Imperial College London

Professor José R Penadés

Faculty of MedicineDepartment of Infectious Disease

Director of the MRC Centre for Molecular Biology & Infection
 
 
 
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Contact

 

j.penades Website

 
 
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Assistant

 

Mrs Anna Lee +44 (0)20 7594 2954

 
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Location

 

Flowers buildingSouth Kensington Campus

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Summary

 

Publications

Publication Type
Year
to

95 results found

Rapun-Araiz B, Haag AF, de Cesare V, Gil C, Dorado-Morales P, Penades JR, Lasa Iet al., 2020, Systematic reconstruction of the complete two-component sensorial network in staphylococcus aureus, mSystems, Vol: 5

© 2020 Rapun-Araiz et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International license. In bacteria, adaptation to changes in the environment is mainly controlled through two-component signal transduction systems (TCSs). Most bacteria contain dozens of TCSs, each of them responsible for sensing a different range of signals and controlling the expression of a repertoire of target genes (regulon). Over the years, identification of the regulon controlled by each individual TCS in different bacteria has been a recurrent question. However, limitations associated with the classical approaches used have left our knowledge far from complete. In this report, using a pioneering approach in which a strain devoid of the complete nonessential TCS network was systematically complemented with the constitutively active form of each response regulator, we have reconstituted the regulon of each TCS of S. aureus in the absence of interference between members of the family. Transcriptome sequencing (RNA-Seq) and proteomics allowed us to determine the size, complexity, and insulation of each regulon and to identify the genes regulated exclusively by one or many TCSs. This gain-of-function strategy provides the first description of the complete TCS regulon in a living cell, which we expect will be useful to understand the pathobiology of this important pathogen. IMPORTANCE Bacteria are able to sense environmental conditions and respond accordingly. Their sensorial system relies on pairs of sensory and regulatory proteins, known as two-component systems (TCSs). The majority of bacteria contain dozens of TCSs, each of them responsible for sensing and responding to a different range of signals. Traditionally, the function of each TCS has been determined by analyzing the changes in gene expression caused by the absence of individual TCSs. Here, we used a bacterial strain deprived of the complete TC sensorial system to introduce

Journal article

Fillol-Salom A, Miguel-Romero L, Marina A, Chen J, Penadés JRet al., 2020, Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation., Curr Opin Microbiol, Vol: 56, Pages: 52-58

Phage satellites are genetic elements that depend on helper phages for induction, packaging and transfer. To promote their lifestyles, they have evolved elegant and sophisticated strategies to inhibit phage reproduction, which will be reviewed here. We will principally focus on the convergent interference mechanisms used by phage-inducible chromosomal islands (PICIs), which are a family of satellite phages present in both Gram-positive and Gram-negative bacteria. While some PICI elements have been extensively studied for their roles in virulence and antibiotic resistance, recent studies have highlighted their relevance in controlling phage ecology and diversity. In many cases, these interference mechanisms are complemented by additional strategies that promote the preferential PICI packaging and dissemination of these elements in nature. Since the PICI-encoded mechanisms target conserved phage mechanisms, we propose here that the PICIs form part of the initial innate immune system that phages must overcome to infect their bacterial host.

Journal article

Kiga K, Tan X-E, Ibarra-Chávez R, Watanabe S, Aiba Y, Sato'o Y, Li F-Y, Sasahara T, Cui B, Kawauchi M, Boonsiri T, Thitiananpakorn K, Taki Y, Azam AH, Suzuki M, Penadés JR, Cui Let al., 2020, Development of CRISPR-Cas13a-based antimicrobials capable of sequence-specific killing of target bacteria, Nature Communications, Vol: 11, ISSN: 2041-1723

