Center of Biological and Industrial Processes for Biofuels - CeProBIO

• Grant number: 09/52840-7
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Thematic Grants
• Duration: July 01, 2011 - June 30, 2015
• Field of knowledge: Biological Sciences - Biochemistry
• Convênio/Acordo: CNPq - Cooperation Brazil-European Commission Program in ​​Second Generation Biofuels
• Principal Investigator: Igor Polikarpov
• Grantee: Igor Polikarpov
• Host Institution: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brazil
• Associated grant(s): 14/50241-7 - Establishing of a joint X-ray crystallographic pipeline for structural analysis of membrane transporters, AP.R
• Associated scholarship(s): 12/22802-9 - Functional and Structural Studies of Carbohydrate Binding Modules of Glycosil Hydrolases, BP.PD

Abstract

CeProBIO is proposing a model of industrial cellulosic ethanol production capable of integration into existing production arrangements present in developed Brazilian regions that can be next implemented in areas where the agro-industry infrastructure is still being put into effect and consolidated. This innovative model provides a drastic decrease and possibly of even total elimination of the need for any input of fossil fuel through the efficient use of waste, effluents and emissions of the bioethanol production and concomitant production of added-value chemicals. Currently, cellulosic ethanol industrial production is not economically viable. Its economic, environmental and social sustainability can only be achieved through an orchestrated effort of initiatives for fundamental, applied and technological scientific research. For this, the CeProBIO is structured into eight major projects listed above, based in the areas of genetics, genomics, molecular and structural biology, physics, chemistry, bioinformatics and computing, agronomic engineering, microbiology, enzymes, and advanced industrial processes. Thus, the mission of CeProBIO is promoting an integrated multidisciplinary and transdisciplinary approach. This entails extending traditional areas to allow for an unprecedented synergy between the groups, which is absolutely necessary for solving problems arising from developing the technology needed for large scale second generation biofuels production. The main problem in ethanol production from cellulosic biomass entails dealing with biomass recalcitrance during the hydrolysis process. For efficient conversion of biomass into simple sugars (pentose and hexose) and their co-products (lignin, waxes, etc.), it is essential to know the cell wall physico-chemical composition and structure. In order to acquire these insights, we need first to acquire a deep understanding of plant genetics and genomics. Projects 1 and 2 are focused on these two goals having sugar cane as their main object of study. Project 3 aims to study other types of biomass such as Panicum maximum Jacq, Brachiaria brisantha, Pennisetum purpureum, wood and eucalyptus bark, Sclerolobium paraense Schizolobium amazonicum and their applicability for cellulosic ethanol production. In addition, Project 4 aims to deeply understand the physical and chemical structures of plant cell walls. In addition, this project deals with questions relating to their synthesis and decomposition. Biomass hydrolysis requires the development of better technology especially targeted to optimizing cellulose, hemicellulose and lignin enzymatic hydrolysis. This development is dependent on the identification and manipulation of microorganisms (mainly fungi and bacteria), enzymes (exo-and endoglucanase, beta-glycosidases) and other auxiliary proteins identification and characterization, and improvement of biomass pre-treatment and hydrolytic process integration. These studies are part of Project 5. In Project 6, we want to establish and implement advanced technological processes for second generation bioethanol production on an industrial scale, optimizing its basic operations (pre-treatment, enzyme preparations production, hydrolysis, fermentation and distillation). Our anticipated outcome is improved performance and added value to the process byproducts. It is part our vision that it is highly beneficial to integrate the first and second-generation cellulosic ethanol production so that it will be possible to continue to use the same loading industrial machinery, mechanical pre-treatment facilities and fermentation and distillation processes of the existing Brazilian first-generation ethanol factories. This also applies to the thermal and electrical systems of the factory. However, we must still resolve several serious scientific and technological challenges. They include pentose fermentation, fermentation inhibition by toxic compounds originating from biomass pre-treatment and optimizing use of by-products from industrial processes, aims which also make part of Project 6. In this project, the vinasse derived from the industrial process will be treated by anaerobic bacterial fermentation to produce biogases fuels (hydrogen, methane) and organic acids (lactic acid, acetic acid and others). The latter serve as inputs for biodegradable plastics production and other "green" chemical products. This technology will contribute to improving our model of industrial closed cycle implementation. To better use wastes generated by the fermentation process, we will develop and implement technological processes for biodiesel production by microalgae (Project 7). In this project we aim to develop an industrial photo bioreactor for microalgae cultivation at extremely high concentrations using vinasse and CO2 generated in the bioethanol production process. Although microalgae are able to accumulate up to 70% of its dry weight in fat, their production demands a very massive cultivation area for the large quantities needed of algal biomass production. Therefore, the development of efficient photo bioreactors able to ensure efficient and large algal mass-growth for biodiesel production is a challenging engineering problem. The bioethanol waste recovery utilization in algal biodiesel production stemming from our industrial design will not only reduce fossil fuels use (diesel used in the transport and collection of sugar cane) but it will also reduce the emission of carbon dioxide gas in the first and second generation phases of bioethanol production. It is important to note that technologies for biofuels production from algae biomass may be linked not only to the bioethanol production, but also to several other industrial processes and energy generation (such as thermoelectric, for example). Optimization of enzymatic catalysis in biodiesel production is also part of project 7. Finally, Project 8 studies various aspects of environmental sustainability and socioeconomic issues. These projects are deeply integrated with the sister SUNLIBB proposal from the European Union. Their plan is to improve the biomass quality and the economic efficiency of biomass conversion into biofuels through obtaining more valuable aggregated co-products, improvements in the conversion process (pre-treatment, identification of new enzymatic activities, integrated process development and computational models for biorefineries). In deference to our project, SUNLIBB will also look at the social and economic impact problems arising from industrial cellulosic ethanol production. Their project complementarity will be maintained through choosing different main biomass sources (sugar cane at CeProBIO and miscanthus in SUNLlBB). In each project, joint studies will identify needed enzymes and new enzyme cocktail types required for: 1) pre-treatment and large-scale saccharification processes; 2) analysis of plant cell wall structures; 3) extraction of co-products and most valuable waxes and chemical compounds. (AU)

