Development of model systems in sorghum and a systems biology approach to unravel the molecular mechanisms controlling lignin metabolism in grasses

• Grant number: 15/02527-1
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• Start date: July 01, 2015
• End date: April 30, 2021
• Field of knowledge: Biological Sciences - Botany - Pant Physiology
• Principal Investigator: Igor Cesarino
• Grantee: Igor Cesarino
• Host Institution: Instituto de Biociências (IB). Universidade de São Paulo (USP). São Paulo , SP, Brazil
• Associated researchers: Renato Vicentini dos Santos
• Associated research grant(s): 21/06142-8 - Steering the shikimate/phenylpropanoid pathway: from gene function discovery to green factories, AP.BIOEN.JP2
• Associated scholarship(s): 19/14604-1 - The ABC of lignification: towards the identification of ABC transporters potentially involved in lignin deposition in Setaria viridis (L.) P.Beauv, BP.IC; 16/06917-1 - Transcriptomic analysis and co-expression network construction in model systems for identification of genes involved in secondary cell wall deposition and lignin metabolism in grasses, BP.PD; 16/07502-0 - Development of a model system based on a single elongating internode to study secondary cell wall deposition in sorghum, BP.IC; 15/18361-5 - Establishment of an inducible suspension cell culture for tracheary element differentiation in Sorghum bicolor L., BP.MS

Abstract

Recently, interest on lignin research has increased significantly since several studies have identified this biopolymer as the main factor responsible for the recalcitrance of cell walls to cellulose-to-glucose conversion for downstream applications, such as the production of biofuels and bio-based materials. Despite recent advances, most of our current knowledge of cell wall formation and lignin metabolism is primarily derived from dicotyledonous species. However, the molecular mechanisms controlling different aspects of lignin metabolism in grasses, such as transcriptional regulation, biosynthesis and polymerization, remains largely unknown, despite of the economic importance of this group of plants. Therefore, comprehensive and systematic studies are needed to unravel specific characteristics of secondary cell wall formation and lignin metabolism in grasses. The present project aims to develop model systems of sorghum and use them in a systems biology approach based on transcriptomics and metabolomics to correlate changes in cell wall composition with changes in gene expression, with a major focus on lignin and phenolic metabolism. The proposed model systems are: i) the elongating internodes system, and ii) inducible cell suspension culture for tracheary element differentiation. Both systems will be characterized for lignin deposition and phenolic profiling and subsequently used in high-throughput transcriptomic analysis using RNAseq. Finally, the transcriptomic data will be used to generate a co-expression network and a database of co-expressed genes, in order to select candidate genes that potentially play a role in secondary cell wall formation and lignin biosynthesis in grasses. The obtained knowledge might be very helpful for future biotechnological strategies to reduce biomass recalcitrance in bioenergy crops, such as sugarcane. (AU)

Scientific publications

(18)

(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)

STEENACKERS, WARD; KLIMA, PETR; QUARESHY, MUSSA; CESARINO, IGOR; KUMPF, ROBERT P.; CORNEILLIE, SANDER; ARAUJO, PEDRO; VIAENE, TOM; GOEMINNE, GEERT; NOWACK, MORITZ K.; et al. cis-Cinnamic Acid Is a Novel, Natural Auxin Efflux Inhibitor That Promotes Lateral Root Formation. Plant Physiology, v. 173, n. 1, p. 552-565, JAN 2017. (15/02527-1)

LI, ZHENG; ZHANG, CHUNTANG; ZHANG, YUAN; ZENG, WEI; CESARINO, IGOR. offee cell walls-composition, influence on cup quality and opportunities for coffee improvement. FOOD QUALITY AND SAFETY, v. 5, JUN 5 2021. (15/02527-1)

