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1.
Int J Mol Sci ; 25(13)2024 Jul 07.
Article in English | MEDLINE | ID: mdl-39000573

ABSTRACT

Mycobacteriophages are viruses that specifically infect bacterial species within the genera Mycobacterium and Mycolicibacterium. Over 2400 mycobacteriophages have been isolated on the host Mycolicibacterium smegmatis and sequenced. This wealth of genomic data indicates that mycobacteriophage genomes are diverse, mosaic, and contain numerous (35-60%) genes for which there is no predicted function based on sequence similarity to characterized orthologs, many of which are essential to lytic growth. To fully understand the molecular aspects of mycobacteriophage-host interactions, it is paramount to investigate the function of these genes and gene products. Here we show that the temperate mycobacteriophage, Alexphander, makes stable lysogens with a frequency of 2.8%. Alexphander gene 94 is essential for lytic infection and encodes a protein predicted to contain a C-terminal MerR family helix-turn-helix DNA-binding motif (HTH) and an N-terminal DinB/YfiT motif, a putative metal-binding motif found in stress-inducible gene products. Full-length and C-terminal gp94 constructs form high-order nucleoprotein complexes on 100-500 base pair double-stranded DNA fragments and full-length phage genomic DNA with little sequence discrimination for the DNA fragments tested. Maximum gene 94 mRNA levels are observed late in the lytic growth cycle, and gene 94 is transcribed in a message with neighboring genes 92 through 96. We hypothesize that gp94 is an essential DNA-binding protein for Alexphander during lytic growth. We proposed that gp94 forms multiprotein complexes on DNA through cooperative interactions involving its HTH DNA-binding motif at sites throughout the phage chromosome, facilitating essential DNA transactions required for lytic propagation.


Subject(s)
DNA-Binding Proteins , Mycobacteriophages , Mycobacterium smegmatis , Viral Proteins , Mycobacteriophages/genetics , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Mycobacterium smegmatis/virology , Mycobacterium smegmatis/genetics , Viral Proteins/genetics , Viral Proteins/metabolism , Viral Proteins/chemistry , Lysogeny/genetics , Genome, Viral , DNA, Viral/genetics
2.
Int J Mol Sci ; 25(11)2024 May 23.
Article in English | MEDLINE | ID: mdl-38891850

ABSTRACT

Clostridioides difficile is a causative agent of antibiotic-associated diarrhea as well as pseudomembranous colitis. So far, all known bacteriophages infecting these bacteria are temperate, which means that instead of prompt lysis of host cells, they can integrate into the host genome or replicate episomally. While C. difficile phages are capable of spontaneous induction and entering the lytic pathway, very little is known about the regulation of their maintenance in the state of lysogeny. In this study, we investigated the properties of a putative major repressor of the recently characterized C. difficile phiCDKH01 bacteriophage. A candidate protein belongs to the XRE family and controls the transcription of genes encoding putative phage antirepressors, known to be involved in the regulation of lytic development. Hence, the putative major phage repressor is likely to be responsible for maintenance of the lysogeny.


Subject(s)
Bacteriophages , Clostridioides difficile , Lysogeny , Clostridioides difficile/virology , Bacteriophages/genetics , Bacteriophages/physiology , Viral Proteins/genetics , Viral Proteins/metabolism , Gene Expression Regulation, Viral , Humans , Repressor Proteins/genetics , Repressor Proteins/metabolism , Genome, Viral
3.
Curr Biol ; 34(13): 2841-2853.e18, 2024 Jul 08.
Article in English | MEDLINE | ID: mdl-38878771

