Analysis of metabolite profiles obtained by mass spectrometry using graphs

• Grant number: 14/01884-2
• Support type: Scholarships in Brazil - Post-Doctorate
• Effective date (Start): July 01, 2014
• Effective date (End): July 31, 2016
• Field of knowledge: Health Sciences - Pharmacy
• Cooperation agreement: Coordination of Improvement of Higher Education Personnel (CAPES)
• Principal researcher: Norberto Peporine Lopes
• Grantee: Ricardo Roberto da Silva
• Home Institution: Faculdade de Ciências Farmacêuticas de Ribeirão Preto (FCFRP). Universidade de São Paulo (USP). Ribeirão Preto , SP, Brazil
• Associated scholarship(s): 15/03348-3 - Improvement of molecular networking using in silico fragmentation and subnetwork storage and search, BE.EP.PD

Abstract

The natural product bioprospection is a complex and laborious process, with a high average cost and intensive manual inspection to isolate and identify active compounds from a natural product source. Brazilian endemic species of Lychnophora (Asteraceae) figure as a rich plant genus that have been used as the source for natural products exploration. Public compendia of molecular information with biological hierarchical organization of catalytic and regulatory genome potential, metabolic pathways and compounds potentially produced by a given organism, are incipient, often lacking for Lychnophora species. Recent studies of genome scale metabolism reconstruction perform exhaustive searches of genetic and biochemical information about a particular organism, reconstructing the known metabolism for the same. This approach allows a better inference of an organism chemical potential, enhancing its biotechnological exploitation. Besides the absence of molecular information compendia for Lychnophora metabolism inference, with conventional methods to analise plant extracts, the spatial information of metabolites in tissue, cells and organelles is lost. The IMS technique (Imaging Mass Spectrometry) allows the mass spectra collection for hundreds to thousands of points at predefined coordinates of a tissue area. With this spectras a map of the tissue distribution of the target substance can be built. The use of a compendium of biologically hierarchical known compounds for Lychnophora, and its compartmentalization in reactions and metabolic pathways, allows the natural product search in spatially defined regions of plant tissue and can be very useful for understanding their biological function as well as to guide its isolation improvement. Given the great complexity of the datasets produced in MALDI-imaging experiments and the lack of databases for metabolite comparison and inference of biochemical processes, this project aims to build a database with hierarchical genetic and biochemical information of Lychnophora phylogenetically related species and perform the inference by graphs of spatially specific metabolic pathways, using data obtained from IMS . (AU)

Scientific publications

(4)

(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)

ELIAS, LARISSA G.; SILVA, DENISE B.; SILVA, RICARDO; PENG, YAN-QIONG; YANG, DA-RONG; LOPES, NORBERTO P.; PEREIRA, RODRIGO A. S. A comparative venomic fingerprinting approach reveals that galling and non-galling fig wasp species have different venom profiles. PLoS One, v. 13, n. 11 NOV 8 2018. Web of Science Citations: 1.

DA SILVA, RICARDO R.; WANG, MINGXUN; NOTHIAS, LOUIS-FELIX; VAN DER HOOFT, JUSTIN J. J.; CARABALLO-RODRIGUEZ, ANDRES MAURICIO; FOX, EVAN; BALUNAS, MARCY J.; KLASSEN, JONATHAN L.; LOPES, NORBERTO PEPORINE; DORRESTEIN, PIETER C. Propagating annotations of molecular networks using in silico fragmentation. PLOS COMPUTATIONAL BIOLOGY, v. 14, n. 4 APR 2018. Web of Science Citations: 28.

