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Hambalko J, Gajdoš P, Nicaud JM, Ledesma-Amaro R, Tupec M, Pichová I, Čertík M. Biosynthesis of Fatty Acid Derivatives by Recombinant Yarrowia lipolytica Containing MsexD2 and MsexD3 Desaturase Genes from Manduca sexta. J Fungi (Basel) 2023; 9:jof9010114. [PMID: 36675935 PMCID: PMC9862095 DOI: 10.3390/jof9010114] [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: 12/19/2022] [Revised: 01/09/2023] [Accepted: 01/11/2023] [Indexed: 01/19/2023] Open
Abstract
One of the most interesting groups of fatty acid derivates is the group of conjugated fatty acids from which the most researched include: conjugated linoleic acid (CLA) and conjugated linolenic acid (CLNA), which are associated with countless health benefits. Sex pheromone mixtures of some insect species, including tobacco horn-worm (Manduca sexta), are typical for the production of uncommon C16 long conjugated fatty acids with two and three conjugated double bonds, as opposed to C18 long CLA and CLNA. In this study, M. sexta desaturases MsexD2 and MsexD3 were expressed in multiple strains of Y. lipolytica with different genotypes. Experiments with the supplementation of fatty acid methyl esters into the medium resulted in the production of novel fatty acids. Using GCxGC-MS, 20 new fatty acids with two or three double bonds were identified. Fatty acids with conjugated or isolated double bonds, or a combination of both, were produced in trace amounts. The results of this study prove that Y. lipolytica is capable of synthesizing C16-conjugated fatty acids. Further genetic optimization of the Y. lipolytica genome and optimization of the fermentation process could lead to increased production of novel fatty acid derivatives with biotechnologically interesting properties.
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Affiliation(s)
- Jaroslav Hambalko
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Peter Gajdoš
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
| | - Jean-Marc Nicaud
- Université Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, Domaine de Vilvert, 78352 Jouy-en-Josas, France
| | - Rodrigo Ledesma-Amaro
- Department of Bioengineering and Imperial College Centre for Synthetic Biology, Faculty of Engineering, Imperial College, London SW7 2AZ, UK
| | - Michal Tupec
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Iva Pichová
- Institute of Organic Chemistry and Biochemistry of the Czech Academy of Sciences, Flemingovo náměstí 542/2, 160 00 Prague 6, Czech Republic
| | - Milan Čertík
- Institute of Biotechnology, Faculty of Chemical and Food Technology, Slovak University of Technology, Radlinského 9, 812 37 Bratislava, Slovakia
- Correspondence:
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New Promoters for Metabolic Engineering of Ashbya gossypii. J Fungi (Basel) 2021; 7:jof7110906. [PMID: 34829195 PMCID: PMC8618306 DOI: 10.3390/jof7110906] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2021] [Revised: 10/21/2021] [Accepted: 10/24/2021] [Indexed: 11/22/2022] Open
Abstract
Ashbya gossypii is a filamentous fungus that is currently exploited for the industrial production of riboflavin. In addition, metabolically engineered strains of A. gossypii have also been described as valuable biocatalysts for the production of different metabolites such as folic acid, nucleosides, and biolipids. Hence, bioproduction in A. gossypii relies on the availability of well-performing gene expression systems both for endogenous and heterologous genes. In this regard, the identification of novel promoters, which are critical elements for gene expression, decisively helps to expand the A. gossypii molecular toolbox. In this work, we present an adaptation of the Dual Luciferase Reporter (DLR) Assay for promoter analysis in A. gossypii using integrative cassettes. We demonstrate the efficiency of the analysis through the identification of 10 new promoters with different features, including carbon source-regulatable abilities, that will highly improve the gene expression platforms used in A. gossypii. Three novel strong promoters (PCCW12, PSED1, and PTSA1) and seven medium/weak promoters (PHSP26, PAGL366C, PTMA10, PCWP1, PAFR038W, PPFS1, and PCDA2) are presented. The functionality of the promoters was further evaluated both for the overexpression and for the underexpression of the A. gossypii MSN2 gene, which induced significant changes in the sporulation ability of the mutant strains.
