a better knowledge of its metabolism, which can be approached by using systems biology tools. To fulfill this objective, we worked out an updated, more comprehensive, and functional genome-scale model of this freshwater cyanobacterium, which was termed iMS837. The model includes 837 genes, 887 reactions, and 801 metabolites. When compared with previous models of S. elongatus PCC 7942, iMS837 is more complete in key physiological and biotechnologically relevant metabolic hubs, such as fatty acid biosynthesis, oxidative phosphorylation, photosynthesis, and transport, among others. iMS837 shows high accuracy when predicting growth performance and gene essentiality. The validated model was further used as a test-bed for the assessment of suitable metabolic engineering strategies, yielding superior production of non-native omega-3 fatty acids such as α-linolenic acid (ALA). As previously reported, the computational analysis demonstrated that fabF overexpression is a feasible metabolic target to increase ALA production, whereas deletion and overexpression of fabH cannot be used for this purpose. Flux scanning based on enforced objective flux, a strain-design algorithm, allowed us to identify not only previously known gene overexpression targets that improve fatty acid synthesis, such as Acetyl-CoA carboxylase and β-ketoacyl-ACP synthase I, but also novel potential targets that might lead to higher ALA yields. Systematic sampling of the metabolic space contained in iMS837 identified a set of ten additional knockout metabolic targets that resulted in higher ALA productions. In silico simulations under photomixotrophic conditions with acetate or glucose as a carbon source boosted ALA production levels, indicating that photomixotrophic nutritional regimens could be potentially exploited in vivo to improve fatty acid production in cyanobacteria. Overall, we show that iMS837 is a powerful computational platform that proposes new metabolic engineering strategies to produce biotechnologically relevant compounds, using S. elongatus PCC 7942 as non-conventional microbial cell factory.
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Affiliation(s)
- María Santos-Merino
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, Spain
- *Correspondence: María Santos-Merino,
| | - Álvaro Gargantilla-Becerra
- 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
| | - Fernando de la Cruz
- Instituto de Biomedicina y Biotecnología de Cantabria, Universidad de Cantabria—CSIC, Santander, Cantabria, 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
- Juan Nogales,
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5
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Satta A, Esquirol L, Ebert BE. Current Metabolic Engineering Strategies for Photosynthetic Bioproduction in Cyanobacteria. Microorganisms 2023; 11:455. [PMID: 36838420 PMCID: PMC9964548 DOI: 10.3390/microorganisms11020455] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 02/04/2023] [Accepted: 02/09/2023] [Indexed: 02/16/2023] Open
Abstract
Cyanobacteria are photosynthetic microorganisms capable of using solar energy to convert CO2 and H2O into O2 and energy-rich organic compounds, thus enabling sustainable production of a wide range of bio-products. More and more strains of cyanobacteria are identified that show great promise as cell platforms for the generation of bioproducts. However, strain development is still required to optimize their biosynthesis and increase titers for industrial applications. This review describes the most well-known, newest and most promising strains available to the community and gives an overview of current cyanobacterial biotechnology and the latest innovative strategies used for engineering cyanobacteria. We summarize advanced synthetic biology tools for modulating gene expression and their use in metabolic pathway engineering to increase the production of value-added compounds, such as terpenoids, fatty acids and sugars, to provide a go-to source for scientists starting research in cyanobacterial metabolic engineering.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
- Department of Biology, University of Padua, 35100 Padua, Italy
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Natha, QLD 4111, Australia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD 4072, Australia
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6
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Diaz CJ, Douglas KJ, Kang K, Kolarik AL, Malinovski R, Torres-Tiji Y, Molino JV, Badary A, Mayfield SP. Developing algae as a sustainable food source. Front Nutr 2023; 9:1029841. [PMID: 36742010 PMCID: PMC9892066 DOI: 10.3389/fnut.2022.1029841] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 12/05/2022] [Indexed: 01/20/2023] Open
Abstract
Current agricultural and food production practices are facing extreme stress, posed by climate change and an ever-increasing human population. The pressure to feed nearly 8 billion people while maintaining a minimal impact on the environment has prompted a movement toward new, more sustainable food sources. For thousands of years, both the macro (seaweed and kelp) and micro (unicellular) forms of algae have been cultivated as a food source. Algae have evolved to be highly efficient at resource utilization and have proven to be a viable source of nutritious biomass that could address many of the current food production issues. Particularly for microalgae, studies of their large-scale growth and cultivation come from the biofuel industry; however, this knowledge can be reasonably translated into the production of algae-based food products. The ability of algae to sequester CO2 lends to its sustainability by helping to reduce the carbon footprint of its production. Additionally, algae can be produced on non-arable land using non-potable water (including brackish or seawater), which allows them to complement rather than compete with traditional agriculture. Algae inherently have the desired qualities of a sustainable food source because they produce highly digestible proteins, lipids, and carbohydrates, and are rich in essential fatty acids, vitamins, and minerals. Although algae have yet to be fully domesticated as food sources, a variety of cultivation and breeding tools exist that can be built upon to allow for the increased productivity and enhanced nutritional and organoleptic qualities that will be required to bring algae to mainstream utilization. Here we will focus on microalgae and cyanobacteria to highlight the current advancements that will expand the variety of algae-based nutritional sources, as well as outline various challenges between current biomass production and large-scale economic algae production for the food market.
