Scientists Elucidate DNA Recognition By BREX System And Program Its Specificity

Bacteriophages, the most abundant life form on Earth, infect bacterial cells and influence the structure of the microbial community. To fend off phage attacks, bacteria have evolved their own defense tools, including the most common restriction-modification (R-M) and CRISPR-Cas systems. In addition, bacteria encode a collection of several hundred more rare and obscure defense systems, some of which, such as BREX, exploit modification of their own DNA to distinguish it from viral DNA and are more complex than the classical R-M systems.

Researchers from the Skoltech Laboratory for Metagenome Analysis, which is led by Assistant Professor Artem Isaev, and their colleagues from the United Kingdom have studied the BREX methyltransferase and determined the protein structure, which helped to program its specificity for DNA sites and significantly enhanced antiviral defense. The research, supported by a grant from the Russian Science Foundation, was published in Nature Communications.

“In our laboratory, we have been studying BREX since its discovery. This rather complex six-protein system is interesting because it combines classical DNA methylation with new antiviral mechanisms. In this study, we tried to find out how BREX distinguishes between self and non-self and what role the BrxX methyltransferase plays in this process. Our colleagues from Dmitry Gilyarov’s laboratory solved the structure of BrxX in a complex with a site-specific DNA substrate and found out how specific nucleotides in the BREX site are recognized. Using this knowledge, we were able to mutagenize BrxX and program it to recognize new DNA sites. Unexpectedly, this also significantly increased the antiviral activity of BREX,” says Alena Drobiazko, the study’s lead author and a Life Sciences PhD student at Skoltech.

“In our work, we also showed that BrxX is an essential element for both the methylation of bacterial DNA and the defense step. Interestingly, this protein, which was inactive in both in vitro and in vivo experiments, was functional after the assembly of a large BREX complex. In simple type II R-M systems, methylase and restrictase are two separate proteins, whereas in BREX, both the methylation of its own DNA and the recognition and restriction of unmethylated viral DNA are performed by the “supramolecular” BREX complex. In our further research, we expect to find out how the BREX system decides between attacking or defending DNA and how the protection mechanism works,” says Mikhail Skutel, a co-author of the paper and a Life Sciences PhD student at Skoltech.

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Skoltech is a private international university in Russia, cultivating a new generation of leaders in technology, science, and business. As a factory of technologies, it conducts research in breakthrough fields and promotes technological innovation to solve critical problems that face Russia and the world. Skoltech focuses on six priority areas: life sciences, health, and agro; telecommunications, photonics, and quantum technologies; artificial intelligence; advanced materials and engineering; energy efficiency and the energy transition; and advanced studies. Established in 2011 in collaboration with the Massachusetts Institute of Technology (MIT), Skoltech was listed among the world’s top 100 young universities by the Nature Index in its both editions (2019, 2021). On Research.com, the Institute ranks as Russian university No. 2 overall and No. 1 for genetics and materials science. In the recent SCImago Institutions Rankings, Skoltech placed first nationwide for computer science. Website: https://www.skoltech.ru/.

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