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Pérez-Valero Á, Serna-Diestro J, Tafur Rangel A, Barbuto Ferraiuolo S, Schiraldi C, Kerkhoven EJ, Villar CJ, Lombó F. Biosynthesis of Hesperetin, Homoeriodictyol, and Homohesperetin in a Transcriptomics-Driven Engineered Strain of Streptomyces albidoflavus. Int J Mol Sci 2024; 25:4053. [PMID: 38612864 PMCID: PMC11012174 DOI: 10.3390/ijms25074053] [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: 03/07/2024] [Revised: 04/01/2024] [Accepted: 04/04/2024] [Indexed: 04/14/2024] Open
Abstract
Flavonoids exhibit various bioactivities including anti-oxidant, anti-tumor, anti-inflammatory, and anti-viral properties. Methylated flavonoids are particularly significant due to their enhanced oral bioavailability, improved intestinal absorption, and greater stability. The heterologous production of plant flavonoids in bacterial factories involves the need for enough biosynthetic precursors to allow for high production levels. These biosynthetic precursors are malonyl-CoA and l-tyrosine. In this work, to enhance flavonoid biosynthesis in Streptomyces albidoflavus, we conducted a transcriptomics study for the identification of candidate genes involved in l-tyrosine catabolism. The hypothesis was that the bacterial metabolic machinery would detect an excess of this amino acid if supplemented with the conventional culture medium and would activate the genes involved in its catabolism towards energy production. Then, by inactivating those overexpressed genes (under an excess of l-tyrosine), it would be possible to increase the intracellular pools of this precursor amino acid and eventually the final flavonoid titers in this bacterial factory. The RNAseq data analysis in the S. albidoflavus wild-type strain highlighted the hppD gene encoding 4-hydroxyphenylpyruvate dioxygenase as a promising target for knock-out, exhibiting a 23.2-fold change (FC) in expression upon l-tyrosine supplementation in comparison to control cultivation conditions. The subsequent knock-out of the hppD gene in S. albidoflavus resulted in a 1.66-fold increase in the naringenin titer, indicating enhanced flavonoid biosynthesis. Leveraging the improved strain of S. albidoflavus, we successfully synthesized the methylated flavanones hesperetin, homoeriodictyol, and homohesperetin, achieving titers of 2.52 mg/L, 1.34 mg/L, and 0.43 mg/L, respectively. In addition, the dimethoxy flavanone homohesperetin was produced as a byproduct of the endogenous metabolism of S. albidoflavus. To our knowledge, this is the first time that hppD deletion was utilized as a strategy to augment the biosynthesis of flavonoids. Furthermore, this is the first report where hesperetin and homoeriodictyol have been synthesized from l-tyrosine as a precursor. Therefore, transcriptomics is, in this case, a successful approach for the identification of catabolism reactions affecting key precursors during flavonoid biosynthesis, allowing the generation of enhanced production strains.
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Affiliation(s)
- Álvaro Pérez-Valero
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Area of Microbiology, Department of Functional Biology, University of Oviedo, 33006 Oviedo, Principality of Asturias, Spain; (Á.P.-V.); (J.S.-D.); (C.J.V.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Principality of Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Principality of Asturias, Spain
| | - Juan Serna-Diestro
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Area of Microbiology, Department of Functional Biology, University of Oviedo, 33006 Oviedo, Principality of Asturias, Spain; (Á.P.-V.); (J.S.-D.); (C.J.V.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Principality of Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Principality of Asturias, Spain
| | - Albert Tafur Rangel
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (A.T.R.); (E.J.K.)
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Simona Barbuto Ferraiuolo
- Section of Biotechnology and Molecular Biology, Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Via De Crecchio 7, 80138 Naples, Italy; (S.B.F.); (C.S.)
| | - Chiara Schiraldi
- Section of Biotechnology and Molecular Biology, Department of Experimental Medicine, University of Campania “Luigi Vanvitelli”, Via De Crecchio 7, 80138 Naples, Italy; (S.B.F.); (C.S.)
| | - Eduard J. Kerkhoven
- Department of Biology and Biological Engineering, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden; (A.T.R.); (E.J.K.)
