scholarly journals Mycobacterium phage Butters-encoded proteins contribute to host defense against viral attack

2020 ◽  
Author(s):  
Catherine M. Mageeney ◽  
Hamidu T. Mohammed ◽  
Marta Dies ◽  
Samira Anbari ◽  
Netta Cudkevich ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Defense Mechanism ◽  
Resistant Bacteria ◽  
Two Component System ◽  
Bacterial Genomes ◽  
Bacterial Host ◽  
Bioinformatics Analyses ◽  
Defense Systems ◽  
Two Component

ABSTRACTA diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within Cluster N mycobacteriophages. In that context, we unveil a novel defense mechanism in Cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two component system articulated by interactions between protein products of genes 30 and 31 confers defense against heterotypic phage infection by PurpleHaze or Alma, but is insufficient to confer defense against attack by the heterotypic phage Island3. Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated.IMPORTANCEMany sequenced bacterial genomes including pathogenic bacteria contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems will be critical to development of phage therapy that circumvents these defenses. Additionally, such knowledge will help engineer phage-resistant bacteria of industrial importance.

scholarly journals Mycobacterium Phage Butters-Encoded Proteins Contribute to Host Defense against Viral Attack

mSystems ◽  
2020 ◽  
Vol 5 (5) ◽  
Author(s):  
Catherine M. Mageeney ◽  
Hamidu T. Mohammed ◽  
Marta Dies ◽  
Samira Anbari ◽  
Netta Cudkevich ◽  
...  
Keyword(s):  
Defense Mechanisms ◽  
Pathogenic Bacteria ◽  
Defense Mechanism ◽  
Viral Infections ◽  
Resistant Bacteria ◽  
Two Component System ◽  
Bioinformatics Analyses ◽  
Content Type ◽  
Defense Systems ◽  
Cluster A

ABSTRACT A diverse set of prophage-mediated mechanisms protecting bacterial hosts from infection has been recently uncovered within cluster N mycobacteriophages isolated on the host, Mycobacterium smegmatis mc2155. In that context, we unveil a novel defense mechanism in cluster N prophage Butters. By using bioinformatics analyses, phage plating efficiency experiments, microscopy, and immunoprecipitation assays, we show that Butters genes located in the central region of the genome play a key role in the defense against heterotypic viral attack. Our study suggests that a two-component system, articulated by interactions between protein products of genes 30 and 31, confers defense against heterotypic phage infection by PurpleHaze (cluster A/subcluster A3) or Alma (cluster A/subcluster A9) but is insufficient to confer defense against attack by the heterotypic phage Island3 (cluster I/subcluster I1). Therefore, based on heterotypic phage plating efficiencies on the Butters lysogen, additional prophage genes required for defense are implicated and further show specificity of prophage-encoded defense systems. IMPORTANCE Many sequenced bacterial genomes, including those of pathogenic bacteria, contain prophages. Some prophages encode defense systems that protect their bacterial host against heterotypic viral attack. Understanding the mechanisms undergirding these defense systems is crucial to appreciate the scope of bacterial immunity against viral infections and will be critical for better implementation of phage therapy that would require evasion of these defenses. Furthermore, such knowledge of prophage-encoded defense mechanisms may be useful for developing novel genetic tools for engineering phage-resistant bacteria of industrial importance.

scholarly journals How to Train Your Phage: The Recent Efforts in Phage Training

Biologics ◽  
2021 ◽  
Vol 1 (2) ◽  
pp. 70-88
Author(s):  
Abdallah Abdelsattar ◽  
Alyaa Dawooud ◽  
Nouran Rezk ◽  
Salsabil Makky ◽  
Anan Safwat ◽  
...  
Keyword(s):  
Host Range ◽  
Pathogenic Bacteria ◽  
Bacterial Resistance ◽  
Phage Therapy ◽  
Current Knowledge ◽  
Lytic Replication ◽  
Resistant Bacteria ◽  
Infection Cycles ◽  
Different Strains ◽  
Specific Species