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Mhlongo SI, Ezeokoli OT, Roopnarain A, Ndaba B, Sekoai PT, Habimana O, Pohl CH. The Potential of Single-Cell Oils Derived From Filamentous Fungi as Alternative Feedstock Sources for Biodiesel Production. Front Microbiol 2021; 12:637381. [PMID: 33584636 PMCID: PMC7876240 DOI: 10.3389/fmicb.2021.637381] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2020] [Accepted: 01/07/2021] [Indexed: 11/13/2022] Open
Abstract
Microbial lipids, also known as single-cell oils (SCOs), are highly attractive feedstocks for biodiesel production due to their fast production rates, minimal labor requirements, independence from seasonal and climatic changes, and ease of scale-up for industrial processing. Among the SCO producers, the less explored filamentous fungi (molds) exhibit desirable features such as a repertoire of hydrolyzing enzymes and a unique pellet morphology that facilitates downstream harvesting. Although several oleaginous filamentous fungi have been identified and explored for SCO production, high production costs and technical difficulties still make the process less attractive compared to conventional lipid sources for biodiesel production. This review aims to highlight the ability of filamentous fungi to hydrolyze various organic wastes for SCO production and explore current strategies to enhance the efficiency and cost-effectiveness of the SCO production and recovery process. The review also highlights the mechanisms and components governing lipogenic pathways, which can inform the rational designs of processing conditions and metabolic engineering efforts for increasing the quality and accumulation of lipids in filamentous fungi. Furthermore, we describe other process integration strategies such as the co-production with hydrogen using advanced fermentation processes as a step toward a biorefinery process. These innovative approaches allow for integrating upstream and downstream processing units, thus resulting in an efficient and cost-effective method of simultaneous SCO production and utilization for biodiesel production.
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Affiliation(s)
- Sizwe I. Mhlongo
- Discipline of Medical Microbiology, School of Laboratory Medicine and Medical Sciences, Medical School, University of KwaZulu-Natal, Durban, South Africa
| | - Obinna T. Ezeokoli
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
| | - Ashira Roopnarain
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Pretoria, South Africa
| | - Busiswa Ndaba
- Microbiology and Environmental Biotechnology Research Group, Institute for Soil, Climate and Water, Agricultural Research Council, Pretoria, South Africa
| | - Patrick T. Sekoai
- The School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Olivier Habimana
- The School of Biological Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Carolina H. Pohl
- Department of Microbial, Biochemical and Food Biotechnology, University of the Free State, Bloemfontein, South Africa
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Silva R, Aguiar TQ, Coelho E, Jiménez A, Revuelta JL, Domingues L. Metabolic engineering of Ashbya gossypii for deciphering the de novo biosynthesis of γ-lactones. Microb Cell Fact 2019; 18:62. [PMID: 30922300 PMCID: PMC6437850 DOI: 10.1186/s12934-019-1113-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 03/20/2019] [Indexed: 02/04/2023] Open
Abstract
Background Lactones are highly valuable cyclic esters of hydroxy fatty acids that find application as pure fragrances or as building blocks of speciality chemicals. While chemical synthesis often leads to undesired racemic mixtures, microbial production allows obtaining optically pure lactones. The production of a specific lactone by biotransformation depends on the supply of the corresponding hydroxy fatty acid, which has economic and industrial value similar to γ-lactones. Hence, the identification and exploration of microorganisms with the rare natural ability for de novo biosynthesis of lactones will contribute to the long-term sustainability of microbial production. In this study, the innate ability of Ashbya gossypii for de novo production of γ-lactones from glucose was evaluated and improved. Results Characterization of the volatile organic compounds produced by nine strains of this industrial filamentous fungus in glucose-based medium revealed the noteworthy presence of seven chemically different γ-lactones. To decipher and understand the de novo biosynthesis of γ-lactones from glucose, we developed metabolic engineering strategies focused on the fatty acid biosynthesis and the β-oxidation pathways. Overexpression of AgDES589, encoding a desaturase for the conversion of oleic acid (C18:1) into linoleic acid (C18:2), and deletion of AgELO624, which encodes an elongase that catalyses the formation of C20:0 and C22:0 fatty acids, greatly increased the production of γ-lactones (up to 6.4-fold; (7.6 ± 0.8) × 103 µg/gCell Dry Weight). Further substitution of AgPOX1, encoding the exclusive acyl-CoA oxidase in A. gossypii, by a codon-optimized POX2 gene from Yarrowia lipolytica, which encodes a specific long chain acyl-CoA oxidase, fine-tuned the biosynthesis of γ-decalactone to a relative production of more than 99%. Conclusions This study demonstrates the potential of A. gossypii as a model and future platform for de novo biosynthesis of γ-lactones. By means of metabolic engineering, key enzymatic steps involved in their production were elucidated. Moreover, the combinatorial metabolic engineering strategies developed resulted in improved de novo biosynthesis of γ-decalactone. In sum, these proof-of-concept data revealed yet unknown metabolic and genetic determinants important for the future exploration of the de novo production of γ-lactones as an alternative to biotransformation processes. Electronic supplementary material The online version of this article (10.1186/s12934-019-1113-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rui Silva
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Tatiana Q Aguiar
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Eduardo Coelho
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Lucília Domingues
- CEB-Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal.
