Library generation for biomass-conversion enzymes from soil metagenome

• Grant number: 08/58037-9
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• Start date: May 01, 2009
• End date: April 30, 2014
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Fábio Márcio Squina
• Grantee: Fábio Márcio Squina
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• Associated research grant(s): 10/18198-3 - Systems biology of sugarcane bagasse microbial decomposition interactions, AV.EXT
• Associated scholarship(s): 13/09541-4 - Genomic studies of global gene expression of Aspergillus niger grown on sugarcane bagasse and stem, BP.MS; 13/03061-0 - Characterization and antioxidant capacity of fractions of lignin extracted from sugarcane bagasse, BP.DR; 12/19040-0 - Characterization of gene expression of Neurospora crassa in response to deconstruction of sugar cane bagasse, BP.PD; + associated scholarships 12/18859-5 - Development of enzymatic model for deconstruction of sugarcane bagasse cell wall, BP.PD; 11/14200-6 - Functional studies of microbial hemicellulases with potential biotechnological application in biorefinery of hemicellulosic biomass, BP.MS; 11/02169-7 - Aspergillus nidulans as a model for heterologous expression of cellulases and hemicellulases, BP.PD; 10/11469-1 - Library generation for biomass-conversion enzymes from soil metagenome, BP.DD - associated scholarships

Abstract

The gradual shift from petroleum to renewable biomass resources is generally seen as an important contribution to the development of a sustainable industrial society and the effective management of green house emissions. Lignocellulosic materiais are an abundant and low-cost source of stored energy in the biosphere. Thus, biomass conversion into feedstock sugars has moved towards the forefront of the biofuel industry. However, the saccharification of plant biomass is a complicated and lengthy process, mainly due to the inherent recalcitrance and the complex heterogeneity of the polymers comprising plant cell walls. Lignocellulosic biomass must go through an intensive pretreatment step, after which enzymes are used to break down the polysaccharides biomass into simple sugar suitable for fermentation and ethanol production. Aiming at the entire exploitation of the plant cell wall polysaccharides, as an environmentally renewable energy source, an extensive repertoire of hydrolytic enzymes would play a major role for biofuel production. The objective of this proposal is the generation of a toolkit of Iignocellulolytic enzymes with a wide range of biotechnological applications, including their use as players for the development of strategies for second generation ethanol production. The prospection of these enzymes will be done from soil metagenome, which contemplates a pioneering strategy towards the prospection of biomass conversion enzymes from microorganisms not conventionally cultivable. Additionally, this study may intensively contribute to the development of the field of bioenergy by improving techniques in rapid detection of hydrolysis using capillary electrophoresis and implementing heterologous gene expression in filamentous fungi. (AU)

Scientific publications

(28)

(References retrieved automatically from Web of Science and SciELO through information on FAPESP grants and their corresponding numbers as mentioned in the publications by the authors)

SQUINA, FABIO MARCIO; PRADE, ROLF ALEXANDER; WANG, HONGLIANG; MURAKAMI, MARIO TYAGO. Expression, purification, crystallization and preliminary crystallographic analysis of an endo-1,5-alpha-L-arabinanase from hyperthermophilic Thermotoga petrophila. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 65, n. 9, p. 902-905, Aug. 2009. (08/58037-9)

BRAGATTO, J.; SEGATO, F.; SQUINA, F. M.. Production of xylooligosaccharides (XOS) from delignified sugarcane bagasse by peroxide-HAc process using recombinant xylanase from Bacillus subtilis. INDUSTRIAL CROPS AND PRODUCTS, v. 51, p. 123-129, NOV 2013. (08/58037-9)

MANDELLI, F.; FRANCO CAIRO, J. P. L.; CITADINI, A. P. S.; BUECHLI, F.; ALVAREZ, T. M.; OLIVEIRA, R. J.; LEITE, V. B. P.; PAES LEME, A. F.; MERCADANTE, A. Z.; SQUINA, F. M.. The characterization of a thermostable and cambialistic superoxide dismutase from Thermus filiformis. Letters in Applied Microbiology, v. 57, n. 1, p. 40-46, JUL 2013. (08/58037-9, 11/17658-3)