ABSTRACT

The developmental choice made by temperate phages, between cell death (lysis) and viral dormancy (lysogeny), is influenced by the relative abundance of viruses and hosts in the environment. The paradigm for this abundance-driven decision is phage lambda of E. coli, whose propensity to lysogenize increases with the number of viruses coinfecting the same bacterium. It is believed that lambda uses this number to infer whether phages or bacteria outnumber each other. However, this interpretation is premised on an accurate mapping between the extracellular phage-to-bacteria ratio and the intracellular multiplicity of infection (MOI). Here, we show this premise to be faulty. By simultaneously labeling phage capsids and genomes, we find that, while the number of phages landing on each cell reliably samples the population ratio, the number of phages entering the cell does not. Single-cell infections, performed in a microfluidic device and interpreted using a stochastic model, reveal that the probability and rate of phage entry decrease with the number of adsorbed phages. This decrease reflects an MOI-dependent perturbation to host physiology caused by phage attachment, as evidenced by compromised membrane integrity and loss of membrane potential. The dependence of entry dynamics on the surrounding medium results in a strong impact on the infection outcome, while the protracted entry of coinfecting phages increases the heterogeneity in infection outcome at a given MOI. Our findings in lambda, and similar results we obtained for phages T5 and P1, demonstrate the previously unappreciated role played by entry dynamics in determining the outcome of bacteriophage infection.


Subject(s)
Bacteriophage lambda , Escherichia coli , Escherichia coli/virology , Escherichia coli/physiology , Bacteriophage lambda/physiology , Bacteriophage lambda/genetics , Lysogeny , Virus Internalization
4.
Ecol Lett ; 27(6): e14464, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38923281

ABSTRACT

Microbiomes are ecosystems, and their stability can impact the health of their hosts. Theory predicts that predators influence ecosystem stability. Phages are key predators of bacteria in microbiomes, but phages are unusual predators because many have lysogenic life cycles. It has been hypothesized that lysogeny can destabilize microbiomes, but lysogeny has no direct analog in classical ecological theory, and no formal theory exists. We studied the stability of computationally simulated microbiomes with different numbers of temperate (lysogenic) and virulent (obligate lytic) phage species. Bacterial populations were more likely to fluctuate over time when there were more temperate phages species. After disturbances, bacterial populations returned to their pre-disturbance densities more slowly when there were more temperate phage species, but cycles engendered by disturbances dampened more slowly when there were more virulent phage species. Our work offers the first formal theory linking lysogeny to microbiome stability.


Subject(s)
Bacteriophages , Lysogeny , Microbiota , Bacteriophages/physiology , Computer Simulation , Bacteria/virology , Models, Biological
5.
mBio ; 15(6): e0050424, 2024 Jun 12.
Article in English | MEDLINE | ID: mdl-38757974

ABSTRACT

A recent demonstration of synergy between a temperate phage and the antibiotic ciprofloxacin suggested a scalable approach to exploiting temperate phages in therapy, termed temperate phage-antibiotic synergy, which specifically interacted with the lysis-lysogeny decision. To determine whether this would hold true across antibiotics, we challenged Escherichia coli with the phage HK97 and a set of 13 antibiotics spanning seven classes. As expected, given the conserved induction pathway, we observed synergy with classes of drugs known to induce an SOS response: a sulfa drug, other quinolones, and mitomycin C. While some ß-lactams exhibited synergy, this appeared to be traditional phage-antibiotic synergy, with no effect on the lysis-lysogeny decision. Curiously, we observed a potent synergy with antibiotics not known to induce the SOS response: protein synthesis inhibitors gentamicin, kanamycin, tetracycline, and azithromycin. The synergy results in an eightfold reduction in the effective minimum inhibitory concentration of gentamicin, complete eradication of the bacteria, and, when administered at sub-optimal doses, drastically decreases the frequency of lysogens emerging from the combined challenge. However, lysogens exhibit no increased sensitivity to the antibiotic; synergy was maintained in the absence of RecA; and the antibiotic reduced the initial frequency of lysogeny rather than selecting against formed lysogens. Our results confirm that SOS-inducing antibiotics broadly result in temperate-phage-specific synergy, but that other antibiotics can interact with temperate phages specifically and result in synergy. This is the first report of a means of chemically blocking entry into lysogeny, providing a new means for manipulating the key lysis-lysogeny decision.IMPORTANCEThe lysis-lysogeny decision is made by most bacterial viruses (bacteriophages, phages), determining whether to kill their host or go dormant within it. With over half of the bacteria containing phages waiting to wake, this is one of the most important behaviors in all of biology. These phages are also considered unusable for therapy because of this behavior. In this paper, we show that many antibiotics bias this behavior to "wake" the dormant phages, forcing them to kill their host, but some also prevent dormancy in the first place. These will be important tools to study this critical decision point and may enable the therapeutic use of these phages.


