Integrative systems approach for the study of gene expression regulatory networks related to biomass production in microalgae

• Grant number: 16/06601-4
• Support Opportunities: Program for Research on Bioenergy (BIOEN) - Young Investigators Grants
• Start date: June 01, 2017
• End date: October 31, 2023
• Field of knowledge: Biological Sciences - Biochemistry - Molecular Biology
• Principal Investigator: Flavia Vischi Winck
• Grantee: Flavia Vischi Winck
• Host Institution: Centro de Energia Nuclear na Agricultura (CENA). Universidade de São Paulo (USP). Piracicaba , SP, Brazil
• City of the host institution: Piracicaba
• Associated researchers: Camila Caldana ; Danielle Izilda Rodrigues da Silva ; Diego Mauricio Riano Pachon ; Paula Barjona do Nascimento Coutinho ; Telma Teixeira Franco ; Thiago Olitta Basso
• Associated research grant(s): 24/06720-0 - American Society of Photobiologists (ASP) 42nd Biennial Meeting, AR.EXT; 23/02511-4 - Multi-user equipment approved in grant 16/06601-4: fluorescence microscope, AP.EMU
• Associated scholarship(s): 22/15431-6 - Proteomics analysis of Arginase-like function inhibition effects on the regulation of neutral lipids synthesis in microalgae, BP.IC; 22/07957-8 - Analysis of the effect of nitric oxide on the molecular physiology of microalgae and biomass production and lipids, BP.TT; 22/06280-4 - Monitoring alterations in the biochemical composition of microalgae biomass under stress conditions, BP.TT; + associated scholarships 22/02790-8 - Functional characterization of transcription factors related to biomass production and lipids biosynthesis, BP.TT; 21/12301-1 - Analysis of the effect of nitric oxide on the molecular physiology of microalgae and biomass production and lipids, BP.TT; 21/02163-0 - Functional characterization of transcription factors related to biomass production and lipids biosynthesis, BP.TT; 21/03080-1 - Monitoring of changes in the biochemical composition of microalgal biomass under stress conditions, BP.TT; 21/01871-1 - Reconstruction and analysis of biological networks related to nitrogen deprivation response in microalgae, BP.IC; 20/10636-3 - Development and application of computational tools for omics data integrative analysis, BP.TT; 20/04900-0 - Development and application of computacional tools for omics integrative data analysis, BP.TT; 18/14661-2 - Establishment of a real time PCR platform for the analysis of gene expression regulatory networks in microalgae., BP.TT; 18/16630-7 - Transcriptomic analysis of the nitrogen deprivation effect in the microalgae Chlamydomonas reinhardtii in photoautotrophy and mixotrophy, BP.MS; 18/14884-1 - Analysis of the effects of alterations on the availability of nitrogen and iron in the biomass formation by the microalgae Chlamydomonas reinhradtii, BP.IC; 18/13276-8 - Analysis of the effects of salt stress in biomass formation in the microalgae Chlamydomonas reinhardtii and the further alterations in the profile of chromatin binding proteins, BP.IC; 17/23674-8 - Analysis of iron and nitrogen interplay in lipids accumulation in microalgae, BP.DR; 17/25859-5 - Omics data knowledge basis development of transcriptional regulation in microalgae, BP.TT - associated scholarships

