24 páginas, 7 figuras, información suplementaria, Arbitrium-coding phages use peptides to communicate and coordinate the decision between lysis and lysogeny. However, the mechanism by which these phages establish lysogeny remains unknown. Here, focusing on the SPbeta phage family's model phages phi3T and SPβ, we report that a six-gene operon called the "SPbeta phages repressor operon" (sro) expresses not one but two master repressors, SroE and SroF, the latter of which folds like a classical phage integrase. To promote lysogeny, these repressors bind to multiple sites in the phage genome. SroD serves as an auxiliary repressor that, with SroEF, forms the repression module necessary for lysogeny establishment and maintenance. Additionally, the proteins SroABC within the operon are proposed to constitute the transducer module, connecting the arbitrium communication system to the activity of the repression module. Overall, this research sheds light on the intricate and specialized repression system employed by arbitrium SPβ-like phages in making lysis-lysogeny decisions., X-ray diffraction data collection
was supported by block allocation group (BAG) DLS Proposal MX28394,
ESRRF Proposal MX-2443 ALBA Proposal 2022075911. Some figures in this
manuscript have been created with Biorender.com. This work was supported
by grants PID2019-108541GB-I00 and PID2022-137201NB-I00 from the
Spanish Government (Ministry of Science and Innovation) and PROMETEO/
2020/012 by Valencian Government to A.M., and grants MR/V000772/1,
MR/X020223/1, and MR/S00940X/1 from the Medical Research Council
(UK), BB/V002376/1 and BB/V009583/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), and EP/X026671/1 from the Engineering and Physical Sciences Research Council (EPSRC, UK) to J.R.P. A.M.
is part of the CSIC’s Global Health Platform (PTI Salud Global). E.C.-Y.
received an FPI predoctoral fellowship from the Spanish Ministry of Science
and Innovation with identifier PRE2020-092531., Peer reviewed

Early life represents a critical window for metabolic, cognitive and immune system development, which is influenced by the maternal microbiome as well as the infant gut microbiome. Antibiotic exposure, mode of delivery and breastfeeding practices modulate the gut microbiome and the reservoir of antibiotic resistance genes (ARGs). Vertical and horizontal microbial gene transfer during early life and the mechanisms behind these transfers are being uncovered. In this review, we aim to provide an overview of the current knowledge on the transfer of antibiotic resistance in the mother-infant dyad through vertical and horizontal transmission and to highlight the main gaps and challenges in this area., This work has been supported by PROMETEO GVA (NEOHEALTH ref. 2020/012). The authors acknowledge the comments and suggestions of Dr. Raul Cabrera-Rubio. who thanks the Generalitat-Valenciana for the grant of the Plan GenT project (CDEIGENT 2020). M.B. thanks to the post-PhD grant 'Juan de la Cierva' (ref. JDC2022-050269-I) supported by the Spanish Ministry of Science, Innovation and Universities/State Investigation Agency (MCIU/AEI) and the European Union 'NextGenerationEU'/PRTR. E.C-Y received a FPI predoctoral fellowship from the Spanish Ministry of Science and Innovation with identifier PRE2020-092531. E.F.V thanks to a Predoctoral grant awarded by the Spanish Ministry of Science and Innovation and the European Social Fund Plus (ESF+) for the training of doctors within the framework of the State Plan for Scientific, Technical and Innovation Research 2021–2023 (ref. CEX2021-001189-S-20-1). A.S. acknowledges Generalitat-Valenciana-European Social Fund (ACIF/2021) for the predoctoral fellowship grant. M.C.C. acknowledges the support by the European Research Council Starting grant (MAMI grant ref. 639226), Horizon Europe Program (INITIALISE ref. 101094099), Spanish Ministry of Science and Innovation (MAMI-Plus ref. PID2022-139475OB-I00), by the Joint Action 'European Joint Programming Initiative “A Healthy Diet for a Healthy Life” (JPI-HDHL)' — FOOD-HYPERSENS call (ECOBIOTIC) and the national funding from Programación Conjunta Internacional (PCI) (ref. PCI2021-122059-2A), Spanish Government (Ministry of Science, Innovation and Universities) and also by Biostime Institute Nutrition & Care (BINC) grant. IATA-CSIC authors also acknowledge the Spanish government Ministry of Science and Innovation/State Investigation Agency (MCIN/AEI) to the Center of Excellence Accreditation Severo Ochoa (CEX2021-001189-S/MCIN/AEI/10.13039/501100011033). A.M. acknowledges the support by grants PID2019-108541GB-I00 and PID2022-137201NB-I00 from Spanish Government (Ministry of Science and Innovation). M.C.C. and A.M. are part of the CSIC's Global Health Platform (PTI Salud Global)., Peer reviewed