Scientific publications

(32)

(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)

GODOY, ANDRE SCHUTZER; CAMILO, CESAR MOISES; KADOWAKI, MARCO ANTONIO; MUNIZ, HELOISA DOS S.; SANTO, MELISSA ESPIRITO; MURAKAMI, MARIO TYAGO; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Crystal structure of beta 1 -> 6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by alpha-galactose. FEBS Journal, v. 283, n. 22, p. 4097-4112, NOV 2016. (09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9, 14/06565-2, 11/05712-3)

LIBERATO, MARCELO VIZONA; GENEROSO, WESLEY CARDOSO; MALAGO, JR., WILSON; HENRIQUE-SILVA, FLAVIO; POLIKARPOV, IGOR. Crystallization and preliminary X-ray diffraction analysis of endoglucanase III from Trichoderma harzianum. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 68, n. 3, p. 306-309, MAR 2012. (09/14333-6, 09/52840-7)

GRANDIS, ADRIANA; LEITE, DEBORA C. C.; TAVARES, EVELINE Q. P.; ARENQUE-MUSA, BRUNA C.; GAIARSA, JONAS W.; MARTINS, MARINA C. M.; DE SOUZA, AMANDA P.; GOMEZ, LEONARDO D.; FABBRI, CLAUDIA; MATTEI, BENEDETTA; et al. Cell wall hydrolases act in concert during aerenchyma development in sugarcane roots. ANNALS OF BOTANY, v. 124, n. 6, SI, p. 1067-1089, NOV 4 2019. (14/50884-5, 09/52840-7, 10/17104-5, 10/17070-3, 08/57908-6)

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. (09/52840-7, 15/13684-0, 11/20505-4)

GRANDIS, ADRIANA; ARENQUE-MUSA, BRUNA C.; MARTINS, MARINA C. M.; MACIEL, THAIS OLIVAR; SIMISTER, RACHAEL; GOMEZ, LEONARDO D.; BUCKERIDGE, MARCOS S.. Senna reticulata: a Viable Option for Bioenergy Production in the Amazonian Region. BioEnergy Research, v. 14, n. 1, p. 91-105, MAR 2021. (14/50884-5, 18/03764-5, 08/57908-6, 09/52840-7)