Subject(s)
Anti-Bacterial Agents , Escherichia coli , Lysogeny , Anti-Bacterial Agents/pharmacology , Escherichia coli/virology , Escherichia coli/drug effects , SOS Response, Genetics/drug effects , Microbial Sensitivity Tests , Coliphages/physiology , Coliphages/drug effects , Drug Synergism , Bacteriophages/physiology , Bacteriophages/drug effects , Mitomycin/pharmacology
6.
ISME J ; 18(1)2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38818736

ABSTRACT

When phage infect their bacterial hosts, they may either lyse the cell and generate a burst of new phage, or lysogenize the bacterium, incorporating the phage genome into it. Phage lysis/lysogeny strategies are assumed to be highly optimized, with the optimal tradeoff depending on environmental conditions. However, in nature, phage of radically different lysis/lysogeny strategies coexist in the same environment, preying on the same bacteria. How can phage preying on the same bacteria coexist if one is more optimal than the other? Here, we address this conundrum within a modeling framework, simulating the population dynamics of communities of phage and their lysogens. We find that coexistence between phage of different lysis/lysogeny strategies is a natural outcome of chaotic population dynamics that arise within sufficiently diverse communities, which ensure no phage is able to absolutely dominate its competitors. Our results further suggest a bet-hedging mechanism at the level of the phage pan-genome, wherein obligate lytic (virulent) strains typically outcompete temperate strains, but also more readily fluctuate to extinction within a local community.


Subject(s)
Bacteria , Bacteriophages , Lysogeny , Bacteriophages/genetics , Bacteriophages/isolation & purification , Bacteriophages/classification , Bacteria/virology , Bacteria/genetics , Bacteria/classification , Population Dynamics , Models, Biological , Genome, Viral
7.
Virus Res ; 346: 199395, 2024 Aug.
Article in English | MEDLINE | ID: mdl-38782263

ABSTRACT

The plague, caused by Yersinia pestis, is a natural focal disease and the presence of Y. pestis in the environment is a critical ecological concern worldwide. The role of Y. pestis phages in the ecological life cycle of the plague is crucial. Previously, a temperature-sensitive phage named vB_YpM_HQ103 was isolated from plague foci in Yunnan province, China. Upon infecting the EV76 strain of Y. pestis, vB_YpM_HQ103 exhibits lysogenic behavior at 21 °C and lytic behavior at 37 °C. Various methods including continuous passage lysogenic tests, in vitro lysis tests, comparative genomic assays, fluorescence quantitative PCR and receptor identification tests were employed to demonstrate that the lysogenic life cycle of this phage is applicable to wild Y. pestis strains; its lysogeny is pseudolysogenic (carrying but not integrating), allowing it to replicate and proliferate within Y. pestis. Furthermore, we have identified the outer membrane protein OmpA of Y. pestis as the receptor for phage infection. In conclusion, our research provides insight into the characteristics and receptors of a novel Y. pestis phage infection with a pseudolysogenic cycle. The findings of this study enhance our understanding of Y. pestis phages and plague microecology, offering valuable insights for future studies on the conservation and genetic evolution of Y. pestis in nature.


