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1.
Cell ; 177(7): 1771-1780.e12, 2019 06 13.
Artículo en Inglés | MEDLINE | ID: mdl-31199917

RESUMEN

Cargo trafficking along microtubules is exploited by eukaryotic viruses, but no such examples have been reported in bacteria. Several large Pseudomonas phages assemble a dynamic, tubulin-based (PhuZ) spindle that centers replicating phage DNA sequestered within a nucleus-like structure. Here, we show that capsids assemble on the membrane and then move rapidly along PhuZ filaments toward the phage nucleus for DNA packaging. The spindle rotates the phage nucleus, distributing capsids around its surface. PhuZ filaments treadmill toward the nucleus at a constant rate similar to the rate of capsid movement and the linear velocity of nucleus rotation. Capsids become trapped along mutant static PhuZ filaments that are defective in GTP hydrolysis. Our results suggest a transport and distribution mechanism in which capsids attached to the sides of filaments are trafficked to the nucleus by PhuZ polymerization at the poles, demonstrating that the phage cytoskeleton evolved cargo-trafficking capabilities in bacteria.


Asunto(s)
Proteínas Bacterianas , Citoesqueleto , ADN Viral , Fagos Pseudomonas , Pseudomonas , Tubulina (Proteína) , Virión , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Proteínas de la Cápside/genética , Proteínas de la Cápside/metabolismo , Citoesqueleto/genética , Citoesqueleto/metabolismo , ADN Viral/biosíntesis , ADN Viral/genética , Pseudomonas/genética , Pseudomonas/metabolismo , Pseudomonas/virología , Fagos Pseudomonas/genética , Fagos Pseudomonas/metabolismo , Tubulina (Proteína)/genética , Tubulina (Proteína)/metabolismo , Virión/genética , Virión/metabolismo
2.
Mol Cell ; 81(3): 420-422, 2021 02 04.
Artículo en Inglés | MEDLINE | ID: mdl-33545057

RESUMEN

Shah et al. (2021) uncover phage-encoded protein Aqs1 that tactically blocks Pseudomonas aeruginosa quorum-sensing receptor LasR immediately upon infection to counteract the host's quorum-sensing program, a defense strategy that is likely conserved in other phages.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Proteínas Bacterianas/genética , Bacteriófagos/genética , Fagos Pseudomonas/genética , Pseudomonas aeruginosa/genética , Percepción de Quorum , Transactivadores
3.
Mol Cell ; 73(3): 601-610.e5, 2019 02 07.
Artículo en Inglés | MEDLINE | ID: mdl-30595438

RESUMEN

CRISPR-Cas immune systems utilize RNA-guided nucleases to protect bacteria from bacteriophage infection. Bacteriophages have in turn evolved inhibitory "anti-CRISPR" (Acr) proteins, including six inhibitors (AcrIIA1-AcrIIA6) that can block DNA cutting and genome editing by type II-A CRISPR-Cas9 enzymes. We show here that AcrIIA2 and its more potent homolog, AcrIIA2b, prevent Cas9 binding to DNA by occluding protein residues required for DNA binding. Cryo-EM-determined structures of AcrIIA2 or AcrIIA2b bound to S. pyogenes Cas9 reveal a mode of competitive inhibition of DNA binding that is distinct from other known Acrs. Differences in the temperature dependence of Cas9 inhibition by AcrIIA2 and AcrIIA2b arise from differences in both inhibitor structure and the local inhibitor-binding environment on Cas9. These findings expand the natural toolbox for regulating CRISPR-Cas9 genome editing temporally, spatially, and conditionally.


Asunto(s)
Proteína 9 Asociada a CRISPR/metabolismo , Sistemas CRISPR-Cas , ADN/metabolismo , Edición Génica/métodos , Fagos Pseudomonas/metabolismo , Pseudomonas aeruginosa/enzimología , ARN Guía de Kinetoplastida/metabolismo , Temperatura , Proteínas Virales/metabolismo , Unión Competitiva , Proteína 9 Asociada a CRISPR/antagonistas & inhibidores , Proteína 9 Asociada a CRISPR/genética , Proteína 9 Asociada a CRISPR/ultraestructura , Microscopía por Crioelectrón , ADN/genética , ADN/ultraestructura , Escherichia coli/enzimología , Escherichia coli/genética , Regulación Bacteriana de la Expresión Génica , Modelos Moleculares , Conformación de Ácido Nucleico , Unión Proteica , Conformación Proteica , Fagos Pseudomonas/genética , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/virología , ARN Guía de Kinetoplastida/genética , ARN Guía de Kinetoplastida/ultraestructura , Relación Estructura-Actividad , Proteínas Virales/genética , Proteínas Virales/ultraestructura
4.
Nature ; 577(7789): 244-248, 2020 01.
Artículo en Inglés | MEDLINE | ID: mdl-31819262

