Integrated multi-omics analysis and metabolic network simulations applied to Saccharomyces cerevisiae for second generation ethanol production

• Grant number: 19/12914-3
• Support Opportunities: Scholarships in Brazil - Post-Doctoral
• Start date: January 01, 2020
• End date: January 31, 2024
• Field of knowledge: Biological Sciences - Genetics - Molecular Genetics and Genetics of Microorganisms
• Principal Investigator: Guido Costa Souza de Araújo
• Grantee: Lucas Miguel de Carvalho
• Host Institution: Instituto de Computação (IC). Universidade Estadual de Campinas (UNICAMP). Campinas , SP, Brazil
• Associated research grant: 13/08293-7 - CCES - Center for Computational Engineering and Sciences, AP.CEPID
• Associated scholarship(s): 20/15065-4 - Improving xylose-fermenting yeast for 2G ethanol production via constraint-based modeling combined with omics data analysis and machine learning, BE.EP.PD

Abstract

Currently, ethanol is the most consumed biofuel in the world and Brazil is a highlight in production. One of the great advances in the production of ethanol is the production from lignocellulosic biomass that is called second-generation ethanol (2G ethanol) or cellulosic ethanol and is considered the largest industrial biotechnology product in the world. Second-generation technology is one of the most promising in the development stage on the planet, and it consists of transforming the polymers of the plant cell wall into ethanol. In order to produce a broad understanding of cellular functioning in the conditions of interest, bioinformatics, in association with the various ómics, has a fundamental role, so as to enable a complete study of cellular metabolism (DNA, mRNA, proteins and metabolites) indicating bottlenecks and also directing to new genetic modifications, in order to maximize the metabolic flow. The tooling needed to analyze and predict the metabolites that will be formed encompasses the use of Machine Learning algorithms (ML), using features related to production, chemical, network and experimental data (such as RNA-Seq and proteomics). Along with Petri Net simulation data from metabolic networks and Flux Balance Analysis (FBA) data. Therefore, this project aims to integrate bioinformatics analysis methodologies, which include metabolic simulations and ML algorithms, to elucidate the metabolic bottlenecks present in the production of 2G ethanol. (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)

DE ABREU, LUIS GUILHERME F.; SILVA, V, NICHOLAS; FERRARI, ALLAN JHONATHAN R.; DE CARVALHO, LUCAS M.; FIAMENGHI, MATEUS B.; CARAZZOLLE, MARCELO F.; FILL, TAICIA P.; PILAU, EDUARDO J.; PEREIRA, GONCALO AMARANTE G.; GRASSI, MARIA CAROLINA B.. Metabolite profiles of energy cane and sugarcane reveal different strategies during the axillary bud outgrowth. Plant Physiology and Biochemistry, v. 167, p. 504-516, OCT 2021. (19/12914-3, 18/10315-2, 19/17007-4)

CARVALHO, LUCAS M.; CARVALHO-NETTO, OSMAR V.; CALDERON, LUIGE L.; GUTIERREZ, MILENA; DE ASSIS, MICHELLE A.; MOFATTO, LUCIANA S.; CAMARGO, ANTONIO P.; DOS SANTOS, LEANDRO V.; BORELLI, GUILHERME; TEMER, BEATRIZ; et al. Understanding the differences in 2G ethanol fermentative scales through omics data integration. FEMS Yeast Research, v. 21, n. 4, JUN 2021. (13/08293-7, 20/06563-0, 19/12914-3)

CARVALHO, LUCAS M.; SILVA, NICHOLAS VINICIUS; DE ABREU, LUIS GUILHERME F.; MARONE, MARINA PUPKE; CARDELLI, ALEXANDRA RUSSOLO; RAYA, FABIO TRIGO; ARAUJO, GUIDO; CARAZZOLLE, MARCELO FALSARELLA; PEREIRA, GONCALO AMARANTE GUIMARAES. Analysis of protein-protein interaction and weighted co-expression networks revealed key modules and genes in multiple organs of Agave sisalana. FRONTIERS IN CHEMICAL ENGINEERING, v. 5, p. 15-pg., 2023-05-26. (20/02524-0, 13/08293-7, 19/12914-3)