Subject(s)
Bacteriophages , Genome, Viral , Lysogeny , Plague , Yersinia pestis , Yersinia pestis/virology , Yersinia pestis/genetics , Bacteriophages/genetics , Bacteriophages/isolation & purification , Bacteriophages/classification , Bacteriophages/physiology , Plague/microbiology , China , Bacterial Outer Membrane Proteins/genetics , Bacterial Outer Membrane Proteins/metabolism
8.
mSystems ; 9(6): e0103623, 2024 Jun 18.
Article in English | MEDLINE | ID: mdl-38727217

ABSTRACT

Temperate bacteriophages (phages) are common features of bacterial genomes and can act as self-amplifying biological weapons, killing susceptible competitors and thus increasing the fitness of their bacterial hosts (lysogens). Despite their prevalence, however, the key characteristics of an effective temperate phage weapon remain unclear. Here, we use systematic mathematical analyses coupled with experimental tests to understand what makes an effective temperate phage weapon. We find that effectiveness is controlled by phage life history traits-in particular, the probability of lysis and induction rate-but that the optimal combination of traits varies with the initial frequency of a lysogen within a population. As a consequence, certain phage weapons can be detrimental when their hosts are rare yet beneficial when their hosts are common, while subtle changes in individual life history traits can completely reverse the impact of an individual phage weapon on lysogen fitness. We confirm key predictions of our model experimentally, using temperate phages isolated from the clinically relevant Liverpool epidemic strain of Pseudomonas aeruginosa. Through these experiments, we further demonstrate that nutrient availability can also play a critical role in driving frequency-dependent patterns in phage-mediated competition. Together, these findings highlight the complex and context-dependent nature of temperate phage weapons and the importance of both ecological and evolutionary processes in shaping microbial community dynamics more broadly. IMPORTANCE: Temperate bacteriophages-viruses that integrate within bacterial DNA-are incredibly common within bacterial genomes and can act as powerful self-amplifying weapons. Bacterial hosts that carry temperate bacteriophages can thus gain a fitness advantage within a given niche by killing competitors. But what makes an effective phage weapon? Here, we first use a simple mathematical model to explore the factors determining bacteriophage weapon utility. Our models suggest that bacteriophage weapons are nuanced and context-dependent; an individual bacteriophage may be beneficial or costly depending upon tiny changes to how it behaves or the bacterial community it inhabits. We then confirm these mathematical predictions experimentally, using phages isolated from cystic fibrosis patients. But, in doing so, we also find that another factor-nutrient availability-plays a key role in shaping bacteriophage-mediated competition. Together, our results provide new insights into how temperate bacteriophages modulate bacterial communities.


Subject(s)
Lysogeny , Pseudomonas aeruginosa , Pseudomonas aeruginosa/virology , Bacteriophages/genetics , Bacteriophages/physiology
9.
ISME J ; 18(1)2024 Jan 08.
Article in English | MEDLINE | ID: mdl-38739683

ABSTRACT

Temperate phages can interact with bacterial hosts through lytic and lysogenic cycles via different mechanisms. Lysogeny has been identified as the major form of bacteria-phage interaction in the coral-associated microbiome. However, the lysogenic-to-lytic switch of temperate phages in ecologically important coral-associated bacteria and its ecological impact have not been extensively investigated. By studying the prophages in coral-associated Halomonas meridiana, we found that two prophages, Phm1 and Phm3, are inducible by the DNA-damaging agent mitomycin C and that Phm3 is spontaneously activated under normal cultivation conditions. Furthermore, Phm3 undergoes an atypical lytic pathway that can amplify and package adjacent host DNA, potentially resulting in lateral transduction. The induction of Phm3 triggered a process of cell lysis accompanied by the formation of outer membrane vesicles (OMVs) and Phm3 attached to OMVs. This unique cell-lysis process was controlled by a four-gene lytic module within Phm3. Further analysis of the Tara Ocean dataset revealed that Phm3 represents a new group of temperate phages that are widely distributed and transcriptionally active in the ocean. Therefore, the combination of lateral transduction mediated by temperate phages and OMV transmission offers a versatile strategy for host-phage coevolution in marine ecosystems.