RESUMEN

All viruses require strategies to inhibit or evade the immune pathways of cells that they infect. The viruses that infect bacteria, bacteriophages (phages), must avoid immune pathways that target nucleic acids, such as CRISPR-Cas and restriction-modification systems, to replicate efficiently1. Here we show that jumbo phage ΦKZ segregates its DNA from immunity nucleases of its host, Pseudomonas aeruginosa, by constructing a proteinaceous nucleus-like compartment. ΦKZ is resistant to many immunity mechanisms that target DNA in vivo, including two subtypes of CRISPR-Cas3, Cas9, Cas12a and the restriction enzymes HsdRMS and EcoRI. Cas proteins and restriction enzymes are unable to access the phage DNA throughout the infection, but engineering the relocalization of EcoRI inside the compartment enables targeting of the phage and protection of host cells. Moreover, ΦKZ is sensitive to Cas13a-a CRISPR-Cas enzyme that targets RNA-probably owing to phage mRNA localizing to the cytoplasm. Collectively, we propose that Pseudomonas jumbo phages evade a broad spectrum of DNA-targeting nucleases through the assembly of a protein barrier around their genome.


Asunto(s)
Proteínas Asociadas a CRISPR/metabolismo , Fagos Pseudomonas/genética , Pseudomonas aeruginosa/inmunología , Pseudomonas aeruginosa/virología , Proteínas Virales/química , Sistemas CRISPR-Cas , ADN Viral/química , Genoma Viral , Fagos Pseudomonas/química
5.
Nucleic Acids Res ; 51(16): 8663-8676, 2023 09 08.
Artículo en Inglés | MEDLINE | ID: mdl-37503841

RESUMEN

Deazaguanine DNA modifications are widespread in phages, particularly in those with pathogenic hosts. Pseudomonas phage iggy substitutes ∼16.5% of its genomic 2'-deoxyguanosine (G) with dPreQ0, and the iggy deazaguanine transglycosylase (DpdA) is unique in having a strict GA target motif, not observed previously. The iggy PreQ0 modification is shown to provide protection against both restriction endonucleases and Cas9 (when present in PAM), thus expanding our understanding of the deazaguanine modification system, its potential, and diversity. Phage iggy represents a new genus of Pseudomonas phages within the Queuovirinae subfamily; which have very little in common with other published phage genomes in terms of nucleotide similarity (<10%) and common proteins (<2%). Interestingly, shared similarity is concentrated in dpdA and preQ0 biosynthesis genes. TEM imaging confirmed a siphovirus morphology with a prolate icosahedral head and a non-contractile flexible tail with one long central tail spike. The observed protective effect of the deazaguanine modification on the iggy DNA may contribute to its broad within-species host range. Phage iggy was isolated on Pseudomonas aeruginosa PAO1, but also infects PDO300, PAK, PA14, as well as 10 of 27 tested environmental isolates and 13 of 20 tested clinical isolates of P. aeruginosa from patients with cystic fibrosis.


Asunto(s)
Bacteriófagos , ADN Viral , Desoxiguanosina , Fagos Pseudomonas , Humanos , Bacteriófagos/genética , Sistemas CRISPR-Cas , Fagos Pseudomonas/genética , Desoxiguanosina/análogos & derivados , ADN Viral/química
6.
J Bacteriol ; 206(5): e0040223, 2024 May 23.
Artículo en Inglés | MEDLINE | ID: mdl-38687034

