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Structural and functional studies of enzymes that participate in complex carbohydrates synthesis and degradation

Grant number: 15/13684-0
Support type:Research Projects - Thematic Grants
Duration: March 01, 2017 - February 28, 2022
Field of knowledge:Biological Sciences - Biophysics
Principal Investigator:Igor Polikarpov
Grantee:Igor Polikarpov
Home Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
Co-Principal Investigators:Francisco Eduardo Gontijo Guimaraes
Assoc. researchers:Alessandro Silva Nascimento ; Camila Alves de Rezende ; Eduardo Ribeiro de Azevedo ; Marcos Silveira Buckeridge ; Munir Salomao Skaf
Associated grant(s):18/22300-0 - Synergistic activities to boost enzymatic lignocellulose oxidation using light and LPMOs, AP.R
Associated scholarship(s):18/24705-7 - Structural and functional studies of enzymes PARTICPATE in complex carbohydrates synthesis and degradation, BP.PD
19/10942-0 - Heterologous expression and characterization of xilanases that belong to GH10 and GH11 families and evaluation of its application in xilan cleavage leading to xylooligossacharides production from lignocelulosic biomass, BP.IC
18/00082-0 - Structural and biochemical studies of enzymes involved in the degradation of glucuronoarabinoxylan (GAX), BP.IC
18/02028-3 - Structural and functional studies of enzymes participate in complex carbohydrates synthesis and degradation, BP.TT

Abstract

Carbohydrates, such as mono- and oligosaccharides, polysaccharides and glycoconjugates, play extremely important roles in all forms of life, participating in host-pathogen interactions, signal transduction, inflammation, intracellular trafficking and differentiation. In addition, carbohydrates make up about three quarters of renewable plant biomass (~ 135 billion tons/year) whose cell walls and reserve carbohydrates represent a sustainable source of energy and renewable materials. However, the diversity of carbohydrates and the complexity of the plant cell walls turn their enzymatic hydrolysis into simple sugars for biofuel production and "green" chemicals into a difficult task. Our current understanding of synthesis and enzymatic degradation of complex carbohydrates in the cell wall context are at least incomplete. Less than 3.8% of enzymes and auxiliary proteins involved in synthesis and degradation of carbohydrates are currently characterized biochemically and less than 0.42% of them are characterized structurally (Lombard et al., Nucl. Acids Res. (2014) 42: D490 - D495). Therefore, in this project we propose to conduct a systematic structural and functional study of the enzymes with potential in depolymerization and, also synthesis of polysaccharides, aiming to understand their specific mechanisms of action in the context of cell wall and also against isolated carbohydrates. The results of this study will shed light on the fundamental questions about enzymatic degradation of biopolymers and may be important for biotechnological applications such as enzymatic hydrolysis of lignocellulosic materials and their transformation in platform molecules and biofuels, among others. (AU)

Scientific publications (25)
(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)
TOMAZINI, ATILIO; HIGASI, PAULA; MANZINE, LIVIA R.; STOTT, MATTHEW; SPARLING, RICHARD; LEVIN, DAVID B.; POLIKARPOV, IGOR. A novel thermostable GH5 beta-xylosidase from Thermogemmatispora sp. T81. NEW BIOTECHNOLOGY, v. 53, p. 57-64, NOV 25 2019. Web of Science Citations: 0.
DO ESPIRITO SANTO, MELISSA CRISTINA; CARDOSO, ELIANO BRITO; GONTIJO GUIMARAES, FRANCISCO EDUARDO; DEAZEVEDO, EDUARDO RIBEIRO; DA CUNHA, GIOVANNI PARO; NOVOTNY, ETELVINO HENRIQUE; ARNOLDI PELLEGRINI, VANESSA DE OLIVEIRA; CHANDEL, ANUJ KUMAR; LUCIANO SILVEIRA, MARCOS HENRIQUE; POLIKARPOV, IGOR. Multifaceted characterization of sugarcane bagasse under different steam explosion severity conditions leading to distinct enzymatic hydrolysis yields. INDUSTRIAL CROPS AND PRODUCTS, v. 139, NOV 1 2019. Web of Science Citations: 0.
