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Functional Metagenomics of the Bovine Rumen Microbiota to Boost Enzyme Discovery for Complex Polymer Breakdown

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Functional Metagenomics of the Bovine Rumen Microbiota to Boost Enzyme Discovery for Complex Polymer Breakdown THÈSE En vue de l'obtention du DOCTORAT DE L’UNIVERSITÉ DE TOULOUSE Délivré par Institut National des Sciences Appliquées de Toulouse (INSA Toulouse) Discipline ou spécialité : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries Présentée et soutenue par Lisa UFARTÉ Le 25 février 2016 Titre : Functional metagenomics of the bovine rumen microbiota to boost enzyme discovery for complex polymer breakdown JURY Dr Gabrielle POTOCKI-VERONESE (LISBP, INRA Toulouse), directrice de thèse Pr. Trevor CHARLES (University of Waterloo, Canada), rapporteur Pr. Thierry GIARDINA (Université Aix Marseille), rapporteur, président du jury Dr Elisabeth LAVILLE (LISBP, INRA Toulouse) Dr Diego MORGAVI (INRA, Theix) Dr Daniel ZALKO (Toxalim, INRA Toulouse) Pr. Magali REMAUD-SIMEON (LISBP, INSA Toulouse), membre invité Ecole doctorale : ED SEVAB : Ingénieries microbienne et enzymatique Unité de recherche : LISBP (UMR CNRS 5504, UMR INRA 792), INSA de Toulouse 2 NOM : UFARTÉ PRÉNOM : Lisa TITRE : Métagénomique fonctionnelle du microbiote du rumen bovin pour la découverte d’enzymes de dégradation de polymères naturels et synthétiques. SPÉCIALITÉ : Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries FILIÈRE : Ingénieries Moléculaires et Enzymatiques ANNÉE : 2016 LIEU : INSA, Toulouse DIRECTRICE DE THÈSE : Dr Gabrielle Potocki-Veronese RÉSUMÉ : Le microbiote du rumen bovin est un écosystème très diversifié et efficace pour la dégradation de substrats complexes, notamment issus de la biomasse végétale. Composé majoritairement de microorganismes non cultivés, il constitue un réservoir très riche de nouvelles enzymes d’intérêt potentiel pour les biotechnologies industrielles, en particulier les bioraffineries et la bioremédiation. Dans le cadre de cette thèse, nous avons mis en œuvre une approche de criblage fonctionnel du métagenome ruminal pour accélérer la découverte d’enzymes de dégradation des lignocelluloses, mais aussi de divers polluants synthétiques. En particulier, de nouvelles estérases capables de dégrader un insecticide de la famille des carbamates, le fenobucarb, ainsi qu’un polyuréthane commercial, l’Impranil DLN, ont pu être identifiées. De plus, le développement d’une nouvelle stratégie de criblage d’oxydoréductases nous a permis d’isoler trois enzymes bactériennes originales, très polyspécifiques, ne requérant ni cuivre ni manganèse pour dégrader différents substrats polycycliques tels que des polluants majeurs de l’industrie textile, mais aussi des dérivés de lignine. Enfin, le criblage de deux banques issues d’enrichissements in vivo et in vitro du microbiome du rumen sur paille de blé a permis d’isoler des cocktails d’enzymes lignocellulolytiques au profil fonctionnel et d’origine taxonomique différents, constitués de glycoside-hydrolases, estérases et oxydoréductases. Quinze nouveaux modules CAZy, correspondant à des familles enzymatiques jamais caractérisées, ont été identifiés. L’ensemble de ces résultats met en lumière l’immense potentiel d’innovation biotechnologique contenu dans les écosystèmes microbiens, en particulier dans le microbiote du rumen bovin. MOTS-CLÉS : métagénomique fonctionelle, rumen bovin, enzymes, criblage haut débit ÉCOLE DOCTORALE: Sciences Ecologiques, Vétérinaires, Agronomiques et Bioingénieries (SEVAB) LABORATOIRE : Laboratoire d’Ingénieries des Systèmes Biologiques et des Procédés (LISBP) INSA/CNRS 5504 - UMR INSA/INRA 792 NAME: UFARTÉ FIRST NAME: Lisa TITLE: Functional metagenomics of the bovine rumen microbiota to boost enzyme discovery for complex polymer breakdown. SPECIALTY: Ecological, Veterinary, Agronomic Sciences and Bioengineering FIELD: Enzymatic and Molecular engineering YEAR: 2016 PLACE: INSA, Toulouse THESIS DIRECTOR: Dr Gabrielle Potocki-Veronese SUMMARY: Bovine rumen microbiota is a highly diverse and efficient ecosystem for the degradation of complex substrates, especially those issued from plant biomass. Predominantly composed of uncultivated microorganisms, it constitutes a rich reservoir of new enzymes of potential interest for industrial biotechnologies, especially biorefineries and bioremediation. As part of this thesis, we used the functional screening of the ruminal metagenome to increase the discovery of enzymes able to degrade lignocelluloses, as well as different synthetic pollutants. In particular, new esterases able to degrade a carbamate insecticide, fenoucarb, and a commercial polyurethane, Impranil DLN, have been identified. Moreover, the development of a new screening strategy for oxidoreductases allowed the isolation of three original bacterial enzymes that are very polyspecific, and do not need copper