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. (11/20505-4, 15/13684-0, 09/52840-7, 10/52362-5, 11/21608-1, 15/50590-4)

SEGATO, FERNANDO; DIAS, BRUNO; BERTO, GABRIELA L.; DE OLIVEIRA, DYONI M.; DE SOUZA, FLAVIO H. M.; CITADINI, ANA PAULA; MURAKAMI, MARIO T.; DAMASIO, ANDRE R. L.; SQUINA, FABIO MARCIO; POLIKARPOV, IGOR. Cloning, heterologous expression and biochemical characterization of a non-specific endoglucanase family 12 from Aspergillus terreus NIH2624. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS, v. 1865, n. 4, p. 395-403, APR 2017. (09/52840-7, 14/18714-2, 13/21545-5)

LEITE, D. C. C.; GRANDIS, A.; TAVARES, E. Q. P.; PIOVEZANI, A. R.; PATTATHIL, S.; AVCI, U.; ROSSINI, A.; CAMBLER, A.; DE SOUZA, A. P.; HAHN, M. G.; et al. Cell wall changes during the formation of aerenchyma in sugarcane roots. ANNALS OF BOTANY, v. 120, n. 5, p. 16-pg., 2017-11-01. (09/52840-7, 10/17104-5, 08/57908-6, 10/12833-9, 10/17070-3)

NASCIMENTO, ALESSANDRO S.; MUNIZ, JOAO RENATO C.; APARICIO, RICARDO; GOLUBEV, ALEXANDER M.; POLIKARPOV, IGOR. Insights into the structure and function of fungal beta-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. FEBS Journal, v. 281, n. 18, p. 14-pg., 2014-09-01. (09/52840-7, 08/56255-9)

LIBERATO, MARCELO V.; SILVEIRA, RODRIGO L.; PRATES, ERICA T.; DE ARAUJO, EVANDRO A.; PELLEGRINI, VANESSA O. A.; CAMILO, CESAR M.; KADOWAKI, MARCO A.; NETO, MARIO DE O.; POPOV, ALEXANDER; SKAF, MUNIR S.; et al. Molecular characterization of a family 5 glycoside hydrolase suggests an induced-fit enzymatic mechanism. SCIENTIFIC REPORTS, v. 6, APR 1 2016. (13/08293-7, 09/52840-7, 10/18773-8, 13/15582-5, 08/56255-9, 14/10448-1)

LIMA, LEONARDO H. F.; SERPA, VIVIANE I.; ROSSETO, FLAVIO R.; SARTORI, GERALDO RODRIGUES; DE OLIVEIRA NETO, MARIO; MARTINEZ, LEANDRO; POLIKARPOV, IGOR. Small-angle X-ray scattering and structural modeling of full-length: cellobiohydrolase I from Trichoderma harzianum. Cellulose, v. 20, n. 4, p. 1573-1585, AUG 2013. (09/52840-7, 07/08706-9, 08/56255-9, 08/05637-9, 10/16947-9)

MIOTTO, LIS SCHWARTZ; DE REZENDE, CAMILA ALVES; BERNARDES, AMANDA; SERPA, VIVIANE ISABEL; TSANG, ADRIAN; POLIKARPOV, IGOR. The Characterization of the Endoglucanase Cel12A from Gloeophyllum trabeum Reveals an Enzyme Highly Active on beta-Glucan. PLoS One, v. 9, n. 9, SEP 24 2014. (09/52840-7, 08/56255-9, 12/22802-9, 10/52362-5, 09/08233-9)

AFIONIS, STAVROS; STRINGER, LINDSAY C.; FAVRETTO, NICOLA; TOMEI, JULIA; BUCKERIDGE, MARCOS S.. Unpacking Brazil's Leadership in the Global Biofuels Arena: Brazilian Ethanol Diplomacy in Africa. GLOBAL ENVIRONMENTAL POLITICS, v. 16, n. 3, p. 127-150, AUG 2016. (08/57908-6, 09/52840-7)

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. (13/21545-5, 14/18714-2, 15/13684-0, 09/52840-7)