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Affiliation(s)
- Crisandra J. Diaz
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Kai J. Douglas
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Kalisa Kang
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Ashlynn L. Kolarik
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Rodeon Malinovski
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Yasin Torres-Tiji
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - João V. Molino
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Amr Badary
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States
| | - Stephen P. Mayfield
- Mayfield Lab, Division of Biological Sciences, Department of Molecular Biology, University of California, San Diego, San Diego, CA, United States,California Center for Algae Biotechnology, University of California, San Diego, La Jolla, CA, United States,*Correspondence: Stephen P. Mayfield,
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Lindberg P, Kenkel A, Bühler K. Introduction to Cyanobacteria. ADVANCES IN BIOCHEMICAL ENGINEERING/BIOTECHNOLOGY 2023; 183:1-24. [PMID: 37009973 DOI: 10.1007/10_2023_217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
Abstract
Cyanobacteria are highly interesting microbes with the capacity for oxygenic photosynthesis. They fulfill an important purpose in nature but are also potent biocatalysts. This chapter gives a brief overview of this diverse phylum and shortly addresses the functions these organisms have in the natural ecosystems. Further, it introduces the main topics covered in this volume, which is dealing with the development and application of cyanobacteria as solar cell factories for the production of chemicals including potential fuels. We discuss cyanobacteria as industrial workhorses, present established chassis strains, and give an overview of the current target products. Genetic engineering strategies aiming at the photosynthetic efficiency as well as approaches to optimize carbon fluxes are summarized. Finally, main cultivation strategies are sketched.
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Affiliation(s)
- Pia Lindberg
- Department of Chemistry-Ångström, Uppsala University, Uppsala, Sweden
| | - Amelie Kenkel
- Helmholtzcenter for Environmental Research, Leipzig, Germany
| | - Katja Bühler
- Helmholtzcenter for Environmental Research, Leipzig, Germany.
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Perez Rojo F, Pillow JJ, Kaur P. Bioprospecting microbes and enzymes for the production of pterocarpans and coumestans. Front Bioeng Biotechnol 2023; 11:1154779. [PMID: 37187887 PMCID: PMC10175578 DOI: 10.3389/fbioe.2023.1154779] [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: 01/31/2023] [Accepted: 04/18/2023] [Indexed: 05/17/2023] Open
Abstract
The isoflavonoid derivatives, pterocarpans and coumestans, are explored for multiple clinical applications as osteo-regenerative, neuroprotective and anti-cancer agents. The use of plant-based systems to produce isoflavonoid derivatives is limited due to cost, scalability, and sustainability constraints. Microbial cell factories overcome these limitations in which model organisms such as Saccharomyces cerevisiae offer an efficient platform to produce isoflavonoids. Bioprospecting microbes and enzymes can provide an array of tools to enhance the production of these molecules. Other microbes that naturally produce isoflavonoids present a novel alternative as production chassis and as a source of novel enzymes. Enzyme bioprospecting allows the complete identification of the pterocarpans and coumestans biosynthetic pathway, and the selection of the best enzymes based on activity and docking parameters. These enzymes consolidate an improved biosynthetic pathway for microbial-based production systems. In this review, we report the state-of-the-art for the production of key pterocarpans and coumestans, describing the enzymes already identified and the current gaps. We report available databases and tools for microbial bioprospecting to select the best production chassis. We propose the use of a holistic and multidisciplinary bioprospecting approach as the first step to identify the biosynthetic gaps, select the best microbial chassis, and increase productivity. We propose the use of microalgal species as microbial cell factories to produce pterocarpans and coumestans. The application of bioprospecting tools provides an exciting field to produce plant compounds such as isoflavonoid derivatives, efficiently and sustainably.