Control of pathogenic bacteria by deliberate application of predatory phages has potential as a powerful therapy against antibiotic-resistant bacteria. The key advantages of phage biocontrol over antibacterial chemotherapy are: (1) an ability to self-propagate inside host bacteria, (2) targeted predation of specific species or strains of bacteria, (3) adaptive molecular machinery to overcome resistance in target bacteria. However, realizing the potential of phage biocontrol is dependent on harnessing or adapting these responses, as many phage species switch between lytic infection cycles (resulting in lysis) and lysogenic infection cycles (resulting in genomic integration) that increase the likelihood of survival of the phage in response to external stress or host depletion. Similarly, host range will need to be optimized to make phage therapy medically viable whilst avoiding the potential for deleteriously disturbing the commensal microbiota. Phage training is a new approach to produce efficient phages by capitalizing on the evolved response of wild-type phages to bacterial resistance. Here we will review recent studies reporting successful trials of training different strains of phages to switch into lytic replication mode, overcome bacterial resistance, and increase their host range. This review will also highlight the current knowledge of phage training and future implications in phage applications and phage therapy and summarize the recent pipeline of the magistral preparation to produce a customized phage for clinical trials and medical applications.

scholarly journals Bacteriophages: the possible solution to treat infections caused by pathogenic bacteria

2017 ◽  
Vol 63 (11) ◽  
pp. 865-879 ◽  
Author(s):  
Ayman El-Shibiny ◽  
Salma El-Sahhar
Keyword(s):  
Bacterial Infections ◽  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Multidrug Resistant ◽  
Clinical Applications ◽  
Western World ◽  
Resistant Bacteria ◽  
Vaccine Production ◽  
Bacterial Populations ◽  
Antibiotic Resistant

Since their discovery in 1915, bacteriophages have been used to treat bacterial infections in animals and humans because of their unique ability to infect their specific bacterial hosts without affecting other bacterial populations. The research carried out in this field throughout the 20th century, largely in Georgia, part of USSR and Poland, led to the establishment of phage therapy protocols. However, the discovery of penicillin and sulfonamide antibiotics in the Western World during the 1930s was a setback in the advancement of phage therapy. The misuse of antibiotics has reduced their efficacy in controlling pathogens and has led to an increase in the number of antibiotic-resistant bacteria. As an alternative to antibiotics, bacteriophages have become a topic of interest with the emergence of multidrug-resistant bacteria, which are a threat to public health. Recent studies have indicated that bacteriophages can be used indirectly to detect pathogenic bacteria or directly as biocontrol agents. Moreover, they can be used to develop new molecules for clinical applications, vaccine production, drug design, and in the nanomedicine field via phage display.

scholarly journals The Concerted Action of Two B3-Like Prophage Genes Excludes Superinfecting Bacteriophages by Blocking DNA Entry into Pseudomonas aeruginosa

2020 ◽  
Vol 94 (15) ◽  
Author(s):  
Marco Antonio Carballo-Ontiveros ◽  
Adrián Cazares ◽  
Pablo Vinuesa ◽  
Luis Kameyama ◽  
Gabriel Guarneros
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Alternative Therapy ◽  
Multidrug Resistant ◽  
Open Reading Frames ◽  
Resistant Bacteria ◽  
Content Type ◽  
Secondary Infections ◽  
Genes Encoding

ABSTRACT In this study, we describe seven vegetative phage genomes homologous to the historic phage B3 that infect Pseudomonas aeruginosa. Like other phage groups, the B3-like group contains conserved (core) and variable (accessory) open reading frames (ORFs) grouped at fixed regions in their genomes; however, in either case, many ORFs remain without assigned functions. We constructed lysogens of the seven B3-like phages in strain Ps33 of P. aeruginosa, a novel clinical isolate, and assayed the exclusion phenotype against a variety of temperate and virulent superinfecting phages. In addition to the classic exclusion conferred by the phage immunity repressor, the phenotype observed in B3-like lysogens suggested the presence of other exclusion genes. We set out to identify the genes responsible for this exclusion phenotype. Phage Ps56 was chosen as the study subject since it excluded numerous temperate and virulent phages. Restriction of the Ps56 genome, cloning of several fragments, and resection of the fragments that retained the exclusion phenotype allowed us to identify two core ORFs, so far without any assigned function, as responsible for a type of exclusion. Neither gene expressed separately from plasmids showed activity, but the concurrent expression of both ORFs is needed for exclusion. Our data suggest that phage adsorption occurs but that phage genome translocation to the host’s cytoplasm is defective. To our knowledge, this is the first report on this type of exclusion mediated by a prophage in P. aeruginosa. IMPORTANCE Pseudomonas aeruginosa is a Gram-negative bacterium frequently isolated from infected immunocompromised patients, and the strains are resistant to a broad spectrum of antibiotics. Recently, the use of phages has been proposed as an alternative therapy against multidrug-resistant bacteria. However, this approach may present various hurdles. This work addresses the problem that pathogenic bacteria may be lysogenized by phages carrying genes encoding resistance against secondary infections, such as those used in phage therapy. Discovering phage genes that exclude superinfecting phages not only assigns novel functions to orphan genes in databases but also provides insight into selection of the proper phages for use in phage therapy.

