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Targeted analysis of microbial lignocellulolytic secretomes: a new approach to enzyme discovery

Processo: 10/52362-5
Modalidade de apoio:Auxílio à Pesquisa - Regular
Vigência: 01 de novembro de 2011 - 31 de agosto de 2015
Área do conhecimento:Ciências Biológicas - Bioquímica - Biologia Molecular
Convênio/Acordo: BBSRC, UKRI
Pesquisador responsável:Igor Polikarpov
Beneficiário:Igor Polikarpov
Pesq. responsável no exterior: Neil Bruce
Instituição no exterior: University of York, Inglaterra
Instituição Sede: Instituto de Física de São Carlos (IFSC). Universidade de São Paulo (USP). São Carlos , SP, Brasil
Bolsa(s) vinculada(s):13/19236-4 - Targeted analysis of microbial lignocellulolytic secretomes: a new approach to enzyme discovery, BP.TT
13/05842-0 - Targeted analysis of microbial lignocellulolytic secretomes: a new approach to enzyme discovery, BP.TT
12/19674-9 - Targeted analysis of microbial lignocellulolytic secretomes: a new approach to enzyme discovery, BP.TT
Assunto(s):Biologia celular  Celulose de madeira 
Publicação FAPESP:https://media.fapesp.br/bv/uploads/pdfs/International...RCUK_4_5.pdf

Resumo

From both a fundamental and industrial biotech viewpoint understanding the deconstruction of lignocellulose in soil and compost is of central importance. In the natural environments microbial communities can efficiently degrade or modify lignin to enable the effective enzymatic hydrolysis of the polysaccharides present in plant cell walls. The aim of this proposal is to use metatranscriptomics and proteomics to determine gene - and protein - centred details to determine new mechanisms and improved methods of lignocellulose deconstruction in mixed microbial communities from composting wheat straw and sugar cane bagasse. Secreted proteins will be tagged, affinity purified and analyzed by LC-ESI-MS. In order to have a picture of the overall community dynamics in terms of species composition during the composting process DNA will be extracted for SSU rRNA profiling: Saccharification of the lignocellulose will be monitored and the lignin content of the straw or bagasse analyzed using FTIR spectroscopy and solid state NMR. Metatranscriptome analysis will be performed by preparing cDNA from samples taken at various time points from the Iignocellulose enriched cultures, the cDNA will be sequenced using the Roche 454 GS FLX Titanium platform. The peptide sequences from the proteomics analysis will allow the identification of full and partial coding sequences in the library. These coding sequences will be cloned and expressed in established recombinant expression systems and the recombinant proteins screened for activity. (AU)

