Imperial College London

Professor José R Penadés

Faculty of MedicineDepartment of Infectious Disease

Director MRC Centre for Molecular Bacteriology & Infection
 
 
 
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Contact

 

+44 (0)20 7594 8533j.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

98 results found

Yebra G, Haag AF, Neamah MM, Wee BA, Richardson EJ, Horcajo P, Granneman S, Angeles Tormo-Mas M, de la Fuente R, Fitzgerald JR, Penades JRet al., 2021, Radical genome remodelling accompanied the emergence of a novel host-restricted bacterial pathogen, PLOS PATHOGENS, Vol: 17, ISSN: 1553-7366

Journal article

Prieto JM, Rapún-Araiz B, Gil C, Penadés JR, Lasa I, Latasa Cet al., 2020, Inhibiting the two-component system GraXRS with verteporfin to combat Staphylococcus aureus infections, Scientific Reports, Vol: 10, ISSN: 2045-2322

Infections caused by Staphylococcus aureus pose a serious and sometimes fatal health issue. With the aim of exploring a novel therapeutic approach, we chose GraXRS, a Two-Component System (TCS) that determines bacterial resilience against host innate immune barriers, as an alternative target to disarm S. aureus. Following a drug repurposing methodology, and taking advantage of a singular staphylococcal strain that lacks the whole TCS machinery but the target one, we screened 1.280 off-patent FDA-approved drug for GraXRS inhibition. Reinforcing the connection between this signaling pathway and redox sensing, we found that antioxidant and redox-active molecules were capable of reducing the expression of the GraXRS regulon. Among all the compounds, verteporfin (VER) was really efficient in enhancing PMN-mediated bacterial killing, while topical administration of such drug in a murine model of surgical wound infection significantly reduced the bacterial load. Experiments relying on the chemical mimicry existing between VER and heme group suggest that redox active residue C227 of GraS participates in the inhibition exerted by this FDA-approved drug. Based on these results, we propose VER as a promising candidate for sensitizing S. aureus that could be helpful to combat persistent or antibiotic-resistant infections.

Journal article

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, Pages: 1-16, ISSN: 2379-5077

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, one by one, the active form of every TCS. This gain-of-function strategy allowed us to identify the changes in gene expression conferred by each TCS wit

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

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 Saccharomyces cerevisiae 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 Staphylococcus aureus and Escherichia coli 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.

Journal article

Fillol-Salom A, Miguel-Romero L, Marina A, Chen J, Penades JRet al., 2020, Beyond the CRISPR-Cas safeguard: PICI-encoded innate immune systems protect bacteria from bacteriophage predation, CURRENT OPINION IN MICROBIOLOGY, Vol: 56, Pages: 52-58, ISSN: 1369-5274

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: 1020-1030.e4, ISSN: 1097-2765

Phage-inducible chromosomal islands (PICIs) represent a novel and universal class of mobile genetic elements, which have broad impact on bacterial virulence. In spite of their relevance, how the Gram-negative PICIs hijack the phage machinery for their own specific packaging and how they block phage reproduction remains to be determined. Using genetic and structural analyses, we solve the mystery here by showing that the Gram-negative PICIs encode a protein that simultaneously performs these processes. This protein, which we have named Rpp (for redirecting phage packaging), interacts with the phage terminase small subunit, forming a heterocomplex. This complex is unable to recognize the phage DNA, blocking phage packaging, but specifically binds to the PICI genome, promoting PICI packaging. Our studies reveal the mechanism of action that allows PICI dissemination in nature, introducing a new paradigm in the understanding of the biology of pathogenicity islands and therefore of bacterial pathogen evolution.