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
- SciLifeLab, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
| | - Claudio J. Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Area of Microbiology, Department of Functional Biology, University of Oviedo, 33006 Oviedo, Principality of Asturias, Spain; (Á.P.-V.); (J.S.-D.); (C.J.V.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Principality of Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Area of Microbiology, Department of Functional Biology, University of Oviedo, 33006 Oviedo, Principality of Asturias, Spain; (Á.P.-V.); (J.S.-D.); (C.J.V.)
- Instituto Universitario de Oncología del Principado de Asturias (IUOPA), 33006 Oviedo, Principality of Asturias, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33006 Oviedo, Principality of Asturias, Spain
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Pérez-Valero Á, Ye S, Magadán-Corpas P, Villar CJ, Lombó F. Metabolic engineering in Streptomyces albidoflavus for the biosynthesis of the methylated flavonoids sakuranetin, acacetin, and genkwanin. Microb Cell Fact 2023; 22:234. [PMID: 37964284 PMCID: PMC10648386 DOI: 10.1186/s12934-023-02247-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 11/09/2023] [Indexed: 11/16/2023] Open
Abstract
Flavonoids are important plant secondary metabolites showing antioxidant, antitumor, anti-inflammatory, and antiviral activities, among others. Methylated flavonoids are particularly interesting compared to non-methylated ones due to their greater stability and intestinal absorption, which improves their oral bioavailability. In this work we have stablished a metabolic engineered strain of Streptomyces albidoflavus with enhanced capabilities for flavonoid production, achieving a 1.6-fold increase in the biosynthesis of naringenin with respect to the parental strain. This improved strain, S. albidoflavus UO-FLAV-004, has been used for the heterologous biosynthesis of the methylated flavonoids sakuranetin, acacetin and genkwanin. The achieved titers of sakuranetin and acacetin were 8.2 mg/L and 5.8 mg/L, respectively. The genkwanin titers were 0.8 mg/L, with a bottleneck identified in this producing strain. After applying a co-culture strategy, genkwanin production titers reached 3.5 mg/L, which represents a 4.4-fold increase. To our knowledge, this study presents the first biosynthesis of methylated flavonoids in not only any Streptomyces species, but also in any Gram-positive bacteria.
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Affiliation(s)
- Álvaro Pérez-Valero
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Suhui Ye
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Patricia Magadán-Corpas
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Claudio J Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain.
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Magadán-Corpas P, Ye S, Pérez-Valero Á, McAlpine PL, Valdés-Chiara P, Torres-Bacete J, Nogales J, Villar CJ, Lombó F. Optimized De Novo Eriodictyol Biosynthesis in Streptomyces albidoflavus Using an Expansion of the Golden Standard Toolkit for Its Use in Actinomycetes. Int J Mol Sci 2023; 24:ijms24108879. [PMID: 37240225 DOI: 10.3390/ijms24108879] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2023] [Revised: 05/12/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
Eriodictyol is a hydroxylated flavonoid displaying multiple pharmaceutical activities, such as antitumoral, antiviral or neuroprotective. However, its industrial production is limited to extraction from plants due to its inherent limitations. Here, we present the generation of a Streptomyces albidoflavus bacterial factory edited at the genome level for an optimized de novo heterologous production of eriodictyol. For this purpose, an expansion of the Golden Standard toolkit (a Type IIS assembly method based on the Standard European Vector Architecture (SEVA)) has been created, encompassing a collection of synthetic biology modular vectors (adapted for their use in actinomycetes). These vectors have been designed for the assembly of transcriptional units and gene circuits in a plug-and-play manner, as well as for genome editing using CRISPR-Cas9-mediated genetic engineering. These vectors have been used for the optimization of the eriodictyol heterologous production levels in S. albidoflavus by enhancing the flavonoid-3'-hydroxylase (F3'H) activity (by means of a chimera design) and by replacing three native biosynthetic gene clusters in the bacterial chromosome with the plant genes matBC (involved in extracellular malonate uptake and its intracellular activation into malonyl-CoA), therefore allowing more malonyl-CoA to be devoted to the heterologous production of plant flavonoids in this bacterial factory. These experiments have allowed an increase in production of 1.8 times in the edited strain (where the three native biosynthetic gene clusters have been deleted) in comparison with the wild-type strain and a 13 times increase in eriodictyol overproduction in comparison with the non-chimaera version of the F3'H enzyme.