RESUMEN

Pseudomonas aeruginosa is an opportunistic bacterial pathogen that commonly causes medical hardware, wound, and respiratory infections. Temperate filamentous Pf phages that infect P. aeruginosa impact numerous virulence phenotypes. Most work on Pf phages has focused on Pf4 and its host P. aeruginosa PAO1. Expanding from Pf4 and PAO1, this study explores diverse Pf phages infecting P. aeruginosa clinical isolates. We describe a simple technique targeting the Pf lysogeny maintenance gene, pflM (PA0718), that enables the effective elimination of Pf prophages from diverse P. aeruginosa hosts. The pflM gene shows diversity among different Pf phage isolates; however, all examined pflM alleles encode the DUF5447 domain. We demonstrate that pflM deletion results in prophage excision but not replication, leading to total prophage loss, indicating a role for lysis/lysogeny decisions for the DUF5447 domain. This study also assesses the effects different Pf phages have on host quorum sensing, biofilm formation, pigment production, and virulence against the bacterivorous nematode Caenorhabditis elegans. We find that Pf phages have strain-specific impacts on quorum sensing and biofilm formation, but nearly all suppress pigment production and increase C. elegans avoidance behavior. Collectively, this research not only introduces a valuable tool for Pf prophage elimination from diverse P. aeruginosa isolates but also advances our understanding of the complex relationship between P. aeruginosa and filamentous Pf phages.IMPORTANCEPseudomonas aeruginosa is an opportunistic bacterial pathogen that is frequently infected by filamentous Pf phages (viruses) that integrate into its chromosome, affecting behavior. Although prior work has focused on Pf4 and PAO1, this study investigates diverse Pf in clinical isolates. A simple method targeting the deletion of the Pf lysogeny maintenance gene pflM (PA0718) effectively eliminates Pf prophages from clinical isolates. The research evaluates the impact Pf prophages have on bacterial quorum sensing, biofilm formation, and virulence phenotypes. This work introduces a valuable tool to eliminate Pf prophages from clinical isolates and advances our understanding of P. aeruginosa and filamentous Pf phage interactions.


Asunto(s)
Profagos , Pseudomonas aeruginosa , Percepción de Quorum , Pseudomonas aeruginosa/virología , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/patogenicidad , Pseudomonas aeruginosa/fisiología , Profagos/genética , Profagos/fisiología , Virulencia , Caenorhabditis elegans/microbiología , Caenorhabditis elegans/virología , Biopelículas/crecimiento & desarrollo , Animales , Lisogenia , Fagos Pseudomonas/genética , Fagos Pseudomonas/fisiología , Infecciones por Pseudomonas/microbiología
7.
J Gen Virol ; 105(6)2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38833289

RESUMEN

Relatively few phages that infect plant pathogens have been isolated and investigated. The Pseudomonas syringae species complex is present in various environments, including plants. It can cause major crop diseases, such as bacterial canker on apricot trees. This study presents a collection of 25 unique phage genomes that infect P. syringae. These phages were isolated from apricot orchards with bacterial canker symptoms after enrichment with 21 strains of P. syringae. This collection comprises mostly virulent phages, with only three being temperate. They belong to 14 genera, 11 of which are newly discovered, and 18 new species, revealing great genetic diversity within this collection. Novel DNA packaging systems have been identified bioinformatically in one of the new phage species, but experimental confirmation is required to define the precise mechanism. Additionally, many phage genomes contain numerous potential auxiliary metabolic genes with diversified putative functions. At least three phages encode genes involved in bacterial tellurite resistance, a toxic metalloid. This suggests that viruses could play a role in bacterial stress tolerance. This research emphasizes the significance of continuing the search for new phages in the agricultural ecosystem to unravel novel ecological diversity and new gene functions. This work contributes to the foundation for future fundamental and applied research on phages infecting phytopathogenic bacteria.


Asunto(s)
Genoma Viral , Enfermedades de las Plantas , Fagos Pseudomonas , Pseudomonas syringae , Pseudomonas syringae/virología , Pseudomonas syringae/genética , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Fagos Pseudomonas/genética , Filogenia , Variación Genética
8.
Environ Microbiol ; 26(6): e16671, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38863081

RESUMEN

The environmental bacterium, Pseudomonas putida, possesses a broad spectrum of metabolic pathways. This makes it highly promising for use in biotechnological production as a cell factory, as well as in bioremediation strategies to degrade various aromatic pollutants. For P. putida to flourish in its environment, it must withstand the continuous threats posed by bacteriophages. Interestingly, until now, only a handful of phages have been isolated for the commonly used laboratory strain, P. putida KT2440, and no phage defence mechanisms have been characterized. In this study, we present a new Collection of Environmental P. putida Phages from Estonia, or CEPEST. This collection comprises 67 double-stranded DNA phages, which belong to 22 phage species and 9 phage genera. Our findings reveal that most phages in the CEPEST collection are more infectious at lower temperatures, have a narrow host range, and require an intact lipopolysaccharide for P. putida infection. Furthermore, we show that cryptic prophages present in the P. putida chromosome provide strong protection against the infection of many phages. However, the chromosomal toxin-antitoxin systems do not play a role in the phage defence of P. putida. This research provides valuable insights into the interactions between P. putida and bacteriophages, which could have significant implications for biotechnological and environmental applications.