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, Pages: 1-19, ISSN: 2165-0497

Staphylococcus aureus is a mammalian commensal and opportunistic pathogen that colonizes niches such as skin, nares and diverse mucosal membranes of about 20-30% of the human population. S. aureus can cause a wide spectrum of diseases in humans and both methicillin-sensitive and methicillin-resistant strains are common causes of nosocomial- and community-acquired infections. Despite the prevalence of literature characterising staphylococcal pathogenesis in humans, S. aureus is a major cause of infection and disease in a plethora of animal hosts leading to a significant impact on public health and agriculture. Infections in animals are deleterious to animal health, and animals can act as a reservoir for staphylococcal transmission to humans.Host-switching events between humans and animals and amongst animals are frequent and have been accentuated with the domestication and/or commercialisation of specific animal species. Host-switching is typically followed by subsequent adaptation through acquisition and/or loss of mobile genetic elements such as phages, pathogenicity islands and plasmids as well as further host-specific mutations allowing it to expand into new host populations.In this chapter, we will be giving an overview of S. aureus in animals, how this bacterial species was, and is, being transferred to new host species and the key elements thought to be involved in its adaptation to new ecological host niches. We will also highlight animal hosts as a reservoir for the development and transfer of antimicrobial resistance determinants.

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: 59-72.e3, ISSN: 1097-2765

Bacillus phages use a communication system, termed “arbitrium,” to coordinate lysis-lysogeny decisions. Arbitrium communication is mediated by the production and secretion of a hexapeptide (AimP) during lytic cycle. Once internalized, AimP reduces the expression of the negative regulator of lysogeny, AimX, by binding to the transcription factor, AimR, promoting lysogeny. We have elucidated the crystal structures of AimR from the Bacillus subtilis SPbeta phage in its apo form, bound to its DNA operator and in complex with AimP. AimR presents intrinsic plasticity, sharing structural features with the RRNPP quorum-sensing family. Remarkably, AimR binds to an unusual operator with a long spacer that interacts nonspecifically with the receptor TPR domain, while the HTH domain canonically recognizes two inverted repeats. AimP stabilizes a compact conformation of AimR that approximates the DNA-recognition helices, preventing AimR binding to the aimX promoter region. Our results establish the molecular basis of the arbitrium communication system.

Journal article

Haag AF, Ross Fitzgerald J, Penadés JR, 2019, Staphylococcus aureus in animals, Gram-Positive Pathogens, Pages: 731-746, ISBN: 9781683670124

The genus Staphylococcus currently comprises 81 species and subspecies (https://www.dsmz.de/bacterial-diversity/prokaryotic-nomenclature-up-to-date/prokaryotic-nomenclature-up-to-date.html), and most members of the genus are mammalian commensals or opportunistic pathogens that colonize niches such as skin, nares, and diverse mucosal membranes. Several species are of significant medical or veterinary importance. Staphylococcus pseudintermedius (1) is a leading cause of pyoderma in dogs and is considered to be a significant reservoir of antimicrobial resistance factors for the genus (2, 3). S. pseudintermedius is very similar to Staphylococcus intermedius and can be distinguished from other coagulase-positive staphylococci by positive arginine dihydrolase and acid production from β-gentiobiose and d-mannitol (4) or by using a multiplex-PCR approach targeting the nuclease gene nuc (5). Staphylococcus saprophyticus is the second leading cause of uncomplicated urinary tract infections (6). While Staphylococcus epidermidis is a normal component of the epidermal microbiota, it is a leading cause of biofilm contamination of medical devices (7). The most promiscuous and most significant human pathogenic staphylococcal species is Staphylococcus aureus, which is the causal agent of a variety of disease symptoms that can range from cosmetic to lethal manifestations. S. aureus is distinguished from most members of the genus by its abundant production of secreted coagulase, an enzyme which converts serum fibrinogen to fibrin and promotes clotting. However, the S. intermedius group and some strains of Staphylococcus lugdunensis have coagulase activity (5, 8, 9).

Book chapter

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: 207-212, ISSN: 0036-8075

Genetic transduction is a major evolutionary force that underlies bacterial adaptation. Here we report that the temperate bacteriophages of Staphylococcus aureus engage in a distinct form of transduction we term lateral transduction. Staphylococcal prophages do not follow the previously described excision-replication-packaging pathway but instead excise late in their lytic program. Here, DNA packaging initiates in situ from integrated prophages, and large metameric spans including several hundred kilobases of the S. aureus genome are packaged in phage heads at very high frequency. In situ replication before DNA packaging creates multiple prophage genomes so that lateral-transducing particles form during normal phage maturation, transforming parts of the S. aureus chromosome into hypermobile regions of gene transfer.

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, 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

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, Pages: 1-23, 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

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

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