scholarly journals Functional Determinants of a Small Protein Controlling a Broadly Conserved Bacterial Sensor Kinase

2020 ◽  
Vol 202 (16) ◽  
Author(s):  
Srujana S. Yadavalli ◽  
Ted Goh ◽  
Jeffrey N. Carey ◽  
Gabriele Malengo ◽  
Sangeevan Vellappan ◽  
...  
Keyword(s):  
Membrane Protein ◽  
Pathogenic Bacteria ◽  
Regulatory Function ◽  
Two Component System ◽  
Alanine Scanning Mutagenesis ◽  
Histidine Kinases ◽  
Component System ◽  
Small Protein ◽  
Content Type ◽  
Two Component

ABSTRACT The PhoQ/PhoP two-component system plays a vital role in the regulation of Mg2+ homeostasis, resistance to acid and hyperosmotic stress, cationic antimicrobial peptides, and virulence in Escherichia coli, Salmonella, and related bacteria. Previous studies have shown that MgrB, a 47-amino-acid membrane protein that is part of the PhoQ/PhoP regulon, inhibits the histidine kinase PhoQ. MgrB is part of a negative-feedback loop modulating this two-component system that prevents hyperactivation of PhoQ and may also provide an entry point for additional input signals for the PhoQ/PhoP pathway. To explore the mechanism of action of MgrB, we analyzed the effects of point mutations, C-terminal truncations, and transmembrane (TM) region swaps on MgrB activity. In contrast to two other known membrane protein regulators of histidine kinases in E. coli, we found that the MgrB TM region is necessary for PhoQ inhibition. Our results indicate that the TM region mediates interactions with PhoQ and that W20 is a key residue for PhoQ/MgrB complex formation. Additionally, mutations of the MgrB cytosolic region suggest that the two N-terminal lysines play an important role in regulating PhoQ activity. Alanine-scanning mutagenesis of the periplasmic region of MgrB further indicated that, with the exception of a few highly conserved residues, most residues are not essential for MgrB’s function as a PhoQ inhibitor. Our results indicate that the regulatory function of the small protein MgrB depends on distinct contributions from multiple residues spread across the protein. Interestingly, the TM region also appears to interact with other noncognate histidine kinases in a bacterial two-hybrid assay, suggesting a potential route for evolving new small-protein modulators of histidine kinases. IMPORTANCE One of the primary means by which bacteria adapt to their environment is through pairs of proteins consisting of a sensor and a response regulator. A small membrane protein, MgrB, impedes the activity of sensor protein PhoQ, thereby affecting the expression of PhoQ regulated virulence genes in pathogenic bacteria. However, it is unknown how such a small protein modulates the activity of PhoQ. Here, we studied the functional determinants of MgrB and identified specific amino acids critical for the protein's inhibitory function. Notably, we find that the membrane-spanning region is important for MgrB interaction with PhoQ. Additionally, this region appears to physically interact with other sensors, a property that may be important for evolving small protein regulators of sensor kinases.

DevR–DevS is a bona fide two-component system of Mycobacterium tuberculosis that is hypoxia-responsive in the absence of the DNA-binding domain of DevR

Microbiology ◽  
2004 ◽  
Vol 150 (4) ◽  
pp. 865-875 ◽  
Author(s):  
Deepak Kumar Saini ◽  
Vandana Malhotra ◽  
Deepanwita Dey ◽  
Neha Pant ◽  
Taposh K. Das ◽  
...  
Keyword(s):  
Mycobacterium Tuberculosis ◽  
Pathogenic Bacteria ◽  
Response Regulator ◽  
Regulatory System ◽  
Site Directed Mutagenesis ◽  
Phosphoryl Transfer ◽  
Dependent Manner ◽  
Two Component System ◽  
Component System ◽  
Two Component

