Advanced search
Start date

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


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)

Articles published in Agência FAPESP Newsletter about the research grant:
Articles published in other media outlets (0 total):
More itemsLess items

Scientific publications (19)
(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)
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, . (09/18354-8, 08/56255-9, 10/11135-6, 10/52362-5, 10/08370-3)
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, . (10/52362-5, 15/13684-0, 11/20505-4, 11/21608-1)
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, . (10/52362-5, 15/13684-0, 11/21608-1)
MELLO, BRUNO LUAN; POLIKARPOV, IGOR. Family 1 carbohydrate binding-modules enhance saccharification rates. AMB EXPRESS, v. 4, . (10/52362-5, 09/05349-6, 08/56255-9)
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, . (09/18354-8, 08/56255-9, 10/11135-6, 10/52362-5, 10/08370-3)
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, . (10/52362-5, 07/08706-9, 09/05349-6, 08/56255-9)
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)
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)
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, . (10/52362-5, 07/08706-9, 09/05349-6, 08/56255-9)
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, . (09/18354-8, 08/56255-9, 10/11135-6, 10/52362-5, 10/08370-3)
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, . (10/52362-5, 11/21608-1)
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, . (12/22802-9, 09/08233-9, 08/56255-9, 09/52840-7, 10/52362-5)
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, . (10/52362-5, 09/05349-6, 12/22802-9, 08/56255-9)
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)
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)
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)
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, . (10/52362-5, 15/13684-0, 14/00769-5, 11/20505-4)
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)

Please report errors in scientific publications list by writing to: