Biology subjects

Penades, J.

Publications and source records attributed to Penades, J..

3 recordsLinked to original sources

bioRxiv2025

An unprecedented DNA recognition-mimicry switch governs induction in arbitrium phages

Temperate phages integrate multiple information sources to regulate lysis-lysogeny transitions. SPBeta-like phages use arbitrium signalling and DNA damage to control repressor activity during lytic induction, but how the repressor functions and is inactivated by the SOS response remains unclear. Here, we show that SroF, the SPBeta-like phage repressor, binds DNA via a novel mechanism involving its integrase-like fold, enabling stable prophage repression. Upon DNA damage, the host SOS response triggers derepression of a newly identified antirepressor, Sar. Sar binds SroF by mimicking the DNA structure recognised by the repressor, inactivating its function and inducing phage. This mechanism is conserved across SP{beta}-like phages, which encode multiple, specific SroF-Sar pairs. Surprisingly, repressor inactivation alone is insufficient for induction when arbitrium levels are high. Our results uncover the mechanism underlying the double layer of control that ensures phage induction occurs only under SOS conditions and in the absence of neighbouring prophages.

molecular biology↗

bioRxiv2025

Phages communicate across species to shape microbial ecosystems

Arbitrium is a communication system that helps bacteriophages decide between lysis and lysogeny via secreted peptides. In arbitrium, the AimP peptide binds its cognate AimR receptor to repress aimX expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we question this view by demonstrating cross-communication between distinct arbitrium systems. Using prototypical arbitrium phages, we demonstrate that AimP peptides bind and repress unrelated AimR receptors, promoting lysogeny and reducing prophage induction. Structural and binding assays reveal conserved residues enabling cross-recognition while preserving specificity. In mixed lysogenic cultures, these interactions shape induction outcomes, demonstrating ecological relevance. We extent these findings to infection contexts, showing that arbitrium signalling influences outcomes in cells harbouring prophages with compatible communicating systems. These findings reveal that phages engage in cross-species communication, a trait restricted to more complex life forms, challenging our understanding of how these elements reshape microbial communities.

microbiology↗

bioRxiv2021

The secret life (cycle) of temperate bacteriophages

Lysogenic induction ends the stable association between a bacteriophage and its host, and the transition to the lytic cycle begins with prophage excision followed by DNA replication and packaging (ERP) - a temporal program that is considered universal for most temperate phages. Here we report that the long-standing ERP program is an artefact of the experimentally favoured Salmonella phage P22 tsc229 heat-inducible mutant, and that wildtype P22 actually follows a replication-packaging-excision (RPE) program. We found that unlike P22 tsc229, P22 delayed excision to just before it was detrimental to phage production. Thus, at minimal expense to itself, P22 has tuned the timing of excision to balance propagation with lateral transduction, powering the evolution of its host through gene transfer in the interest of self-preservation. One Sentence SummaryGenetic analyses propose a new life cycle for temperate bacteriophages.

microbiology↗