Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems

Anna A Kudryavtseva; Eva Cséfalvay; Evgeniy Yu Gnuchikh; Darya D Yanovskaya; Mikhail A Skutel; Artem B Isaev; Sergey V Bazhenov; Anna A Utkina; Ilya V Manukhov

doi:10.3389/fmicb.2023.1133144

Broadness and specificity: ArdB, ArdA, and Ocr against various restriction-modification systems

Front Microbiol. 2023 Apr 17:14:1133144. doi: 10.3389/fmicb.2023.1133144. eCollection 2023.

Authors

Anna A Kudryavtseva¹, Eva Cséfalvay², Evgeniy Yu Gnuchikh³, Darya D Yanovskaya⁴, Mikhail A Skutel⁴, Artem B Isaev⁴, Sergey V Bazhenov^{1

5

6}, Anna A Utkina¹, Ilya V Manukhov^{1

5

6}

Affiliations

¹ Laboratory for Molecular Genetics, Moscow Institute of Physics and Technology, Dolgoprudny, Russia.
² Laboratory of Structural Biology and Bioinformatics, Institute of Microbiology, Academy of Sciences of the Czech Republic, Nové Hrady, Czechia.
³ Kurchatov Genomic Center, National Research Center Kurchatov Institute, Moscow, Russia.
⁴ Center of Cellular and Molecular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia.
⁵ Laboratory for Microbiology, BIOTECH University, Moscow, Russia.
⁶ Faculty of Physics, HSE University, Moscow, Russia.

Abstract

ArdB, ArdA, and Ocr proteins inhibit the endonuclease activity of the type I restriction-modification enzymes (RMI). In this study, we evaluated the ability of ArdB, ArdA, and Ocr to inhibit different subtypes of Escherichia coli RMI systems (IA, IB, and IC) as well as two Bacillus licheniformis RMI systems. Furthermore we explored, the antirestriction activity of ArdA, ArdB, and Ocr against a type III restriction-modification system (RMIII) EcoPI and BREX. We found that DNA-mimic proteins, ArdA and Ocr exhibit different inhibition activity, depending on which RM system tested. This effect might be linked to the DNA mimicry nature of these proteins. In theory, DNA-mimic might competitively inhibit any DNA-binding proteins; however, the efficiency of inhibition depend on the ability to imitate the recognition site in DNA or its preferred conformation. In contrast, ArdB protein with an undescribed mechanism of action, demonstrated greater versatility against various RMI systems and provided similar antirestriction efficiency regardless of the recognition site. However, ArdB protein could not affect restriction systems that are radically different from the RMI such as BREX or RMIII. Thus, we assume that the structure of DNA-mimic proteins allows for selective inhibition of any DNA-binding proteins depending on the recognition site. In contrast, ArdB-like proteins inhibit RMI systems independently of the DNA recognition site.

Keywords: ArdA; ArdB; RMI; antirestriction; conjugative plasmid.

Grants and funding

The study of AK on antirestriction activity against gram-negative and gram-positive RMI systems was supported by RSF grant 22-74-00027. The study of AI, MS, and DY on the antirestriction activity against BREX and EcoPI was supported by grants from RSF (22-14-00004) and the Ministry of Science and Higher Education of the Russian Federation (075-10-2021-114). AI was supported by the Skoltech Systems Biology Fellowship. The study of EG on working with gram-positive bacteria and searching RM-I genes in gram-positive bacteria was supported by the Ministry of Science and Higher Education of the Russian Federation, Grant 075-15-2019-1659. The study of IM on manuscript edition and supervision was supported by the Ministry of Science and Higher Education of the RF, project FSMF-2022-0007; Development of technology for rational and highly productive use of agro- and bioresources, their efficient processing and obtaining safe and high-quality sources of food and non-food products.