Asunto(s)
Especificidad del Huésped , Pseudomonas putida , Pseudomonas putida/virología , Pseudomonas putida/genética , Pseudomonas putida/metabolismo , Profagos/genética , Fagos Pseudomonas/genética , Fagos Pseudomonas/aislamiento & purificación , Estonia , Bacteriófagos/genética , Bacteriófagos/aislamiento & purificación
9.
BMC Microbiol ; 24(1): 207, 2024 Jun 10.
Artículo en Inglés | MEDLINE | ID: mdl-38858621

RESUMEN

BACKGROUND: Quorum sensing (QS) is a cell density-based intercellular communication system that controls virulence gene expression and biofilm formation. In Pseudomonas aeruginosa (P. aeruginosa), the LasR system sits at the top of the QS hierarchy and coordinates the expression of a series of important traits. However, the role of lasR in phage infection remains unclear. This study aims to investigate the role of lasR QS in phage infection. METHODS: The P. aeruginosa phage was isolated from sewage, and its biological characteristics and whole genome were analyzed. The adsorption receptor was identified via a phage adsorption assay. Following lasR gene knockout, the adsorption rate and bactericidal activity of phage were analyzed. Finally, real-time quantitative polymerase chain reaction (RT-qPCR) was conducted to explore how lasR promoting phage infection. RESULTS: The lytic phage vB_Pae_PLY was isolated and lipopolysaccharide (LPS) was identified as its adsorption receptor. The adsorption rate and bactericidal activity of vB_Pae_PLY were reduced after lasR knockout. RT-qPCR results showed that the expression of galU, a key gene involved in LPS synthesis, was down-regulated, and several genes related to type IV pili (T4P) were also down-regulated in the lasR mutant PaΔlasR. CONCLUSIONS: The study showed that QS lasR may promote phage vB_Pae_PLY infection by involving in the synthesis of LPS and T4P. This study provides an example of QS in promoting phage infection and deepens the understanding of phage-bacteria interactions.


Asunto(s)
Proteínas Bacterianas , Pseudomonas aeruginosa , Percepción de Quorum , Transactivadores , Pseudomonas aeruginosa/virología , Pseudomonas aeruginosa/genética , Percepción de Quorum/genética , Transactivadores/genética , Transactivadores/metabolismo , Proteínas Bacterianas/genética , Proteínas Bacterianas/metabolismo , Fagos Pseudomonas/genética , Fagos Pseudomonas/fisiología , Aguas del Alcantarillado/virología , Aguas del Alcantarillado/microbiología , Regulación Bacteriana de la Expresión Génica , Lipopolisacáridos/metabolismo , Técnicas de Inactivación de Genes
10.
Virus Genes ; 60(3): 295-308, 2024 Jun.
Artículo en Inglés | MEDLINE | ID: mdl-38594490

RESUMEN

Pseudomonas syringae is a gram-negative plant pathogen that infects plants such as tomato and poses a threat to global crop production. In this study, a novel lytic phage infecting P. syringae pv. tomato DC3000, named phage D6, was isolated and characterized from sediments in a karst cave. The latent period of phage D6 was found to be 60 min, with a burst size of 16 plaque-forming units per cell. Phage D6 was stable at temperatures between 4 and 40 °C but lost infectivity when heated to 70 °C. Its infectivity was unaffected at pH 6-10 but became inactivated at pH ≤ 5 or ≥ 12. The genome of phage D6 is a linear double-stranded DNA of 307,402 bp with a G + C content of 48.43%. There is a codon preference between phage D6 and its host, and the translation of phage D6 gene may not be entirely dependent on the tRNA library provided by the host. A total of 410 open reading frames (ORFs) and 14 tRNAs were predicted in its genome, with 92 ORFs encoding proteins with predicted functions. Phage D6 showed low genomic similarity to known phage genomes in the GenBank and Viral sequence databases. Genomic and phylogenetic analyses revealed that phage D6 is a novel phage. The tomato plants were first injected with phage D6, and subsequently with Pst DC3000, using the foliar spraying and root drenching inoculum approach. Results obtained after 14 days indicated that phage D6 inoculation decreased P. syringae-induced symptoms in tomato leaves and inhibited the pathogen's growth in the leaves. The amount of Pst DC3000 was reduced by 150- and 263-fold, respectively. In conclusion, the lytic phage D6 identified in this study belongs to a novel phage within the Caudoviricetes class and has potential for use in biological control of plant diseases.