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Affiliation(s)
- Fernando Perez Rojo
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Fernando Perez Rojo, ; Parwinder Kaur,
| | - J. Jane Pillow
- UWA School of Human Sciences, The University of Western Australia, Perth, WA, Australia
| | - Parwinder Kaur
- UWA School of Agriculture and Environment, The University of Western Australia, Perth, WA, Australia
- *Correspondence: Fernando Perez Rojo, ; Parwinder Kaur,
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Satta A, Esquirol L, Ebert BE, Newman J, Peat TS, Plan M, Schenk G, Vickers CE. Molecular characterization of cyanobacterial short-chain prenyltransferases and discovery of a novel GGPP phosphatase. FEBS J 2022; 289:6672-6693. [PMID: 35704353 PMCID: PMC9796789 DOI: 10.1111/febs.16556] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 06/03/2022] [Accepted: 06/14/2022] [Indexed: 01/07/2023]
Abstract
Cyanobacteria are photosynthetic prokaryotes with strong potential to be used for industrial terpenoid production. However, the key enzymes forming the principal terpenoid building blocks, called short-chain prenyltransferases (SPTs), are insufficiently characterized. Here, we examined SPTs in the model cyanobacteria Synechococcus elongatus sp. PCC 7942 and Synechocystis sp. PCC 6803. Each species has a single putative SPT (SeCrtE and SyCrtE, respectively). Sequence analysis identified these as type-II geranylgeranyl pyrophosphate synthases (GGPPSs) with high homology to GGPPSs found in the plastids of green plants and other photosynthetic organisms. In vitro analysis demonstrated that SyCrtE is multifunctional, producing geranylgeranyl pyrophosphate (GGPP; C20 ) primarily but also significant amounts of farnesyl pyrophosphate (FPP, C15 ) and geranyl pyrophosphate (GPP, C10 ); whereas SeCrtE appears to produce only GGPP. The crystal structures were solved to 2.02 and 1.37 Å, respectively, and the superposition of the structures against the GGPPS of Synechococcus elongatus sp. PCC 7002 yield a root mean square deviation of 0.8 Å (SeCrtE) and 1.1 Å (SyCrtE). We also discovered that SeCrtE is co-encoded in an operon with a functional GGPP phosphatase, suggesting metabolic pairing of these two activities and a putative function in tocopherol biosynthesis. This work sheds light on the activity of SPTs and terpenoid synthesis in cyanobacteria. Understanding native prenyl phosphate metabolism is an important step in developing approaches to engineering the production of different chain-length terpenoids in cyanobacteria.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia
| | - Birgitta E. Ebert
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Janet Newman
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Thomas S. Peat
- CSIRO Biomedical ProgramParkvilleAustralia,School of Biotechnology and Biomolecular SciencesUniversity of New South WalesKensingtonAustralia
| | - Manuel Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and NanotechnologyThe University of QueenslandSt. LuciaAustralia
| | - Gerhard Schenk
- Australian Institute for Bioengineering and BiotechnologyThe University of QueenslandSt. LuciaAustralia,School of Chemistry and Molecular BiosciencesThe University of QueenslandSt. LuciaAustralia,Sustainable Minerals InstituteThe University of QueenslandSt. LuciaAustralia
| | - Claudia E. Vickers
- CSIRO Synthetic Biology Future Science PlatformBrisbaneAustralia,Centre for Cell Factories and Biopolymers, Griffith Institute for Drug DiscoveryGriffith UniversityNathanAustralia,ARC Centre of Excellence in Synthetic BiologyQueensland University of TechnologyBrisbaneAustralia
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10
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Baldanta S, Guevara G, Navarro-Llorens JM. SEVA-Cpf1, a CRISPR-Cas12a vector for genome editing in cyanobacteria. Microb Cell Fact 2022; 21:103. [PMID: 35643551 PMCID: PMC9148489 DOI: 10.1186/s12934-022-01830-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/13/2022] [Indexed: 12/01/2022] Open