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Affiliation(s)
- Patricia Magadán-Corpas
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Suhui Ye
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Álvaro Pérez-Valero
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Patrick L McAlpine
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Paula Valdés-Chiara
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Jesús Torres-Bacete
- Department of Systems Biology, Centro Nacional de Biotecnologia, CSIC, 28049 Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain
| | - Juan Nogales
- Department of Systems Biology, Centro Nacional de Biotecnologia, CSIC, 28049 Madrid, Spain
- Interdisciplinary Platform for Sustainable Plastics towards a Circular Economy-Spanish National Research Council (SusPlast-CSIC), 28040 Madrid, Spain
| | - Claudio J Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, 33006 Oviedo, Spain
- IUOPA (Instituto Universitario de Oncología del Principado de Asturias), 33006 Oviedo, Spain
- ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), 33006 Oviedo, Spain
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Martínez-García E, Fraile S, Algar E, Aparicio T, Velázquez E, Calles B, Tas H, Blázquez B, Martín B, Prieto C, Sánchez-Sampedro L, Nørholm MH, Volke D, Wirth N, Dvořák P, Alejaldre L, Grozinger L, Crowther M, Goñi-Moreno A, Nikel P, Nogales J, de Lorenzo V. SEVA 4.0: an update of the Standard European Vector Architecture database for advanced analysis and programming of bacterial phenotypes. Nucleic Acids Res 2023; 51:D1558-D1567. [PMID: 36420904 PMCID: PMC9825617 DOI: 10.1093/nar/gkac1059] [Citation(s) in RCA: 20] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Revised: 10/22/2022] [Accepted: 10/24/2022] [Indexed: 11/27/2022] Open
Abstract
The SEVA platform (https://seva-plasmids.com) was launched one decade ago, both as a database (DB) and as a physical repository of plasmid vectors for genetic analysis and engineering of Gram-negative bacteria with a structure and nomenclature that follows a strict, fixed architecture of functional DNA segments. While the current update keeps the basic features of earlier versions, the platform has been upgraded not only with many more ready-to-use plasmids but also with features that expand the range of target species, harmonize DNA assembly methods and enable new applications. In particular, SEVA 4.0 includes (i) a sub-collection of plasmids for easing the composition of multiple DNA segments with MoClo/Golden Gate technology, (ii) vectors for Gram-positive bacteria and yeast and [iii] off-the-shelf constructs with built-in functionalities. A growing collection of plasmids that capture part of the standard-but not its entirety-has been compiled also into the DB and repository as a separate corpus (SEVAsib) because of its value as a resource for constructing and deploying phenotypes of interest. Maintenance and curation of the DB were accompanied by dedicated diffusion and communication channels that make the SEVA platform a popular resource for genetic analyses, genome editing and bioengineering of a large number of microorganisms.
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Affiliation(s)
- Esteban Martínez-García
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Sofía Fraile
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Algar
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Tomás Aparicio
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Elena Velázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Belén Calles
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Huseyin Tas
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Blas Blázquez
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | | | | | | | - Morten H H Nørholm
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Daniel C Volke
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Nicolas T Wirth
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Pavel Dvořák
- Department of Experimental Biology, Faculty of Science, Masaryk University, Brno 62500 Czech Republic
| | - Lorea Alejaldre
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Lewis Grozinger
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Matthew Crowther
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
- School of Computing, Newcastle University, NE4 5TG, UK
| | - Angel Goñi-Moreno
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid (INIA-CSIC), Pozuelo de Alarcón 28223, Spain
| | - Pablo I Nikel
- The Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kongens Lyngby, Denmark
| | - Juan Nogales
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
| | - Víctor de Lorenzo
- Systems Biology Department, Centro Nacional de Biotecnología (CNB-CSIC), 28049 Cantoblanco-Madrid, Spain
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Dolan SK, Matilla MA. Tools of the trade: plasmid repositories and standardized plasmid manipulation for molecular and synthetic biology. Microb Biotechnol 2022; 15:1318-1320. [PMID: 35137542 PMCID: PMC9049604 DOI: 10.1111/1751-7915.14012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 01/19/2022] [Indexed: 11/29/2022] Open
Abstract
Plasmids are extrachromosomal genetic elements capable of autonomous replication within a host cell. They play a key role in bacterial ecology and evolution, facilitating the mobilization of accessory genes by horizontal gene transfer. Crucially, plasmids also serve as valuable tools in modern molecular biology. Here, we highlight recent articles aimed at implementing standardized plasmid assembly techniques and plasmid repositories to promote open science as well as to improve experimental reproducibility across laboratories. Research focused on assisting these fundamental aims is a further step towards improving standardization in molecular and synthetic biology.