Subject(s)
Anthozoa , Halomonas , Prophages , Halomonas/virology , Halomonas/genetics , Anthozoa/microbiology , Anthozoa/virology , Prophages/genetics , Prophages/physiology , Animals , Lysogeny , Transduction, Genetic , Mitomycin/pharmacology
10.
Cell Host Microbe ; 32(5): 727-738.e6, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38579715

ABSTRACT

Many, if not all, bacteria use quorum sensing (QS) to control collective behaviors, and more recently, QS has also been discovered in bacteriophages (phages). Phages can produce communication molecules of their own, or "listen in" on the host's communication processes, to switch between lytic and lysogenic modes of infection. Here, we study the interaction of Vibrio cholerae with the lysogenic phage VP882, which is activated by the QS molecule DPO. We discover that induction of VP882 results in the binding of phage transcripts to the major RNA chaperone Hfq, which in turn outcompetes and downregulates host-encoded small RNAs (sRNAs). VP882 itself also encodes Hfq-binding sRNAs, and we demonstrate that one of these sRNAs, named VpdS, promotes phage replication by regulating host and phage mRNA levels. We further show that host-encoded sRNAs can antagonize phage replication by downregulating phage mRNA expression and thus might be part of the host's phage defense arsenal.


Subject(s)
Bacteriophages , Host Factor 1 Protein , Quorum Sensing , Vibrio cholerae , Vibrio cholerae/virology , Vibrio cholerae/genetics , Quorum Sensing/genetics , Bacteriophages/genetics , Bacteriophages/physiology , Host Factor 1 Protein/metabolism , Host Factor 1 Protein/genetics , Virus Replication , Lysogeny , RNA, Viral/genetics , RNA, Viral/metabolism , RNA, Small Untranslated/genetics , RNA, Small Untranslated/metabolism , Gene Expression Regulation, Bacterial , RNA, Bacterial/genetics , RNA, Bacterial/metabolism , RNA, Messenger/metabolism , RNA, Messenger/genetics , Host Microbial Interactions/genetics
11.
Nat Microbiol ; 9(5): 1312-1324, 2024 May.
Article in English | MEDLINE | ID: mdl-38565896

ABSTRACT

Dormant prophages protect lysogenic cells by expressing diverse immune systems, which must avoid targeting their cognate prophages upon activation. Here we report that multiple Staphylococcus aureus prophages encode Tha (tail-activated, HEPN (higher eukaryotes and prokaryotes nucleotide-binding) domain-containing anti-phage system), a defence system activated by structural tail proteins of incoming phages. We demonstrate the function of two Tha systems, Tha-1 and Tha-2, activated by distinct tail proteins. Interestingly, Tha systems can also block reproduction of the induced tha-positive prophages. To prevent autoimmunity after prophage induction, these systems are inhibited by the product of a small overlapping antisense gene previously believed to encode an excisionase. This genetic organization, conserved in S. aureus prophages, allows Tha systems to protect prophages and their bacterial hosts against phage predation and to be turned off during prophage induction, balancing immunity and autoimmunity. Our results show that the fine regulation of these processes is essential for the correct development of prophages' life cycle.


Subject(s)
Prophages , Staphylococcus aureus , Prophages/genetics , Staphylococcus aureus/virology , Staphylococcus aureus/immunology , Autoimmunity , Lysogeny , Staphylococcus Phages/genetics , Staphylococcus Phages/immunology , Staphylococcus Phages/physiology , Viral Tail Proteins/genetics , Viral Tail Proteins/metabolism , Bacteriophages/genetics , Bacteriophages/immunology , Bacteriophages/physiology
12.
J Bacteriol ; 206(5): e0040223, 2024 May 23.
Article in English | MEDLINE | ID: mdl-38687034

ABSTRACT

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.


