Library generation for biomass conversion enzymes from soil metagenome

Author(s)

Thabata Maria Alvarez

• Document type: Doctoral Thesis
• Press: Campinas, SP.
• Institution: Universidade Estadual de Campinas (UNICAMP). Instituto de Biologia
• Defense date: 2013-08-28

Examining board members

Fabio Marcio Squina; Carmen Veríssima Ferreira; Marie Anne Van Sluys; Igor Polikarpov; Hiroshi Aoyama

• Advisor: Fabio Marcio Squina

Abstract

Due to the necessity of development of renewable sources of energy, it is of great interest the discovery of novel enzymes involved in plant cell wall deconstruction for biofuels production. Metagenomics is a powerful tool for the discovery of novel genes in microbial communities that are not liable to cultivation by traditional techniques. In this context, the aim of this thesis was the development of metagenomic strategies for prospection of novel enzymes involved in plant biomass degradation in sugarcane field soil metagenome and functional characterization of the identified enzymes. The metagenomic library constructed with DNA extracted from a microbial consortium specialized in degradation of steam exploded delignified sugarcane bagasse was used in the experiments of high-performance functional screening. As a result, we identified three positive clones with cellulolytic activity and two clones with xylanolytic activity. The analysis of the inserts from each clone resulted in the location of ORFs whose amino acid sequences showed identity to conserved domains of glycoside hydrolase family 5 (cellulases E-1 and E-2), family 6 (cellulase E-3), family 10 (xylanase X-1) and family 16 (glycoside hydrolase X-2). Cellulase E-1 exhibited in addition to the catalytic domain, E-1 Cat, a carbohydrate binding module, called E-1 CBM, which showed no sequence identity with known conserved domains. Functional analysis of E-1 CBM showed that it is a CBM specific for glucan chains with a degree of polymerization of at least five units of glucose. Assays with a set of different substrates revealed that E-1 Cat hydrolyzed specifically ß(1,4) glycoside bonds between glucose residues. The highest value of enzymatic activity was obtained at pH 7.0 and temperature of 50°C. The kinetic parameters Km, Vmax and catalytic efficiency kcat/Km calculated using CMC were 6.05 ± 0.37 mg/mL, 42.51 ± 1.2 ?mol/min/mg and 4.06 mL/mg/s, respectively. The enzyme showed thermal stability at 40°C for five hours. The enzymatic activity of E-1 Cat in crystalline cellulose and steam exploded sugarcane bagasse resulted in the release of soluble sugars, demonstrating its potential application in processes of biomass conversion. The xylanase X-1 showed higher enzyme activity in debranched xylan, in reactions conducted in pH 6.0 and temperature of 45°C. The kinetic parameters Km, Vmax and catalytic efficiency kcat/Km calculated using beechwood xylan were 2.18 ± 0.13 mg/mL, 1,435 ± 30.4 ?mol/min/mg and 496.32 mL/mg/s, respectively. In relation to thermal stability, the enzyme was stable at 40°C and 50°C for six hours. The hydrolysis of complex substrates resulted in the release of xylo-oligosaccharides, xylobiose and xylose, which are compounds that have potential application in food and biofuels industries. The results of this study validated the metagenomic approach developed for the discovery of novel genes coding for glycoside hydrolases. Moreover, the strategy described in this work can be extended to the discovery of a myriad of byproducts of biotechnological interest (AU)

• FAPESP's process: 10/11469-1 - Library generation for biomass-conversion enzymes from soil metagenome
• Grantee: Thabata Maria Alvarez
• Support Opportunities: Scholarships in Brazil - Doctorate (Direct)