The emergence of antimicrobial-resistant bacteria is an increasingly serious threat to global health, necessitating the development of innovative antimicrobials. Here we report the development of a series of CRISPR-Cas13a-based antibacterial nucleocapsids, termed CapsidCas13a(s), capable of sequence-specific killing of carbapenem-resistant Escherichia coli and methicillin-resistant Staphylococcus aureus by recognizing corresponding antimicrobial resistance genes. CapsidCas13a constructs are generated by packaging programmed CRISPR-Cas13a into a bacteriophage capsid to target antimicrobial resistance genes. Contrary to Cas9-based antimicrobials that lack bacterial killing capacity when the target genes are located on a plasmid, the CapsidCas13a(s) exhibit strong bacterial killing activities upon recognizing target genes regardless of their location. Moreover, we also demonstrate that the CapsidCas13a(s) can be applied to detect bacterial genes through gene-specific depletion of bacteria without employing nucleic acid manipulation and optical visualization devices. Our data underscore the potential of CapsidCas13a(s) as both therapeutic agents against antimicrobial-resistant bacteria and nonchemical agents for detection of bacterial genes.

Journal article

Ibarra-Chávez R, Haag AF, Dorado-Morales P, Lasa I, Penadés JRet al., 2020, Rebooting Synthetic Phage-Inducible Chromosomal Islands: One Method to Forge Them All, BioDesign Research, Vol: 2020, Pages: 1-14

<jats:p>Phage-inducible chromosomal islands (PICIs) are a widespread family of mobile genetic elements, which have an important role in bacterial pathogenesis. These elements mobilize among bacterial species at extremely high frequencies, representing an attractive tool for the delivery of synthetic genes. However, tools for their genetic manipulation are limited and timing consuming. Here, we have adapted a synthetic biology approach for rapidly editing of PICIs in <jats:italic>Saccharomyces cerevisiae</jats:italic> based on their ability to excise and integrate into the bacterial chromosome of their cognate host species. As proof of concept, we engineered several PICIs from <jats:italic>Staphylococcus aureus</jats:italic> and <jats:italic>Escherichia coli</jats:italic> and validated this methodology for the study of the biology of these elements by generating multiple and simultaneous mutations in different PICI genes. For biotechnological purposes, we also synthetically constructed PICIs as Trojan horses to deliver different CRISPR-Cas9 systems designed to either cure plasmids or eliminate cells carrying the targeted genes. Our results demonstrate that the strategy developed here can be employed universally to study PICIs and enable new approaches for diagnosis and treatment of bacterial diseases.</jats:p>

Journal article

Bacigalupe R, Angeles Tormo-Mas M, Penades JR, Fitzgerald JRet al., 2019, A multihost bacterial pathogen overcomes continuous population bottlenecks to adapt to new host species, Science Advances, Vol: 5, ISSN: 2375-2548

While many bacterial pathogens are restricted to single host species, some have the capacity to undergo host switches, leading to the emergence of new clones that are a threat to human and animal health. However, the bacterial traits that underpin a multihost ecology are not well understood. Following transmission to a new host, bacterial populations are influenced by powerful forces such as genetic drift that reduce the fixation rate of beneficial mutations, limiting the capacity for host adaptation. Here, we implement a novel experimental model of bacterial host switching to investigate the ability of the multihost pathogen Staphylococcus aureus to adapt to new species under continuous population bottlenecks. We demonstrate that beneficial mutations accumulated during infection can overcome genetic drift and sweep through the population, leading to host adaptation. Our findings highlight the remarkable capacity of some bacteria to adapt to distinct host niches in the face of powerful antagonistic population forces.

Journal article

Fillol-Salom A, Bacarizo J, Alqasmi M, Rafael Ciges-Tomas J, Martinez-Rubio R, Roszak AW, Cogdell RJ, Chen J, Marina A, Penades JRet al., 2019, Hijacking the Hijackers: Escherichia coli Pathogenicity Islands Redirect Helper Phage Packaging for Their Own Benefit, MOLECULAR CELL, Vol: 75, Pages: 1020-+, ISSN: 1097-2765

Journal article

Ciges-Tomas JR, Alite C, Humphrey S, Donderisl J, Bowring J, Salvatella X, Penades JR, Marina Aet al., 2019, The structure of a polygamous repressor reveals how phage-inducible chromosomal islands spread in nature, Nature Communications, Vol: 10, ISSN: 2041-1723