Abstract
Background Cyanobacteria are photosynthetic autotrophs that have tremendous potential for fundamental research and industrial applications due to their high metabolic plasticity and ability to grow using CO2 and sunlight. CRISPR technology using Cas9 and Cpf1 has been applied to different cyanobacteria for genome manipulations and metabolic engineering. Despite significant advances with genome editing in several cyanobacteria strains, the lack of proper genetic toolboxes is still a limiting factor compared to other model laboratory species. Among the limitations, it is essential to have versatile plasmids that could ease the benchwork when using CRISPR technology. Results In the present study, several CRISPR-Cpf1 vectors were developed for genetic manipulations in cyanobacteria using SEVA plasmids. SEVA collection is based on modular vectors that enable the exchangeability of diverse elements (e.g. origins of replication and antibiotic selection markers) and the combination with many cargo sequences for varied end-applications. Firstly, using SEVA vectors containing the broad host range RSF1010 origin we demonstrated that these vectors are replicative not only in model cyanobacteria but also in a new cyanobacterium specie, Chroococcidiopsis sp., which is different from those previously published. Then, we constructed SEVA vectors by harbouring CRISPR elements and showed that they can be easily assimilated not only by conjugation, but also by natural transformation. Finally, we used our SEVA-Cpf1 tools to delete the nblA gene in Synechocystis sp. PCC 6803, demonstrating that our plasmids can be applied for CRISPR-based genome editing technology. Conclusions The results of this study provide new CRISPR-based vectors based on the SEVA (Standard European Vector Architecture) collection that can improve editing processes using the Cpf1 nuclease in cyanobacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12934-022-01830-4.
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11
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Chen J, Huang Y, Shu Y, Hu X, Wu D, Jiang H, Wang K, Liu W, Fu W. Recent Progress on Systems and Synthetic Biology of Diatoms for Improving Algal Productivity. Front Bioeng Biotechnol 2022; 10:908804. [PMID: 35646842 PMCID: PMC9136054 DOI: 10.3389/fbioe.2022.908804] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 04/29/2022] [Indexed: 11/13/2022] Open
Abstract
Microalgae have drawn much attention for their potential applications as a sustainable source for developing bioactive compounds, functional foods, feeds, and biofuels. Diatoms, as one major group of microalgae with high yields and strong adaptability to the environment, have shown advantages in developing photosynthetic cell factories to produce value-added compounds, including heterologous bioactive products. However, the commercialization of diatoms has encountered several obstacles that limit the potential mass production, such as the limitation of algal productivity and low photosynthetic efficiency. In recent years, systems and synthetic biology have dramatically improved the efficiency of diatom cell factories. In this review, we discussed first the genome sequencing and genome-scale metabolic models (GEMs) of diatoms. Then, approaches to optimizing photosynthetic efficiency are introduced with a focus on the enhancement of biomass productivity in diatoms. We also reviewed genome engineering technologies, including CRISPR (clustered regularly interspaced short palindromic repeats) gene-editing to produce bioactive compounds in diatoms. Finally, we summarized the recent progress on the diatom cell factory for producing heterologous compounds through genome engineering to introduce foreign genes into host diatoms. This review also pinpointed the bottlenecks in algal engineering development and provided critical insights into the future direction of algal production.