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Ledesma-Amaro R, Jiménez A, Revuelta JL. Pathway Grafting for Polyunsaturated Fatty Acids Production in Ashbya gossypii through Golden Gate Rapid Assembly. ACS Synth Biol 2018; 7:2340-2347. [PMID: 30261136 DOI: 10.1021/acssynbio.8b00287] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Here we present a Golden Gate assembly system adapted for the rapid genomic engineering of the industrial fungus Ashbya gossypii. This biocatalyst is an excellent biotechnological chassis for synthetic biology applications and is currently used for the industrial production of riboflavin. Other bioprocesses such as the production of folic acid, nucleosides, amino acids and biolipids have been recently reported in A. gossypii. In this work, an efficient assembly system for the expression of heterologous complex pathways has been designed. The expression platform comprises interchangeable DNA modules, which provides flexibility for the use of different loci for integration, selection markers and regulatory sequences. The functionality of the system has been applied to engineer strains able to synthesize polyunsaturated fatty acids (up to 35% of total fatty acids). The production of the industrially relevant arachidonic, eicosapentanoic and docosahexanoic acids remarks the potential of A. gossypii to produce these functional lipids.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Imperial College Centre for Synthetic Biology and Department of Bioengineering, Imperial College London, London SW7 2AZ, U.K
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Alberto Jiménez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - José Luis Revuelta
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
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Semenova EF, Shpichka AI, Presnyakova EV. Aromatic and monoterpene alcohol accumulation by Eremothecium ashbyi strains differing in riboflavinogenesis. APPL BIOCHEM MICRO+ 2017. [DOI: 10.1134/s0003683817030139] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Díaz-Fernández D, Lozano-Martínez P, Buey RM, Revuelta JL, Jiménez A. Utilization of xylose by engineered strains of Ashbya gossypii for the production of microbial oils. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:3. [PMID: 28053663 PMCID: PMC5209892 DOI: 10.1186/s13068-016-0685-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2016] [Accepted: 12/09/2016] [Indexed: 05/24/2023]
Abstract
BACKGROUND Ashbya gossypii is a filamentous fungus that is currently exploited for the industrial production of riboflavin. The utilization of A. gossypii as a microbial biocatalyst is further supported by its ability to grow in low-cost feedstocks, inexpensive downstream processing and the availability of an ease to use molecular toolbox for genetic and genomic modifications. Consequently, A. gossypii has been also introduced as an ideal biotechnological chassis for the production of inosine, folic acid, and microbial oils. However, A. gossypii cannot use xylose, the most common pentose in hydrolysates of plant biomass. RESULTS In this work, we aimed at designing A. gossypii strains able to utilize xylose as the carbon source for the production of biolipids. An endogenous xylose utilization pathway was identified and overexpressed, resulting in an A. gossypii xylose-metabolizing strain showing prominent conversion rates of xylose to xylitol (up to 97% after 48 h). In addition, metabolic flux channeling from xylulose-5-phosphate to acetyl-CoA, using aheterologous phosphoketolase pathway, increased the lipid content in the xylose-metabolizing strain a 54% over the parental strain growing in glucose-based media. This increase raised to 69% when lipid accumulation was further boosted by blocking the beta-oxidation pathway. CONCLUSIONS Ashbya gossypii has been engineered for the utilization of xylose. We present here a proof-of-concept study for the production of microbial oils from xylose in A. gossypii, thus introducing a novel biocatalyst with very promising properties in developing consolidated bioprocessing to produce fine chemicals and biofuels from xylose-rich hydrolysates of plant biomass.