nor manganese to degrade different polycyclic substrates, like major pollutants of the textile industry, as well as lignin derivatives. Finally, the screening of two libraries from in vivo and in vitro enrichments of the ruminal microbiome on wheat straw allowed the isolation of lignocellulolytic enzymatic cocktails, with different functional profiles and taxonomical origins, comprising glycoside- hydrolases, esterases and oxidoreductases. Fifteen novel CAZy modules, related to enzymatic families never characterized, were identified. All these results highlight the vast potential of microbial ecosystems, in particular the bovine rumen microbiota, for biotechnological innovation. KEYWORDS: functional metagenomics, bovine rumen, enzymes, high-throughput screening DOCTORAL SCHOOL: Ecological, Veterinary, Agronomic Sciences and Bioengineering (SEVAB) LABORATORY: Laboratory of Biosystems and Chemical Engineering (LISBP) INSA/CNRS 5504 - UMR INSA/INRA 792 2 PUBLICATIONS Peer reviewed journal articles: Ufarté L., Potocki-Veronese G., Laville E. (2015). Discovery of new protein families and functions: new challenges in functional metagenomics for biotechnologies and microbial ecology. Front. Microbiol. 6:563. doi: 10.3389/fmicb.2015.00563 Ufarté L., Duquesne S., Laville E., Potocki-Veronese G. (2015) Metagenomics for the discovery of pollutant degrading enzymes. Biotechnology Advances. doi: 10.1016/j.biotechadv.2015.10.009 Passerini D.*, Vuillemin M.*, Ufarté L., Morel S., Loux V., Fontagné-Faucher C., Monsan P., Remaud-Siméon M., Moulis C. (2015) Inventory of the GH70 enzymes encoded by Leuconostoc citreum NRRL B-1299: identification of three novel a-transglucosylases. FEBS Journal 282, 2115–2130. doi:10.1111/febs.13261 * Contributed equally Ufarté L., Potocki-Veronese G., Cecchini D., Rizzo A., Morgavi D., Cathala B., Moreau C., Cleret M., Robe P., Klopp C., Bozonnet S., Laville E. Highly promiscuous oxidases discovered by functional exploration of the bovine rumen microbiome. To be submitted 2016. Ufarté L., Laville E., Cecchini D., Rizzo A., Amblard E., Drula E., Henrissat B., Cleret M., Lazuka A., Hernandez G., Morgavi D., Dumon C., Robe P., Klopp C., Bozonnet S., Potocki-Veronese G. Functional exploration of naturally and artificially enriched rumen microbiomes reveals novel enzymatic synergies involved in polysaccharide breakdown. To be submitted 2016. Ufarté L., Laville E., Duquesne S., Morgavi D., Robe P., Klopp C., Rizzo A., Bozonnet S. and Potocki-Veronese G. Discovery of carbamate degrading enzymes by functional metagenomics. To be submitted 2016 Book chapter: Laville E., Ufarté L., Potocki-Veronese G. (2015) Découverte de nouvelles fonctions et familles protéiques: nouveaux défis pour les biotechnologies et l’écologie microbienne. In La métagénomique: développements et futures applications. Quae. Ufarté L., Bozonnet S., Laville E., Cecchini D. A., Pizzut-Serin S., Jacquiod S., Demanèche S., Simonet P., Franqueville L., Potocki-Veronese G. Functional metagenomics: construction and high-throughput screening of fosmid libraries for discovery of novel carbohydrate-active enzymes. In Martin, F., Uroz, S. (Eds.), Microbial 3 Environmental Genomics (MEG). Springer New York, New York, NY, pp. 257–271. doi : 10.1007/978-1-4939-3369-3_15 ORAL COMMUNICATIONS Ufarté L., Laville E., Morgavi D., Ladeveze S., Bozonnet S., Robe P., Henrissat B., Remaud- Simeon M., Monsan P., Potocki-Veronese G. Functional metagenomics boosts enzyme discovery for complex polymer breakdown. SEVAB Doctoral school day, Toulouse (France), 5 march 2015. Ufarté L., Laville E., Morgavi D., Ladeveze S., Bozonnet S., Robe P., Henrissat B., Remaud- Simeon M., Monsan P., Potocki-Veronese G Functional metagenomics boosts enzyme discovery for complex polymer breakdown 2nd International Symposium on Green Chemistry (ISGC), La Rochelle (France), 3-7 may 2015. Ufarté L., Tauzin A., Gherbovet O., Lebaz N., Lazuka A., Abot A. Transverse approaches for the optimization of lignocellulose degradation. 1st PhD and Post-Doctoral Students Day, LISBP, Toulouse (France), 8 july 2015. POSTER COMMUNICATIONS Ufarté L., Morgavi D., Laville E., Potocki-Veronese G. Functional metagenomics for biocatalyst discovery: applications for environmental biotechnologies and green chemistry SEVAB doctoral school day, Toulouse (France), 12 November 2013. Third place for best poster. Ufarté L., Morgavi D., Laville E., Potocki-Veronese G. Functional metagenomics for biocatalyst discovery: applications for environmental biotechnologies and green chemistry Club Bioconversions en Synthèse Organique (CBSO) 25 th symposium, Carry-le-Rouet (France), 3-6 June 2014. Ufarté L., Laville E., Morgavi D., Hernandez-Raquet G., Bozonnet S., Dumon C., Robe P., Henrissat B., Potocki-Veronese G. Functional metagenomics boosts enzyme discovery for plant cell wall polymer breakdown. 11th Carbohydrate Bioengineering Meeting (CBM),
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