FRANCO CAIRO, JOAO P. L.; CARAZZOLLE, MARCELO F.; LEONARDO, FLAVIA C.; MOFATTO, LUCIANA S.; BRENELLI, LIVIA B.; GONCALVES, THIAGO A.; UCHIMA, CRISTIANE A.; DOMINGUES, ROMANIA R.; ALVAREZ, THABATA M.; TRAMONTINA, ROBSON; et al. Expanding the Knowledge on Lignocellulolytic and Redox Enzymes of Worker and Soldier Castes from the Lower Termite Coptotermes gestroi. FRONTIERS IN MICROBIOLOGY, v. 7, OCT 13 2016. (15/06971-3, 14/20576-7, 14/50371-8, 12/19040-0, 14/10351-8, 11/20977-3, 13/03061-0, 10/11469-1, 08/58037-9)

COTA, JUNIO; CORREA, THAMY L. R.; DAMASIO, ANDRE R. L.; DIOGO, JOSE A.; HOFFMAM, ZAIRA B.; GARCIA, WANIUS; OLIVEIRA, LEANDRO C.; PRADE, ROLF A.; SQUINA, FABIO M.. Comparative analysis of three hyperthermophilic GH1 and GH3 family members with industrial potential. NEW BIOTECHNOLOGY, v. 32, n. 1, p. 13-20, JAN 25 2015. (12/21054-9, 11/13242-7, 08/58037-9, 10/18198-3)

ALVAREZ, THABATA M.; PAIVA, JOICE H.; RUIZ, DIEGO M.; CAIRO, JOAO PAULO L. F.; PEREIRA, ISABELA O.; PAIXAO, DOUGLAS A. A.; DE ALMEIDA, RODRIGO F.; TONOLI, CELISA C. C.; RULLER, ROBERTO; SANTOS, CAMILA R.; et al. Structure and Function of a Novel Cellulase 5 from Sugarcane Soil Metagenome. PLoS One, v. 8, n. 12, DEC 17 2013. (13/13309-0, 11/20977-3, 10/11469-1, 09/08312-6, 08/58037-9)

FRANCO CAIRO, JOAO PAULO L.; OLIVEIRA, LEANDRO C.; UCHIMA, CRISTIANE A.; ALVAREZ, THABATA M.; CITADINI, ANA PAULA DA S.; COTA, JUNIO; LEONARDO, FLAVIA COSTA; COSTA-LEONARDO, ANA M.; CARAZZOLLE, MARCELO F.; COSTA, FERNANDO F.; et al. Deciphering the synergism of endogenous glycoside hydrolase families 1 and 9 from Coptotermes gestroi. Insect Biochemistry and Molecular Biology, v. 43, n. 10, p. 970-981, OCT 2013. (12/19040-0, 11/08609-9, 11/20977-3, 11/13242-7, 10/11469-1, 08/58037-9)

COLUSSI, FRANCIELI; DA SILVA, VIVIAM M.; MILLER, IAN; COTA, JUNIO; DE OLIVEIRA, LEANDRO C.; DE OLIVEIRA NETO, MARIO; SQUINA, FABIO M.; GARCIA, WANIUS. Oligomeric state and structural stability of two hyperthermophilic beta-glucosidases from Thermotoga petrophila. Amino Acids, v. 47, n. 5, p. 937-948, MAY 2015. (12/21054-9, 08/58037-9, 12/03503-0, 11/13242-7)

DE OLIVEIRA, LEANDRO C.; DA SILVA, VIVIAM M.; COLUSSI, FRANCIELI; CABRAL, ALINE D.; DE OLIVEIRA NETO, MARIO; SQUINA, FABIO M.; GARCIA, WANIUS. Conformational Changes in a Hyperthermostable Glycoside Hydrolase: Enzymatic Activity Is a Consequence of the Loop Dynamics and Protonation Balance. PLoS One, v. 10, n. 2, FEB 27 2015. (12/21054-9, 08/58037-9, 12/03503-0, 11/13242-7)

