Identification and characterization of the first exo-xylanase from glycosil hydrolase family 11 from the study of the metatranscriptome of a compost-derived consortia

Author(s)

Bruno Luan Soares Paula de Mello

• Document type: Doctoral Thesis
• Press: São Carlos.
• Institution: Universidade de São Paulo (USP). Instituto de Física de São Carlos (IFSC/BT)
• Defense date: 2017-08-23

Examining board members

Igor Polikarpov; Nelma Regina Segnini Bossolan; Ronaldo Alves Pinto Nagem; Aline Maria da Silva; Cristina Paiva de Sousa

• Advisor: Igor Polikarpov

Abstract

Using of the globally abundant crop residues as carbon source for energy generation seems a promising solution to reduce our dependency on fossil fuels. In nature, such as in compost habitats, microbial communities create complex metabolic networks that efficiently degrade the available plant biomass using a set of synergistic enzymes. However, deconstruction of lignocellulose remains a challenge for industry due to recalcitrant nature of the substrate and enzymes low activity, raising the price of the produced biofuel. Metagenomics and metatranscriptomics studies on complex microbial communities can assess the metabolic functions employed by the lignocellulolytic consortia and unveil novel biocatalysts that could improve industrial lignocellulose conversion. Here, using 16S rRNA amplicon metagenomic approach, we examined the diversity of microorganisms obtained in the laboratory setting when a nutrient-limited or nutrient-rich media are used. Then, a microbial community derived from compost was grown in minimal medium with sugarcane bagasse as a sole carbon source. The substrate degradation was monitored and the metatranscriptome from the resulting cultures was sequenced; several target genes were selected and functional characterized. During a five-week time course, the microbial community grown in minimal medium showed greater diversity and enrichment in lignocellulose-degrading microorganisms than the one grown in nutrient rich medium. Metatranscriptomics analysis revealed the first glycoside hydrolase from family 11 with exo-xylanase activity (C21). C21 crystal structure, refined at 1.76 Å, explained the molecular basis of exo-xylanase activity due to two extra loops previously unseen in the other reported structures from members from glycoside hydrolase family 11. A supplementation of commercial enzyme mix with C21 showed improvement in Avicel hydrolysis in the presence of inhibitory xylooligomers. The combination of metagenomic and metatranscriptomic analysis of compost-derived microbial community showed that nutrient-limited medium may displace bacterial generalist species, leading to an enriched source for mining novel enzymes for biotechnology applications. It also unveiled a diversity of mechanisms involved in lignocellulose degradation in situ. (AU)

• FAPESP's process: 11/21608-1 - Identification and characterization of new enzymes with potential for lignocellulosic biomass conversion
• Grantee: Bruno Luan Soares Paula de Mello
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)