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Nature Communications Feb 2024Bacteria have evolved diverse antiviral defence mechanisms to protect themselves against phage infection. Phages integrated into bacterial chromosomes, known as...
Bacteria have evolved diverse antiviral defence mechanisms to protect themselves against phage infection. Phages integrated into bacterial chromosomes, known as prophages, also encode defences that protect the bacterial hosts in which they reside. Here, we identify a type of anti-phage defence that interferes with the virion assembly pathway of invading phages. The protein that mediates this defence, which we call Tab (for 'Tail assembly blocker'), is constitutively expressed from a Pseudomonas aeruginosa prophage. Tab allows the invading phage replication cycle to proceed, but blocks assembly of the phage tail, thus preventing formation of infectious virions. While the infected cell dies through the activity of the replicating phage lysis proteins, there is no release of infectious phage progeny, and the bacterial community is thereby protected from a phage epidemic. Prophages expressing Tab are not inhibited during their own lytic cycle because they express a counter-defence protein that interferes with Tab function. Thus, our work reveals an anti-phage defence that operates by blocking virion assembly, thereby both preventing formation of phage progeny and allowing destruction of the infected cell due to expression of phage lysis genes.
Topics: Humans; Bacteriophages; Prophages; Pseudomonas Infections; Virion
PubMed: 38388474
DOI: 10.1038/s41467-024-45892-x -
Nature Mar 2022Colibactin is a chemically unstable small-molecule genotoxin that is produced by several different bacteria, including members of the human gut microbiome. Although the...
Colibactin is a chemically unstable small-molecule genotoxin that is produced by several different bacteria, including members of the human gut microbiome. Although the biological activity of colibactin has been extensively investigated in mammalian systems, little is known about its effects on other microorganisms. Here we show that colibactin targets bacteria that contain prophages, and induces lytic development through the bacterial SOS response. DNA, added exogenously, protects bacteria from colibactin, as does expressing a colibactin resistance protein (ClbS) in non-colibactin-producing cells. The prophage-inducing effects that we observe apply broadly across different phage-bacteria systems and in complex communities. Finally, we identify bacteria that have colibactin resistance genes but lack colibactin biosynthetic genes. Many of these bacteria are infected with predicted prophages, and we show that the expression of their ClbS homologues provides immunity from colibactin-triggered induction. Our study reveals a mechanism by which colibactin production could affect microbiomes and highlights a role for microbial natural products in influencing population-level events such as phage outbreaks.
Topics: Bacteria; Bacterial Toxins; Bacteriolysis; Microbial Interactions; Peptides; Polyketides; Prophages; SOS Response, Genetics; Virus Activation
PubMed: 35197633
DOI: 10.1038/s41586-022-04444-3 -
MBio Feb 2024Bacteriophages are large and diverse components of the biosphere, and many phages are temperate. Upon infection, temperate phages can establish lysogeny in which a...
Bacteriophages are large and diverse components of the biosphere, and many phages are temperate. Upon infection, temperate phages can establish lysogeny in which a prophage is typically integrated into the bacterial chromosome. Here, we describe the phenomenon of tRNA-dependent lysogeny, a previously unrecognized behavior of some temperate phages. tRNA-dependent lysogeny is characterized by two unusual features. First, a phage-encoded tyrosine family integrase mediates site-specific recombination between a phage site and a bacterial site overlapping a host tRNA gene. However, and share only a short (~10 bp) common core such that a functional tRNA is not reconstructed upon integration. Second, the phage encodes a tRNA of the same isotype as the disrupted but essential host tRNA, complementing its loss, and consequently is required for the survival of lysogenic progeny. As expected, an integrase-defective phage mutant forms turbid plaques, and bacterial progeny are immune to superinfection, but they lack stability, and the prophage is rapidly lost. In contrast, a tRNA-defective phage mutant forms clear plaques and more closely resembles a repressor mutant, and lysogens are recovered only at very low frequency through the use of secondary attachment sites elsewhere in the host genome. Integration-proficient plasmids derived from these phages must also carry a cognate phage tRNA gene for efficient integration, and these may be useful tools for mycobacterial genetics. We show that tRNA-dependent lysogeny is used by phages within multiple different groups of related viruses and may be prevalent elsewhere in the broader phage community.IMPORTANCEBacteriophages are the most numerous biological entities in the biosphere, and a substantial proportion of phages are temperate, forming stable lysogens in which a prophage copy of the genome integrates into the bacterial chromosome. Many phages encode a variety of tRNA genes whose roles are poorly understood, although it has been proposed that they enhance translational efficiencies in lytic growth or that they counteract host defenses that degrade host tRNAs. Here, we show that phage-encoded tRNAs play key roles in the establishment of lysogeny of some temperate phages. They do so by compensating for the loss of tRNA function when phages integrate at an site overlapping a tRNA gene but fail to reconstruct the tRNA at the attachment junction. In this system of tRNA-dependent lysogeny, the phage-encoded tRNA is required for lysogeny, and deletion of the phage tRNA gives rise to a clear plaque phenotype and obligate lytic growth.