SQUINA, FABIO MARCIO; PRADE, ROLF ALEXANDER; WANG, HONGLIANG; MURAKAMI, MARIO TYAGO. Expression, purification, crystallization and preliminary crystallographic analysis of an endo-1,5-alpha-L-arabinanase from hyperthermophilic Thermotoga petrophila. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 65, p. 4-pg., 2009-09-01. (08/58037-9)

CONTESINI, FABIANO JARES; LIBERATO, MARCELO VIZONA; RUBIO, MARCELO VENTURA; CALZADO, FELIPE; ZUBIETA, MARIANE PALUDETTI; RIANO-PACHON, DIEGO MAURICIO; SQUINA, FABIO MARCIO; BRACHT, FABRICIO; SKAF, MUNIR S.; DAMASIO, ANDRE RICARDO. Structural and functional characterization of a highly secreted alpha-L-arabinofuranosidase (GH62) from Aspergillus nidulans grown on sugarcane bagasse. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1865, n. 12, p. 1758-1769, DEC 2017. (13/08293-7, 12/20549-4, 14/04105-4, 14/15403-6, 13/24988-5, 14/23051-2, 08/58037-9)

HAHN SCHNEIDER, WILLIAN DANIEL; GONCALVES, THIAGO AUGUSTO; UCHIMA, CRISTIANE AKEMI; DOS REIS, LAISA; FONTANA, ROSELEI CLAUDETE; SQUINA, FABIO MARCIO; PINHEIRO DILLON, ALDO JOSE; CAMASSOLA, MARLI. Comparison of the production of enzymes to cell wall hydrolysis using different carbon sources by Penicillium echinulaturn strains and its hydrolysis potential for lignocelullosic biomass. Process Biochemistry, v. 66, p. 162-170, MAR 2018. (08/58037-9)

DE LIMA DAMASIO, ANDRE RICARDO; RUBIO, MARCELO VENTURA; GONCALVES, THIAGO AUGUSTO; PERSINOTI, GABRIELA FELIX; SEGATO, FERNANDO; PRADE, ROLF ALEXANDER; CONTESINI, FABIANO JARES; DE SOUZA, AMANDA PEREIRA; BUCKERIDGE, MARCOS SILVEIRA; SQUINA, FABIO MARCIO. Xyloglucan breakdown by endo-xyloglucanase family 74 from Aspergillus fumigatus. Applied Microbiology and Biotechnology, v. 101, n. 7, p. 2893-2903, APR 2017. (11/02169-7, 08/58037-9, 12/20549-4, 14/18714-2)

FRANCO CAIRO, JOAO PAULO L.; LEONARDO, FLAVIA C.; ALVAREZ, THABATA M.; RIBEIRO, DANIELA A.; BUECHLI, FERNANDA; COSTA-LEONARDO, ANA M.; CARAZZOLLE, MARCELO F.; COSTA, FERNANDO F.; PAES LEME, ADRIANA F.; PEREIRA, GONCALO A. G.; et al. Functional characterization and target discovery of glycoside hydrolases from the digestome of the lower termite Coptotermes gestroi. BIOTECHNOLOGY FOR BIOFUELS, v. 4, NOV 14 2011. (08/58037-9, 10/11469-1)

CAMPOS, BRUNA MEDEIA; LIBERATO, MARCELO VIZONA; ALVAREZ, THABATA MARIA; ZANPHORLIN, LETICIA MARIA; EMATSU, GABRIELA CRISTINA; BARUD, HERNANE; POLIKARPOV, IGOR; RULLER, ROBERTO; GILBERT, HARRY J.; DE MATTOS ZERI, ANA CAROLINA; et al. A Novel Carbohydrate-binding Module from Sugar Cane Soil Metagenome Featuring Unique Structural and Carbohydrate Affinity Properties. Journal of Biological Chemistry, v. 291, n. 45, p. 23734-23743, NOV 4 2016. (13/06336-0, 08/58037-9, 14/04105-4, 10/11469-1)