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Affiliation(s)
- Jiwei Chen
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Yifan Huang
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Yuexuan Shu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Xiaoyue Hu
- Center for Data Science, Zhejiang University, Hangzhou, China
- School of Mathematical Sciences, Zhejiang University, Hangzhou, China
| | - Di Wu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Hangjin Jiang
- Center for Data Science, Zhejiang University, Hangzhou, China
| | - Kui Wang
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
| | - Weihua Liu
- School of Mathematical Sciences, Zhejiang University, Hangzhou, China
| | - Weiqi Fu
- Department of Marine Science, Ocean College, Zhejiang University, Hangzhou, China
- Center for Systems Biology and Faculty of Industrial Engineering, Mechanical Engineering and Computer Science, School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
- *Correspondence: Weiqi Fu,
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12
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Theodosiou E, Tüllinghoff A, Toepel J, Bühler B. Exploitation of Hetero- and Phototrophic Metabolic Modules for Redox-Intensive Whole-Cell Biocatalysis. Front Bioeng Biotechnol 2022; 10:855715. [PMID: 35497353 PMCID: PMC9043136 DOI: 10.3389/fbioe.2022.855715] [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: 01/15/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
The successful realization of a sustainable manufacturing bioprocess and the maximization of its production potential and capacity are the main concerns of a bioprocess engineer. A main step towards this endeavor is the development of an efficient biocatalyst. Isolated enzyme(s), microbial cells, or (immobilized) formulations thereof can serve as biocatalysts. Living cells feature, beside active enzymes, metabolic modules that can be exploited to support energy-dependent and multi-step enzyme-catalyzed reactions. Metabolism can sustainably supply necessary cofactors or cosubstrates at the expense of readily available and cheap resources, rendering external addition of costly cosubstrates unnecessary. However, for the development of an efficient whole-cell biocatalyst, in depth comprehension of metabolic modules and their interconnection with cell growth, maintenance, and product formation is indispensable. In order to maximize the flux through biosynthetic reactions and pathways to an industrially relevant product and respective key performance indices (i.e., titer, yield, and productivity), existing metabolic modules can be redesigned and/or novel artificial ones established. This review focuses on whole-cell bioconversions that are coupled to heterotrophic or phototrophic metabolism and discusses metabolic engineering efforts aiming at 1) increasing regeneration and supply of redox equivalents, such as NAD(P/H), 2) blocking competing fluxes, and 3) increasing the availability of metabolites serving as (co)substrates of desired biosynthetic routes.
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Affiliation(s)
- Eleni Theodosiou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thessaloniki, Greece
| | - Adrian Tüllinghoff
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Jörg Toepel
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
| | - Bruno Bühler
- Department of Solar Materials, Helmholtz Centre for Environmental Research GmbH—UFZ, Leipzig, Germany
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13
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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]
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14
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Liu Y, Wang Z, Cui Z, Qi Q, Hou J. Progress and perspectives for microbial production of farnesene. BIORESOURCE TECHNOLOGY 2022; 347:126682. [PMID: 35007732 DOI: 10.1016/j.biortech.2022.126682] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2021] [Revised: 12/30/2021] [Accepted: 01/02/2022] [Indexed: 06/14/2023]
Abstract
Farnesene is increasingly used in industry, agriculture, and other fields due to its unique and excellent properties, necessitating its efficient synthesis. Microbial synthesis is an ideal farnesene production method. Recently, researchers have used several strategies to optimize the production performance of microorganisms. This review summarized these strategies, including regulation of farnesene synthesis pathways, and proposed some emerging tools and methods in stain engineering. Meanwhile, new farnesene biosynthetic pathways and effective farnesene production from cheap or waste substrates were emphatically introduced. Finally, future farnesene biosynthesis challenges were discussed.
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Affiliation(s)
- Yinghang Liu
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhaoxuan Wang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Zhiyong Cui
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Qingsheng Qi
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China
| | - Jin Hou
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao 266237, PR China.
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15
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Abstract
Synthetic biology applications rely on a well-characterized set of microbial strains, with an established toolbox of molecular biology methods for their genetic manipulation. Since there are no thermophiles with such attributes, most biotechnology and synthetic biology studies use organisms that grow in the mesophilic temperature range. As a result, thermophiles, a heterogenous group of microbes that thrive at high (>50 °C) temperatures, are largely overlooked, with respect to their biotechnological potential, even though they share several favorable traits. Thermophilic bacteria tend to grow at higher rates compared to their mesophilic counterparts, while their growth has lower cooling requirements and is less prone to contamination. Over the last few years, there has been renewed interest in developing tools and methods for thermophile bioengineering. In this perspective, we explain why it is a good idea to invest time and effort into developing a thermophilic synthetic biology direction, which is the state of the art, and why we think that the implementation of a thermophilic synthetic biology platform—a thermochassis—will take synthetic biology to the extremes.