Topics: Lysogeny; Bacteriophages; Prophages; Integrases; Plasmids
PubMed: 38236026
DOI: 10.1128/mbio.03260-23 -
MBio Oct 2022The formation of membrane vesicles (MVs) by Gram-positive bacteria has gained increasing attention over the last decade. Recently, models of vesicle formation have been...
The formation of membrane vesicles (MVs) by Gram-positive bacteria has gained increasing attention over the last decade. Recently, models of vesicle formation have been proposed and involve the digestion of the cell wall by prophage-encoded or stress-induced peptidoglycan (PG) hydrolases and the inhibition of PG synthesis by β-lactam antibiotics. The impact of these mechanisms on vesicle formation is largely dependent on the strain and growth conditions. To date, no information on the production of vesicles by the lactobacilli family has been reported. Here, we aimed to characterize the MVs released by the Gram-positive bacteria BL23 and also investigated the mechanisms involved in vesicle formation. Using electron microscopy, we established that the size of the majority of BL23 vesicles ranged from 50 to 100 nm. Furthermore, we showed that the vesicles were released consistently throughout the growth of the bacteria in standard culture conditions. The protein composition of the vesicles released in the supernatant was identified and a significant number of prophage proteins was detected. Moreover, using a mutant strain harboring a defective PLE2 prophage, we were able to show that the spontaneous and mitomycin-triggered induction of the prophage PLE2 contribute to the production of MVs by BL23. Finally, we also demonstrated the influence of prophages on the membrane integrity of bacteria. Overall, our results suggest a key role of the prophage PLE2 in the production of MVs by BL23 in the absence or presence of genotoxic stress. The last few decades have demonstrated that membrane vesicles (MVs) produced by microorganisms can have a wide variety of functions. This diversity places MVs at the crossroads of major research topics in current microbiology such as antibiotic resistance, horizontal gene transfer, cell communication, biofilm development, bacteriophage resistance, and pathogenesis. In particular, vesicles produced by probiotic strains have been shown to play a significant role in their beneficial effects. Thus, the study of vesicle biogenesis is a key element for promoting and improving their release. Overall, our results suggest a key role of spontaneous and mitomycin-triggered prophage induction in MV production by the Gram-positive bacteria BL23. This phenomenon is of great interest as prophage-induced MVs could potentially influence bacterial behavior, stress resistance, and vesicle functions.
Topics: Peptidoglycan; Virus Activation; Lacticaseibacillus casei; Prophages; N-Acetylmuramoyl-L-alanine Amidase; Anti-Bacterial Agents; Mitomycins; beta-Lactams
PubMed: 36200778
DOI: 10.1128/mbio.02375-22 -
International Journal of Molecular... May 2023is a common human commensal and opportunistic pathogen. In recent years, the clinical isolation and resistance rates of have shown a yearly increase, leading to a...
is a common human commensal and opportunistic pathogen. In recent years, the clinical isolation and resistance rates of have shown a yearly increase, leading to a special interest in mobile genetic elements. Prophages are a representative class of mobile genetic elements that can carry host-friendly genes, transfer horizontally between strains, and coevolve with the host's genome. In this study, we identified 15,946 prophages from the genomes of 1437 fully assembled deposited in the NCBI database, with 9755 prophages on chromosomes and 6191 prophages on plasmids. We found prophages to be notably diverse and widely disseminated in the genomes. The prophages encoded multiple putative virulence factors and antibiotic resistance genes. The comparison of strain types with prophage types suggests that the two may be related. The differences in GC content between the same type of prophages and the genomic region in which they were located indicates the alien properties of the prophages. The overall distribution of GC content suggests that prophages integrated on chromosomes and plasmids may have different evolutionary characteristics. These results suggest a high prevalence of prophages in the genome and highlight the effect of prophages on strain characterization.