Stl is a master repressor encoded by Staphylococcus aureus pathogenicity islands (SaPIs) that maintains integration of these elements in the bacterial chromosome. After infection or induction of a resident helper phage, SaPIs are de-repressed by specific interactions of phage proteins with Stl. SaPIs have evolved a fascinating mechanism to ensure their promiscuous transfer by targeting structurally unrelated proteins performing identically conserved functions for the phage. Here we decipher the molecular mechanism of this elegant strategy by determining the structure of SaPIbov1 Stl alone and in complex with two structurally unrelated dUTPases from different S. aureus phages. Remarkably, SaPIbov1 Stl has evolved different domains implicated in DNA and partner recognition specificity. This work presents the solved structure of a SaPI repressor protein and the discovery of a modular repressor that acquires multispecificity through domain recruiting. Our results establish the mechanism that allows widespread dissemination of SaPIs in nature.

Journal article

Chiang YN, Penades JR, Chen J, 2019, Genetic transduction by phages and chromosomal islands: The new and noncanonical, PLoS Pathogens, Vol: 15, Pages: 1-7, ISSN: 1553-7366

Journal article

Fillol-Salom A, Alsaadi A, de Sousa JAM, Zhong L, Foster KR, Rocha EPC, Penades JR, Ingmer H, Haaber Jet al., 2019, Bacteriophages benefit from generalized transduction, PLoS Pathogens, Vol: 15, ISSN: 1553-7366

Temperate phages are bacterial viruses that as part of their life cycle reside in the bacterial genome as prophages. They are found in many species including most clinical strains of the human pathogens, Staphylococcus aureus and Salmonella enterica serovar Typhimurium. Previously, temperate phages were considered as only bacterial predators, but mounting evidence point to both antagonistic and mutualistic interactions with for example some temperate phages contributing to virulence by encoding virulence factors. Here we show that generalized transduction, one type of bacterial DNA transfer by phages, can create conditions where not only the recipient host but also the transducing phage benefit. With antibiotic resistance as a model trait we used individual-based models and experimental approaches to show that antibiotic susceptible cells become resistant to both antibiotics and phage by i) integrating the generalized transducing temperate phages and ii) acquiring transducing phage particles carrying antibiotic resistance genes obtained from resistant cells in the environment. This is not observed for non-generalized transducing temperate phages, which are unable to package bacterial DNA, nor for generalized transducing virulent phages that do not form lysogens. Once established, the lysogenic host and the prophage benefit from the existence of transducing particles that can shuffle bacterial genes between lysogens and for example disseminate resistance to antibiotics, a trait not encoded by the phage. This facilitates bacterial survival and leads to phage population growth. We propose that generalized transduction can function as a mutualistic trait where temperate phages cooperate with their hosts to survive in rapidly-changing environments. This implies that generalized transduction is not just an error in DNA packaging but is selected for by phages to ensure their survival.

Journal article

Haag AF, Fitzgerald JR, Penades JR, 2019, Staphylococcus aureus in Animals, MICROBIOLOGY SPECTRUM, Vol: 7, ISSN: 2165-0497

Journal article

Gallego del Sol F, Penades JR, Marina A, 2019, Deciphering the Molecular Mechanism Underpinning Phage Arbitrium Communication Systems, MOLECULAR CELL, Vol: 74, Pages: 59-+, ISSN: 1097-2765

Journal article

Manning KA, Quiles-Puchalt N, Penades JR, Dokland Tet al., 2018, A novel ejection protein from bacteriophage 80 alpha that promotes lytic growth, VIROLOGY, Vol: 525, Pages: 237-247, ISSN: 0042-6822

Journal article

Chen J, Quiles-Puchalt N, Chiang YN, Bacigalupe R, Fillol-Salom A, Chee MSJ, Fitzgerald JR, Penades JRet al., 2018, Genome hypermobility by lateral transduction, SCIENCE, Vol: 362, Pages: 207-+, ISSN: 0036-8075