Abstract

The socioeconomicand environmental challenges associated with the use of fossil fuels and the increase onglobal energy demand and air and water pollutants can be faced through the development of sustainableproduction of clean energy and chemicals. The integration of microalgaebasedbioremediation and production ofrenewable biomass appears as a promising sustainable path for the production of bioenergy and chemicals.Despite the advances in microalgae cultivation, the generation of biomass for massive fuel and chemicalsproduction is still limiting. Therefore, a better understanding on how changes of environmental factors, such ascarbon source, nutrients and light affect microalgae biomass composition and accumulation is necessary.External abiotic stimuli (e.g., temperature, light, CO2) can induce phenotypic alterations through changes in theunderlying gene regulatory networks (e.g., transcriptional profile, network rewiring). The identification of thecomponents of gene regulatory networks (GRNs), including cis and transregulatoryelements, and theconcomitant quantification of gene transcripts, proteins and metabolites in a time resolved manner is of crucial importance to understand the actual regulatory network structure and its dynamic behavior. Thus, in the presentproposal, we aim to generate and to integrate multiomicsdata in a timeresolvedsystems biology framework toelucidate, in the microalgae Chlamydomonas reinhardtii, GRNs related to the control of cellular responses tonitrogen deprivation and salt stress under photoautotrophic and mixotrophic conditions. This approach will allowus to uncover biological and regulatory subnetworksresponsible for the control of biomass production andaccumulation of chemicals of biotechnological interest. The data generated will be useful for theoretical modelingand simulations and it will serve as the basis for the development of metabolic engineering and synthetic biologyapplications in microalgae, with possibilities to be extended to land plants and yeast strains in the future. (AU)

Scientific publications

(6)

(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)

RASHEED, RASEENA NASEEMA; POURBAKHTIAR, ASMA; ALLAF, MALIHE MEHDIZADEH; BAHARLOOEIAN, MAEDEH; RAFIEI, NAHID; ARATBONI, HOSSEIN ALISHAH; MORONES-RAMIREZ, JOSE RUBEN; WINCK, FLAVIA VISCHI. Microalgal co-cultivation -recent methods, trends in omic-studies, applications, and future challenges. FRONTIERS IN BIOENGINEERING AND BIOTECHNOLOGY, v. 11, p. 25-pg., 2023-09-20. (16/06601-4)

VOLPI, MARIA PAULA. C.; MAGALHAES, LARISSA O.; WINCK, FLAVIA V.; LABATE, MONICA T. V.; MORAES, BRUNA S.. Metaproteomic Analysis of the Anaerobic Community Involved in the Co-Digestion of Residues from Sugarcane Ethanol Production for Biogas Generation. BIOMASS-SWITZERLAND, v. 2, n. 4, p. 16-pg., 2022-12-05. (16/16438-3, 18/09893-1, 16/06601-4)

MAGALHAES, LARISSA DE OLIVEIRA; DE MELLO, FABIO NUNES; WINCK, FLAVIA VISCHI. Characterization of the Nuclear Proteome of Chlamydomonas in Response to Salt Stress. PHYCOLOGY, v. 2, n. 3, p. 17-pg., 2022-09-01. (16/06601-4)

LAVANDOSQUE, L. L.; MASTRANGELO, C. B.; CARVALHO, H. W. P. C.; GUIMARA, R. R.; ARAKI, K.; WINCK, F. V.. Fast multispectral imaging analysis as phenotyping platform: Effect of titanium dioxide nanoparticles on microalgae physiology. ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, v. 78, p. 12-pg., 2024-02-16. (18/03793-5, 16/06601-4, 22/15431-6)

VIDOTTI, ANNAMARIA D. S.; RIANO-PACHON, DIEGO M.; MATTIELLO, LUCIA; GIRALDI, LAIS ALBUQUERQUE; WINCK, FLAVIA V.; FRANCO, TELMA T.. Analysis of autotrophic, mixotrophic and heterotrophic phenotypes in the microalgae Chlorella vulgaris using time-resolved proteomics and transcriptomics approaches. ALGAL RESEARCH-BIOMASS BIOFUELS AND BIOPRODUCTS, v. 51, p. 15-pg., 2020-10-01. (16/06601-4)

MONTEIRO, LUCCA DE FILIPE REBOCHO; GIRALDI, LAIS ALBUQUERQUE; WINCK, FLAVIA VISCHI. From Feasting to Fasting: The Arginine Pathway as a Metabolic Switch in Nitrogen-Deprived Chlamydomonas reinhardtii. CELLS, v. 12, n. 10, p. 19-pg., 2023-05-13. (16/06601-4, 16/19152-3)