Topics: Humans; Prophages; Klebsiella pneumoniae; Plasmids; Genomics; Virulence Factors; Anti-Bacterial Agents; Genome, Bacterial
PubMed: 37298067
DOI: 10.3390/ijms24119116 -
Nature Communications Oct 2023Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity,...
Bacteriophages (phages) are the most abundant biological entities on Earth, exerting a significant influence on the dissemination of bacterial virulence, pathogenicity, and antimicrobial resistance. Temperate phages integrate into the bacterial chromosome in a dormant state through intricate regulatory mechanisms. These mechanisms repress lytic genes while facilitating the expression of integrase and the CI master repressor. Upon bacterial SOS response activation, the CI repressor undergoes auto-cleavage, producing two fragments with the N-terminal domain (NTD) retaining significant DNA-binding ability. The process of relieving CI NTD repression, essential for prophage induction, remains unknown. Here we show a specific interaction between the ClpX protease and CI NTD repressor fragment of phages Ф11 and 80α in Staphylococcus aureus. This interaction is necessary and sufficient for prophage activation after SOS-mediated CI auto-cleavage, defining the final stage in the prophage induction cascade. Our findings unveil unexpected roles of bacterial protease ClpX in phage biology.
Topics: Virus Activation; Staphylococcus aureus; Peptide Hydrolases; Bacteriophages; Prophages
PubMed: 37852980
DOI: 10.1038/s41467-023-42413-0 -
Viruses Nov 2021Prophage 919TP is widely distributed among and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage...
Prophage 919TP is widely distributed among and is induced to produce free φ919TP phage particles. However, the interactions between prophage φ919TP, the induced phage particle, and its host remain unknown. In particular, phage resistance mechanisms and potential fitness trade-offs, resulting from phage resistance, are unresolved. In this study, we examined a prophage 919TP-deleted variant of and its interaction with a modified lytic variant of the induced prophage (φ919TP ). Specifically, the phage-resistant mutant was isolated by challenging a prophage-deleted variant with lytic phage φ919TP . Further, the comparative genomic analysis of wild-type and φ919TP -resistant mutant predicted that phage φ919TP selects for phage-resistant mutants harboring a mutation in key steps of lipopolysaccharide (LPS) O-antigen biosynthesis, causing a single-base-pair deletion in gene . Our study showed that the -mediated O-antigen defect can cause pleiotropic phenotypes, e.g., cell autoaggregation and reduced swarming motility, emphasizing the role of phage-driven diversification in . The developed approach assists in the identification of genetic determinants of host specificity and is used to explore the molecular mechanism underlying phage-host interactions. Our findings contribute to the understanding of prophage-facilitated horizontal gene transfer and emphasize the potential for developing new strategies to optimize the use of phages in bacterial pathogen control.
Topics: Bacterial Proteins; Cholera; Host Microbial Interactions; Host Specificity; Lysogeny; O Antigens; Prophages; Vibrio cholerae O1; Virus Activation
PubMed: 34960610
DOI: 10.3390/v13122342 -
Nucleic Acids Research Dec 2021The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of...
The life cycle of temperate phages includes a lysogenic cycle stage when the phage integrates into the host genome and becomes a prophage. However, the identification of prophages that are highly divergent from known phages remains challenging. In this study, by taking advantage of the lysis-lysogeny switch of temperate phages, we designed Prophage Tracer, a tool for recognizing active prophages in prokaryotic genomes using short-read sequencing data, independent of phage gene similarity searching. Prophage Tracer uses the criterion of overlapping split-read alignment to recognize discriminative reads that contain bacterial (attB) and phage (attP) att sites representing prophage excision signals. Performance testing showed that Prophage Tracer could predict known prophages with precise boundaries, as well as novel prophages. Two novel prophages, dsDNA and ssDNA, encoding highly divergent major capsid proteins, were identified in coral-associated bacteria. Prophage Tracer is a reliable data mining tool for the identification of novel temperate phages and mobile genetic elements. The code for the Prophage Tracer is publicly available at https://github.com/WangLab-SCSIO/Prophage_Tracer.