Journal article

Fillol-Salom A, Martinez-Rubio R, Abdulrahman RF, Chen J, Davies R, Penades JRet al., 2018, Phage-inducible chromosomal islands are ubiquitous within the bacterial universe, The ISME Journal: multidisciplinary journal of microbial ecology, Vol: 12, Pages: 2114-2128, ISSN: 1751-7362

Phage-inducible chromosomal islands (PICIs) are a recently discovered family of pathogenicity islands that contribute substantively to horizontal gene transfer, host adaptation and virulence in Gram-positive cocci. Here we report that similar elements also occur widely in Gram-negative bacteria. As with the PICIs from Gram-positive cocci, their uniqueness is defined by a constellation of features: unique and specific attachment sites, exclusive PICI genes, a phage-dependent mechanism of induction, conserved replication origin organization, convergent mechanisms of phage interference, and specific packaging of PICI DNA into phage-like infectious particles, resulting in very high transfer frequencies. We suggest that the PICIs represent two or more distinct lineages, have spread widely throughout the bacterial world, and have diverged much more slowly than their host organisms or their prophage cousins. Overall, these findings represent the discovery of a universal class of mobile genetic elements.

Journal article

Fernandez L, Gonzalez S, Quiles-Puchalt N, Gutierrez D, Penades JR, Garcia P, Rodriguez Aet al., 2018, Lysogenization of Staphylococcus aureus RN450 by phages phi 11 and phi 80 alpha leads to the activation of the SigB regulon, Scientific Reports, Vol: 8, ISSN: 2045-2322

Staphylococcus aureus is a major opportunistic pathogen that commonly forms biofilms on various biotic and abiotic surfaces. Also, most isolates are known to carry prophages in their genomes. With this in mind, it seems that acquiring a better knowledge of the impact of prophages on the physiology of S. aureus biofilm cells would be useful for developing strategies to eliminate this pathogen. Here, we performed RNA-seq analysis of biofilm cells formed by S. aureus RN450 and two derived strains carrying prophages ϕ11 and ϕ80α. The lysogenic strains displayed increased biofilm formation and production of the carotenoid pigment staphyloxanthin. These phenotypes could be partly explained by the differences in gene expression displayed by prophage-harboring strains, namely an activation of the alternative sigma factor (SigB) regulon and downregulation of genes controlled by the Agr quorum-sensing system, especially the decreased transcription of genes encoding dispersion factors like proteases. Nonetheless, spontaneous lysis of part of the population could also contribute to the increased attached biomass. Interestingly, it appears that the phage CI protein plays a role in orchestrating these phage-host interactions, although more research is needed to confirm this possibility. Likewise, future studies should examine the impact of these two prophages during the infection.

Journal article

Villanueva M, Garcia B, Valle J, Rapun B, Ruiz de los Mozos I, Solano C, Marti M, Penades JR, Toledo-Arana A, Lasa Iet al., 2018, Sensory deprivation in Staphylococcus aureus, Nature Communications, Vol: 9, ISSN: 2041-1723

Bacteria use two-component systems (TCSs) to sense and respond to environmental changes. The core genome of the major human pathogen Staphylococcus aureus encodes 16 TCSs, one of which (WalRK) is essential. Here we show that S. aureus can be deprived of its complete sensorial TCS network and still survive under growth arrest conditions similarly to wild-type bacteria. Under replicating conditions, however, the WalRK system is necessary and sufficient to maintain bacterial growth, indicating that sensing through TCSs is mostly dispensable for living under constant environmental conditions. Characterization of S. aureus derivatives containing individual TCSs reveals that each TCS appears to be autonomous and self-sufficient to sense and respond to specific environmental cues, although some level of cross-regulation between non-cognate sensor-response regulator pairs occurs in vivo. This organization, if confirmed in other bacterial species, may provide a general evolutionarily mechanism for flexible bacterial adaptation to life in new niches.