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16
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Improved polyhydroxybutyrate production by Cupriavidus necator and the photocatalyst graphitic carbon nitride from fructose under low light intensity. Int J Biol Macromol 2022; 203:526-534. [PMID: 35120931 DOI: 10.1016/j.ijbiomac.2022.01.179] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Revised: 01/26/2022] [Accepted: 01/28/2022] [Indexed: 11/21/2022]
Abstract
The photocatalyst graphitic carbon nitride (g-C3N4) is known to photostimulate the production of the bioplastic polyhydroxybutyrate (PHB) by Cupriavidus necator. In previous studies, the combination of C. necator and g-C3N4 increased PHB yield from either an organic or inorganic carbon substrate under a light intensity of 4200 lx. Here, different parameters including light intensity, pH, temperature, nitrogen and carbon concentrations, aeration, and inoculum size were explored to maximize PHB production by hybrid photosynthesis from fructose and visible light. A g-C3N4/C. necator culture grown with a lower light intensity of 2100 lx, an inoculum size of 128.30 × 106 CFU ml-1, and constant aeration produced 7.16 g l-1 d-1 PHB with a product yield from fructose of 60.94%. Furthermore, the ratio of incident photons harvested by g-C3N4 converted into NADPH+H+ by C. necator for PHB production was improved to 19.74% after the process optimization. In comparison, the PHB production rate of a non-optimized g-C3N4/C. necator system exposed to 4200 lx was only 2.94 g l-1 d-1 with a product yield from fructose of 33.29%. These results demonstrate that hybrid photosynthesis productivity can be significantly augmented by decreasing light intensity and adjusting other parameters, which is promising for future bioproduction applications.
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17
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Satta A, Lu Z, Plan MR, Esquirol L, Ebert BE. Microbial Production, Extraction, and Quantitative Analysis of Isoprenoids. Methods Mol Biol 2022; 2469:239-259. [PMID: 35508844 DOI: 10.1007/978-1-0716-2185-1_20] [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: 06/14/2023]
Abstract
Isoprenoids, also known as terpenes or terpenoids, are compounds made of one or more isoprene (C5H8) moieties and constitute the largest class of natural products. They play diverse roles in biology and have broad industrial uses as flavors, fragrances, biofuels, polymers, agricultural chemicals, and medicines. Most isoprenoids are secondary plant metabolites and only produced in very low amounts. To make these valuable compounds economically accessible, significant efforts in the culture and engineering of microbial cells for isoprenoid biosynthesis have been made in the last decades. The protocols presented here describe lab-scale cultivation of microbes, either naturally producing or engineered, for isoprenoid production, the extraction of products and their quantification by high-performance liquid chromatography. Examples of isoprenoids covered in this chapter include (C10) mono-, (C15) sesqui-, (C20) di-, (C30) tri-, and (C40) tetraterpenoids. We focus on yeast and cyanobacteria as production systems, but the protocols can be adapted for other organisms.
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Affiliation(s)
- Alessandro Satta
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Zeyu Lu
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Manuel R Plan
- Metabolomics Australia (Queensland Node), Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia
| | - Lygie Esquirol
- Centre for Cell Factories and Biopolymers, Griffith Institute for Drug Discovery, Griffith University, Nathan, QLD, Australia
| | - Birgitta E Ebert
- Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St Lucia, QLD, Australia.
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18
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Lane TW. Barriers to microalgal mass cultivation. Curr Opin Biotechnol 2021; 73:323-328. [PMID: 34710649 DOI: 10.1016/j.copbio.2021.09.013] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/25/2021] [Accepted: 09/30/2021] [Indexed: 12/23/2022]
Abstract
Economically successful microalgal mass cultivation is dependent on overcoming several barriers that contribute to the cost of production. The severity of these barriers is dependent on the market value of the final product. These barriers prevent the commercially viable production of algal biofuels but are also faced by any producers of any algal product. General barriers include the cost of water and limits on recycling, costs and recycling of nutrients, CO2 utilization, energy costs associated with harvesting and biomass loss due to biocontamination and pond crashes. In this paper, recent advances in overcoming these barriers are discussed.
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Affiliation(s)
- Todd W Lane
- Bioresource and Environmental Security Department, Sandia National Laboratories, P.O. Box 969, Livermore, CA 94550, USA.
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19
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Funk C, Jensen PE, Skjermo J. Blue economy in the North: Scandinavian algal biotechnology to the rescue. PHYSIOLOGIA PLANTARUM 2021; 173:479-482. [PMID: 34528273 DOI: 10.1111/ppl.13534] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Accepted: 08/24/2021] [Indexed: 06/13/2023]
Affiliation(s)
| | - Poul Erik Jensen
- Department of Food Science, University of Copenhagen, Copenhagen, Denmark
| | - Jorunn Skjermo
- Department of Fisheries and New Biomarine Industry, SINTEF Ocean, Trondheim, Norway
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