Subject(s)
Prophages , Pseudomonas aeruginosa , Quorum Sensing , Pseudomonas aeruginosa/virology , Pseudomonas aeruginosa/genetics , Pseudomonas aeruginosa/pathogenicity , Pseudomonas aeruginosa/physiology , Prophages/genetics , Prophages/physiology , Virulence , Caenorhabditis elegans/microbiology , Caenorhabditis elegans/virology , Biofilms/growth & development , Animals , Lysogeny , Pseudomonas Phages/genetics , Pseudomonas Phages/physiology , Pseudomonas Infections/microbiology
13.
Virology ; 595: 110087, 2024 Jul.
Article in English | MEDLINE | ID: mdl-38636362

ABSTRACT

Vibrio parahaemolyticus is a globally important bacterium related to climate warming and health threat to human and marine animals. Yet, there is limited knowledge about its polylysogeny harboring multiple prophages and the genetic information. In this study, two prophages (VPS05ph1 and VPS05ph2) were identified in a V. parahaemolyticus isolate through genomic and transcriptional analyses. Both prophages were determined as HP1-like phages, located in a novel phylogenetic lineage of Peduoviridae. They shared a moderate genome-wide sequence similarity with each other and high synteny with the closest relatives, but showed low identities to the repressor counterparts of the representative phages within the family. In addition, no bacterial virulence genes, antibiotic resistance genes and known phage-encoded lytic proteins were identified on both prophage genomes. Moreover, the V. parahaemolyticus isolate was induced with mitomycin, which caused aberrant cellular morphology and nonviability of bacterial cells and excision of prophage VPS05ph1, accompanied by the respective inhibition and promotion of transcriptions of the cI-like and cox-like regulator genes for phage decision making. Results in this study provide the genetic context of polylysogeny in the V. parahaemolyticus isolate, support the diversity and prevalence of HP1-like phages in vibrios, and promote to explore interactions between the HP1-like prophage and its vibrio host.


Subject(s)
Genome, Viral , Phylogeny , Prophages , Vibrio parahaemolyticus , Vibrio parahaemolyticus/virology , Vibrio parahaemolyticus/genetics , Prophages/genetics , Prophages/isolation & purification , Prophages/physiology , Lysogeny
14.
Environ Microbiol ; 26(4): e16630, 2024 Apr.
Article in English | MEDLINE | ID: mdl-38643972

ABSTRACT

Horizontal gene transfer (HGT) is a fundamental process in prokaryotic evolution, contributing significantly to diversification and adaptation. HGT is typically facilitated by mobile genetic elements (MGEs), such as conjugative plasmids and phages, which often impose fitness costs on their hosts. However, a considerable number of bacterial genes are involved in defence mechanisms that limit the propagation of MGEs, suggesting they may actively restrict HGT. In our study, we investigated whether defence systems limit HGT by examining the relationship between the HGT rate and the presence of 73 defence systems across 12 bacterial species. We discovered that only six defence systems, three of which were different CRISPR-Cas subtypes, were associated with a reduced gene gain rate at the species evolution scale. Hosts of these defence systems tend to have a smaller pangenome size and fewer phage-related genes compared to genomes without these systems. This suggests that these defence mechanisms inhibit HGT by limiting prophage integration. We hypothesize that the restriction of HGT by defence systems is species-specific and depends on various ecological and genetic factors, including the burden of MGEs and the fitness effect of HGT in bacterial populations.


Subject(s)
Bacteria , Gene Transfer, Horizontal , Gene Transfer, Horizontal/genetics , Bacteria/classification , Bacteria/genetics , Interspersed Repetitive Sequences/genetics , CRISPR-Cas Systems/genetics , Lysogeny/genetics , Species Specificity , Evolution, Molecular
15.
Curr Biol ; 34(8): 1739-1749.e7, 2024 04 22.
Article in English | MEDLINE | ID: mdl-38599209