FERREIRA, SAVIO SIQUEIRA; GOEMINNE, GEERT; SIMOES, MARCELLA SIQUEIRA; DE ALMEIDA PINA, ANDRE VICIOLI; ALVES DE LIMA, LEYDSON GABRIEL; PEZARD, JADE; GUTIERREZ, ANA; RENCORET, JORGE; MORTIMER, JENNY C.; DEL RIO, JOSE C.; et al. Transcriptional and metabolic changes associated with internode development and reduced cinnamyl alcohol dehydrogenase activity in sorghum. Journal of Experimental Botany, v. 73, n. 18, p. 27-pg., 2022-07-05. (16/06917-1, 15/02527-1, 19/14604-1, 15/18361-5)

STEENACKERS, WARD; CESARINO, IGOR; KLIMA, PETR; QUARESHY, MUSSA; VANHOLME, RUBEN; CORNEILLIE, SANDER; KUMPF, ROBERT PETER; VAN DE WOUWER, DORIEN; LJUNG, KARIN; GOEMINNE, GEERT; et al. The Allelochemical MDCA Inhibits Lignification and Affects Auxin Homeostasis. Plant Physiology, v. 172, n. 2, p. 874-888, OCT 2016. (15/02527-1)

FIGUEIREDO, RAQUEL; CESARINO, IGOR; MAZZAFERA, PAULO. Suberin as an Extra Barrier to Grass Digestibility: a Closer Look to Sugarcane Forage. TROPICAL PLANT BIOLOGY, v. 9, n. 2, p. 96-108, JUN 2016. (15/02527-1, 15/05437-3)

SORIANO SALEME, MARINA DE LYRA; CESARINO, IGOR; VARGAS, LIVIA; KIM, HOON; VANHOLME, RUBEN; GOEMINNE, GEERT; VAN ACKER, REBECCA; DE ASSIS FONSECA, FERNANDO CAMPOS; PALLIDIS, ANDREAS; VOOREND, WANNES; et al. Silencing CAFFEOYL SHIKIMATE ESTERASE Affects Lignification and Improves Saccharification in Poplar. Plant Physiology, v. 175, n. 3, p. 1040-1057, NOV 2017. (15/02527-1)

SUNG, BIANCA MEEIHUA; CARVALHO, GABRIEL GARON; WAIRICH, ANDRIELE; CESARINO, IGOR. Searching for Novel Transcriptional Regulators of Lignin Deposition Within the PIRIN Family in the Model C4 Grass Setaria Viridis. TROPICAL PLANT BIOLOGY, v. 14, n. 2, p. 93-105, JUN 2021. (15/02527-1)

SIMOES, MARCELLA SIQUEIRA; CARVALHO, GABRIEL GARON; FERREIRA, SAVIO SIQUEIRA; HERNANDES-LOPES, JOSE; DE SETTA, NATHALIA; CESARINO, IGOR. Genome-wide characterization of the laccase gene family in Setaria viridis reveals members potentially involved in lignification. PLANTA, v. 251, n. 2, JAN 9 2020. (15/02527-1, 16/06917-1, 16/50189-0)

ARAUJO, PEDRO; TOLENTINO, FELIPE THADEU; CESARINO, IGOR; GALLINARI, RAFAEL HENRIQUE; STEENACKERS, WARD; SAMPAIO MAYER, JULIANA LISCHKA; MAZZAFERA, PAULO. Expression of Eucalyptus globulus LACCASE48 Restores Lignin Content of Arabidopsis thaliana lac17 Mutant. PLANT MOLECULAR BIOLOGY REPORTER, v. 37, n. 5-6, p. 488-498, DEC 2019. (14/23230-4, 15/02527-1)

SIMOES, MARCELLA SIQUEIRA; FERREIRA, SAVIO SIQUEIRA; GRANDIS, ADRIANA; RENCORET, JORGE; PERSSON, STAFFAN; FLOH, ENY IOCHEVET SEGAL; FERRAZ, ANDRE; DEL RIO, JOSE C.; BUCKERIDGE, MARCOS SILVEIRA; CESARINO, IGOR. Differentiation of Tracheary Elements in Sugarcane Suspension Cells Involves Changes in Secondary Wall Deposition and Extensive Transcriptional Reprogramming. FRONTIERS IN PLANT SCIENCE, v. 11, DEC 18 2020. (14/50884-5, 16/50189-0, 15/02527-1, 19/13936-0, 15/18361-5, 16/06917-1, 16/17541-2)