HAHN SCHNEIDER, WILLIAN DANIEL; GONCALVES, THIAGO AUGUSTO; UCHIMA, CRISTIANE AKEMI; COUGER, MATTHEW BRIAN; PRADE, ROLF; SQUINA, FABIO MARCIO; PINHEIRO DILLON, ALDO JOSE; CAMASSOLA, MARLI. Penicillium echinulatum secretome analysis reveals the fungi potential for degradation of lignocellulosic biomass. BIOTECHNOLOGY FOR BIOFUELS, v. 9, MAR 17 2016. (14/06923-6, 08/58037-9, 12/19040-0)

TRAMONTINA, ROBSON; FRANCO CAIRO, JOAO PAULO L.; LIBERATO, MARCELO V.; MANDELLI, FERNANDA; SOUSA, AMANDA; SANTOS, SAMANTHA; RABELO, SARITA CANDIDA; CAMPOS, BRUNA; IENCZAK, JACIANE; RULLER, ROBERTO; et al. The Coptotermes gestroi aldo-keto reductase: a multipurpose enzyme for biorefinery applications. BIOTECHNOLOGY FOR BIOFUELS, v. 10, JAN 3 2017. (13/06336-0, 12/20549-4, 14/20576-7, 14/04105-4, 08/58037-9)

PIMENTEL, AGNES C.; EMATSU, GABRIELA C. G.; LIBERATO, MARCELO V.; PAIXAO, DOUGLAS A. A.; FRANCO CAIRO, JOAO PAULO L.; MANDELLI, FERNANDA; TRAMONTINA, ROBSON; GANDIN, CESAR A.; DE OLIVEIRA NETO, MARIO; SQUINA, FABIO M.; et al. Biochemical and biophysical properties of a metagenome-derived GH5 endoglucanase displaying an unconventional domain architecture. International Journal of Biological Macromolecules, v. 99, p. 384-393, JUN 2017. (14/06923-6, 14/04105-4, 16/01926-2, 10/11469-1, 14/12861-3, 08/58037-9)

MANDELLI, F.; BRENELLI, L. B.; ALMEIDA, R. F.; GOLDBECK, R.; WOLF, L. D.; HOFFMAM, Z. B.; RULLER, R.; ROCHA, G. J. M.; MERCADANTE, A. Z.; SQUINA, F. M.. Simultaneous production of xylooligosaccharides and antioxidant compounds from sugarcane bagasse via enzymatic hydrolysis. INDUSTRIAL CROPS AND PRODUCTS, v. 52, p. 770-775, JAN 2014. (13/03061-0, 08/58037-9, 11/14200-6, 12/18859-5)

ALVAREZ, THABATA MARIA; LIBERATO, MARCELO VIZONA; FRANCO CAIRO, JOO PAULO L.; PAIXO, DOUGLAS A. A.; CAMPOS, BRUNA M.; FERREIRA, MARCEL R.; ALMEIDA, RODRIGO F.; PEREIRA, ISABELA O.; BERNARDES, AMANDA; EMATSU, GABRIELA C. G.; et al. A Novel Member of GH16 Family Derived from Sugarcane Soil Metagenome. Applied Biochemistry and Biotechnology, v. 177, n. 2, p. 304-317, SEP 2015. (08/58037-9, 10/11469-1)

DAMASIO, ANDRE R. L.; RUBIO, MARCELO V.; OLIVEIRA, LEANDRO C.; SEGATO, FERNANDO; DIAS, BRUNO A.; CITADINI, ANA P.; PAIXAO, DOUGLAS A.; SQUINA, FABIO M.. Understanding the Function of Conserved Variations in the Catalytic Loops of Fungal Glycoside Hydrolase Family 12. Biotechnology and Bioengineering, v. 111, n. 8, p. 1494-1505, AUG 2014. (11/13242-7, 08/58037-9, 12/12859-3)

