Biology subjects

Mancheno-Bonillo, J.

Publications and source records attributed to Mancheno-Bonillo, 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↗

bioRxiv2019

A reversible memory switch for plant synthetic biology based on the phage PhiC31 integration system

Plant synthetic biology aims to contribute to global food security by engineering plants with new or improved functionalities. In recent years, synthetic biology has rapidly advanced from the setup of basic genetic devices to the design of increasingly complex gene circuits able to provide organisms with novel functions. While many bacterial, fungal and mammalian unicellular chassis have been extensively engineered, this progress has been delayed in plants due to their complex multicellular nature and the lack of reliable DNA devices that allow an accurate design of more sophisticated biological circuits. Among these basic devices, gene switches are crucial to deploying new layers of regulation into the engineered organisms. Of special interest are bistable genetic toggle switches, which allow a living organism to exist in two alternative states and switch between them with a minimal metabolic burden. Naturally occurring toggle switches control important decision-making processes such as cell fate and developmental events. We sought to engineer whole plants with an orthogonal genetic toggle switch to be able to regulate artificial functions with minimal interference with their natural pathways. Here we report a bistable toggle memory switch for whole plants based on the phage PhiC31 serine integrase and its cognate recombination directionality factor (RDF). This genetic device was designed to control the transcription of two genes of interest by inversion of a central DNA regulatory element. Each state of the device is defined by one transcriptionally active gene of interest, while the other one remains inactive. The state of the switch can be reversibly modified by the action of the recombination actuators, which were administered externally (e.g. via agroinfiltration), or produced internally in response to an inducible chemical stimulus. We extensively characterized the kinetics, memory, and reversibility of this genetic switch in Nicotiana benthamiana through transient and stable transformation experiments using transgenic plants and hairy roots. Finally, we coupled the integrase expression to an estradiol-inducible promoter as a proof of principle of inducible activation of the switch.

synthetic biology↗