25 págs, 5 figuras, Supplementary material: 8 figs, 2 tablas, 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., This work was supported by grants PID2019-108541GB-I00 and
PID2022-137201NB-I00 from the Spanish Government (Ministerio
de Ciencia e Innovación), PROMETEO/2020/012 by the Valencian
Government and the European Commission NextGenerationEU fund
(EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud
Global) to A.M., and grants MR/M003876/1, MR/V000772/1 and MR/
S00940X/1 from the Medical Research Council (UK), BB/N002873/1,
BB/V002376/1 and BB/S003835/1 from the Biotechnology and
Biological Sciences Research Council (BBSRC, UK), ERC-ADG-2014
Proposal no. 670932 Dut-signal (from EU), and Wellcome Trust
201531/Z/16/Z to J.R.P. A.F.-R. received an FPU predoctoral fellowship
from the Spanish Ministry of Universities, reference FPU19/00433, Peer reviewed

The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter (<S2>) of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA., This research was funded by Consellería de Innovacion, ´ Universidades, Ciencia y Sociedad Digital (Generalitat Valenciana) [CIAICO 2021/0135 to ACA and JLN and PROMETEO/2020/012 to AM], Ministerio de Ciencia e Innovacion ´ (PID2020-118816 GB-I00 to AC and
PID2022-137201NB-I00 to AM) and by the European Commission
NextGenerationEU fund (EU 2020/2094), through CSIC’s Global Health
Platform (PTI Salud Global) to AM. We thank Dr. Sudakshina Ganguly
from PDBe for his help during the deposition of the coordinates of SipA.
The funders had no role in the study design, data collection and analysis,
decision to publish, or preparation of the manuscript., Peer reviewed

The AlfB α-L-fucosidase from Lacticaseibacillus paracasei exhibits high specificity on fucosyl-α1,3-N-acetylglucosamine, achieving yields of 30 % in transfucosylation reactions for its synthesis. By random mutagenesis we selected AlfB variants with enhanced transfucosylation activity. Expression of a collection of alfB mutants in E. coli resulted in the isolation of eighteen clones with reduced activity on p-nitrophenyl-α-L-fucopyranoside. The AlfB variants carried diverse amino substitutions, leading to modifications in their enzymatic parameters. In some cases, these changes increased transfucosylation yields, although no direct correlation was observed between kcat or Km values and the yields. One particular AlfB mutant (M58) achieved 100 % yield in the synthesis of fucosyl-α1,3-N-acetylglucosamine. This enzyme contained three amino acid substitutions (N196S, V261M and N346K); however, further analysis confirmed that the N346K mutation was sufficient to generate the maximum yield. Elucidation of the tridimensional structure of AlfB and AlfBM58 through X-ray crystallography allowed us to propose a mechanism by which the mutation at position 346, located in a loop close to the active site of an adjacent monomer in the protein tetramer, enhanced transfucosylation over hydrolysis of fucosyl-α1,3-N-acetylglucosamine. This study paves the way for designing novel AlfB variants as tools for the efficient enzymatic synthesis of regio-specific fucosyl-oligosaccharides of biotechnological interest., This work was supported by Grants PID2020-115403RB (C21 and C22) and PID2023-148094OB (C21 and C22) to M.J.Y. and J.R.D., and PID2022-137201NB-I00 to A.M., funded by the Spanish Ministry of Science and Innovation (MICIN)/Spanish State Research Agency (AEI)/10.13039/501100011033; by Valencian Government grants AICO/2021/033 to M.J.Y. and J.R.D. and CIPROM/2023/30 to A.M.; grant ERC-2023-SyG Proposal no 101118890 TalkingPhages (from EU) to A.M., and the European Commission NextGenerationEU fund (EU 2020/2094), through CSIC’s Global Health Platform (PTI Salud Global) to A.M., With funding from the Spanish government through the ‘Severo Ochoa Centre of Excellence’ accreditation (CEX2021-001189-S), Peer reviewed