EVANGELISTA, DANILO ELTON; ARNOLDI PELLEGRIN, VANESSA DE OLIVEIRA; SANTO, MELISSA ESPIRITO; MCQUEEN-MASON, SIMON; BRUCE, NEIL C.; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS shape of a novel GH11 exo-1,4-beta-xylanase identified in a microbial consortium. Applied Microbiology and Biotechnology, v. 103, n. 19, p. 8035-8049, OCT 2019. Web of Science Citations: 0.
SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Structural insights into the hydrolysis pattern and molecular dynamics simulations of GH45 subfamily a endoglucanase from Neurospora crassa OR74A. Biochimie, v. 165, p. 275-284, OCT 2019. Web of Science Citations: 0.
PUHL, ANA C.; PRATES, ERICA T.; ROSSETO, FLAVIO R.; MANZINE, LIVIA R.; STANKOVIC, IVANA; DE ARAUJO, SIMARA S.; ALVAREZ, THABATA M.; SQUINA, FABIO M.; SKAF, MUNIR S.; POLIKARPOV, IGOR. Crystallographic structure and molecular dynamics simulations of the major endoglucanase from Xanthomonas campestris pv. campestris shed light on its oligosaccharide products release pattern. International Journal of Biological Macromolecules, v. 136, p. 493-502, SEP 1 2019. Web of Science Citations: 0.
DE AZEVEDO, ERIKA CHANG; NASCIMENTO, ALESSANDRO S. Energy landscape of the domain movement in Staphylococcus aureus UDP-N-acetylglucosamine 2-epimerase. Journal of Structural Biology, v. 207, n. 2, p. 158-168, AUG 1 2019. Web of Science Citations: 0.
SARTORI, GERALDO RODRIGUES; NASCIMENTO, ALESSANDRO S. Comparative Analysis of Electrostatic Models for Ligand Docking. FRONTIERS IN MOLECULAR BIOSCIENCES, v. 6, JUL 3 2019. Web of Science Citations: 0.
SONODA, MILTON T.; GODOY, ANDRE S.; PELLEGRINI, VANESSA O. A.; KADOWAKI, MARCO A. S.; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Structure and dynamics of Trichoderma harzianum Cel7B suggest molecular architecture adaptations required for a wide spectrum of activities on plant cell wall polysaccharides. BIOCHIMICA ET BIOPHYSICA ACTA-GENERAL SUBJECTS, v. 1863, n. 6, p. 1015-1026, JUN 2019. Web of Science Citations: 0.
BERNARDES, A.; PELLEGRINI, V. O. A.; CURTOLO, F.; CAMILO, C. M.; MELLO, B. L.; JOHNS, M. A.; SCOTT, J. L.; GUIMARAES, F. E. C.; POLIKARPOV, I. Carbohydrate binding modules enhance cellulose enzymatic hydrolysis by increasing access of cellulases to the substrate. Carbohydrate Polymers, v. 211, p. 57-68, MAY 1 2019. Web of Science Citations: 1.
VIEIRA, F. R.; PECCHIA, J. A.; SEGATO, F.; POLIKARPOV, I. Exploring oyster mushroom (Pleurotus ostreatus) substrate preparation by varying phase I composting time: changes in bacterial communities and physicochemical composition of biomass impacting mushroom yields. Journal of Applied Microbiology, v. 126, n. 3, p. 931-944, MAR 2019. Web of Science Citations: 0.
DE ARAUJO, EVANDRO ARES; DE OLIVEIRA NETO, MARIO; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS structure of two-domain endoglucanase BlCel9 from Bacillus licheniformis. Applied Microbiology and Biotechnology, v. 103, n. 3, p. 1275-1287, FEB 2019. Web of Science Citations: 1.