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Affiliation(s)
- Stephen K Dolan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA, 30332, USA.,Center for Microbial Dynamics and Infection, Georgia Institute of Technology, Atlanta, GA, 30332, USA
| | - Miguel A Matilla
- Department of Biotechnology and Environmental Protection, Estación Experimental del Zaidín, Consejo Superior de Investigaciones Científicas, Prof. Albareda 1, Granada, 18008, Spain
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Challenges and opportunities in biological funneling of heterogeneous and toxic substrates beyond lignin. Curr Opin Biotechnol 2021; 73:1-13. [PMID: 34242853 DOI: 10.1016/j.copbio.2021.06.007] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2021] [Revised: 06/02/2021] [Accepted: 06/07/2021] [Indexed: 12/12/2022]
Abstract
Significant developments in the understanding and manipulation of microbial metabolism have enabled the use of engineered biological systems toward a more sustainable energy and materials economy. While developments in metabolic engineering have primarily focused on the conversion of carbohydrates, substantial opportunities exist for using these same principles to extract value from more heterogeneous and toxic waste streams, such as those derived from lignin, biomass pyrolysis, or industrial waste. Funneling heterogeneous substrates from these streams toward valuable products, termed biological funneling, presents new challenges in balancing multiple catabolic pathways competing for shared cellular resources and engineering against perturbation from toxic substrates. Solutions to many of these challenges have been explored within the field of lignin valorization. This perspective aims to extend beyond lignin to highlight the challenges and discuss opportunities for use of biological systems to upgrade previously inaccessible waste streams.
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Marín L, Gutiérrez-Del-Río I, Villar CJ, Lombó F. De novo biosynthesis of garbanzol and fustin in Streptomyces albus based on a potential flavanone 3-hydroxylase with 2-hydroxylase side activity. Microb Biotechnol 2021; 14:2009-2024. [PMID: 34216097 PMCID: PMC8449655 DOI: 10.1111/1751-7915.13874] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/07/2021] [Accepted: 06/10/2021] [Indexed: 11/26/2022] Open
Abstract
Flavonoids are important plant secondary metabolites, which were shown to have antioxidant, anti-inflammatory or antiviral activities. Heterologous production of flavonoids in engineered microbial cell factories is an interesting alternative to their purification from plant material representing the natural source. The use of engineered bacteria allows to produce specific compounds, independent of soil, climatic or other plant-associated production parameters. The initial objective of this study was to achieve an engineered production of two interesting flavanonols, garbanzol and fustin, using Streptomyces albus as the production host. Unexpectedly, the engineered strain produced several flavones and flavonols in the absence of the additional expression of a flavone synthase (FNS) or flavonol synthase (FLS) gene. It turned out that the heterologous flavanone 3-hydroxylase (F3H) has a 2-hydroxylase side activity, which explains the observed production of 7,4'-dihydroxyflavone, resokaempferol, kaempferol and apigenin, as well as the biosynthesis of the extremely rare 2-hydroxylated intermediates 2-hydroxyliquiritigenin, 2-hydroxynaringenin and probably licodione. Other related metabolites, such as quercetin, dihydroquercetin and eriodictyol, have also been detected in culture extracts of this recombinant strain. Hence, the enzymatic versatility of S. albus can be conveniently exploited for the heterologous production of a large diversity of plant metabolites of the flavonoid family.