OZPARPUCU, MERVE; GIERLINGER, NOTBURGA; CESARINO, IGOR; BURGERT, INGO; BOERJAN, WOUT; RUGGEBERG, MARKUS. Significant influence of lignin on axial elastic modulus of poplar wood at low microfibril angles under wet conditions. Journal of Experimental Botany, v. 70, n. 15, p. 4039-4047, AUG 1 2019. (15/02527-1)

CESARINO, IGOR. Structural features and regulation of lignin deposited upon biotic and abiotic stresses. CURRENT OPINION IN BIOTECHNOLOGY, v. 56, p. 209-214, APR 2019. (15/02527-1)

FERREIRA, SAVIO SIQUEIRA; SIMOES, MARCELLA SIQUEIRA; CARVALHO, GABRIEL GARON; ALVES DE LIMA, LEYDSON GABRIEL; DE ALMEIDA SVARTMAN, RAPHAEL MENDES; CESARINO, IGOR. The lignin toolbox of the model grass Setaria viridis. Plant Molecular Biology, v. 101, n. 3, p. 235-255, OCT 2019. (16/06917-1, 16/50189-0, 15/02527-1)

ELOY, NUBIA B.; VOOREND, WANNES; LAN, WU; SALEME, MARINA DE LYRA SORIANO; CESARINO, IGOR; VANHOLME, RUBEN; SMITH, REBECCA A.; GOEMINNE, GEERT; PALLIDIS, ANDREAS; MORREEL, KRIS; et al. Silencing CHALCONE SYNTHASE in Maize Impedes the Incorporation of Tricin into Lignin and Increases Lignin Content. Plant Physiology, v. 173, n. 2, p. 998-1016, FEB 2017. (15/02527-1)

OZPARPUCU, MERVE; RUGGEBERG, MARKUS; GIERLINGER, NOTBURGA; CESARINO, IGOR; VANHOLME, RUBEN; BOERJAN, WOUT; BURGERT, INGO. Unravelling the impact of lignin on cell wall mechanics: a comprehensive study on young poplar trees downregulated for CINNAMYL ALCOHOL DEHYDROGENASE (CAD). Plant Journal, v. 91, n. 3, p. 480-490, AUG 2017. (15/02527-1)

CESARINO, IGOR; SIMOES, MARCELLA SIQUEIRA; BRITO, MICHAEL DOS SANTOS; FANELLI, AMANDA; SILVA, TATIANE DA FRANCA; ROMANEL, ELISSON. Building the wall: recent advances in understanding lignin metabolism in grasses. ACTA PHYSIOLOGIAE PLANTARUM, v. 38, n. 11, NOV 2016. (14/06923-6, 15/02527-1, 14/23017-9, 14/17486-6, 14/08468-4, 15/18361-5)

FIGUEIREDO, RAQUEL; PORTILLA LLERENA, JUAN PABLO; KIYOTA, EDUARDO; FERREIRA, SAVIO SIQUEIRA; CARDELI, BARBARA ROCHA; RIBEIRO DE SOUZA, SARAH CAROLINE; BRITO, MICHAEL DOS SANTOS; SODEK, LADASLAV; CESARINO, IGOR; MAZZAFERA, PAULO. The sugarcane ShMYB78 transcription factor activates suberin biosynthesis inNicotiana benthamiana. Plant Molecular Biology, v. 104, n. 4-5, AUG 2020. (15/02527-1, 15/05437-3)

CESARINO, IGOR; DELLO IOIO, RAFFAELE; KIRSCHNER, GWENDOLYN K.; OGDEN, MICHAEL S.; PICARD, KELSEY L.; RAST-SOMSSICH, I, MADLEN; SOMSSICH, MARC. Plant science's next top models. ANNALS OF BOTANY, v. 126, n. 1, p. 1-23, JUN 29 2020. (16/50189-0, 15/02527-1)