PIIADOV, VASSILI; DE ARAUJO, EVANDRO ARES; OLIVEIRA NETO, MARIO; CRAIEVICH, ALDO FELIX; POLIKARPOV, IGOR. SAXSMoW 2.0: Online calculator of the molecular weight of proteins in dilute solution from experimental SAXS data measured on a relative scale. Protein Science, v. 28, n. 2, p. 454-463, FEB 2019. Web of Science Citations: 5.
BERTO, GABRIELA LEILA; VELASCO, JOSMAN; CABOS RIBEIRO, CAIO TASSO; ZANPHORLIN, LETICIA MARIA; DOMINGUES, MARIANE NORONHA; MURAKAMI, MARIO TYAGO; POLIKARPOV, IGOR; DE OLIVEIRA, LEANDRO CRISTANTE; FERRAZ, ANDRE; SEGATO, FERNANDO. Functional characterization and comparative analysis of two heterologous endoglucanases from diverging subfamilies of glycosyl hydrolase family 45. Enzyme and Microbial Technology, v. 120, p. 23-35, JAN 2019. Web of Science Citations: 2.
BESSER, KATRIN; MALYON, GRAHAM P.; EBORALL, WILLIAM S.; DA CUNHA, GIOVANNI PARO; FILGUEIRAS, JEFFERSON G.; DOWLE, ADAM; GARCIA, LOURDES CRUZ; PAGE, SAMUEL J.; DUPREE, RAY; KERN, MARCELO; GOMEZ, LEONARDO D.; LI, YI; ELIAS, LUISA; SABBADIN, FEDERICO; MOHAMAD, SHAZA E.; PESANTE, GIOVANNA; STEELE-KING, CLARE; DE AZEVEDO, EDUARDO RIBEIRO; POLIKARPOV, IGOR; DUPREE, PAUL; CRAGG, SIMON M.; BRUCE, NEIL C.; MCQUEEN-MASON, SIMON J. Hemocyanin facilitates lignocellulose digestion by wood-boring marine crustaceans. NATURE COMMUNICATIONS, v. 9, DEC 3 2018. Web of Science Citations: 2.
FARRO, ERICK GIANCARLO S.; LEITE, ANA ELISA T.; SILVA, ISABELA A.; FILGUEIRAS, JEFFERSON G.; DE AZEVEDO, EDUARDO R.; POLIKARPOV, IGOR; NASCIMENTO, ALESSANDRO S. GH43 endo-arabinanase from Bacillus licheniformis: Structure, activity and unexpected synergistic effect on cellulose enzymatic hydrolysis. International Journal of Biological Macromolecules, v. 117, p. 7-16, OCT 1 2018. Web of Science Citations: 1.
SEIKI KADOWAKI, MARCO ANTONIO; DE GODOY, MARIANA ORTIZ; KUMAGAI, PATRICIA SUEMY; DA COSTA-FILHO, ANTONIO JOSE; MORT, ANDREW; PRADE, ROLF ALEXANDER; POLIKARPOV, IGOR. Characterization of a New Glyoxal Oxidase from the Thermophilic Fungus Myceliophthora thermophila M77: Hydrogen Peroxide Production Retained in 5-Hydroxymethylfurfural Oxidation. CATALYSTS, v. 8, n. 10 OCT 2018. Web of Science Citations: 0.
KADOWAKI, MARCO A. S.; VARNAI, ANIKO; JAMESON, JOHN-KRISTIAN; LEITE, ANA E. T.; COSTA-FILHO, ANTONIO J.; KUMAGAI, PATRICIA S.; PRADE, ROLF A.; POLIKARPOV, IGOR; EIJSINK, VINCENT G. H. Functional characterization of a lytic polysaccharide monooxygenase from the thermophilic fungus Myceliophthora thermophila. PLoS One, v. 13, n. 8 AUG 20 2018. Web of Science Citations: 3.