Topics: Animals; Anthozoa; Bacteria; Genome, Archaeal; Genome, Bacterial; Interspersed Repetitive Sequences; Prophages; Sequence Alignment; Sequence Analysis, DNA; Software
PubMed: 34551431
DOI: 10.1093/nar/gkab824 -
Oxidative Medicine and Cellular... 2016Virulence of enterohemorrhagic Escherichia coli (EHEC) strains depends on production of Shiga toxins. These toxins are encoded in genomes of lambdoid bacteriophages... (Review)
Review
Virulence of enterohemorrhagic Escherichia coli (EHEC) strains depends on production of Shiga toxins. These toxins are encoded in genomes of lambdoid bacteriophages (Shiga toxin-converting phages), present in EHEC cells as prophages. The genes coding for Shiga toxins are silent in lysogenic bacteria, and prophage induction is necessary for their efficient expression and toxin production. Under laboratory conditions, treatment with UV light or antibiotics interfering with DNA replication are commonly used to induce lambdoid prophages. Since such conditions are unlikely to occur in human intestine, various research groups searched for other factors or agents that might induce Shiga toxin-converting prophages. Among other conditions, it was reported that treatment with H2O2 caused induction of these prophages, though with efficiency significantly lower relative to UV-irradiation or mitomycin C treatment. A molecular mechanism of this phenomenon has been proposed. It appears that the oxidative stress represents natural conditions provoking induction of Shiga toxin-converting prophages as a consequence of H2O2 excretion by either neutrophils in infected humans or protist predators outside human body. Finally, the recently proposed biological role of Shiga toxin production is described in this paper, and the "bacterial altruism" and "Trojan Horse" hypotheses, which are connected to the oxidative stress, are discussed.
Topics: Animals; Enterohemorrhagic Escherichia coli; Humans; Hydrogen Peroxide; Oxidative Stress; Prophages; Shiga Toxin
PubMed: 26798420
DOI: 10.1155/2016/3578368 -
BMC Research Notes Oct 2019Staphylococcus aureus is considered an important pathogen with a variety of virulence factors in communities and hospitals all around the world. Prophage typing is a...
OBJECTIVE
Staphylococcus aureus is considered an important pathogen with a variety of virulence factors in communities and hospitals all around the world. Prophage typing is a practical technique for categorizing this bacterium. In this study, we focused on the detection of prophage patterns in methicillin-resistant S. aureus (MRSA) and methicillin-sensitive S. aureus (MSSA) strains based on their virulence factors, antimicrobial resistance patterns, and molecular typing by rep-PCR.
RESULTS
Out of 126 S. aureus isolates, 45 (35.7%) were identified as MRSA. In total, 17 different prophage types were detected and 112 strains out of 126 strains contained at least one prophage. There was a statistically significant relationship between hld, hlg, eta and SGA, SGA, and SGFb, respectively. The results of the rep-PCR analysis revealed 14 different patterns among the MRSA and MSSA isolates. In conclusion, the presence of different prophage-encoded virulence factors and antibiotic-resistant genes among MRSA strains enables them to produce a broad range of diseases. Thus, diverse MRSA strains which have these prophages can be considered as a potential threat to the patient's health in either the hospital or the community.
Topics: Anti-Bacterial Agents; Community-Acquired Infections; Drug Resistance, Bacterial; Gene Expression; Genes, Bacterial; Humans; Iran; Methicillin-Resistant Staphylococcus aureus; Microbial Sensitivity Tests; Polymerase Chain Reaction; Prophages; Staphylococcal Infections; Staphylococcus aureus; Virulence Factors
PubMed: 31639052
DOI: 10.1186/s13104-019-4711-4