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"DNA's dark matter": Brazilians unveil key to increasing biofuel production
Identified in Brazilian soil, the bacterium produces an enzyme containing copper particles that boost cellulose breakdown in agricultural residues used for fuel production
Metalloenzyme comes from the bacterium Candidatus Telluricellulosum braziliensis, found in Brazilian soil, which is part of a group never cultivated in a laboratory before – Photo: Reproduction /CNPEM
Brazilian researchers have found the key to increasing the production of biofuels from agricultural residues in the “dark matter” of soil bacteria genes. Scientists have identified bacteria in sugarcane crops that generate an enzyme that uses copper to facilitate the breakdown of cellulose in residues, providing raw materials for fuels, paper, and textiles, among other products. The proposed name for the bacterium is Candidatus Telluricellulosum braziliensis because it was isolated in Brazil and because of its effect on cellulose. The discovery, in which USP researchers participated, is described in an article published in the journal Nature. “In this particular work, we looked at unknown genes of unknown microorganisms from soils covered in sugarcane residues, showing potential for cellulose biotransformation, what we call the ‘DNA’s dark matter,’” says researcher Mario Murakami, from the Brazilian Center for Research in Energy and Materials (CNPEM) in Campinas (São Paulo), lead author of the article, told Jornal da USP. “This research has the impact of improving the process of transforming plant residues into bioproducts such as biofuels.”
Murakami says that the “DNA’s dark matter” refers to the genetic material of microorganisms that we can’t grow in the laboratory. “It’s like a hidden world of genetic information that we’re only just beginning to explore,” he points out. “This ‘dark matter’ could be the key to discovering new enzymes and biological processes.”
Mario Murakami - Photo: Erik Nardini/CNPEM
The researcher explains that the metalloenzyme comes from the bacterium of which the proposed name is Candidatus Telluricellulosum braziliensis, found in Brazilian soil. “It was discovered in a group of bacteria called UBP4, standing for ‘uncultured bacterial phylum 4’, which are relatively unknown and have never been cultured in the laboratory before,” he says. “The metalloenzyme, called CelOCE [Cellulose Oxidative Cleaving Enzyme], is a special type of enzyme that uses copper to help break down cellulose.”
“Our research group participated in the enzyme’s characterization stage of the copper metal center. When metals are present in enzyme structures, this means that they participate in the process of catalysis [breaking down molecules] carried out by the enzyme, i.e. they are essential for its role,” Professor Antônio José da Costa Filho, from the Physics Department of USP’s Faculty of Philosophy, Sciences and Letters of Ribeirão Preto (FFCLRP), and one of the article’s authors, explains to Jornal da USP. “Therefore, it is relevant to know what type of metal is present and if the surrounding structure changes in the presence of molecules that bind to the enzyme or if the environmental conditions change.”
Antônio José da Costa Filho - Photo: IEA
Antônio José da Costa Filho - Photo: IEA
“Using a technique known as Electron Paramagnetic Resonance, we detected the presence of the copper ion and changes in its arrangement resulting from the presence of some other molecules with which the enzyme interacts,” the FFCLRP professor describes. “It was a participation that helped to compose the robust set of data available in the work.”
Opening molecular locks
“Currently, cellulose is degraded using enzymes called glycoside hydrolases and monooxygenases, working like ‘molecular scissors’, cutting cellulose into its basic constituent, glucose,” Murakami notes. “Unlike these enzymes, CelOCE works by binding to the end of the cellulose chain and ‘cutting’ a single unit, producing cellobionic acid. It alone is unable to release glucose, but it acts by opening molecular ‘locks’ for the action of other known enzymes.”
Proposed model for the simultaneous interaction of the CelOCE enzyme with cellulose, aiming to generate hydrogen peroxide, essential for the breakdown of the molecules - Image: taken from the article
According to the researcher, CelOCE has the potential to significantly improve the production of biofuels and other bioproducts from plant residues. “When combined with existing enzyme cocktails, it can increase the amount of sugar obtained from cellulose, making the process more efficient and economical,” he points out. “For comparison purposes, LPMO enzymes, which were the last major revolution in the area of carbohydrate enzymology more than 20 years ago, provide an increase of approximately 10%, while CelOCE increases by more than 20% under the conditions tested in the pilot plant.”
“This process is vital for various industrial sectors, including the production of biofuels, paper, and textiles. We can turn plant residues into valuable products by breaking down cellulose,” Murakami emphasizes. “This discovery changes the paradigm of cellulose degradation by microbial life, adding a new class of structurally and functionally distinct enzymes. The specific bacterium in which the enzyme was found was proposed to be called Candidatus Telluricellulosum braziliensis, as it was isolated in Brazil and has cellulolytic potential.”
According to the researcher, the work is one of the outcomes of a CNPEM research and innovation program for mapping the genetic heritage of Brazilian biodiversity and subsequent mining for biotechnological purposes. Applications include industrial biotransformation, biofuels, human health, animal nutrition, and agriculture.
“Using an interdisciplinary approach from multi-meta-omics, enzymology, genetic engineering, through solving the 3D structure of the enzyme in the Sirius particle accelerator to scaling up in CNPEM’s pilot plant for validation,” says Murakami, “we discovered a new class of enzymes that act specifically on cellulose, the most abundant polymer on the planet.”
Researchers from CNPEM, USP, Aix Marseille University, CNRS (France), and the Technical University of Denmark contributed to the study. “It’s worth mentioning that all the experiments were performed in Brazil, with the covalidation of some experiments performed in laboratories abroad,” the researcher concludes.
English version: Nexus Traduções
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A reprodução de matérias e fotografias é livre mediante a citação do Jornal da USP e do autor. No caso dos arquivos de áudio, deverão constar dos créditos a Rádio USP e, em sendo explicitados, os autores. Para uso de arquivos de vídeo, esses créditos deverão mencionar a TV USP e, caso estejam explicitados, os autores. Fotos devem ser creditadas como USP Imagens e o nome do fotógrafo.