Asunto(s)
Genoma Viral , Filogenia , Enfermedades de las Plantas , Pseudomonas syringae , Solanum lycopersicum , Pseudomonas syringae/virología , Pseudomonas syringae/genética , Pseudomonas syringae/patogenicidad , Genoma Viral/genética , Solanum lycopersicum/virología , Solanum lycopersicum/microbiología , Enfermedades de las Plantas/microbiología , Enfermedades de las Plantas/virología , Fagos Pseudomonas/genética , Fagos Pseudomonas/aislamiento & purificación , Fagos Pseudomonas/clasificación , Composición de Base , Sistemas de Lectura Abierta , Secuenciación Completa del Genoma , ADN Viral/genética
11.
Antimicrob Agents Chemother ; 67(12): e0065423, 2023 12 14.
Artículo en Inglés | MEDLINE | ID: mdl-37931230

RESUMEN

Antibiotic-resistant bacteria present an emerging challenge to human health. Their prevalence has been increasing across the globe due in part to the liberal use of antibiotics that has pressured them to develop resistance. Those bacteria that acquire mobile genetic elements are especially concerning because those plasmids may be shared readily with other microbes that can then also become antibiotic resistant. Serious infections have recently been related to the contamination of preservative-free eyedrops with extensively drug-resistant (XDR) isolates of Pseudomonas aeruginosa, already resulting in three deaths. These drug-resistant isolates cannot be managed with most conventional antibiotics. We sought to identify alternatives to conventional antibiotics for the lysis of these XDR isolates and identified multiple bacteriophages (viruses that attack bacteria) that killed them efficiently. We found both jumbo phages (>200 kb in genome size) and non-jumbo phages that were active against these isolates, the former killing more efficiently. Jumbo phages effectively killed the three separate XDR P. aeruginosa isolates both on solid and liquid medium. Given the ongoing nature of the XDR P. aeruginosa eyedrop outbreak, the identification of phages active against them provides physicians with several novel potential alternatives for treatment.


Asunto(s)
Bacteriófagos , Infecciones por Pseudomonas , Fagos Pseudomonas , Humanos , Bacteriófagos/genética , Infecciones por Pseudomonas/microbiología , Antibacterianos/farmacología , Antibacterianos/uso terapéutico , Plásmidos , Pseudomonas aeruginosa , Fagos Pseudomonas/genética
12.
Virus Genes ; 59(1): 132-141, 2023 Feb.
Artículo en Inglés | MEDLINE | ID: mdl-36357763

RESUMEN

Pseudomonas aeruginosa is an opportunistic human pathogen that can lead to nosocomial infections which are in turn life threatening. The increase in antibiotic resistance, at an alarming rate, has resulted in a pressing need for alternative therapeutic approaches such as phage therapy, which hold promise according to several studies. This study featured the isolation and characterization of vB_PaeS_TUMS_P81, a new lytic Pseudomonas phage. The whole-genome sequencing indicated that it has a genome of 73,167 bp containing 93 predicted coding sequences. Genes involved in virulence or lysogeny pathway were nowhere to be found in the genome, so it is potentially safe when it comes to therapeutic applications. Genomic and phylogenetic analysis indicated that vB_PaeS_TUMS_P81 is a member of the genus Litunavirus, belonging to Schitoviridae family. The present study lays the groundwork for further research on treatment of P. aeruginosa infections.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Humanos , Bacteriófagos/genética , Pseudomonas aeruginosa/genética , Filogenia , Genómica , Fagos Pseudomonas/genética , Genoma Viral/genética
13.
Nucleic Acids Res ; 49(1): 584-594, 2021 01 11.
Artículo en Inglés | MEDLINE | ID: mdl-33332569

RESUMEN

CRISPR-Cas systems are adaptive immune systems in bacteria and archaea to defend against mobile genetic elements (MGEs) and have been repurposed as genome editing tools. Anti-CRISPR (Acr) proteins are produced by MGEs to counteract CRISPR-Cas systems and can be used to regulate genome editing by CRISPR techniques. Here, we report the cryo-EM structures of three type I-F Acr proteins, AcrIF4, AcrIF7 and AcrIF14, bound to the type I-F CRISPR-Cas surveillance complex (the Csy complex) from Pseudomonas aeruginosa. AcrIF4 binds to an unprecedented site on the C-terminal helical bundle of Cas8f subunit, precluding conformational changes required for activation of the Csy complex. AcrIF7 mimics the PAM duplex of target DNA and is bound to the N-terminal DNA vise of Cas8f. Two copies of AcrIF14 bind to the thumb domains of Cas7.4f and Cas7.6f, preventing hybridization between target DNA and the crRNA. Our results reveal structural detail of three AcrIF proteins, each binding to a different site on the Csy complex for inhibiting degradation of MGEs.


