Enzymatic mechanisms from the microbiome of aquatic herbivores for depolymerization and metabolism of complex carbohydrates

• Grant number: 21/04891-3
• Support Opportunities: Research Projects - Thematic Grants
• Start date: August 01, 2023
• End date: July 31, 2028
• Field of knowledge: Biological Sciences - Biochemistry - Chemistry of Macromolecules
• Principal Investigator: Mário Tyago Murakami
• Grantee: Mário Tyago Murakami
• Host Institution: Centro Nacional de Pesquisa em Energia e Materiais (CNPEM). Ministério da Ciência, Tecnologia e Inovação (Brasil). Campinas , SP, Brazil
• Associated researchers: Andrey Fabricio Ziem Nascimento ; Bernard Henrissat ; Camila Ramos dos Santos ; Carme Rovira Virgili ; Clelton Aparecido dos Santos ; Evandro Ares de Araújo ; Felippe Mariano Colombari ; Gabriela Felix Persinoti ; Mariana Abrahão Bueno de Morais ; Nicolas Terrapon ; Tatiani Brenelli de Lima
• Associated research grant(s): 25/08135-0 - 2025 Gordon Research Conference on Carbohydrate-Active Enzymes for Glycan Conversions, AR.EXT
• Associated scholarship(s): 25/00385-7 - Mechanistic study of enzymes involved in carbohydrate processing and prospected from the microbiota of Amazonian manatee, BP.DD; 24/05551-0 - Bioprospecting of new microorganisms and biosynthetic gene clusters associated with the intestinal microbiota of herbivores from Brazilian biodiversity, BP.DD; 24/15257-1 - Use of classical and quantum molecular dynamics simulations to study new glycoside hydrolases identified through omics studies, BP.DD; 24/15182-1 - Discovery and mechanistic investigation of carbohydrate-active enzymes from the intestinal microbiota of aquatic herbivores, BP.PD; 21/09793-0 - Discovery and mechanistic investigation of carbohydrate-active enzymes from the gut microbiota of Manatee, BP.PD

Abstract

This project aims to elucidate enzymatic systems and molecular mechanisms associated with the depolymerization and metabolism of complex carbohydrates by microorganisms present in the gut microbiota of herbivores. The processing of carbohydrates by the gut microbiota plays a central role in the generation of energy (nutrition) for the host, in addition to other functions such as modulation of the immune system, protection against pathogen invasion and metabolism. In addition, herbivores play an important role in the maintenance and dynamics of ecosystems by controlling the type, distribution and structure of vegetation, whether terrestrial or aquatic. The understanding of molecular bases underpinning the utilization of highly diverse and recalcitrant carbohydrates by gut microbial communities represents an important advance in the knowledge of carbohydrate enzymology, an area of great importance for biotechnology, health and animal nutrition. The knowledge generated has the potential to expand and/or modify our understanding of microbial mechanisms to overcome carbohydrate recalcitrance, which may contribute to accelerating the transition to a circular and sustainable bioeconomy. For this purpose, an interdisciplinary approach will be employed that integrates state-of-the-art omics, biochemical, structural and computational methods to investigate highly specialized niches in the deconstruction of carbohydrates such as the gut microbiomes of semiaquatic and aquatic herbivores that are yet underexplored when compared terrestrial monogastric herbivores and ruminants. The relevance of these biological systems is supported by the recent discoveries from our group on the gut microbiome of the capybara (a semiaquatic herbivore), which allowed the founding of two new families in the CAZy database and revealed a significant number of proteins with unknown function with potential lytic action on carbohydrates, reinforcing the concept that such organisms are untapped sources of microorganisms and enzymatic systems for processing complex carbohydrates (Cabral et al., Nature Communications 2022). In addition, the group has sought to work on the frontier of the discovery and mechanistic elucidation of carbohydrate-active enzymes (CAZymes) exemplified by the functional and mechanistic dissection of an entire family of glucanases through sequence similarity networks (Santos et al., Nature Chemical Biology 2020) and the combination of X-ray crystallography with quantum computational simulations to unravel alternative catalytic pathways of exo-enzymes that change the currently proposed model on catalytic reactions of glycosidic hydrolases (Morais et al., Nature Communications 2021). Also in 2021, the group unveiled the enzymatic machinery for the processing of xyloglucan by proteobacteria and its role in virulence in plant pathogenic species (Vieira et al., Nature Communications, 2021). More recently, we showed how probiotic bacteria from the genus Bifidobacterium are capable of deconstructing and metabolizing N-glycans, which explains a possible molecular strategy for their perennial presence in the gut microbiota of adult and elderly mammals (Cordeiro et al., Nature Chemical Biology 2023). In conclusion, both biological systems ((semi-)aquatic herbivores) and experimental/theoretical approaches have great potential to result in breakthrough discoveries in glycobiology, either in the fundamental understanding of microbial communities and their enzymatic strategies or in the applied field for biotechnological purposes. (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)

MANDELLI, FERNANDA; MARTINS, MARCELE PANDELO; CHINAGLIA, MARIANA; DE LIMA, EVANDRO ANTONIO; MORAIS, MARIANA ABRAHAO BUENO; LIMA, TATIANI BRENELLI; CABRAL, LUCELIA; PIROLLA, RENAN AUGUSTO SIQUEIRA; FUZITA, FELIPE JUN; PAIXAO, DOUGLAS ANTONIO ALVAREDO; et al. A functionally augmented carbohydrate utilization locus from herbivore gut microbiota fueled by dietary β-glucans. NPJ BIOFILMS AND MICROBIOMES, v. 10, n. 1, p. 13-pg., 2024-10-14. (21/04891-3, 22/03059-5, 21/09793-0)

SANTOS, CLELTON A.; MORAIS, MARIANA A. B.; MANDELLI, FERNANDA; LIMA, EVANDRO A.; MIYAMOTO, RENAN Y.; HIGASI, PAULA M. R.; ARAUJO, EVANDRO A.; PAIXAO, DOUGLAS A. A.; JUNIOR, JOAQUIM M.; MOTTA, MARIA L.; et al. A metagenomic 'dark matter' enzyme catalyses oxidative cellulose conversion. Nature, v. N/A, p. 29-pg., 2025-02-12. (21/04891-3, 22/03059-5)

ANDRADE, LILIANE PIRES; RODRIGUES, MARIA ISABEL; MURAKAMI, MARIO TYAGO; DE MORAES ROCHA, GEORGE JACKSON. Pilot-scale high-consistency mechanical refining improves enzymatic saccharification of lignocellulosic feedstock. SCIENTIFIC REPORTS, v. 15, n. 1, p. 10-pg., 2025-03-27. (21/04891-3)