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Communication Dans Un Congrès Année : 2021

Large scale exploration of the biocatalytic capability of biodiversity for biocatalysis & synthetic biology applications

Résumé

Nature appears as the veteran protein engineer since it began its bioengineering ‘experiments’ billions years ago[1]. The emergence of high-throughput sequencing (or Next Generation Sequencing, NGS) in the mid-2000s has generated an incredible amount of protein and gene sequences deposited in the databases. In addition, the deep sequencing of metagenomes from diverse environments offers a huge reservoir of unexploited enzymes which reflect specific metabolic requirements for a defined process (e.g. waste water treatment, bioremediation), or a particular ecological niche. Protein databases are therefore gold mines for discovering novel enzymes for biocatalysis and metabolic engineering for synthetic chemistry and synthetic biology. Unfortunately, the rate of protein functional elucidation lags far behind the rate of gene and protein sequence discovery, leading to an accumulation of proteins with no known (or poorly characterised) function. The experimental exploration of the extraordinary amount of available genomic resources is then needed and can be rationalized to optimize the experimental effort by computational methods that try to reveal the sequence/function relationships of proteins. In addition, the ability of an enzyme to transform not only its metabolic substrate, but to catalyze also the same chemical transformation for a range of different substrates (enzyme promiscuity), expands the field of conversion possibilities expands the chemical capability of enzymes and the chemistry performed by living cells that cannot be predicted efficiently. The research unit “Génomique Métabolique” of Genoscope, the French sequencing center, has developed a multidisciplinary approach for the rational genome mining by bioinformatics methods combined with the set up a high throughput cloning and screening platform that explores and exploits a large prokaryote strain library[2, 3] leading to the discovery of new biocatalysts from diverse enzyme families (nitrilases[2] , transaminases[4], aldolases[5, 6, 7], Baeyer villigerases[8], levansucrases[9], …) including new enzyme families as amine deshydrogenases[10] for chemical synthesis and enzymes for metabolic engineering of terpen synthesis[11]. [1] L. Fernández-Arrojo, ME. Guazzaroni, N. López-Cortés, A. Beloqui, M. Ferrer, Curr. Opin. Biotechnol., 2010, 21, 725. [2] C. Vergne-Vaxelaire, F. Bordier, A. Fossey, M. Besnard-Gonnet, A. Debard, A. Mariage, V. Pellouin, A. Perret, JL Petit, M. Stam, M. Salanoubat, J. Weissenbach, V. de Berardinis, A. Zaparucha Adv. Synth. Catal., 2013, 355, 1763–1779. [3] Chapter book: “Genome Mining for Enzyme Discovery” A. Zaparucha, , V. de Berardinis, C. Vergne-Vaxelaire, “Modern Biocatalysis: Advances Towards Synthetic Biological Systems”Editors: Gavin Williams, Mélanie Hall- Ed. Royal Society of Chemisty, Cambridge (2018) [4 ] E. Heuson, JL Petit, A. Debard, A. Job, F. Charmantray, V. de Berardinis, T. Gefflaut, Appl Microbiol Biotechnol, 2016, 100:397–408 [5] V. de Berardinis, C. Guérard-Hélaine, E. Darii, K. Bastard,V. Hélaine, A. Mariage, JL Petit, N. Poupard, I. Sánchez-Moreno, M. Stam, T. Gefflaut, M. Salanoubat and M. Lemaire Green Chem., 2017, 19, 519–526. [6] V. Laurent, E. Darii, A. Aujon, M. Debacker, JL Petit, V. Hélaine, T. Liptaj, M. Breza, A. Mariage, L. Nauton, M. Trakia, M. Salanoubat, M. Lemaire, C. Guérard-Hélaine, and V. de Berardinis, Angew. Chem. Int. Ed., 2018, 57, 5467–5471. [7] D. Chambre, C. Guerard-Hélaine, E. Darii, A. Mariage, JL Petit, M. Salanoubat, V. de Berardinis, M. Lemaire and V. Hélaine. Chem. Commun., 2019, 55, 7498 [8] T. Reignier, V. de Berardinis, JL Petit,A. Mariage, K. Hamze, K. Duquesne and V. Alphand. Chem. Commun 2014 DOI: 10.1039/c4cc02541e [9] A. Hill, L. Chen, A. Mariage, JL Petit,V. de Berardinis and S. Karboune. Catal. Sci. Technol., 2019, 9, 2931 [10] O. Mayol, K. Bastard, L. Beloti, A. Frese, J.P. Turkenburg, JL Petit, A. Mariage, A. Debard, V. Pellouin, A. Perret, V. de Berardinis, A. Zaparucha, G. Grogan and C. Vergne-Vaxelaire. Nature Catalysis 2019, vol 2, 324–333 [11] J. Rico, K. Duquesne, JL Petit, A. Mariage, E. Darii, F. Peruch, V. de Berardinis, G. Iacazio, Microb. Cell Fact., 2019, 18, 23.
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hal-04315412 , version 1 (30-11-2023)

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  • HAL Id : hal-04315412 , version 1

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Véronique de Berardinis, Jean-Louis Petit, Carine Vergne-Vaxelaire, David Vallenet, Anne Zaparucha. Large scale exploration of the biocatalytic capability of biodiversity for biocatalysis & synthetic biology applications. First International symposium on High-Throughput Catalysts Design, Jun 2021, Virtual conference (Lille), France. ⟨hal-04315412⟩
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