Two-component systems play a central role in the adaptation of pathogenic bacteria to the environment prevailing within host tissues. The genes encoding the response regulator DevR (Rv3133c/DosR) and the cytoplasmic portion (DevS201) of the histidine kinase DevS (Rv3132c/DosS), a putative two-component system of Mycobacterium tuberculosis, were cloned and the protein products were overexpressed, purified and refolded as N-terminally His6-tagged proteins from Escherichia coli. DevS201 underwent autophosphorylation and participated in rapid phosphotransfer to DevR in a Mg2+-dependent manner. Chemical stability analysis and site-directed mutagenesis implicated the highly conserved residues His395 and Asp54 as the sites of phosphorylation in DevS and DevR, respectively. Mutations in Asp8 and Asp9 residues, postulated to form the acidic Mg2+-binding pocket, and the invariant Lys104 of DevR, abrogated phosphoryl transfer from DevS201 to DevR. DevR–DevS was thus established as a typical two-component regulatory system based on His-to-Asp phosphoryl transfer. Expression of the Rv3134c–devR–devS operon was induced at the RNA level in hypoxic cultures of M. tuberculosis H37Rv and was associated with an increase in the level of DevR protein. However, in a devR mutant strain expressing the N-terminal domain of DevR, induction was observed at the level of RNA expression but not at that of protein. DevS was translated independently of DevR and induction of devS transcripts was not associated with an increase in protein level in either wild-type or mutant strains, reflecting differential regulation of this locus during hypoxia.

scholarly journals Microbiota and Phage Therapy: Future Challenges in Medicine

2018 ◽  
Vol 6 (4) ◽  
pp. 86 ◽  
Author(s):  
Armelle Paule ◽  
Domenico Frezza ◽  
Marvin Edeas
Keyword(s):  
Gut Microbiota ◽  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Fecal Microbiota Transplantation ◽  
Wide Spectrum ◽  
Fecal Microbiota ◽  
Resistant Bacteria ◽  
Low Grade ◽  
Future Challenges ◽  
Mitochondria Dynamics

An imbalance of bacterial quantity and quality of gut microbiota has been linked to several pathologies. New strategies of microbiota manipulation have been developed such as fecal microbiota transplantation (FMT); the use of pre/probiotics; an appropriate diet; and phage therapy. The presence of bacteriophages has been largely underestimated and their presence is a relevant component for the microbiome equilibrium. As a promising treatment, phage therapy has been extensively used in Eastern Europe to reduce pathogenic bacteria and has arisen as a new method to modulate microbiota diversity. Phages have been selected and “trained” to infect a wide spectrum of bacteria or tailored to infect specific antibiotic resistant bacteria present in patients. The new development of genetically modified phages may be an efficient tool to treat the gut microbiota dysbiosis associated with different pathologies and increased production of bacterial metabolites and subsequently decrease systemic low-grade chronic inflammation associated with chronic diseases. Microbiota quality and mitochondria dynamics can be remodulated and manipulated by phages to restore the equilibrium and homeostasis of the system. Our aim is to highlight the great interest for phages not only to eliminate and control pathogenic bacterial infection but also in the near future to modulate the microbiota by adding new functions to selected bacteria species and rebalance the dynamic among phages and bacteria. The challenge for the medicine of tomorrow is to re-think and redesign strategies differently and far from our traditional thinking.

scholarly journals Parallel evolution of phage resistance - virulence trade - offs during in vitro and nasal Pseudomonas aeruginosa phage treatment

2021 ◽  
Author(s):  
Meaghan Castledine ◽  
Daniel Padfield ◽  
Pawel Sierocinski ◽  
Jesica Soria Pascual ◽  
Adam Hughes ◽  
...  
Keyword(s):  
Pathogenic Bacteria ◽  
Evolutionary Dynamics ◽  
Phage Therapy ◽  
De Novo ◽  
Resistant Bacteria ◽  
Phage Resistance ◽  
Lower Growth ◽  
Trade Offs