GOLDBECK, ROSANA; DAMASIO, ANDRE R. L.; GONCALVES, THIAGO A.; MACHADO, CARLA B.; PAIXAO, DOUGLAS A. A.; WOLF, LUCIA D.; MANDELLI, FERNANDA; ROCHA, GEORGE J. M.; RULLER, ROBERTO; SQUINA, FABIO M.. Development of hemicellulolytic enzyme mixtures for plant biomass deconstruction on target biotechnological applications. Applied Microbiology and Biotechnology, v. 98, n. 20, p. 8513-8525, OCT 2014. (13/18910-3, 08/58037-9, 12/18859-5)

SEGATO, FERNANDO; DAMASIO, ANDRE R. L.; DE LUCAS, ROSYMAR C.; SQUINA, FABIO M.; PRADE, ROLF A.. Genomics Review of Holocellulose Deconstruction by Aspergilli. MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS, v. 78, n. 4, p. 588-613, DEC 2014. (13/18910-3, 12/20549-4, 08/58037-9, 10/18198-3)

ALVAREZ, THABATA M.; GOLDBECK, ROSANA; DOS SANTOS, CAMILA RAMOS; PAIXAO, DOUGLAS A. A.; GONCALVES, THIAGO A.; FRANCO CAIRO, JOAO PAULO L.; ALMEIDA, RODRIGO FERREIRA; PEREIRA, ISABELA DE OLIVEIRA; JACKSON, GEORGE; COTA, JUNIO; et al. Development and Biotechnological Application of a Novel Endoxylanase Family GH10 Identified from Sugarcane Soil Metagenome. PLoS One, v. 8, n. 7, JUL 29 2013. (11/20977-3, 08/58037-9, 10/11469-1)

DAMASIO, ANDRE R. L.; PINTO BRAGA, CLEITON MARCIO; BRENELLI, LIVIA B.; CITADINI, ANA PAULA; MANDELLI, FERNANDA; COTA, JUNIO; DE ALMEIDA, RODRIGO FERREIRA; SALVADOR, VICTOR HUGO; ALVAREDO PAIXAO, DOUGLAS ANTONIO; SEGATO, FERNANDO; et al. Biomass-to-bio-products application of feruloyl esterase from Aspergillus clavatus. Applied Microbiology and Biotechnology, v. 97, n. 15, p. 6759-6767, AUG 2013. (11/02169-7, 09/17956-4, 08/58037-9)

COTA, JUNIO; OLIVEIRA, LEANDRO C.; DAMASIO, ANDRE R. L.; CITADINI, ANA P.; HOFFMAM, ZAIRA B.; ALVAREZ, THABATA M.; CODIMA, CARLA A.; LEITE, VITOR B. P.; PASTORE, GLAUCIA; DE OLIVEIRA-NETO, MARIO; et al. Assembling a xylanase-lichenase chimera through all-atom molecular dynamics simulations. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1834, n. 8, p. 1492-1500, AUG 2013. (11/13242-7, 11/02169-7, 08/58037-9)

HOFFMAM, ZAIRA B.; OLIVEIRA, LEANDRO C.; COTA, JUNIO; ALVAREZ, THABATA M.; DIOGO, JOS A.; NETO, MARIO DE OLIVEIRA; CITADINI, ANA PAULA S.; LEITE, VITOR B. P.; SQUINA, FABIO M.; MURAKAMI, MARIO T.; et al. Characterization of a Hexameric Exo-Acting GH51 alpha-l-Arabinofuranosidase from the Mesophilic Bacillus subtilis. MOLECULAR BIOTECHNOLOGY, v. 55, n. 3, p. 260-267, NOV 2013. (10/51890-8, 11/14200-6, 11/13242-7, 08/58037-9, 11/17658-3)

DIOGO, JOSE A.; HOFFMAM, ZAIRA B.; ZANPHORLIN, LETICIA M.; COTA, JUNIO; MACHADO, CARLA B.; WOLF, LUCIA D.; SQUINA, FABIO; DAMASIO, ANDRE R. L.; MURAKAMI, MARIO T.; RULLER, ROBERTO. Development of a chimeric hemicellulase to enhance the xylose production and thermotolerance. Enzyme and Microbial Technology, v. 69, p. 31-37, FEB 2015. (11/14200-6, 13/10443-7, 08/58037-9)

Filed patent(s) as a result of this research project