Journal article

Haaber J, Penades JR, Ingmer H, 2017, Transfer of Antibiotic Resistance in Staphylococcus aureus, TRENDS IN MICROBIOLOGY, Vol: 25, Pages: 893-905, ISSN: 0966-842X

Journal article

Alite C, Humphrey S, Donderis J, Maiques E, Ciges-Tomas JR, Penades JR, Marina Aet al., 2017, Dissecting the link between the enzymatic activity and the SaPI inducing capacity of the phage 80 alpha dUTPase, Scientific Reports, Vol: 7, ISSN: 2045-2322

The trimeric staphylococcal phage-encoded dUTPases (Duts) are signalling molecules that induce the cycle of some Staphylococcal pathogenicity islands (SaPIs) by binding to the SaPI-encoded Stl repressor. To perform this regulatory role, these Duts require an extra motif VI, as well as the Dut conserved motifs IV and V. While the apo form of Dut is required for the interaction with the Stl repressor, usually only those Duts with normal enzymatic activity can induce the SaPI cycle. To understand the link between the enzymatic activities and inducing capacities of the Dut protein, we analysed the structural, biochemical and physiological characteristics of the Dut80α D95E mutant, which loses the SaPI cycle induction capacity despite retaining enzymatic activity. Asp95 is located at the threefold central channel of the trimeric Dut where it chelates a divalent ion. Here, using state-of-the-art techniques, we demonstrate that D95E mutation has an epistatic effect on the motifs involved in Stl binding. Thus, ion binding in the central channel correlates with the capacity of motif V to twist and order in the SaPI-inducing disposition, while the tip of motif VI is disturbed. These alterations in turn reduce the affinity for the Stl repressor and the capacity to induce the SaPI cycle.

Journal article

Donderis J, Bowring J, Maiques E, Ciges-Tomas JR, Alite C, Mehmedov I, Tormo-Mas MA, Penades JR, Marina Aet al., 2017, Convergent evolution involving dimeric and trimeric dUTPases in pathogenicity island mobilization, PLoS Pathogens, Vol: 13, ISSN: 1553-7366

The dUTPase (Dut) enzymes, encoded by almost all free-living organisms and some viruses, prevent the misincorporation of uracil into DNA. We previously proposed that trimeric Duts are regulatory proteins involved in different cellular processes; including the phage-mediated transfer of the Staphylococcus aureus pathogenicity island SaPIbov1. Recently, it has been shown that the structurally unrelated dimeric Dut encoded by phage ϕNM1 is similarly able to mobilize SaPIbov1, suggesting dimeric Duts could also be regulatory proteins. How this is accomplished remains unsolved. Here, using in vivo, biochemical and structural approaches, we provide insights into the signaling mechanism used by the dimeric Duts to induce the SaPIbov1 cycle. As reported for the trimeric Duts, dimeric Duts contain an extremely variable region, here named domain VI, which is involved in the regulatory capacity of these enzymes. Remarkably, our results also show that the dimeric Dut signaling mechanism is modulated by dUTP, as with the trimeric Duts. Overall, our results demonstrate that although unrelated both in sequence and structure, dimeric and trimeric Duts control SaPI transfer by analogous mechanisms, representing a fascinating example of convergent evolution. This conserved mode of action highlights the biological significance of Duts as regulatory molecules.

Journal article

Bowring J, Neamah MM, Donderis J, Mir-Sanchis I, Alite C, Rafael Ciges-Tomas J, Maiques E, Medmedov I, Marina A, Penades JRet al., 2017, Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer, ELIFE, Vol: 6, ISSN: 2050-084X

Journal article

Bowring J, Neamah MM, Donderis J, Mir-Sanchis I, Alite C, Ciges-Tomas JR, Maiques E, Medmedov I, Marina A, Penadés JRet al., 2017, Pirating conserved phage mechanisms promotes promiscuous staphylococcal pathogenicity island transfer, eLife, Vol: 6, ISSN: 2050-084X

