In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli
Abstract Background Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an earl...
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doaj-f25dc7239b8a4460a3d5f4a96e21e08c2020-11-25T03:31:03ZengBMCMicrobial Cell Factories1475-28592020-09-0119111610.1186/s12934-020-01432-yIn vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coliFabien Le Chevalier0Isabelle Correia1Lucrèce Matheron2Morgan Babin3Mireille Moutiez4Nicolas Canu5Muriel Gondry6Olivier Lequin7Pascal Belin8Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRSSorbonne Université, Institut de Biologie Paris Seine (IBPS), FRE3631Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Laboratoire des Biomolécules (LBM), Sorbonne Université, Ecole Normale Supérieure, PSL University, CNRSUniversité Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC)Abstract Background Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an early role in the chemical diversification of cyclodipeptides by introducing Cα-Cβ dehydrogenations. Although the activities of more than 100 CDPSs have been determined, the activities of only a few CDOs have been characterized. Furthermore, the assessment of the CDO activities on chemically-synthesized cyclodipeptides has shown these enzymes to be relatively promiscuous, making them interesting tools for cyclodipeptide chemical diversification. The purpose of this study is to provide the first completely microbial toolkit for the efficient bioproduction of a variety of dehydrogenated 2,5-diketopiperazines. Results We mined genomes for CDOs encoded in biosynthetic gene clusters of CDPS-dependent pathways and selected several for characterization. We co-expressed each with their associated CDPS in the pathway using Escherichia coli as a chassis and showed that the cyclodipeptides and the dehydrogenated derivatives were produced in the culture supernatants. We determined the biological activities of the six novel CDOs by solving the chemical structures of the biologically produced dehydrogenated cyclodipeptides. Then, we assessed the six novel CDOs plus two previously characterized CDOs in combinatorial engineering experiments in E. coli. We co-expressed each of the eight CDOs with each of 18 CDPSs selected for the diversity of cyclodipeptides they synthesize. We detected more than 50 dehydrogenated cyclodipeptides and determined the best CDPS/CDO combinations to optimize the production of 23. Conclusions Our study establishes the usefulness of CDPS and CDO for the bioproduction of dehydrogenated cyclodipeptides. It constitutes the first step toward the bioproduction of more complex and diverse 2,5-diketopiperazines.http://link.springer.com/article/10.1186/s12934-020-01432-ySynthetic biologyCombinatorial biosynthesisNatural products2,5-diketopiperazineCyclodipeptide synthaseCyclodipeptide oxidase |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Fabien Le Chevalier Isabelle Correia Lucrèce Matheron Morgan Babin Mireille Moutiez Nicolas Canu Muriel Gondry Olivier Lequin Pascal Belin |
spellingShingle |
Fabien Le Chevalier Isabelle Correia Lucrèce Matheron Morgan Babin Mireille Moutiez Nicolas Canu Muriel Gondry Olivier Lequin Pascal Belin In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli Microbial Cell Factories Synthetic biology Combinatorial biosynthesis Natural products 2,5-diketopiperazine Cyclodipeptide synthase Cyclodipeptide oxidase |
author_facet |
Fabien Le Chevalier Isabelle Correia Lucrèce Matheron Morgan Babin Mireille Moutiez Nicolas Canu Muriel Gondry Olivier Lequin Pascal Belin |
author_sort |
Fabien Le Chevalier |
title |
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli |
title_short |
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli |
title_full |
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli |
title_fullStr |
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli |
title_full_unstemmed |
In vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in Escherichia coli |
title_sort |
in vivo characterization of the activities of novel cyclodipeptide oxidases: new tools for increasing chemical diversity of bioproduced 2,5-diketopiperazines in escherichia coli |
publisher |
BMC |
series |
Microbial Cell Factories |
issn |
1475-2859 |
publishDate |
2020-09-01 |
description |
Abstract Background Cyclodipeptide oxidases (CDOs) are enzymes involved in the biosynthesis of 2,5-diketopiperazines, a class of naturally occurring compounds with a large range of pharmaceutical activities. CDOs belong to cyclodipeptide synthase (CDPS)-dependent pathways, in which they play an early role in the chemical diversification of cyclodipeptides by introducing Cα-Cβ dehydrogenations. Although the activities of more than 100 CDPSs have been determined, the activities of only a few CDOs have been characterized. Furthermore, the assessment of the CDO activities on chemically-synthesized cyclodipeptides has shown these enzymes to be relatively promiscuous, making them interesting tools for cyclodipeptide chemical diversification. The purpose of this study is to provide the first completely microbial toolkit for the efficient bioproduction of a variety of dehydrogenated 2,5-diketopiperazines. Results We mined genomes for CDOs encoded in biosynthetic gene clusters of CDPS-dependent pathways and selected several for characterization. We co-expressed each with their associated CDPS in the pathway using Escherichia coli as a chassis and showed that the cyclodipeptides and the dehydrogenated derivatives were produced in the culture supernatants. We determined the biological activities of the six novel CDOs by solving the chemical structures of the biologically produced dehydrogenated cyclodipeptides. Then, we assessed the six novel CDOs plus two previously characterized CDOs in combinatorial engineering experiments in E. coli. We co-expressed each of the eight CDOs with each of 18 CDPSs selected for the diversity of cyclodipeptides they synthesize. We detected more than 50 dehydrogenated cyclodipeptides and determined the best CDPS/CDO combinations to optimize the production of 23. Conclusions Our study establishes the usefulness of CDPS and CDO for the bioproduction of dehydrogenated cyclodipeptides. It constitutes the first step toward the bioproduction of more complex and diverse 2,5-diketopiperazines. |
topic |
Synthetic biology Combinatorial biosynthesis Natural products 2,5-diketopiperazine Cyclodipeptide synthase Cyclodipeptide oxidase |
url |
http://link.springer.com/article/10.1186/s12934-020-01432-y |
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