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Affiliation(s)
- David Díaz-Fernández
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Patricia Lozano-Martínez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Rubén M. Buey
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - José Luis Revuelta
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
| | - Alberto Jiménez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007 Salamanca, Spain
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Lozano-Martínez P, Buey RM, Ledesma-Amaro R, Jiménez A, Revuelta JL. Engineering Ashbya gossypii strains for de novo lipid production using industrial by-products. Microb Biotechnol 2016; 10:425-433. [PMID: 28008713 PMCID: PMC5328814 DOI: 10.1111/1751-7915.12487] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Revised: 11/14/2016] [Accepted: 11/16/2016] [Indexed: 11/27/2022] Open
Abstract
Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin, and it is currently exploited for the industrial production of this vitamin. The utilization of A. gossypii for biotechnological applications presents important advantages such as the utilization of low-cost culture media, inexpensive downstream processing and a wide range of molecular tools for genetic manipulation, thus making A. gossypii a valuable biotechnological chassis for metabolic engineering. A. gossypii has been shown to accumulate high levels of lipids in oil-based culture media; however, the lipid biosynthesis capacity is rather limited when grown in sugar-based culture media. In this study, by altering the fatty acyl-CoA pool and manipulating the regulation of the main ∆9 desaturase gene, we have obtained A. gossypii strains with significantly increased (up to fourfold) de novo lipid biosynthesis using glucose as the only carbon source in the fermentation broth. Moreover, these strains were efficient biocatalysts for the conversion of carbohydrates from sugarcane molasses to biolipids, able to accumulate lipids up to 25% of its cell dry weight. Our results represent a proof of principle showing the promising potential of A. gossypii as a competitive microorganism for industrial biolipid production using cost-effective feed stocks.
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Affiliation(s)
- Patricia Lozano-Martínez
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Rodrigo Ledesma-Amaro
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain
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Serrano-Amatriain C, Ledesma-Amaro R, López-Nicolás R, Ros G, Jiménez A, Revuelta JL. Folic Acid Production by Engineered Ashbya gossypii. Metab Eng 2016; 38:473-482. [PMID: 27989803 DOI: 10.1016/j.ymben.2016.10.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Revised: 09/13/2016] [Accepted: 10/25/2016] [Indexed: 11/17/2022]
Abstract
Folic acid (vitamin B9) is the common name of a number of chemically related compounds (folates), which play a central role as cofactors in one-carbon transfer reactions. Folates are involved in the biosynthesis and metabolism of nucleotides and amino acids, as well as supplying methyl groups to a broad range of substrates, such as hormones, DNA, proteins, and lipids, as part of the methyl cycle. Humans and animals cannot synthesize folic acid and, therefore, need them in the diet. Folic acid deficiency is an important and underestimated problem of micronutrient malnutrition affecting billions of people worldwide. Therefore, the addition of folic acid as food additive has become mandatory in many countries thus contributing to a growing demand of the vitamin. At present, folic acid is exclusively produced by chemical synthesis despite its associated environmental burdens. In this work, we have metabolically engineered the industrial fungus Ashbya gossypii in order to explore its potential as a natural producer of folic acid. Overexpression of FOL genes greatly enhanced the synthesis of folates and identified GTP cyclohydrolase I as the limiting step. Metabolic flux redirection from competing pathways also stimulated folic acid production. Finally, combinatorial engineering synergistically increased the production of different bioactive forms of the folic vitamin. Overall, strains were constructed which produce 146-fold (6595µg/L) more vitamin than the wild-type and by far represents the highest yield reported.
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Affiliation(s)
- Cristina Serrano-Amatriain
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Rodrigo Ledesma-Amaro
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - Rubén López-Nicolás
- Department of Food Science and Nutrition, Faculty of Veterinary Sciences, University of Murcia, Campus de Espinardo, 30071 Espinardo (Murcia), Spain
| | - Gaspar Ros
- Department of Food Science and Nutrition, Faculty of Veterinary Sciences, University of Murcia, Campus de Espinardo, 30071 Espinardo (Murcia), Spain
| | - Alberto Jiménez
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Department of Microbiology and Genetics, University of Salamanca, Campus Miguel de Unamuno, E-37007 Salamanca, Spain.