Targeting conserved and essential processes is a successful strategy to combat enemies. Remarkably, the clinically important Staphylococcus aureus pathogenicity islands (SaPIs) use this tactic to spread in nature. SaPIs reside passively in the host chromosome, under the control of the SaPI-encoded master repressor, Stl. It has been assumed that SaPI de-repression is effected by specific phage proteins that bind to Stl, initiating the SaPI cycle. Different SaPIs encode different Stl repressors, so each targets a specific phage protein for its de-repression. Broadening this narrow vision, we report here that SaPIs ensure their promiscuous transfer by targeting conserved phage mechanisms. This is accomplished because the SaPI Stl repressors have acquired different domains to interact with unrelated proteins, encoded by different phages, but in all cases performing the same conserved function. This elegant strategy allows intra- and inter-generic SaPI transfer, highlighting these elements as one of nature's most fascinating subcellular parasites.

Journal article

Neamah MM, Mir-Sanchis I, Lopez-Sanz M, Acosta S, Baquedano I, Haag AF, Marina A, Ayora S, Penades JRet al., 2017, Sak and Sak4 recombinases are required for bacteriophage replication in Staphylococcus aureus, Nucleic Acids Research, Vol: 45, Pages: 6507-6519, ISSN: 0305-1048

DNA-single strand annealing proteins (SSAPs) are recombinases frequently encoded in the genome of many bacteriophages. As SSAPs can promote homologous recombination among DNA substrates with an important degree of divergence, these enzymes are involved both in DNA repair and in the generation of phage mosaicisms. Here, analysing Sak and Sak4 as representatives of two different families of SSAPs present in phages infecting the clinically relevant bacterium Staphylococcus aureus, we demonstrate for the first time that these enzymes are absolutely required for phage reproduction. Deletion of the genes encoding these enzymes significantly reduced phage replication and the generation of infectious particles. Complementation studies revealed that these enzymes are required both in the donor (after prophage induction) and in the recipient strain (for infection). Moreover, our results indicated that to perform their function SSAPs require the activity of their cognate single strand binding (Ssb) proteins. Mutational studies demonstrated that the Ssb proteins are also required for phage replication, both in the donor and recipient strain. In summary, our results expand the functions attributed to the Sak and Sak4 proteins, and demonstrate that both SSAPs and Ssb proteins are essential for the life cycle of temperate staphylococcal phages.

Journal article

Martinez-Rubio R, Quiles-Puchalt N, Marti M, Humphrey S, Ram G, Smyth D, Chen J, Novick RP, Penades JRet al., 2017, Phage-inducible islands in the Gram-positive cocci, ISME JOURNAL, Vol: 11, Pages: 1029-1042, ISSN: 1751-7362

Journal article

Haaber J, Leisner JJ, Cohn MT, Catalan-Moreno A, Nielsen JB, Westh H, Penades JR, Ingmer Het al., 2016, Bacterial viruses enable their host to acquire antibiotic resistance genes from neighbouring cells, Nature Communications, Vol: 7, ISSN: 2041-1723

Prophages are quiescent viruses located in the chromosomes of bacteria. In the human pathogen, Staphylococcus aureus, prophages are omnipresent and are believed to be responsible for the spread of some antibiotic resistance genes. Here we demonstrate that release of phages from a subpopulation of S. aureus cells enables the intact, prophage-containing population to acquire beneficial genes from competing, phage-susceptible strains present in the same environment. Phage infection kills competitor cells and bits of their DNA are occasionally captured in viral transducing particles. Return of such particles to the prophage-containing population can drive the transfer of genes encoding potentially useful traits such as antibiotic resistance. This process, which can be viewed as ‘auto-transduction’, allows S. aureus to efficiently acquire antibiotic resistance both in vitro and in an in vivo virulence model (wax moth larvae) and enables it to proliferate under strong antibiotic selection pressure. Our results may help to explain the rapid exchange of antibiotic resistance genes observed in S. aureus.

