Research at the CNPEM published in Nature Chemical Biology investigates the mechanism by which bacteria that use the sugars in milk as their primary energy source adapt their metabolism to remain in human intestinal microbiota, even after weaning
A study by researchers at the Brazilian Center for Research in Energy and Materials (CNPEM) published in Nature Chemical Biology brings together a series of data that reveals an obscure facet of the carbohydrate metabolism of the probiotic bacteria that inhabit our intestines. Advances in the understanding of these complex mechanisms were detailed by Lucy Crouch, a renowned specialist on this topic, in a text in the same publication.
The organism in the study model is a bacteria in the genus Bifidobacterium, one of the largest groups of bacteria that comprise our intestinal microbiota and are generally referred to as bifidobacteria. They function like probiotics, which play an important role in health, production of bioactive molecules, neuronal modulation, and mechanisms associated with immunity in mammals.
With support from the São Paulo Research Foundation (FAPESP), this study at the CNPEM investigated the activity, function, specificity, and structures of all the enzymatic components utilized by this type of bacteria to use complex carbohydrates as a source of energy and carbon instead of milk sugars, which give these bacteria a competitive advantage within the intestinal microbiota even after mammals stop nursing.
“We know that these bacteria feed on oligosaccharides from milk as an energy source. But in the adult and elderly phases of life, these bacteria require supplementary sources of energy and carbon, which were not yet entirely understood. This work demonstrates how these bacteria can use N-glycans, complex carbohydrates produced by the host as a perennial source of energy and carbon,” explains Mario Murakami, a researcher at CNPEM who coordinated the study.
Revealing molecules and a new metabolic pathway
The CNPEM study revealed that probiotic bifidobacteria contain a set of genes (operons) responsible for producing nine enzymes that work synergistically to completely depolymerize the N-glycans. Along with the atomic structures of these molecules, the study identified how these enzymes work in a new metabolic pathway through which the bacteria obtain energy from the N-glycans when oligosaccharide-type carbohydrates from milk in the diet are absent.
High-resolution images of the three-dimensional structures of these key enzymes were obtained for the first time using electronic cryomicroscopy.
“Obtaining three-dimensional protein structures in high resolution allows us to appreciate essential details for understanding how they work. In this case it was possible to determine fundamental information about the mechanisms for recognizing and cleavage of complex carbohydrates like N-glycans. It is important to emphasize that the CNPEM makes its electronic cryomicroscopy infrastructure available and trains its users, and is open to the entire scientific community, which benefits a variety of studies in the areas of health and biotechnology,” says Rodrigo Portugal, a CNPEM researcher responsible for the electronic cryomicroscopy facility.
The study made it possible to understand the entire metabolic pathway, from breakdown of the N-glycans to the unique sugar fermentation pathway in bifidobacteria known as the bifid shunt. Unlike other phyla of bacteria, these bacteria utilize various alpha-mannosidase-type enzymes that efficiently respond to the distinct chemical bonds that exist in N-glycans. Furthermore, these bacteria can utilize immature N-glycans thanks to an alpha-glycosidase-type enzyme, and the product of the degradation of these N-glycans is directed toward a fermentation pathway through a non-conventional reaction in which chemical modifications like phosphorylation (adding a phosphoryl group to a molecule) occurs after the sugar mannose is converted into fructose, an unusual process in bacteria.
“The molecular sophistication of this enzymatic system is unique among bacterial phyla, and understanding the puzzle of specificity and the mechanisms by which multiple enzymes work within the chemical N-glycan complex was extremely challenging. It required over 6 years of research, and involved doctoral students, post-docs, and collaborators from Brazil and abroad,” adds Murakami.
Next steps
The intestinal microbiota have been shown to play an essential role in health and metabolism, with implications for the immune system, inflammatory processes, and various diseases. Understanding how the main groups of bacteria survive and act within the intestinal microbiota is fundamental to explore their full potential for human and animal health, particularly for the bacterial groups that are well-known as probiotics.
“These bacteria can be added to formulations and we can think about genetic modifications, where characteristics like this, like N-glycan utilization, are encouraged. We can boost the expression of these genes in a fundamental way, expanding the competitiveness of this group of bacteria in intestinal colonization. This study shows the possibility of such applications, and also advances basic knowledge on probiotic bacteria,” explains Murakami.
About CNPEM
Sophisticated and effervescent environment for research and development, unique in Brazil and present in few scientific centers in the world, the Brazilian Center for Research in Energy and Materials (CNPEM) is a private non-profit organization, under the supervision of the Ministry of Science, Technology and Innovation (MCTI). The Center operates four National Laboratories and is the birthplace of the most complex project in Brazilian science – Sirius – one of the most advanced synchrotron light sources in the world. CNPEM brings together highly specialized multi-thematic teams, globally competitive laboratory infrastructures open to the scientific community, strategic lines of investigation, innovative projects in partnership with the productive sector and training of researchers and students. The Center is an environment driven by the search for solutions with impact in the areas of Health, Energy and Renewable Materials, Agro-environment, and Quantum Technologies. As of 2022, with the support of the Ministry of Education (MEC), CNPEM expanded its activities with the opening of the Ilum School of Science. The interdisciplinary higher course in Science, Technology and Innovation adopts innovative proposals with the aim of offering excellent, free, full-time training with immersion in the CNPEM research environment. Through the CNPEM 360 Platform, it is possible to explore, in a virtual and immersive way, the main environments and activities of the Center, visit: https://pages.cnpem.br/cnpem360/