GODOY, ANDRE SCHUTZER; CAMILO, CESAR MOISES; KADOWAKI, MARCO ANTONIO; MUNIZ, HELOISA DOS S.; SANTO, MELISSA ESPIRITO; MURAKAMI, MARIO TYAGO; NASCIMENTO, ALESSANDRO S.; POLIKARPOV, IGOR. Crystal structure of beta 1 -> 6-galactosidase from Bifidobacterium bifidum S17: trimeric architecture, molecular determinants of the enzymatic activity and its inhibition by alpha-galactose. FEBS Journal, v. 283, n. 22, p. 16-pg., 2016-11-01. (11/05712-3, 09/52840-7, 11/20505-4, 14/06565-2, 08/56255-9, 09/05328-9)

GODOY, ANDRE S.; DE LIMA, MARIANA Z. T.; CAMILO, CESAR M.; POLIKARPOV, IGOR. Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 72, n. 4, p. 288-293, APR 2016. (09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9, 11/05712-3)

NASCIMENTO, ALESSANDRO S.; MUNIZ, JOAO RENATO C.; APARICIO, RICARDO; GOLUBEV, ALEXANDER M.; POLIKARPOV, IGOR. Insights into the structure and function of fungal beta-mannosidases from glycoside hydrolase family 2 based on multiple crystal structures of the Trichoderma harzianum enzyme. FEBS Journal, v. 281, n. 18, SI, p. 4165-4178, SEP 2014. (08/56255-9, 09/52840-7)

LEITE, D. C. C.; GRANDIS, A.; TAVARES, E. Q. P.; PIOVEZANI, A. R.; PATTATHIL, S.; AVCI, U.; ROSSINI, A.; CAMBLER, A.; DE SOUZA, A. P.; HAHN, M. G.; et al. Cell wall changes during the formation of aerenchyma in sugarcane roots. ANNALS OF BOTANY, v. 120, n. 5, SI, p. 693-708, NOV 2017. (09/52840-7, 10/12833-9, 10/17104-5, 10/17070-3, 08/57908-6)

SEGATO, FERNANDO; BERTO, GABRIELA L.; DE ARAUJO, EVANDRO ARES; MUNIZ, JOAO RENATO; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-beta-1,4-glucanase from glycoside hydrolase family 12. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 70, n. 2, p. 267-270, FEB 2014. (08/05637-9, 09/52840-7, 10/16947-9)

DOS REIS, CAIO VINICIUS; BERNARDES, AMANDA; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Bifidobacterium adolescentis xylose isomerase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, n. 5, p. 588-591, MAY 2013. (08/56255-9, 09/52840-7)

TEXTOR, LARISSA C.; SANTOS, JADEMILSON C.; HIDALGO CUADRADO, NAZARET; ROIG, MANUEL G.; ZHADAN, GALINA G.; SHNYROV, VALERY L.; POLIKARPOV, IGOR. Purification, crystallization and preliminary crystallographic analysis of peroxidase from the palm tree Chamaerops excelsa. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 67, n. 12, p. 1641-1644, DEC 2011. (09/14333-6, 09/52840-7)

TAVARES, E. Q. P.; GRANDIS, A.; LEMBKE, C. G.; SOUZA, G. M.; PURGATTO, E.; DE SOUZA, A. P.; BUCKERIDGE, M. S.. Roles of auxin and ethylene in aerenchyma formation in sugarcane roots. PLANT SIGNALING & BEHAVIOR, v. 13, n. 3, 2018. (09/52840-7, 13/16225-1, 11/07586-5, 10/17104-5, 08/57908-6)

PELLEGRINI, VANESSA O. A.; SERPA, VIVIANE ISABEL; GODOY, ANDRE S.; CAMILO, CESAR M.; BERNARDES, AMANDA; REZENDE, CAMILA A.; PEREIRA JUNIOR, NEI; CAIRO, JOAO PAULO L. FRANCO; SQUINA, FABIO M.; POLIKARPOV, IGOR. Recombinant Trichoderma harzianum endoglucanase I (Cel7B) is a highly acidic and promiscuous carbohydrate-active enzyme. Applied Microbiology and Biotechnology, v. 99, n. 22, p. 9591-9604, NOV 2015. (09/52840-7, 10/18773-8, 08/56255-9, 11/20977-3, 09/05328-9, 11/05712-3)