Asunto(s)
Proteínas Asociadas a CRISPR/antagonistas & inhibidores , Sistemas CRISPR-Cas , Fagos Pseudomonas/química , Pseudomonas aeruginosa/metabolismo , Proteínas Virales/química , Secuencia de Aminoácidos , Proteínas Asociadas a CRISPR/metabolismo , Microscopía por Crioelectrón , ADN Bacteriano/metabolismo , Conjuntos de Datos como Asunto , Ensayo de Cambio de Movilidad Electroforética , Procesamiento de Imagen Asistido por Computador , Modelos Moleculares , Unión Proteica , Conformación Proteica , Dominios Proteicos , Mapeo de Interacción de Proteínas , Fagos Pseudomonas/genética , Estructuras R-Loop , Proteínas Recombinantes/química , Proteínas Recombinantes/metabolismo , Proteínas Virales/metabolismo
14.
J Biol Chem ; 297(6): 101357, 2021 12.
Artículo en Inglés | MEDLINE | ID: mdl-34756887

RESUMEN

It has been shown that phages have evolved anti-CRISPR (Acr) proteins to inhibit host CRISPR-Cas systems. Most acr genes are located upstream of anti-CRISPR-associated (aca) genes, which is instrumental for identifying these acr genes. Thus far, eight Aca families (Aca1-Aca8) have been identified, all proteins of which share low sequence homology and bind to different target DNA sequences. Recently, Aca1 and Aca2 proteins were discovered to function as repressors by binding to acr-aca promoters, thus implying a potential anti-anti-CRISPR mechanism. However, the structural basis for the repression roles of Aca proteins is still unknown. Here, we elucidated apo-structures of Aca1 and Aca2 proteins and their complex structures with their cognate operator DNA in two model systems, the Pseudomonas phage JBD30 and the Pectobacterium carotovorum template phage ZF40. In combination with biochemical and cellular assays, our study unveils dimerization and DNA-recognition mechanisms of Aca1 and Aca2 family proteins, thus revealing the molecular basis for Aca1-and Aca2-mediated anti-CRISPR repression. Our results also shed light on understanding the repression roles of other Aca family proteins and autoregulation roles of acr-aca operons.


Asunto(s)
Bacteriófagos/metabolismo , Repeticiones Palindrómicas Cortas Agrupadas y Regularmente Espaciadas , Operón , Pectobacterium carotovorum/virología , Pseudomonas aeruginosa/virología , Proteínas Virales/metabolismo , Bacteriófagos/química , Bacteriófagos/genética , Modelos Moleculares , Pectobacterium carotovorum/genética , Pectobacterium carotovorum/metabolismo , Conformación Proteica , Multimerización de Proteína , Fagos Pseudomonas/química , Fagos Pseudomonas/genética , Fagos Pseudomonas/metabolismo , Pseudomonas aeruginosa/genética , Pseudomonas aeruginosa/metabolismo , Proteínas Virales/química , Proteínas Virales/genética
15.
Antimicrob Agents Chemother ; 66(8): e0023922, 2022 08 16.
Artículo en Inglés | MEDLINE | ID: mdl-35862755

RESUMEN

Bacteriophage (phage) therapy is an alternative to traditional antibiotic treatments that is particularly important for multidrug-resistant pathogens, such as Pseudomonas aeruginosa. Unfortunately, phage resistance commonly arises during treatment as bacteria evolve to survive phage predation. During in vitro phage treatment of a P. aeruginosa-type strain, we observed the emergence of phage-resistant mutants with brown pigmentation that was indicative of pyomelanin. As increased pyomelanin (due to hmgA gene mutation) was recently associated with enhanced resistance to hydrogen peroxide and persistence in experimental lung infection, we questioned if therapeutic phage applications could inadvertently select for hypervirulent populations. Pyomelanogenic phage-resistant mutants of P. aeruginosa PAO1 were selected for upon treatment with three distinct phages. Phage-resistant pyomelanogenic mutants did not possess increased survival of pyomelanogenic ΔhmgA in hydrogen peroxide. At the genomic level, large (~300 kb) deletions in the phage-resistant mutants resulted in the loss of ≥227 genes, many of which had roles in survival, virulence, and antibiotic resistance. Phage-resistant pyomelanogenic mutants were hypersusceptible to cationic peptides LL-37 and colistin and were more easily cleared in human whole blood, serum, and a murine infection model. Our findings suggest that hyperpigmented phage-resistant mutants that may arise during phage therapy are markedly less virulent than their predecessors due to large genomic deletions. Thus, their existence does not present a contraindication to using anti-pseudomonal phage therapy, especially considering that these mutants develop drug susceptibility to the familiar FDA-approved antibiotic, colistin.


