Identifying gene co-expression modules with novel transcription factors involved in hemicellulose biosynthesis in C4 grasses

• Grant number: 21/11057-0
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: October 01, 2022
• End date: September 30, 2025
• Field of knowledge: Biological Sciences - Genetics - Plant Genetics
• Principal Investigator: Diego Mauricio Riano Pachon
• Grantee: Renato Augusto Corrêa dos Santos
• Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• Company: Universidade de São Paulo (USP). Escola Politécnica (EP)
• Associated research grant: 20/15230-5 - Research Centre for Greenhouse Gas Innovation - RCG2I, AP.PCPE
• Associated scholarship(s): 23/11133-3 - Integrating metataxonomics and host transcriptomics data in maize, BE.EP.PD

Abstract

Biofuels are important contributors to a more sustainable planet, due to reduced greenhouse gas emissions and substitution of fossil fuels. In this context, grasses are particularly relevant because their lignocellulosic biomass is abundant in nature and can be used to produce biofuel that does not compete with the food industry. C4 grasses are of particular relevance as they have an improved efficiency for conversion of carbon into biomass through photosynthesis compared to C3. Among these plants, sugarcane is an important crop in Brazil which fixes carbon and uses water efficiently, for which the bagasse can be used to produce second generation bioethanol. However, the production of biofuels from lignocellulosic material is hampered by its high biomass recalcitrance, including the deposition of hydrophobic lignin and cross-linked arabinoxylan components, in particular the hydroxycinnamic acids, p-coumaric and ferulic acids, in the plant secondary cell wall. Understanding of the gene regulatory elements involved in biosynthesis and cross-linking of arabinoxylan would make it possible to engineer more digestible plants and, therefore, facilitate biofuel production processes. Our groups have already studies some gene families (BAHDs: acyltransferases and XATs: xylan arabinosyltransferases) that have a role in the digestibility of plant cell wall in sugarcane and in Setaria viridis, a C4 grass model. We plan to exploit public omics datasets to discover new genes involved in the control of biomass saccharification. The increasing availability of plant RNA-Seq experiments in public databases will allow us to gain new biological insights. By using these transcriptomics data, systems biology methods can be used to predict coexpression networks. A high correlation in gene expression of different genes (i.e. coexpressed modules) indicate possible biological relationships, such as regulation. Transcription factors (TFs) comprise important regulatory elements which can easily be identified using conserved protein domains. Co-expressed clusters of genes will aid to pinpoint probable regulatory relationships (TF - target pairs). Identified putative TF - target pairs can be tested in the wet-lab relatively easily, using e.g., yeast one-hybrid assays. This project aims: (i) to reconstruct co-expression networks using RNA-Seq experiments of C4 grass species obtained from public databases; (ii) to identify conserved modules of co-expressed genes including TFs and already known genes, involved in C4 grass biomass digestibility; and (iii) to validate three selected TF-DNA interactions experimentally (yeast one-hybrid assays) based on Setaria viridis genes. We expect to obtain novel candidate regulatory genes in grasses that can be further used in plant biotechnology to improve biomass digestibility in crop plants such as sugarcane. (AU)

Scientific publications

(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)

PELLEGRINETTI, THIERRY ALEXANDRE; MONTEIRO, GABRIEL GUSTAVO TAVARES NUNES; LEMOS, LEANDRO NASCIMENTO; DOS SANTOS, RENATO AUGUSTO CORREA; BARROS, ARTUR GOMES; MENDES, LUCAS WILLIAM. PGPg finder : A comprehensive and user-friendly pipeline for identifying plant growth-promoting genes in genomic and metagenomic data. RHIZOSPHERE, v. 30, p. 9-pg., 2024-06-01. (23/07080-1, 19/16043-7, 21/11057-0, 23/11133-3)