BUCKERIDGE, MARCOS S.; DE SOUZA, AMANDA P.. Breaking the ``Glycomic Code{''} of Cell Wall Polysaccharides May Improve Second-Generation Bioenergy Production from Biomass. BioEnergy Research, v. 7, n. 4, p. 1065-1073, DEC 2014. (09/52840-7, 08/57908-6)

JOHNS, M. A.; BERNARDES, A.; RIBEIRO DE AZEVEDO, E.; GUIMARAES, F. E. G.; LOWE, J. P.; GALE, E. M.; POLIKARPOV, I.; SCOTT, J. L.; SHARMA, R. I.. On the subtle tuneability of cellulose hydrogels: implications for binding of biomolecules demonstrated for CBM 1. JOURNAL OF MATERIALS CHEMISTRY B, v. 5, n. 21, p. 3879-3887, JUN 7 2017. (09/52840-7)

DE SOUZA, AMANDA P.; LEITE, DEBORA C. C.; PATTATHIL, SIVAKUMAR; HAHN, MICHAEL G.; BUCKERIDGE, MARCOS S.. Composition and Structure of Sugarcane Cell Wall Polysaccharides: Implications for Second-Generation Bioethanol Production. BioEnergy Research, v. 6, n. 2, p. 564-579, JUN 2013. (08/57908-6, 09/52840-7)

GRANDIS, ADRIANA; LEITE, DEBORA C. C.; TAVARES, EVELINE Q. P.; ARENQUE-MUSA, BRUNA C.; GAIARSA, JONAS W.; MARTINS, MARINA C. M.; DE SOUZA, AMANDA P.; GOMEZ, LEONARDO D.; FABBRI, CLAUDIA; MATTEI, BENEDETTA; et al. Cell wall hydrolases act in concert during aerenchyma development in sugarcane roots. ANNALS OF BOTANY, v. 124, n. 6, p. 23-pg., 2019-11-04. (09/52840-7, 10/17104-5, 08/57908-6, 14/50884-5, 10/17070-3)

GODOY, ANDRE S.; DE LIMA, MARIANA Z. T.; CAMILO, CESAR M.; POLIKARPOV, IGOR. Crystal structure of a putative exo-beta-1,3-galactanase from Bifidobacterium bifidum S17. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 72, p. 6-pg., 2016-04-01. (11/05712-3, 09/52840-7, 11/20505-4, 08/56255-9, 09/05328-9)

DOS REIS, CAIO VINICIUS; BERNARDES, AMANDA; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Bifidobacterium adolescentis xylose isomerase. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, p. 4-pg., 2013-05-01. (09/52840-7, 08/56255-9)

TEXTOR, LARISSA C.; SANTOS, JADEMILSON C.; HIDALGO CUADRADO, NAZARET; ROIG, MANUEL G.; ZHADAN, GALINA G.; SHNYROV, VALERY L.; POLIKARPOV, IGOR. Purification, crystallization and preliminary crystallographic analysis of peroxidase from the palm tree Chamaerops excelsa. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 67, p. 4-pg., 2011-12-01. (09/52840-7, 08/56255-9, 09/14333-6)

LIBERATO, MARCELO VIZONA; GENEROSO, WESLEY CARDOSO; MALAGO, WILSON, JR.; HENRIQUE-SILVA, FLAVIO; POLIKARPOV, IGOR. Crystallization and preliminary X-ray diffraction analysis of endoglucanase III from Trichoderma harzianum. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 68, p. 4-pg., 2012-03-01. (09/52840-7, 08/56255-9, 09/14333-6)

SEGATO, FERNANDO; BERTO, GABRIELA L.; DE ARAUJO, EVANDRO ARES; MUNIZ, JOAO RENATO; POLIKARPOV, IGOR. Expression, purification, crystallization and preliminary X-ray diffraction analysis of Aspergillus terreus endo-beta-1,4-glucanase from glycoside hydrolase family 12. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 70, p. 4-pg., 2014-02-01. (09/52840-7, 08/05637-9, 10/16947-9)