Asunto(s)
Bacteriófagos , Infecciones por Pseudomonas , Fagos Pseudomonas , Animales , Antibacterianos/farmacología , Bacteriófagos/genética , Colistina , Humanos , Peróxido de Hidrógeno , Inmunidad Innata , Ratones , Infecciones por Pseudomonas/tratamiento farmacológico , Infecciones por Pseudomonas/microbiología , Fagos Pseudomonas/genética , Pseudomonas aeruginosa/genética
16.
Microb Pathog ; 172: 105767, 2022 Nov.
Artículo en Inglés | MEDLINE | ID: mdl-36096457

RESUMEN

The emergence of highly virulent multidrug-resistant P. aeruginosa has become increasingly evident among hospital-acquired infections and has raised the need for alternative therapies. Phage therapy can be one such alternative to antibiotic therapy to combat multidrug-resistant pathogenic bacteria, but this requires the availability of phages with a broad host range. In this study, isolation and molecular characterisation of P. aeruginosa specific phages were carried out. A total of 17 phages isolated showed different spectra of activity and efficiency of lysis against 82 isolates of P. aeruginosa obtained from clinical samples (n = 13), hospital effluent (n = 46) and fish processing plant effluent (n = 23). Antibiotic susceptibility test results revealed multi-drug resistance in 61 of the total 82 isolates. Three new jumbo lytic P. aeruginosa specific broad host range phages were isolated and characterised in this present study belonged to the family Myoviridae (order Caudovirales). The genetic analysis of ɸU5 revealed that phage has a genome size of 282.6 kbp with 373 putative open reading frames (ORFs), and its genetic architecture is similar to phiKZ like jumbo phages infecting P. aeruginosa. The bacteriophages isolated in this study had lytic ability against biofilm-forming and multidrug-resistant P. aeruginosa and could be candidates for further studies towards phage therapy.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Pseudomonas aeruginosa/genética , Fagos Pseudomonas/genética , Bacteriófagos/genética , Genoma Viral , Antibacterianos/farmacología
17.
J Evol Biol ; 35(11): 1475-1487, 2022 11.
Artículo en Inglés | MEDLINE | ID: mdl-36168737

RESUMEN

Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms-race dynamics (ARD) and fluctuating-selection dynamics (FSD). Here, we tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory, whether ARD versus FSD coevolution occurred, and how coevolution affected a predicted phenotypic trade-off between phage resistance and antibiotic sensitivity. We used a unique "deep" sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage infection and resistance to antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD, whereas the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade-off. Whole genome sequencing revealed that treatment populations of bacteria accrued more de novo mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type-IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade-off in the ARD-coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria-phage system and that occurrence of predicted phage-driven evolutionary trade-offs may depend on the genetics underlying evolution of phage resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Humanos , Pseudomonas aeruginosa , Bacterias , Antibacterianos , Fagos Pseudomonas/genética
18.
Arch Virol ; 168(1): 8, 2022 Dec 24.
Artículo en Inglés | MEDLINE | ID: mdl-36565337

RESUMEN

Pseudomonas aeruginosa is an opportunistic human pathogen that can cause life-threatening nosocomial infections. The alarming increase in antibiotic resistance has led to an urgent need for alternative therapeutic approaches, such as phage therapy, which has shown promising results in many studies. In this study, P121, a new lytic Pseudomonas phage, was isolated and characterized. Whole-genome sequencing showed that it has a genome of 73,001 bp that contains 91 predicted coding sequences. No genes involved in virulence or lysogeny were found in the genome, thus making it potentially safe for therapeutic applications. Genomic and phylogenetic analysis indicated that P121 is a member of the genus Litunavirus, family Schitoviridae. The present study provides some basic information for further research on treatment of P. aeruginosa infections.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Humanos , Bacteriófagos/genética , Pseudomonas aeruginosa , Filogenia , Genoma Viral , Genómica/métodos , Fagos Pseudomonas/genética
19.
J Appl Microbiol ; 133(3): 1353-1362, 2022 Sep.
Artículo en Inglés | MEDLINE | ID: mdl-35616159