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Bioproduction of riboflavin: a bright yellow history. J Ind Microbiol Biotechnol 2016; 44:659-665. [PMID: 27696023 DOI: 10.1007/s10295-016-1842-7] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2016] [Accepted: 09/23/2016] [Indexed: 10/20/2022]
Abstract
Riboflavin (vitamin B2) is an essential nutrient for humans and animals that must be obtained from the diet. To ensure an optimal supply, riboflavin is used on a large scale as additive in the food and feed industries. Here, we describe a historical overview of the industrial process of riboflavin production starting from its discovery and the need to produce the vitamin in bulk at prices that would allow for their use in human and animal nutrition. Riboflavin was produced industrially by chemical synthesis for many decades. At present, the development of economical and eco-efficient fermentation processes, which are mainly based on Bacillus subtilis and Ashbya gossypii strains, has replaced the synthetic process at industrial scale. A detailed account is given of the development of the riboflavin overproducer strains as well as future prospects for its improvement.
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11
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Ledesma-Amaro R, Revuelta JL. Synthetic biology and metabolic engineering to produce microbial oils: towards a sustainable source of fuels, chemicals and nutraceuticals. N Biotechnol 2016. [DOI: 10.1016/j.nbt.2015.10.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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Ledesma-Amaro R, Buey RM, Revuelta JL. The filamentous fungus Ashbya gossypii as a competitive industrial inosine producer. Biotechnol Bioeng 2016; 113:2060-3. [PMID: 26927228 DOI: 10.1002/bit.25965] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 02/04/2016] [Accepted: 02/21/2016] [Indexed: 01/06/2023]
Abstract
Inosine is a nucleoside with growing biotechnological interest due to its recently attributed beneficial health effects and as a convenient precursor of the umami flavor. At present, most of the industrial inosine production relies on bacterial fermentations. In this work, we have metabolically engineered the filamentous fungus Ashbya gossypii to obtain strains able to excrete high amounts of inosine to the culture medium. We report that the disruption of only two key genes of the purine biosynthetic pathway efficiently redirect the metabolic flux, increasing 200-fold the excretion of inosine with respect to the wild type, up to 2.2 g/L. These results allow us to propose A. gossypii as a convenient candidate for large-scale nucleoside production, especially in view of the several advantages that Ashbya has with respect to the bacterial systems used at present for the industrial production of this food additive. Biotechnol. Bioeng. 2016;113: 2060-2063. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Metabolic Engineering Group, Departamento de Microbiologia y Genetica, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, 37007, Spain
| | - Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiologia y Genetica, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, 37007, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiologia y Genetica, Universidad de Salamanca, Campus Miguel de Unamuno, Salamanca, 37007, Spain.
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Ledesma-Amaro R, Lozano-Martínez P, Jiménez A, Revuelta JL. Engineering Ashbya gossypii for efficient biolipid production. Bioengineered 2016; 6:119-23. [PMID: 25625436 DOI: 10.1080/21655979.2015.1011525] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
Abstract
Ashbya gossypii is a filamentous fungus that naturally overproduces riboflavin. Indeed, engineered strains are currently used for the industrial production of riboflavin, replacing the chemical synthesis processes formerly used. The utilization of A. gossypii for biotechnological applications affords significant advantages that involve low-cost media use and cheap downstream processing for some applications. Although A. gossypii cannot be considered a bona fide oleaginous microorganism, the accumulation of lipid droplets within hyphae has been described. In view of the genomic and molecular tools available for its manipulation, the metabolism of A. gossypii was engineered aiming to increase total lipid accumulation. Blocking the β-oxidation pathway through the knock-out of the AgPOX1 gene was sufficient to obtain strains with high lipid yields, comparable to those of the best oleaginous microorganisms. Thus, the poxΔ strain of A. gossypii constitutes a novel promising tool for the production of microbial oils in forthcoming modified A. gossypii strains.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- a Departamento de Microbiología y Genética; Universidad de Salamanca ; Campus Miguel de Unamuno ; Salamanca , Spain
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Ledesma-Amaro R, Nicaud JM. Yarrowia lipolytica as a biotechnological chassis to produce usual and unusual fatty acids. Prog Lipid Res 2016; 61:40-50. [DOI: 10.1016/j.plipres.2015.12.001] [Citation(s) in RCA: 165] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 12/02/2015] [Accepted: 12/08/2015] [Indexed: 10/22/2022]
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Aguiar TQ, Silva R, Domingues L. Ashbya gossypii beyond industrial riboflavin production: A historical perspective and emerging biotechnological applications. Biotechnol Adv 2015; 33:1774-86. [DOI: 10.1016/j.biotechadv.2015.10.001] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2015] [Revised: 09/28/2015] [Accepted: 10/04/2015] [Indexed: 10/22/2022]
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16