With rising antibiotic resistance, there has been increasing interest in the treatment of pathogenic bacteria with bacteriophages (phage therapy). One limitation of phage therapy is the ease at which bacteria can evolve resistance. The negative effects of resistance may be partially mitigated when resistance results in reduced bacterial growth and virulence, or when phage coevolve to overcome resistance. Resistance evolution and its consequences are highly contingent on the particular combination of bacteria and phage and the ecological context they interact in, making therapeutic outcomes hard to predict. One solution might be to conduct ″in vitro evolutionary simulations″ using the bacteria-phage combinations specific to the therapeutic context. Here, we investigate parallels between in vitro experiments and in vivo dynamics in a human participant. Evolutionary dynamics were similar in vivo and in vitro, with high levels of de novo resistance evolving quickly with limited evidence of phage evolution. Moreover, resistant bacteria – evolved both in vitro and in vivo – had lower virulence when measured in an insect model. In vivo, this was linked to lower growth rates of resistant isolates, whereas in vitro isolates evolved greater biofilm production with phage resistance. Population sequencing suggests resistance was typically the result of selection on de novo mutations rather than sorting of existing variants in the population. These results highlight the speed at which resistance to phages can evolve in vivo, and that in vitro evolution may give useful insights for evolutionary outcomes in vivo.

scholarly journals Determination of the optimal bacteriophage dose to control Pseudomonas aeruginosa using evolutionary programming and stochastic kinetics

2016 ◽  
Author(s):  
Diana C Ardila ◽  
Juan D Castro ◽  
Angela V Holguín ◽  
Viviana Clavijo ◽  
Catalina Prada ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Reverse Engineering ◽  
Pathogenic Bacteria ◽  
Phage Therapy ◽  
Evolutionary Programming ◽  
Stochastic Simulations ◽  
Resistant Bacteria ◽  
Multiple Drug ◽  
Promising Alternative

Phage-therapy is a promising alternative against pathogenic, multiple drug resistant bacteria. In this work we propose an algorithm to determine the optimal bacteriophage dose able to minimize a population of Pseudomonas aeruginosa. Reverse engineering was used to determine the kinetic parameters; subsequently, a bi-level optimization platform was implemented for a model based on evolutionary programming. Our prediction of optimal dose was tested in vitro with planktonic cultures of P. aeruginosa. From the data obtained, we conclude that reverse engineering and stochastic simulations are a useful approach to find optimal phage doses against pathogenic bacteria, an important step for the implementation of phage-therapy.

The relationship between the phageome and human health: are bacteriophages beneficial or harmful microbes?

2021 ◽  
pp. 1-14
Author(s):  
L. Fernández ◽  
A.C. Duarte ◽  
A. Rodríguez ◽  
P. García
Keyword(s):  
Antibiotic Resistance ◽  
Human Health ◽  
Pathogenic Bacteria ◽  
Antimicrobial Agents ◽  
Phage Therapy ◽  
Negative Impact ◽  
Antibiotic Resistance Genes ◽  
Resistant Bacteria ◽  
Potential Risks

In the context of the global antibiotic resistance crisis, bacteriophages are increasingly becoming promising antimicrobial agents against multi-resistant bacteria. Indeed, a huge effort is being made to bring phage-derived products to the market, a process that will also require revising the current regulations in order to facilitate their approval. However, despite the evidence supporting the safety of phages for humans, the general public would still be reluctant to use ‘viruses’ for therapeutic purposes. In this scenario, we consider that it is important to discuss the role of these microorganisms in the equilibrium of the microbiota and how this relates to human health. To do that, this review starts by examining the role of phages as key players in bacterial communities (including those that naturally inhabit the human body), modulating the species composition and contributing to maintain a ‘healthy’ status quo. Additionally, in specific situations, e.g. an infectious disease, bacteriophages can be used as target-specific antimicrobials against pathogenic bacteria (phage therapy), while being harmless to the desirable microbiota. Apart from that, incipient research shows the potential application of these viruses to treat diseases caused by bacterial dysbiosis. This latter application would be comparable to the use of probiotics or prebiotics, since bacteriophages can indirectly improve the growth of beneficial bacteria in the gastrointestinal tract by removing undesirable competitors. On the other hand, possible adverse effects do not appear to be an impediment to promote phage therapy. Nonetheless, it is important to remember their potentially negative impact, mainly concerning their immunogenicity or their potential spread of virulence and antibiotic resistance genes, especially by temperate phages. Overall, we believe that phages should be largely considered beneficial microbes, although it is paramount not to overlook their potential risks.

Sign in / Sign up

Export Citation Format

Share Document