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Publicações científicas (21)
(Referências obtidas automaticamente do Web of Science e do SciELO, por meio da informação sobre o financiamento pela FAPESP e o número do processo correspondente, incluída na publicação pelos autores)
LIMA, MARISA A.; LAVORENTE, GABRIELA B.; DA SILVA, HANA K. P.; BRAGATTO, JULIANO; REZENDE, CAMILA A.; BERNARDINELLI, OIGRES D.; DEAZEVEDO, EDUARDO R.; GOMEZ, LEONARDO D.; MCQUEEN-MASON, SIMON J.; LABATE, CARLOS A.; et al. Effects of pretreatment on morphology, chemical composition and enzymatic digestibility of eucalyptus bark: a potentially valuable source of fermentable sugars for biofuel production - part 1. BIOTECHNOLOGY FOR BIOFUELS, v. 6, . (10/11135-6, 08/56255-9, 10/08370-3, 10/52362-5, 09/18354-8)
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, . (11/21608-1, 10/52362-5, 15/13684-0)
LIMA, MARISA A.; GOMEZ, LEONARDO D.; STEELE-KING, CLARE G.; SIMISTER, RACHAEL; BERNARDINELLI, OIGRES D.; CARVALHO, MARCELO A.; REZENDE, CAMILA A.; LABATE, CARLOS A.; DEAZEVEDO, EDUARDO R.; MCQUEEN-MASON, SIMON J.; et al. Evaluating the composition and processing potential of novel sources of Brazilian biomass for sustainable biorenewables production. BIOTECHNOLOGY FOR BIOFUELS, v. 7, . (10/11135-6, 08/56255-9, 10/08370-3, 10/52362-5, 09/18354-8)
MELLO, BRUNO LUAN; POLIKARPOV, IGOR. Family 1 carbohydrate binding-modules enhance saccharification rates. AMB EXPRESS, v. 4, . (08/56255-9, 10/52362-5, 09/05349-6)
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, . (11/20505-4, 11/21608-1, 10/52362-5, 15/13684-0)
ROSSETO, FLAVIO R.; PUHL, ANA C.; ANDRADE, MAXUEL O.; POLIKARPOV, IGOR. Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, p. 4-pg., . (10/52362-5, 09/05349-6, 08/56255-9, 07/08706-9)
DE ARAUJO, EVANDRO ARES; TOMAZINI, JR., ATILIO; SEIKI KADOWAKI, MARCO ANTONIO; MURAKAMI, MARIO TYAGO; POLIKARPOV, IGOR. Crystallization and preliminary X-ray diffraction analysis of a new xyloglucanase from Xanthomonas campestris pv. campestris. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, n. 6, p. 676-678, . (09/05349-6, 10/52362-5, 07/08706-9, 08/56255-9)
ROSSETO, FLAVIO R.; PUHL, ANA C.; ANDRADE, MAXUEL O.; POLIKARPOV, IGOR. Crystallization and preliminary diffraction analysis of the catalytic domain of major extracellular endoglucanase from Xanthomonas campestris pv. campestris. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, n. 2, p. 137-140, . (08/56255-9, 10/52362-5, 07/08706-9, 09/05349-6)
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, . (11/20505-4, 15/13684-0, 09/52840-7, 10/52362-5, 11/21608-1, 15/50590-4)
ALESSI, ANNA M.; BIRD, SUSANNAH M.; OATES, NICOLA C.; LI, YI; DOWLE, ADAM A.; NOVOTNY, ETELVINO H.; DEAZEVEDO, EDUARDO R.; BENNETT, JOSEPH P.; POLIKARPOV, IGOR; YOUNG, J. PETER W.; et al. Defining functional diversity for lignocellulose degradation in a microbial community using multi-omics studies. BIOTECHNOLOGY FOR BIOFUELS, v. 11, . (10/52362-5)
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, . (10/52362-5, 15/13684-0)
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, . (14/00769-5, 11/20505-4, 10/52362-5, 15/13684-0)
ALESSI, ANNA M.; BIRD, SUSANNAH M.; BENNETT, JOSEPH P.; OATES, NICOLA C.; LI, YI; DOWLE, ADAM A.; POLIKARPOV, IGOR; YOUNG, J. PETER W.; MCQUEEN-MASON, SIMON J.; BRUCE, NEIL C.. Revealing the insoluble metasecretome of lignocellulose-degrading microbial communities. SCIENTIFIC REPORTS, v. 7, . (10/52362-5)
TOMAZINI JUNIOR, ATILIO; DOLCE, LUCIANO GRACIANI; DE OLIVEIRA NETO, MARIO; POLIKARPOV, IGOR. Xanthomonas campestris expansin-like X domain is a structurally disordered beta-sheet macromolecule capable of synergistically enhancing enzymatic efficiency of cellulose hydrolysis. Biotechnology Letters, v. 37, n. 12, p. 2419-2426, . (08/56255-9, 10/52362-5, 07/08706-9, 09/05349-6)
BERNARDINELLI, OIGRES DANIEL; LIMA, MARISA APARECIDA; REZENDE, CAMILA ALVES; POLIKARPOV, IGOR; DEAZEVEDO, EDUARDO RIBEIRO. Quantitative C-13 MultiCP solid-state NMR as a tool for evaluation of cellulose crystallinity index measured directly inside sugarcane biomass. BIOTECHNOLOGY FOR BIOFUELS, v. 8, . (10/11135-6, 08/56255-9, 10/08370-3, 10/52362-5, 09/18354-8)
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, . (09/52840-7, 08/56255-9, 12/22802-9, 10/52362-5, 09/08233-9)
BERNARDES, AMANDA; TEXTOR, LARISSA C.; SANTOS, JADEMILSON C.; CUADRADO, NAZARET HIDALGO; KOSTETSKY, EDUARD YA.; ROIG, MANUEL G.; BAVRO, VASSILIY N.; MUNIZ, JOAO R. C.; SHNYROV, VALERY L.; POLIKARPOV, IGOR. Crystal structure analysis of peroxidase from the palm tree Chamaerops excelsa. Biochimie, v. 111, p. 58-69, . (12/22802-9, 10/52362-5, 08/56255-9, 09/05349-6)
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.; et al. Structure, computational and biochemical analysis of PcCel45A endoglucanase from Phanerochaete chrysosporium and catalytic mechanisms of GH45 subfamily C members. SCIENTIFIC REPORTS, v. 8, . (15/13684-0, 11/21608-1, 10/52362-5, 11/20505-4)
MELLO, BRUNO L.; ALESSI, ANNA M.; MCQUEEN-MASON, SIMON; BRUCE, NEIL C.; POLIKARPOV, IGOR. Nutrient availability shapes the microbial community structure in sugarcane bagasse compost-derived consortia. SCIENTIFIC REPORTS, v. 6, . (11/21608-1, 10/52362-5)
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, . (15/13684-0, 11/21608-1, 10/52362-5, 11/20505-4)
DE ARAUJO, EVANDRO ARES; TOMAZINI, ATILIO, JR.; SEIKI KADOWAKI, MARCO ANTONIO; MURAKAMI, MARIO TYAGO; POLIKARPOV, IGOR. Crystallization and preliminary X-ray diffraction analysis of a new xyloglucanase from Xanthomonas campestris pv. campestris. ACTA CRYSTALLOGRAPHICA SECTION F-STRUCTURAL BIOLOGY COMMUNICATIONS, v. 69, p. 3-pg., . (09/05349-6, 10/52362-5, 08/56255-9, 07/08706-9)

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