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Guanine nucleotide binding to the Bateman domain mediates the allosteric inhibition of eukaryotic IMP dehydrogenases. Nat Commun 2015; 6:8923. [PMID: 26558346 PMCID: PMC4660370 DOI: 10.1038/ncomms9923] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 10/16/2015] [Indexed: 12/26/2022] Open
Abstract
Inosine-5′-monophosphate dehydrogenase (IMPDH) plays key roles in purine nucleotide metabolism and cell proliferation. Although IMPDH is a widely studied therapeutic target, there is limited information about its physiological regulation. Using Ashbya gossypii as a model, we describe the molecular mechanism and the structural basis for the allosteric regulation of IMPDH by guanine nucleotides. We report that GTP and GDP bind to the regulatory Bateman domain, inducing octamers with compromised catalytic activity. Our data suggest that eukaryotic and prokaryotic IMPDHs might have developed different regulatory mechanisms, with GTP/GDP inhibiting only eukaryotic IMPDHs. Interestingly, mutations associated with human retinopathies map into the guanine nucleotide-binding sites including a previously undescribed non-canonical site and disrupt allosteric inhibition. Together, our results shed light on the mechanisms of the allosteric regulation of enzymes mediated by Bateman domains and provide a molecular basis for certain retinopathies, opening the door to new therapeutic approaches. IMP dehydrogenase (IMPDH) plays essential roles in purine metabolism and cell proliferation. Here Buey et al. describe a guanine nucleotides regulated molecular mechanism for allosteric communication between the regulatory and catalytic domains of IMPDH.
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Ledesma-Amaro R, Serrano-Amatriain C, Jiménez A, Revuelta JL. Metabolic engineering of riboflavin production in Ashbya gossypii through pathway optimization. Microb Cell Fact 2015; 14:163. [PMID: 26463172 PMCID: PMC4605130 DOI: 10.1186/s12934-015-0354-x] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/04/2015] [Indexed: 12/21/2022] Open
Abstract
Background The industrial production of riboflavin mostly relies on the microbial fermentation of flavinogenic microorganisms and Ashbya gossypii is the main industrial producer of the vitamin. Accordingly, bioengineering strategies aimed at increasing riboflavin production in A. gossypii are highly valuable for industry. Results
We analyze the contribution of all the RIB genes to the production of riboflavin in A. gossypii. Two important metabolic rate-limiting steps that limit the overproduction of riboflavin have been found: first, low mRNA levels of the RIB genes hindered the overproduction of riboflavin; second, the competition of the AMP branch for purinogenic precursors also represents a limitation for riboflavin overproduction. Thus, overexpression of the RIB genes resulted in a significant increase in riboflavin yield. Moreover, both the inactivation and the underexpression of the ADE12 gene, which controls the first step of the AMP branch, also proved to have a positive effect on riboflavin production. Accordingly, a strain that combines both the overexpression of the RIB genes and the underexpression of the ADE12 gene was engineered. This strain produced 523 mg/L of riboflavin (5.4-fold higher than the wild-type), which is the highest titer of riboflavin obtained by metabolic engineering in A. gossypii so far. Conclusions Riboflavin production in A. gossypii is limited by a low transcription activity of the RIB genes. Flux limitation towards AMP provides committed substrate GTP for riboflavin overproduction without detrimental effects on biomass formation. A multiple-engineered Ashbya strain that produces up to 523 mg/L of riboflavin was generated. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0354-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Cristina Serrano-Amatriain
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Alberto Jiménez
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - José Luis Revuelta
- Departamento de Microbiología y Genética, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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Zhang H, Zhang L, Chen H, Chen YQ, Chen W, Song Y, Ratledge C. Enhanced lipid accumulation in the yeast Yarrowia lipolytica by over-expression of ATP:citrate lyase from Mus musculus. J Biotechnol 2015; 192 Pt A:78-84. [PMID: 25450640 DOI: 10.1016/j.jbiotec.2014.10.004] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2014] [Revised: 09/15/2014] [Accepted: 10/01/2014] [Indexed: 12/18/2022]
Abstract
Yarrowia lipolytica can accumulate large amounts of storage lipids and has considerable potential for the production of polyunsaturated fatty acids and other lipids for biofuels. When the nitrogen source is exhausted in the medium, the key intermediate, citrate, is converted to acetyl-CoA by ATP:citrate lyase (ACL) for lipid accumulation. However, in this yeast most of the citrate is also secreted into the culture medium. To increase the endogenous substrate (acetyl-CoA) level for lipid biosynthesis, the acl gene from Mus musculus was over-expressed in Y. lipolytica with mono-copy integration vector pINA1312sp and multi-copy integration vector pINA1292sp. This increased the lipid content from 7.3% to between 11% and 23% (w/w) of the cell dry weight. Cell growth was only slightly affected. Multi-copy integration transformants had higher lipid contents than mono-copy integration transformants; the lipid content of the transformants was consistent with the copy number of acl gene integrated. Over-expression of ACL had no significant effect on fatty acid profile of the yeast. These results suggested that ACL is an important acetyl-CoA producer and plays a vital role in lipid accumulation in oleaginous yeast Y. lipolytica.