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The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedicatio, Ministerio de Ciencia e Innovación (MCIN), 9HYX.pdb, Peer reviewed

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The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedicatio, Ministerio de Ciencia e Innovación (MCIN), 9HZ1.pdb, Peer reviewed

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The wwPDB policy states that data files contained in the PDB archive are available under the CC0 1.0 Universal (CC0 1.0) Public Domain Dedicatio, Ministerio de Ciencia e Innovación (MCIN), 8OZU.pdb, Peer reviewed

24 páginas, 7 figuras, 1 tabla, Temperate phages integrate multiple information sources to regulate lysis-lysogeny transitions. SPbeta-like phages use arbitrium signaling 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 mechanism involving its integrase-like fold, enabling stable prophage repression. Upon DNA damage, the host SOS response triggers derepression of an antirepressor, Sar. Sar binds SroF by mimicking the DNA structure recognized by the repressor, thereby inactivating its function and inducing phage. This mechanism is conserved across SPbeta-like phages, which encode multiple, specific SroF-Sar pairs. Surprisingly, repressor inactivation alone is insufficient for efficient induction when arbitrium levels are high. Our results uncover the mechanism underlying a double layer of control that ensures phage induction occurs only under SOS conditions and in the absence of neighboring prophages., We thank the IBV-CSIC Crystallogenesis Facility for protein crystallization screenings. Data collection experiments for the crystallographic structures were carried out at the XALOC beamline at ALBA Synchrotron with the collaboration of ALBA staff. X-ray diffraction data collection was supported by block allocation group (BAG)ALBAProposal2024078509.Weacknowledgesupport from the Scientific Network Conexio´n Resistencia Antimicrobianos funded by the Consejo Superior de Investigaciones Cientı´ficas (CSIC), Spain. This work was supported by grants PID2022-137201NB-I00 from the Spanish Government (Ministerio de Ciencia e Innovacio´n), CIPROM/2023/30 from the Valencian Government, and the European Commission NextGenerationEU fund (EU 2020/2094), through CSIC’s Global. Health Platform (PTI Salud Global) to A.M. and grants MR/X020223/1, MR/M003876/1, MR/V000772/1, and MR/S00940X/1 from the Medical Research Council (UK); BB/V002376/1 and BB/V009583/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK); and EP/X026671/1 from the Engineering and Physical Sciences Research Council (EPSRC, UK) to J.R.P. A.M., A.E., and J.R.P. are funded by European Research Council grant 101118890 (TalkingPhages)., Peer reviewed