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Affiliation(s)
- Laura Marín
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Ignacio Gutiérrez-Del-Río
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Claudio Jesús Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Principality of Asturias, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Principality of Asturias, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Principality of Asturias, Spain
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Mitousis L, Thoma Y, Musiol-Kroll EM. An Update on Molecular Tools for Genetic Engineering of Actinomycetes-The Source of Important Antibiotics and Other Valuable Compounds. Antibiotics (Basel) 2020; 9:E494. [PMID: 32784409 PMCID: PMC7460540 DOI: 10.3390/antibiotics9080494] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/06/2020] [Accepted: 08/07/2020] [Indexed: 02/06/2023] Open
Abstract
The first antibiotic-producing actinomycete (Streptomyces antibioticus) was described by Waksman and Woodruff in 1940. This discovery initiated the "actinomycetes era", in which several species were identified and demonstrated to be a great source of bioactive compounds. However, the remarkable group of microorganisms and their potential for the production of bioactive agents were only partially exploited. This is caused by the fact that the growth of many actinomycetes cannot be reproduced on artificial media at laboratory conditions. In addition, sequencing, genome mining and bioactivity screening disclosed that numerous biosynthetic gene clusters (BGCs), encoded in actinomycetes genomes are not expressed and thus, the respective potential products remain uncharacterized. Therefore, a lot of effort was put into the development of technologies that facilitate the access to actinomycetes genomes and activation of their biosynthetic pathways. In this review, we mainly focus on molecular tools and methods for genetic engineering of actinomycetes that have emerged in the field in the past five years (2015-2020). In addition, we highlight examples of successful application of the recently developed technologies in genetic engineering of actinomycetes for activation and/or improvement of the biosynthesis of secondary metabolites.
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Affiliation(s)
| | | | - Ewa M. Musiol-Kroll
- Interfaculty Institute for Microbiology and Infection Medicine Tübingen (IMIT), Microbiology/Biotechnology, University of Tübingen, Auf der Morgenstelle 28, 72076 Tübingen, Germany; (L.M.); (Y.T.)
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García-Gutiérrez C, Aparicio T, Torres-Sánchez L, Martínez-García E, de Lorenzo V, Villar CJ, Lombó F. Multifunctional SEVA shuttle vectors for actinomycetes and Gram-negative bacteria. Microbiologyopen 2020; 9:1135-1149. [PMID: 32170856 PMCID: PMC7294301 DOI: 10.1002/mbo3.1024] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2019] [Revised: 02/07/2020] [Accepted: 02/14/2020] [Indexed: 11/10/2022] Open
Abstract
Actinomycetales, such as the genus Streptomyces, are well‐known cell factories employed to produce a wide variety of secondary metabolites for industrial use. However, not only is the genetic engineering of Streptomyces more complicated and tedious than other model laboratory species, such as Escherichia coli, there is also a considerable lack of genetic tools, hindering its adoption as a common chassis for synthetic biology. In this work, 23 novel shuttle vectors are presented that follow the canonical SEVA (Standard European Vector Architecture) common architecture with the goal of increasing the genetic toolbox repertoire for Streptomyces and other actinomycetes. The ORI module of these plasmids is composed of the combination of two origins of replication, one for Gram‐negative bacteria and the other for Streptomyces, a Gram‐positive bacteria. Origins of replication have been included in the collection for integrative, low‐copy number, and medium‐to‐high‐copy number vectors for Streptomyces. Also, a new selection marker has been developed that confers resistance to apramycin. The functionality of these plasmids was tested via the heterologous expression of GFP and the heterologous production of the plant flavonoid apigenin in Streptomyces albus J1074, with successful results in both cases, therefore expanding the current repertoire of genetic manipulation tools in Streptomyces species.
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Affiliation(s)
- Coral García-Gutiérrez
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Spain
| | - Tomás Aparicio
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Lucía Torres-Sánchez
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Spain
| | | | - Víctor de Lorenzo
- Systems Biology Program, Centro Nacional de Biotecnología (CNB-CSIC), Madrid, Spain
| | - Claudio J Villar
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Spain
| | - Felipe Lombó
- Research Group BIONUC (Biotechnology of Nutraceuticals and Bioactive Compounds), Departamento de Biología Funcional, Área de Microbiología, Universidad de Oviedo, Oviedo, Spain.,IUOPA (Instituto Universitario de Oncología del Principado de Asturias), Oviedo, Spain.,ISPA (Instituto de Investigación Sanitaria del Principado de Asturias), Oviedo, Spain
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