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Buey RM, Ledesma-Amaro R, Balsera M, de Pereda JM, Revuelta JL. Increased riboflavin production by manipulation of inosine 5'-monophosphate dehydrogenase in Ashbya gossypii. Appl Microbiol Biotechnol 2015; 99:9577-89. [PMID: 26150243 DOI: 10.1007/s00253-015-6710-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2015] [Revised: 05/15/2015] [Accepted: 05/19/2015] [Indexed: 12/13/2022]
Abstract
Guanine nucleotides are the precursors of essential biomolecules including nucleic acids and vitamins such as riboflavin. The enzyme inosine-5'-monophosphate dehydrogenase (IMPDH) catalyzes the ratelimiting step in the guanine nucleotide de novo biosynthetic pathway and plays a key role in controlling the cellular nucleotide pools. Thus, IMPDH is an important metabolic bottleneck in the guanine nucleotide synthesis, susceptible of manipulation by means of metabolic engineering approaches. Herein, we report the functional and structural characterization of the IMPDH enzyme from the industrial fungus Ashbya gossypii. Our data show that the overexpression of the IMPDH gene increases the metabolic flux through the guanine pathway and ultimately enhances 40 % riboflavin production with respect to the wild type. Also, IMPDH disruption results in a 100-fold increase of inosine excretion to the culture media. Our results contribute to the developing metabolic engineering toolbox aiming at improving the production of metabolites with biotechnological interest in A. gossypii.
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Affiliation(s)
- Rubén M Buey
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | | | - Mónica Balsera
- Department Abiotic Stress, Instituto de Recursos Naturales y Agrobiología, Consejo Superior de Investigaciones Científicas, C/ Cordel de Merinas 40-52, 37008, Salamanca, Spain
| | - José María de Pereda
- Instituto de Biología Celular y Molecular del Cáncer, Consejo Superior de Investigaciones Científicas, Universidad de Salamanca, Campus Miguel de Unamuno, 37007, Salamanca, Spain
| | - José Luis Revuelta
- Metabolic Engineering Group, Departamento de Microbiología y Genética, Universidad de Salamanca, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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Dulermo T, Lazar Z, Dulermo R, Rakicka M, Haddouche R, Nicaud JM. Analysis of ATP-citrate lyase and malic enzyme mutants of Yarrowia lipolytica points out the importance of mannitol metabolism in fatty acid synthesis. Biochim Biophys Acta Mol Cell Biol Lipids 2015; 1851:1107-17. [PMID: 25959598 DOI: 10.1016/j.bbalip.2015.04.007] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2015] [Revised: 04/27/2015] [Accepted: 04/29/2015] [Indexed: 12/20/2022]
Abstract
The role of the two key enzymes of fatty acid (FA) synthesis, ATP-citrate lyase (Acl) and malic enzyme (Mae), was analyzed in the oleaginous yeast Yarrowia lipolytica. In most oleaginous yeasts, Acl and Mae are proposed to provide, respectively, acetyl-CoA and NADPH for FA synthesis. Acl was mainly studied at the biochemical level but no strain depleted for this enzyme was analyzed in oleaginous microorganisms. On the other hand the role of Mae in FA synthesis in Y. lipolytica remains unclear since it was proposed to be a mitochondrial NAD(H)-dependent enzyme and not a cytosolic NADP(H)-dependent enzyme. In this study, we analyzed for the first time strains inactivated for corresponding genes. Inactivation of ACL1 decreases FA synthesis by 60 to 80%, confirming its essential role in FA synthesis in Y. lipolytica. Conversely, inactivation of MAE1 has no effects on FA synthesis, except in a FA overaccumulating strain where it improves FA synthesis by 35%. This result definitively excludes Mae as a major key enzyme for FA synthesis in Y. lipolytica. During the analysis of both mutants, we observed a negative correlation between FA and mannitol level. As mannitol and FA pathways may compete for carbon storage, we inactivated YlSDR, encoding a mannitol dehydrogenase converting fructose and NADPH into mannitol and NADP+. The FA content of the resulting mutant was improved by 60% during growth on fructose, demonstrating that mannitol metabolism may modulate FA synthesis in Y. lipolytica.