Journal article

Carpena N, Manning KA, Dokland T, Marina A, Penades JRet al., 2016, Convergent evolution of pathogenicity islands in helper cos phage interference, Philosophical Transactions of the Royal Society B: Biological Sciences, Vol: 371, ISSN: 0962-8436

Staphylococcus aureus pathogenicity islands (SaPIs) are phage satellites that exploit the life cycle of their helper phages for their own benefit. Most SaPIs are packaged by their helper phages using a headful (pac) packaging mechanism. These SaPIs interfere with pac phage reproduction through a variety of strategies, including the redirection of phage capsid assembly to form small capsids, a process that depends on the expression of the SaPI-encoded cpmA and cpmB genes. Another SaPI subfamily is induced and packaged by cos-type phages, and although these cos SaPIs also block the life cycle of their inducing phages, the basis for this mechanism of interference remains to be deciphered. Here we have identified and characterized one mechanism by which the SaPIs interfere with cos phage reproduction. This mechanism depends on a SaPI-encoded gene, ccm, which encodes a protein involved in the production of small isometric capsids, compared with the prolate helper phage capsids. As the Ccm and CpmAB proteins are completely unrelated in sequence, this strategy represents a fascinating example of convergent evolution. Moreover, this result also indicates that the production of SaPI-sized particles is a widespread strategy of phage interference conserved during SaPI evolution.

Journal article

Bowring JZ, Marina A, Penadés JR, Quiles-Puchalt Net al., 2016, Bacteriophage Moonlighting Proteins in the Control of Bacterial Pathogenicity, Moonlighting Proteins: Novel Virulence Factors in Bacterial Infections, Pages: 387-412, ISBN: 9781118951118

© 2017 John Wiley & Sons, Inc. This chapter describes the dual role of bacteria-encoded proteins along with their impact on the bacteriophage biology and the repercussion in bacterial pathogenicity. The use of bacteriophage-encoded proteins as de-repressor proteins is an elegant strategy that allows the Staphylococcus aureus pathogenicity islands (SaPI) to be induced only when the helper phage has entered the lytic cycle. The chapter examines the dual role of various well-known and well-characterized bacteriophage moonlighting proteins and their impact on bacterial pathogenicity. The first example of moonlighting proteins studied was the homing endonuclease T4 I-TevI encoded by the T4 bacteriophage. This homing endonuclease, in addition to its main cleavage activity, has a role as a transcriptional regulator controlling its own transfer. Understanding the biology of bacteriophages is of great importance due to their crucial role in bacterial pathogenicity, as well as for the study of the different proteins and functions that they have for their own biology.

Book chapter

Taglialegna A, Navarro S, Ventura S, Garnett JA, Matthews S, Penades JR, Lasa I, Valle Jet al., 2016, Staphylococcal Bap Proteins Build Amyloid Scaffold Biofilm Matrices in Response to Environmental Signals, PLOS Pathogens, Vol: 12, ISSN: 1553-7366

Biofilms are communities of bacteria that grow encased in an extracellular matrix that often contains proteins. The spatial organization and the molecular interactions between matrix scaffold proteins remain in most cases largely unknown. Here, we report that Bap protein of Staphylococcus aureus self-assembles into functional amyloid aggregates to build the biofilm matrix in response to environmental conditions. Specifically, Bap is processed and fragments containing at least the N-terminus of the protein become aggregation-prone and self-assemble into amyloid-like structures under acidic pHs and low concentrations of calcium. The molten globule-like state of Bap fragments is stabilized upon binding of the cation, hindering its self-assembly into amyloid fibers. These findings define a dual function for Bap, first as a sensor and then as a scaffold protein to promote biofilm development under specific environmental conditions. Since the pH-driven multicellular behavior mediated by Bap occurs in coagulase-negative staphylococci and many other bacteria exploit Bap-like proteins to build a biofilm matrix, the mechanism of amyloid-like aggregation described here may be widespread among pathogenic bacteria.

