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Instruments / Technical Area	Publication Details	Published
I24-Microfocus Macromolecular Crystallography	Insights into the mechanism of action of the arbitrium communication system in SPbeta phages Francisca Gallego Del Sol , Nuria Quiles-Puchalt , Aisling Brady , José R. Penadés , Alberto Marina Nature Communications 13 DOI: 10.1038/s41467-022-31144-3 Diamond Proposal Number(s): [28394] Open Access Show Abstract ▼ Abstract: The arbitrium system is employed by phages of the SPbeta family to communicate with their progeny during infection to decide either to follow the lytic or the lysogenic cycle. The system is controlled by a peptide, AimP, that binds to the regulator AimR, inhibiting its DNA-binding activity and expression of aimX. Although the structure of AimR has been elucidated for phages SPβ and phi3T, there is still controversy regarding the molecular mechanism of AimR function, with two different proposed models for SPβ. In this study, we deepen our understanding of the system by solving the structure of an additional AimR that shows chimerical characteristics with the SPβ receptor. The crystal structures of this AimR (apo, AimP-bound and DNA-bound) together with in vitro and in vivo analyses confirm a mechanism of action by AimP-induced conformational restriction, shedding light on peptide specificity and cross regulation with relevant biological implications.	Jun 2022
I04-Macromolecular Crystallography	Antagonistic interactions between phage and host factors control arbitrium lysis–lysogeny decision Sara Zamora-Caballero , Cora Chmielowska , Nuria Quiles-Puchalt , Aisling Brady , Francisca Gallego Del Sol , Javier Mancheño-Bonillo , Alonso Felipe-Ruíz , Wilfried J. J. Meijer , José R. Penadés , Alberto Marina Nature Microbiology 9, 161 - 172 DOI: 10.1038/s41564-023-01550-4 Diamond Proposal Number(s): [2452] Open Access Show Abstract ▼ Abstract: Phages can use a small-molecule communication arbitrium system to coordinate lysis–lysogeny decisions, but the underlying mechanism remains unknown. Here we determined that the arbitrium system in Bacillus subtilis phage phi3T modulates the bacterial toxin–antitoxin system MazE–MazF to regulate the phage life cycle. We show that phi3T expresses AimX and YosL, which bind to and inactivate MazF. AimX also inhibits the function of phi3T_93, a protein that promotes lysogeny by binding to MazE and releasing MazF. Overall, these mutually exclusive interactions promote the lytic cycle of the phage. After several rounds of infection, the phage-encoded AimP peptide accumulates intracellularly and inactivates the phage antiterminator AimR, a process that eliminates aimX expression from the aimP promoter. Therefore, when AimP increases, MazF activity promotes reversion back to lysogeny, since AimX is absent. Altogether, our study reveals the evolutionary strategy used by arbitrium to control lysis–lysogeny by domesticating and fine-tuning a phage-defence mechanism.	Jan 2024
I04-Macromolecular Crystallography I24-Microfocus Macromolecular Crystallography	Structure and rational engineering of the PglX methyltransferase and specificity factor for BREX phage defence Sam C. Went , David M. Picton , Richard D. Morgan , Andrew Nelson , Aisling Brady , Giuseppina Mariano , David T. F. Dryden , Darren L. Smith , Nicolas Wenner , Jay C. D. Hinton , Tim R. Blower Nature Communications 15 DOI: 10.1038/s41467-024-51629-7 Diamond Proposal Number(s): [24948] Open Access Show Abstract ▼ Abstract: Bacteria have evolved a broad range of systems that provide defence against their viral predators, bacteriophages. Bacteriophage Exclusion (BREX) systems recognise and methylate 6 bp non-palindromic motifs within the host genome, and prevent replication of non-methylated phage DNA that encodes these same motifs. How BREX recognises cognate motifs has not been fully understood. In this study we characterise BREX from pathogenic Salmonella and present X-ray crystallographic structures of the conserved BREX protein, PglX. The PglX N-terminal domain encodes the methyltransferase, whereas the C-terminal domain is for motif recognition. We also present the structure of PglX bound to the phage-derived DNA mimic, Ocr, an inhibitor of BREX activity. Our analyses propose modes for DNA-binding by PglX and indicate that both methyltransferase activity and defence require larger BREX complexes. Through rational engineering of PglX we broaden both the range of phages targeted, and the host motif sequences that are methylated by BREX. Our data demonstrate that PglX is used to recognise specific DNA sequences for BREX activity, contributing to motif recognition for both phage defence and host methylation.	Aug 2024

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