DE ARAUJO, EVANDRO ARES; MANZINE, LIVIA REGINA; PIIADOV, VASSILI; SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Biochemical characterization, low-resolution SAXS structure and an enzymatic cleavage pattern of BlCel48 from Bacillus licheniformis. International Journal of Biological Macromolecules, v. 111, p. 302-310, MAY 2018. Web of Science Citations: 1.
EVANGELISTA, DANILO ELTON; SEIKI KADOWAKI, MARCO ANTONIO; MELLO, BRUNO LUAN; POLIKARPOV, IGOR. Biochemical and biophysical characterization of novel GH10 xylanase prospected from a sugar cane bagasse compost-derived microbial consortia. International Journal of Biological Macromolecules, v. 109, p. 560-568, APR 2018. Web of Science Citations: 4.
PELLEGRINI, VANESSA O. A.; BERNARDES, AMANDA; REZENDE, CAMILA A.; POLIKARPOV, IGOR. Cellulose fiber size defines efficiency of enzymatic hydrolysis and impacts degree of synergy between endo- and exoglucanases. Cellulose, v. 25, n. 3, p. 1865-1881, MAR 2018. Web of Science Citations: 2.
SANTO, MELISSA ESPIRITO; REZENDE, CAMILA A.; BERNARDINELLI, OIGRES D.; PEREIRA, JR., NEI; CURVELO, ANTONIO A. S.; DEAZEVEDO, EDUARDO R.; GUIMARAES, FRANSCISCO E. G.; POLIKARPOV, IGOR. Structural and compositional changes in sugarcane bagasse subjected to hydrothermal and organosolv pretreatments and their impacts on enzymatic hydrolysis. INDUSTRIAL CROPS AND PRODUCTS, v. 113, p. 64-74, MAR 2018. Web of Science Citations: 11.
GODOY, ANDRE S.; PEREIRA, CAROLINE S.; RAMIA, MARINA PAGLIONE; SILVEIRA, RODRIGO L.; CAMILO, CESAR M.; KADOWAKI, MARCO A.; LANGE, LENE; BUSK, PETER K.; NASCIMENTO, ALESSANDRO S.; SKAF, MUNIR S.; POLIKARPOV, IGOR. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. SCIENTIFIC REPORTS, v. 8, FEB 27 2018. Web of Science Citations: 3.
KADOWAKI, MARCO A. S.; HIGASI, PAULA; DE GODOY, MARIANA O.; PRADE, ROLF A.; POLIKARPOV, IGOR. Biochemical and structural insights into a thermostable cellobiohydrolase from Myceliophthora thermophila. FEBS Journal, v. 285, n. 3, p. 559-579, FEB 2018. Web of Science Citations: 1.
MELLO, BRUNO L.; ALESSI, ANNA M.; RIANO-PACHON, DIEGO M.; DEAZEVEDO, EDUARDO R.; GUIMARAES, FRANCISCO E. G.; ESPIRITO SANTO, MELISSA C.; MCQUEEN-MASON, SIMON; BRUCE, NEIL C.; POLIKARPOV, IGOR. Targeted metatranscriptomics of compost-derived consortia reveals a GH11 exerting an unusual exo-1,4-beta-xylanase activity. BIOTECHNOLOGY FOR BIOFUELS, v. 10, NOV 2 2017. Web of Science Citations: 7.
EVANGELISTA, DANILO ELTON; DE ARAUJO, EVANDRO A.; OLIVEIRA NETO, MARIO; SEIKI KADOWAKI, MARCO ANTONIO; POLIKARPOV, IGOR. Biochemical characterization and low-resolution SAXS structure of an exopolygalacturonase from Bacillus licheniformis. NEW BIOTECHNOLOGY, v. 40, n. B, p. 268-274, JAN 25 2017. Web of Science Citations: 3.

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