Journal article

Maiques E, Quiles-Puchalt N, Donderis J, Rafael Ciges-Tomas J, Alite C, Bowring JZ, Humphrey S, Penades JR, Marina Aet al., 2016, Another look at the mechanism involving trimeric dUTPases in Staphylococcus aureus pathogenicity island induction involves novel players in the party, Nucleic Acids Research, Vol: 44, Pages: 5457-5469, ISSN: 0305-1048

We have recently proposed that the trimeric staphylococcal phage encoded dUTPases (Duts) are signaling molecules that act analogously to eukaryotic G-proteins, using dUTP as a second messenger. To perform this regulatory role, the Duts require their characteristic extra motif VI, present in all the staphylococcal phage coded trimeric Duts, as well as the strongly conserved Dut motif V. Recently, however, an alternative model involving Duts in the transfer of the staphylococcal islands (SaPIs) has been suggested, questioning the implication of motifs V and VI. Here, using state-of the-art techniques, we have revisited the proposed models. Our results confirm that the mechanism by which the Duts derepress the SaPI cycle depends on dUTP and involves both motifs V and VI, as we have previously proposed. Surprisingly, the conserved Dut motif IV is also implicated in SaPI derepression. However, and in agreement with the proposed alternative model, the dUTP inhibits rather than inducing the process, as we had initially proposed. In summary, our results clarify, validate and establish the mechanism by which the Duts perform regulatory functions.

Journal article

Li X, Koc C, Kuehner P, Stierhof Y-D, Krismer B, Enright MC, Penades JR, Wolz C, Stehle T, Cambillau C, Peschel A, Xia Get al., 2016, An essential role for the baseplate protein Gp45 in phage adsorption to Staphylococcus aureus, Scientific Reports, Vol: 6, ISSN: 2045-2322

Despite the importance of phages in driving horizontal gene transfer (HGT) among pathogenic bacteria, the underlying molecular mechanisms mediating phage adsorption to S. aureus are still unclear. Phage ϕ11 is a siphovirus with a high transducing efficiency. Here, we show that the tail protein Gp45 localized within the ϕ11 baseplate. Phage ϕ11 was efficiently neutralized by anti-Gp45 serum and its adsorption to host cells was inhibited by recombinant Gp45 in a dose-dependent manner. Flow cytometry analysis demonstrated that biotin-labelled Gp45 efficiently stained the wild-type S. aureus cell but not the double knockout mutant ΔtarM/S, which lacks both α- and β-O-GlcNAc residues on its wall teichoic acids (WTAs). Additionally, adsorption assays indicate that GlcNAc residues on WTAs and O-acetyl groups at the 6-position of muramic acid residues in peptidoglycan are essential components of the ϕ11 receptor. The elucidation of Gp45-involved molecular interactions not only broadens our understanding of siphovirus-mediated HGT, but also lays the groundwork for the development of sensitive affinity-based diagnostics and therapeutics for S. aureus infection.

Journal article

Frigols B, Quiles-Puchalt N, Mir-Sanchis I, Donderis J, Elena SF, Buckling A, Novick RP, Marina A, Penades JRet al., 2015, Virus satellites drive viral evolution and ecology, PLoS Genetics, Vol: 11, ISSN: 1553-7390

Virus satellites are widespread subcellular entities, present both in eukaryotic and in prokaryotic cells. Their modus vivendi involves parasitism of the life cycle of their inducing helper viruses, which assures their transmission to a new host. However, the evolutionary and ecological implications of satellites on helper viruses remain unclear. Here, using staphylococcal pathogenicity islands (SaPIs) as a model of virus satellites, we experimentally show that helper viruses rapidly evolve resistance to their virus satellites, preventing SaPI proliferation, and SaPIs in turn can readily evolve to overcome phage resistance. Genomic analyses of both these experimentally evolved strains as well as naturally occurring bacteriophages suggest that the SaPIs drive the coexistence of multiple alleles of the phage-coded SaPI inducing genes, as well as sometimes selecting for the absence of the SaPI depressing genes. We report similar (accidental) evolution of resistance to SaPIs in laboratory phages used for Staphylococcus aureus typing and also obtain the same qualitative results in both experimental evolution and phylogenetic studies of Enterococcus faecalis phages and their satellites viruses. In summary, our results suggest that helper and satellite viruses undergo rapid coevolution, which is likely to play a key role in the evolution and ecology of the viruses as well as their prokaryotic hosts.

Journal article

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