10 páginas, 5 figuras, Despite the high incidence of influenza virus infections, one-fifth of people infected with influenza remain asymptomatic. The mechanisms associated with this immune resilience are, however, unknown. Here, we show that the human antimicrobial peptide dermcidin has antiviral activity against influenza viruses through binding to hemagglutinin and extends its effect to taxonomically unrelated respiratory viruses such as measles virus and human coronavirus OC43. We show that dermcidin is present in all anatomical regions associated with the entry routes of respiratory viruses, that its levels increase during viral respiratory infections, and that it protects mice against influenza disease. Notably, dermcidin levels were higher in asymptomatic individuals than in susceptible peers, suggesting a role in the onset of disease symptoms. Thus, we show that dermcidin inhibits influenza virus infection in vitro and in vivo, with potential as a human-derived product for the prevention and treatment of respiratory viral infections., This study was supported by grants INNVAL20/19/006 and INNVA2/2021/3 from the Valencian Innovation Agency (AVI), FISABIO Innovation grant PAPIRO UGP-21-047, an EXPLORA Action from the Spanish Ministry of Science and Innovation with code SAF2013-505553-EXP, CIPROM/2023/30 from Regional Ministry of Education, Culture, Universities, and Employment of the Valencian Government, PID2022-137201NB-I00 from the Spanish Ministry of Science and Innovation and by the Carlos III Health Institute, under file code CP22/00036, pursuant to the Resolution of the Director of the Carlos III Health Institute, O.A., M.P., dated December 7, 2022, granting the Miguel Servet Contracts, and cofinanced by the European Union. We thank the patients and the IBSP-CV Biobank (PT17/0015/0017) integrated in the Spanish National Biobanks Network and in the Valencian Biobanking Network for collaboration. We also thank the Central Service for Experimental Research of Universitat de València for the sequencing. Finally, we express our gratitude to Dr. Elena Tapia, Eduardo Romanos, Dr. Julián Pardo, and Dr. Maykel Arias from Instituto Aragonés de Ciencias de la Salud for assistance with the animal experiments, to Dr. Florian Krammer for kindly providing baculoviruses expressing PR8 HA ectodomain, Dr. Jeronimo Bravo for sharing insect High Five cells and to Kenneth McCreath for helpful comments on the manuscript. E.A. and A.M.F.-E. thank Dr. Carmen Gil and Dr. Ana Martínez for valuable advice and for providing access to computational resources. Some of the figure graphics were created by using BioRender.com., Peer reviewed

27 páginas, 7 figuas, información suplementaria de material y métodos, Arbitrium is a communication system that helps bacteriophages to decide between lysis and lysogeny through secreted peptides. In this system, the arbitrium communication peptide (AimP) binds its cognate arbitrium receptor (AimR) to repress aimX (a negative regulator of lysogeny) expression, promoting lysogeny. It has been assumed that each AimR responds exclusively to its own AimP. Here, we challenge this view by demonstrating cross-communication between arbitrium systems. Using prototypical arbitrium phages, we show that AimP peptides can bind and repress non-cognate AimR receptors, promoting lysogeny and reducing prophage induction. Structural and biochemical analyses reveal conserved receptor features that permit cross-recognition of non-cognate peptides while preserving recognition of cognate partners. In mixed lysogenic cultures, these interactions alter induction outcomes, underscoring their ecological significance. Extending to infection contexts, we demonstrate that crosstalk favors lysogeny of incoming phages in cells harboring compatible systems. These findings establish that phages engage in cross-species communication via peptide signaling, reshaping microbial communities in unexpected ways., This work was supported by grants PID2022-137201NB-I00 from the Spanish Government (Ministerio de Ciencia e Innovacio´n), CIPROM/2023/30 from the Valencian Government, and the European Commission NextGenerationEU fund (EU 2020/2094) through CSIC’s Global Health Platform (PTI Salud Global) to A.M.; grants MR/X020223/1, MR/M003876/1, MR/V000772/1, and MR/ S00940X/1 from the Medical Research Council (UK), BB/V002376/1 and BB/ V009583/1 from the Biotechnology and Biological Sciences Research Council (BBSRC, UK), and EP/X026671/1 from the Engineering and Physical Sciences Research Council (EPSRC, UK) to J.R.P.; and A.M. and J.R.P. are funded by ERC-2023-SyG Project 101118890—TalkingPhages. D.S. is funded by the Croucher Foundation Scholarship for Doctoral Study., Peer reviewed