ABSTRACT

Prophages, viral sequences integrated into bacterial genomes, can be beneficial and costly. Despite the risk of prophage activation and subsequent bacterial death, active prophages are present in most bacterial genomes. However, our understanding of the selective forces that maintain prophages in bacterial populations is limited. Combining experimental evolution with stochastic modeling, we show that prophage maintenance and loss are primarily determined by environmental conditions that alter the net fitness effect of a prophage on its bacterial host. When prophages are too costly, they are rapidly lost through environment-specific sequences of selective sweeps. Conflicting selection pressures that select against the prophage but for a prophage-encoded accessory gene can maintain prophages. The dynamics of prophage maintenance additionally depend on the sociality of this accessory gene. Prophage-encoded genes that exclusively benefit the lysogen maintain prophages at higher frequencies compared with genes that benefit the entire population. That is because the latter can protect phage-free "cheaters," reducing the benefit of maintaining the prophage. Our simulations suggest that environmental variation plays a larger role than mutation rates in determining prophage maintenance. These findings highlight the complexity of selection pressures that act on mobile genetic elements and challenge our understanding of the role of environmental factors relative to random chance events in shaping the evolutionary trajectory of bacterial populations. By shedding light on the key factors that shape microbial populations in the face of environmental changes, our study significantly advances our understanding of the complex dynamics of microbial evolution and diversification.


Subject(s)
Prophages , Prophages/genetics , Prophages/physiology , Selection, Genetic , Mutation , Environment , Lysogeny/genetics , Evolution, Molecular
16.
Cell Rep ; 43(3): 113849, 2024 Mar 26.
Article in English | MEDLINE | ID: mdl-38427560

ABSTRACT

CRISPR-Cas immune systems provide bacteria with adaptive immunity against bacteriophages, but they are often transcriptionally repressed to mitigate auto-immunity. In some cases, CRISPR-Cas expression increases in response to a phage infection, but the mechanisms of induction are largely unknown, and it is unclear whether induction occurs strongly and quickly enough to benefit the bacterial host. In S. pyogenes, Cas9 is both an immune effector and auto-repressor of CRISPR-Cas expression. Here, we show that phage-encoded anti-CRISPR proteins relieve Cas9 auto-repression and trigger a rapid increase in CRISPR-Cas levels during a single phage infective cycle. As a result, fewer cells succumb to lysis, leading to a striking survival benefit after multiple rounds of infection. CRISPR-Cas induction also reduces lysogeny, thereby limiting a route for horizontal gene transfer. Altogether, we show that Cas9 is not only a CRISPR-Cas effector and repressor but also a phage sensor that can mount an anti-anti-CRISPR transcriptional response.


Subject(s)
Bacteriophages , Bacteriophages/physiology , CRISPR-Cas Systems/genetics , Bacteria/metabolism , Lysogeny , Viral Proteins/genetics , Viral Proteins/metabolism
17.
Methods Mol Biol ; 2793: 257-271, 2024.
Article in English | MEDLINE | ID: mdl-38526735

ABSTRACT

We present here a CRISPR-interference-based protocol to trigger prophage induction, even for non-inducible prophages. This method can also be used to cure the prophage from the bacterial host. The method is based on silencing of the phage's repressor transcription, thanks to CRISPR interference. Plasmid electroporation is used to bring the CRISPRi system into the bacteria, specifically on a plasmid carrying spacers targeting the prophage repressor. This method enables prophage induction and curation in a week or two with a high efficiency.


Subject(s)
Lysogeny , Prophages , Prophages/genetics , Clustered Regularly Interspaced Short Palindromic Repeats/genetics , Virus Activation , Plasmids/genetics
18.
Arch Virol ; 169(4): 81, 2024 Mar 23.
Article in English | MEDLINE | ID: mdl-38519716

ABSTRACT

Bacillus subtilis is a Gram-positive bacterium that is widely used in fermentation and in the pharmaceutical industry. Phage contamination occasionally occurs in various fermentation processes and causes significant economic loss. Here, we report the isolation and characterization of a temperate B. subtilis phage, termed phi18-2, from spore powder manufactured in a fermentation plant. Transmission electron microscopy showed that phi18-2 has a symmetrical polyhedral head and a long noncontractile tail. Receptor analysis showed that phi18-2 recognizes wall teichoic acid (WTA) for infection. The phage virions have a linear double-stranded DNA genome of 64,467 bp with identical direct repeat sequences of 309 bp at each end of the genome. In lysogenic cells, the phage genome was found to be present in the cytoplasm without integration into the host cell chromosome, and possibly as a linear phage-plasmid with unmodified ends. Our data may provide some insight into the molecular basis of the unique lysogenic cycle of phage phi18-2.