RESUMEN

AIM: Bacteriophages are effective natural antimicrobial agents against drug-resistant pathogens. Therefore, identification and detailed characterization of bacteriophages become essential to explore their therapeutic potential. This study aims to isolate and characterize a lytic bacteriophage against drug-resistant Pseudomonas aeruginosa. METHODS AND RESULTS: The Pseudomonas phage AIIMS-Pa-A1, isolated from the river Ganga water against drug-resistant P. aeruginosa, showed a clear lytic zone on spot assay. The phage revealed an icosahedral head (58.20 nm diameter) and a small tail (6.83 nm) under a transmission electron microscope. The growth kinetics showed an adsorption constant of 1.5 × 10-9 phage particles cell-1 ml-1 min-1 and a latent period of approximately 15 min with the burst size of 27 phages per infected cell. The whole-genome sequencing depicted a GC-rich genome of 40.97 kb having a lysis cassette of holin, endolysin and Rz protein, with features of the family Autographiviridae. The comparative genome analysis, Ortho-average nucleotide identity value, and phylogenetic analysis indicated the novelty of the phage AIIMS-Pa-A1. CONCLUSIONS: The study concludes that the Pseudomonas phage AIIMS-Pa-A1 is a novel member of the Autographiviridae family, truly lytic in nature for drug-resistant P. aeruginosa. SIGNIFICANCE AND IMPACT OF THE STUDY: The Pseudomonas phage AIIMS-Pa-A1 is having promising potential for future therapeutic intervention to treat drug-resistant P. aeruginosa infections.


Asunto(s)
Bacteriófagos , Fagos Pseudomonas , Bacteriófagos/genética , Genoma Viral , Filogenia , Fagos Pseudomonas/genética , Pseudomonas aeruginosa , Ríos
20.
Nucleic Acids Res ; 48(1): 445-459, 2020 01 10.
Artículo en Inglés | MEDLINE | ID: mdl-31724707

RESUMEN

Bacterial viruses encode a vast number of ORFan genes that lack similarity to any other known proteins. Here, we present a 2.20 Å crystal structure of N4-related Pseudomonas virus LUZ7 ORFan gp14, and elucidate its function. We demonstrate that gp14, termed here as Drc (ssDNA-binding RNA Polymerase Cofactor), preferentially binds single-stranded DNA, yet contains a structural fold distinct from other ssDNA-binding proteins (SSBs). By comparison with other SSB folds and creation of truncation and amino acid substitution mutants, we provide the first evidence for the binding mechanism of this unique fold. From a biological perspective, Drc interacts with the phage-encoded RNA Polymerase complex (RNAPII), implying a functional role as an SSB required for the transition from early to middle gene transcription during phage infection. Similar to the coliphage N4 gp2 protein, Drc likely binds locally unwound middle promoters and recruits the phage RNA polymerase. However, unlike gp2, Drc does not seem to need an additional cofactor for promoter melting. A comparison among N4-related phage genera highlights the evolutionary diversity of SSB proteins in an otherwise conserved transcription regulation mechanism.


Asunto(s)
ADN de Cadena Simple/química , ADN Viral/química , Proteínas de Unión al ADN/química , Fagos Pseudomonas/genética , Pseudomonas/virología , Proteínas Virales/química , Secuencia de Aminoácidos , Sustitución de Aminoácidos , Sitios de Unión , Clonación Molecular , ADN de Cadena Simple/genética , ADN de Cadena Simple/metabolismo , ADN Viral/genética , ADN Viral/metabolismo , Proteínas de Unión al ADN/genética , Proteínas de Unión al ADN/metabolismo , ARN Polimerasas Dirigidas por ADN/química , ARN Polimerasas Dirigidas por ADN/genética , ARN Polimerasas Dirigidas por ADN/metabolismo , Escherichia coli/genética , Escherichia coli/metabolismo , Expresión Génica , Vectores Genéticos/química , Vectores Genéticos/metabolismo , Modelos Moleculares , Conformación de Ácido Nucleico , Sistemas de Lectura Abierta , Regiones Promotoras Genéticas , Unión Proteica , Conformación Proteica en Hélice alfa , Conformación Proteica en Lámina beta , Dominios y Motivos de Interacción de Proteínas , Multimerización de Proteína , Fagos Pseudomonas/metabolismo , Proteínas Recombinantes/química , Proteínas Recombinantes/genética , Proteínas Recombinantes/metabolismo , Transcripción Genética , Proteínas Virales/genética , Proteínas Virales/metabolismo
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