18 páginas, 6 figuras, 2 tablas, Fungal antifungal proteins (AFPs) are promising biofungicides. PeAfpA and PeAfpB from Penicillium expansum show different activity profiles and potency, with PeAfpA being more active. Based on the PeAfpB solved structure, we had previously designed PeAfpB-PeAfpA chimeras that showed different properties. From these, we engineer here two additional variants, chPeAFPV6 and chPeAFPV7, that revealed novel aspects of the AFP structure, antifungal determinants and mechanism. chPeAFPV6, with a single E11K mutation in the loop L1 that is part of the γ-core motif, increased PeAfpB antifungal activity to that of PeAfpA against filamentous fungi but not yeasts, and promoted internalisation into Penicillium digitatum hyphae. However, changes in loop L3 of PeAfpB as in chPeAFPV7 abolished this increase, resulting in an inactive protein that still internalised. Overall, internalisation is neither sufficient nor essential for killing P. digitatum. Antifungal activity did not correlate with reactive oxygen species production, suggesting that oxidative burst is a fungal stress defence rather than a killing mechanism. Although cell permeabilisation was associated with antifungal activity, it does not seem to be a primary mode of action. Structural analysis showed interactions between the γ-core motif and loop L3, and suggests the importance of the conformation of the E7 residue of PeAfpB. Additionally, PeAfpA was identified as a protein able to penetrate Candida auris by a cell wall-dependent mechanism, and kill yeast cells. This study highlights the potential of the PeAfpB scaffold for engineering new-to-nature AFPs and provides novel insights into their modes of action, paving the way for future applications. KEY POINTS: A single amino acid change in the γ-core of PeAfpB enhances antifungal potency Loop L3 of PeAfpB may block activity through interaction with the γ-core Antifungal activity does not correlate with ROS production., Funding Open Access funding provided thanks to the CRUECSIC agreement with Springer Nature. This work was supported by grants PID2021-125858OB-I00, PID2024-162516OB-I00 (to PM and JFM), PID2022-1372 01NB-I00 (to AM) funded by MCIN/AEI/10.13039/501100011033, the Severo Ochoa Excellence Program
CEX2021-001189-S by “ERDF, a way of making Europe”,
and CIPROM/2023/30 (to AM) by Valencian Government (Conselleria
de Educación, Investigación, Cultura y Deporte). MGL
was a recipient of the predoctoral grant FPU19/02066 funded by
MCIN/AEI/10.13039/501100011033 and by ESF-Investing in your
future, respectively. MGL international exchange was supported by
EST23/00233 grant (funded by MCIN/AEI/10.13039/501100011033
and by ESF-Investing in your future) and SEG10314 EMBO Scientific
Exchange Grant. We acknowledge funding from the MRC Centre
for Medical Mycology at the University of Exeter (MR/N006364/2
and MR/V033417/1), the NIHR Exeter Biomedical Research Centre
(NIHR203320). The views expressed are those of the authors and
not necessarily those of the NIHR or the Department of Health and
Social Care. The structural results reported in this article derive from
measurements made at the synchrotron ALBA (Cerdanyola del Valles,
Spain) and ESRF (Grenoble, France). Data collection experiments for
the best crystals were carried at XALOC beamlines at ALBA. X-ray
diffraction data collection was supported by block allocation group
(BAG) ALBA Proposal 2023077633 and ESRF proposal MX-25s7., Peer reviewed

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The small, 78-residue long, regulator SipA interacts with the non-bleaching sensor histidine kinase (NblS). We have solved the solution structure of SipA on the basis of 990 nuclear Overhauser effect- (NOE-) derived distance constraints. The average pairwise root-mean-square deviation (RMSD) for the twenty best structures for the backbone residues, obtained by CYANA, was 1.35 ± 0.21 Å, and 1.90 ± 0.16 Å when all heavy atoms were considered (the target function of CYANA was 0.540 ± 0.08). The structure is that of a β-II class protein, basically formed by a five-stranded β-sheet composed of antiparallel strands following the arrangement: Gly6-Leu11 (β-strand 1), which packs against Leu66-Val69 (β-strand 5) on one side, and against Gly36-Thr42 (β-strand 2) on the other side; Trp50-Phe54 (β-strand 3); and Gly57-Leu60 (β-strand 4). The protein is highly mobile, as shown by measurements of R1, R2, NOE and ηxy relaxation parameters, with an average order parameter (<S2>) of 0.70; this mobility encompasses movements in different time scales. We hypothesize that this high flexibility allows the interaction with other proteins (among them NblS), and it explains the large conformational stability of SipA.