WANG, MINGXUN; CARVER, JEREMY J.; PHELAN, VANESSA V.; SANCHEZ, LAURA M.; GARG, NEHA; PENG, YAO; NGUYEN, DON DUY; WATROUS, JERAMIE; KAPONO, CLIFFORD A.; LUZZATTO-KNAAN, TAL; PORTO, CARLA; BOUSLIMANI, AMINA; MELNIK, ALEXEY V.; MEEHAN, MICHAEL J.; LIU, WEI -TING; CRIISEMANN, MAX; BOUDREAU, PAUL D.; ESQUENAZI, EDUARDO; SANDOVAL-CALDERON, MARIO; KERSTEN, ROLAND D.; PACE, LAURA A.; QUINN, ROBERT A.; DUNCAN, KATHERINE R.; HSU, CHENG-CHIH; FLOROS, DIMITRIOS J.; GAVILAN, RONNIE G.; KLEIGREWE, KARIN; NORTHEN, TRENT; DUTTON, RACHEL J.; PARROT, DELPHINE; CARLSON, ERIN E.; AIGLE, BERTRAND; MICHELSEN, CHARLOTTE F.; JELSBAK, LARS; SOHLENKAMP, CHRISTIAN; PEVZNER, PAVEL; EDLUND, ANNA; MCLEAN, JEFFREY; PIEL, JORN; MURPHY, BRIAN T.; GERWICK, LENA; LIAW, CHIH-CHUANG; YANG, YU-LIANG; HUMPF, HANS-ULRICH; MAANSSON, MARIA; KEYZERS, ROBERT A.; SIMS, AMY C.; JOHNSON, ANDREW R.; SIDEBOTTOM, ASHLEY M.; SEDIO, BRIAN E.; KLITGAARD, ANDREAS; LARSON, CHARLES B.; BOYA P, CRISTOPHER A.; TORRES-MENDOZA, DANIEL; GONZALEZ, DAVID J.; SILVA, DENISE B.; MARQUES, LUCAS M.; DEMARQUE, DANIEL P.; POCIUTE, EGLE; O'NEILL, ELLIS C.; BRIAND, ENORA; HELFRICH, ERIC J. N.; GRANATOSKY, EVE A.; GLUKHOV, EVGENIA; RYFFEL, FLORIAN; HOUSON, HAILEY; MOHIMANI, HOSEIN; KHARBUSH, JENAN J.; ZENG, YI; VORHOLT, JULIA A.; KURITA, KENJI L.; CHARUSANTI, PEP; MCPHAIL, KERRY L.; NIELSEN, KRISTIAN FOG; VUONG, LISA; ELFEKI, MARYAM; TRAXLER, MATTHEW F.; ENGENE, NICLAS; KOYAMA, NOBUHIRO; VINING, OLIVER B.; BARIC, RALPH; SILVA, RICARDO R.; MASCUCH, SAMANTHA J.; TOMASI, SOPHIE; JENKINS, STEFAN; MACHERLA, VENKAT; HOFFMAN, THOMAS; AGARWAL, VINAYAK; WILLIAMS, PHILIP G.; DAI, JINGQUI; NEUPANE, RAM; GURR, JOSHUA; RODRIGUEZ, ANDRES M. C.; LAMSA, ANNE; ZHANG, CHEN; DORRESTEIN, KATHLEEN; DUGGAN, BRENDAN M.; ALMALITI, JEHAD; ALLARD, PIERRE-MARIE; PHAPALE, PRASAD; NOTHIAS, LOUIS-FELIX; ALEXANDROVR, THEODORE; LITAUDON, MARC; WOLFENDER, JEAN-LUC; KYLE, JENNIFER E.; METZ, THOMAS O.; PERYEA, TYLER; NGUYEN, DAC-TRUNG; VANLEER, DANIELLE; SHINN, PAUL; JADHAV, AJIT; MULLER, ROLF; WATERS, KATRINA M.; SHI, WENYUAN; LIU, XUETING; ZHANG, LIXIN; KNIGHT, ROB; JENSEN, PAUL R.; PALSSON, BERNHARD O.; POGLIANO, KIT; LININGTON, ROGER G.; GUTIERREZ, MARCELINO; LOPES, NORBERTO P.; GERWICK, WILLIAM H.; MOORE, BRADLEY S.; DORRESTEIN, PIETER C.; BANDEIRA, NUNO. Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking. NATURE BIOTECHNOLOGY, v. 34, n. 8, p. 828-837, AUG 2016. Web of Science Citations: 383.

NUNES, TULIO M.; MATEUS, SIDNEI; FAVARIS, ARODI P.; AMARAL, MONICA F. Z. J.; VON ZUBEN, LUCAS G.; CLOSOSKI, GIULIANO C.; BENTO, JOSE M. S.; OLDROYD, BENJAMIN P.; SILVA, RICARDO; ZUCCHI, RONALDO; SILVA, DENISE B.; LOPES, NORBERTO P. Queen signals in a stingless bee: suppression of worker ovary activation and spatial distribution of active compounds. SCIENTIFIC REPORTS, v. 4, DEC 12 2014. Web of Science Citations: 25.