Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

Alena Drobiazko; Myfanwy C. Adams; Mikhail Skutel; Kristina Potekhina; Oksana Kotovskaya; Anna Trofimova; Mikhail Matlashov; Daria Yatselenko; Karen L. Maxwell; Tim R. Blower; Konstantin Severinov; Dmitry Ghilarov; Artem Isaev

doi:10.1038/s41467-025-57006-2

Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

Alena Drobiazko, Myfanwy C. Adams, Mikhail Skutel, Kristina Potekhina, Oksana Kotovskaya, Anna Trofimova, Mikhail Matlashov, Daria Yatselenko, Karen L. Maxwell, Tim R. Blower, Konstantin Severinov, Dmitry Ghilarov, Artem Isaev

Research output: Contribution to journal › Article › peer-review

Abstract

Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.

Original language	American English
Article number	1825
Journal	Nature communications
Volume	16
Issue number	1
DOIs	https://doi.org/10.1038/s41467-025-57006-2
State	Published - Dec 2025
Externally published	Yes

ASJC Scopus subject areas

General Chemistry
General Biochemistry, Genetics and Molecular Biology
General Physics and Astronomy

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10.1038/s41467-025-57006-2

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title = "Molecular basis of foreign DNA recognition by BREX anti-phage immunity system",

abstract = "Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-{\AA} cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.",

author = "Alena Drobiazko and Adams, {Myfanwy C.} and Mikhail Skutel and Kristina Potekhina and Oksana Kotovskaya and Anna Trofimova and Mikhail Matlashov and Daria Yatselenko and Maxwell, {Karen L.} and Blower, {Tim R.} and Konstantin Severinov and Dmitry Ghilarov and Artem Isaev",

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doi = "10.1038/s41467-025-57006-2",

language = "American English",

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T1 - Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

AU - Drobiazko, Alena

AU - Adams, Myfanwy C.

AU - Skutel, Mikhail

AU - Potekhina, Kristina

AU - Kotovskaya, Oksana

AU - Trofimova, Anna

AU - Matlashov, Mikhail

AU - Yatselenko, Daria

AU - Maxwell, Karen L.

AU - Blower, Tim R.

AU - Severinov, Konstantin

AU - Ghilarov, Dmitry

AU - Isaev, Artem

PY - 2025/12

Y1 - 2025/12

N2 - Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.

AB - Anti-phage systems of the BREX (BacteRiophage EXclusion) superfamily rely on site-specific epigenetic DNA methylation to discriminate between the host and invading DNA. We demonstrate that in Type I BREX systems, defense and methylation require BREX site DNA binding by the BrxX (PglX) methyltransferase employing S-adenosyl methionine as a cofactor. We determined 2.2-Å cryoEM structure of Escherichia coli BrxX bound to target dsDNA revealing molecular details of BREX DNA recognition. Structure-guided engineering of BrxX expands its DNA specificity and dramatically enhances phage defense. We show that BrxX alone does not methylate DNA, and BREX activity requires an assembly of a supramolecular BrxBCXZ immune complex. Finally, we present a cryoEM structure of BrxX bound to a phage-encoded inhibitor Ocr that sequesters BrxX in an inactive dimeric form. We propose that BrxX-mediated foreign DNA sensing is a necessary first step in activation of BREX defense.

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Molecular basis of foreign DNA recognition by BREX anti-phage immunity system

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