Subject(s)
Bacillus Phages , Bacteriophages , Bacteriophages/genetics , Bacillus Phages/genetics , DNA, Viral/genetics , Lysogeny , Genome, Viral , Plasmids/genetics , Cytoplasm
19.
J Basic Microbiol ; 64(6): e2400027, 2024 Jun.
Article in English | MEDLINE | ID: mdl-38548701

ABSTRACT

Bacteriophages infecting Mycobacterium smegmatis mc2155 are numerous and, hence, are classified into clusters based on nucleotide sequence similarity. Analyzing phages belonging to clusters/subclusters can help gain deeper insights into their biological features and potential therapeutic applications. In this study, for genomic characterization of B1 subcluster mycobacteriophages, a framework of online tools was developed, which enabled functional annotation of about 55% of the previously deemed hypothetical proteins in B1 phages. We also studied the phenotype, lysogeny status, and antimycobacterial activity of 10 B1 phages against biofilm and an antibiotic-resistant M. smegmatis strain (4XR1). All 10 phages belonged to the Siphoviridae family, appeared temperate based on their spontaneous release from the putative lysogens and showed antibiofilm activity. The highest inhibitory and disruptive effects on biofilm were 64% and 46%, respectively. This systematic characterization using a combination of genomic and experimental tools is a promising approach to furthering our understanding of viral dark matter.


Subject(s)
Biofilms , Genome, Viral , Genomics , Lysogeny , Mycobacteriophages , Mycobacterium smegmatis , Mycobacteriophages/genetics , Mycobacteriophages/physiology , Biofilms/growth & development , Genome, Viral/genetics , Mycobacterium smegmatis/virology , Mycobacterium smegmatis/genetics , Phylogeny
20.
Nucleic Acids Res ; 52(8): 4659-4675, 2024 May 08.
Article in English | MEDLINE | ID: mdl-38554102

ABSTRACT

RexA and RexB function as an exclusion system that prevents bacteriophage T4rII mutants from growing on Escherichia coli λ phage lysogens. Recent data established that RexA is a non-specific DNA binding protein that can act independently of RexB to bias the λ bistable switch toward the lytic state, preventing conversion back to lysogeny. The molecular interactions underlying these activities are unknown, owing in part to a dearth of structural information. Here, we present the 2.05-Å crystal structure of the λ RexA dimer, which reveals a two-domain architecture with unexpected structural homology to the recombination-associated protein RdgC. Modelling suggests that our structure adopts a closed conformation and would require significant domain rearrangements to facilitate DNA binding. Mutagenesis coupled with electromobility shift assays, limited proteolysis, and double electron-electron spin resonance spectroscopy support a DNA-dependent conformational change. In vivo phenotypes of RexA mutants suggest that DNA binding is not a strict requirement for phage exclusion but may directly contribute to modulation of the bistable switch. We further demonstrate that RexA homologs from other temperate phages also dimerize and bind DNA in vitro. Collectively, these findings advance our mechanistic understanding of Rex functions and provide new evolutionary insights into different aspects of phage biology.


Subject(s)
Bacteriophage lambda , DNA-Binding Proteins , Models, Molecular , Viral Proteins , Bacteriophage lambda/genetics , Crystallography, X-Ray , Viral Proteins/metabolism , Viral Proteins/chemistry , Viral Proteins/genetics , DNA-Binding Proteins/chemistry , DNA-Binding Proteins/metabolism , DNA-Binding Proteins/genetics , Protein Binding , Protein Multimerization , DNA, Viral/genetics , DNA, Viral/metabolism , Mutation , Lysogeny , Escherichia coli/virology , Escherichia coli/genetics , Escherichia coli/metabolism , DNA/metabolism , DNA/chemistry
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