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Affiliation(s)
- Thierry Dulermo
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Zbigniew Lazar
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37/41, 51-630 Wroclaw, Poland
| | - Rémi Dulermo
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Magdalena Rakicka
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France; Department of Biotechnology and Food Microbiology, Wroclaw University of Environmental and Life Sciences, Chełmońskiego 37/41, 51-630 Wroclaw, Poland
| | - Ramedane Haddouche
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France
| | - Jean-Marc Nicaud
- INRA, UMR1319 Micalis, F-78350 Jouy-en-Josas, France; AgroParisTech, UMR Micalis, Jouy-en-Josas, France.
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Ledesma-Amaro R, Buey RM, Revuelta JL. Increased production of inosine and guanosine by means of metabolic engineering of the purine pathway in Ashbya gossypii. Microb Cell Fact 2015; 14:58. [PMID: 25889888 PMCID: PMC4407346 DOI: 10.1186/s12934-015-0234-4] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Accepted: 03/25/2015] [Indexed: 11/25/2022] Open
Abstract
Background Inosine and guanosine monophosphate nucleotides are convenient sources of the umami flavor, with attributed beneficial health effects that have renewed commercial interest in nucleotide fermentations. Accordingly, several bacterial strains that excrete high levels of inosine and guanosine nucleosides are currently used in the food industry for this purpose. Results In the present study, we show that the filamentous fungus Ashbya gossypii, a natural riboflavin overproducer, excretes high amounts of inosine and guanosine nucleosides to the culture medium. Following a rational metabolic engineering approach of the de novo purine nucleotide biosynthetic pathway, we increased the excreted levels of inosine up to 27-fold. Conclusions We generated Ashbya gossypii strains with improved production titers of inosine and guanosine. Our results point to Ashbya gossypii as the first eukaryotic microorganism representing a promising candidate, susceptible to further manipulation, for industrial nucleoside fermentation. Electronic supplementary material The online version of this article (doi:10.1186/s12934-015-0234-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Ruben M Buey
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
| | - Jose Luis Revuelta
- Departamento de Microbiología y Genética, Metabolic Engineering Group, Universidad de Salamanca, Laboratory 323, Edificio Departamental, Campus Miguel de Unamuno, 37007, Salamanca, Spain.
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Ledesma-Amaro R. Microbial oils: A customizable feedstock through metabolic engineering. EUR J LIPID SCI TECH 2014. [DOI: 10.1002/ejlt.201400181] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética, Metabolic Engineering Group; Universidad de Salamanca; Salamanca Spain
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23
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Ledesma-Amaro R, Santos MA, Jiménez A, Revuelta JL. Tuning single-cell oil production inAshbya gossypiiby engineering the elongation and desaturation systems. Biotechnol Bioeng 2014; 111:1782-91. [DOI: 10.1002/bit.25245] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Revised: 03/11/2014] [Accepted: 03/19/2014] [Indexed: 01/01/2023]
Affiliation(s)
- Rodrigo Ledesma-Amaro
- Departamento de Microbiología y Genética; Universidad de Salamanca; Campus Miguel de Unamuno E-37007 Salamanca Spain
| | - María-Angeles Santos
- Departamento de Microbiología y Genética; Universidad de Salamanca; Campus Miguel de Unamuno E-37007 Salamanca Spain
| | - Alberto Jiménez
- Departamento de Microbiología y Genética; Universidad de Salamanca; Campus Miguel de Unamuno E-37007 Salamanca Spain
| | - José Luis Revuelta
- Departamento de Microbiología y Genética; Universidad de Salamanca; Campus Miguel de Unamuno E-37007 Salamanca Spain
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