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Prophage

The concept of the prophage was introduced by André Lwoff in the early 1950s through his studies on lysogeny at the Pasteur Institute. Lwoff demonstrated that temperate bacteriophages could integrate their genome into the bacterial chromosome as a dormant prophage, which could later be induced to enter the lytic cycle. This discovery, shared in the 1965 Nobel Prize in Physiology or Medicine with François Jacob and Jacques Monod, revolutionized understanding of viral-bacterial interactions.^[1] A prophage is the dormant, integrated form of a temperate bacteriophage genome within the chromosome of a bacterial host, where it replicates passively alongside the host's DNA without producing new virions or lysing the cell.^[2] This integration typically occurs via site-specific recombination at attachment sites (attB) on the bacterial chromosome, mediated by phage-encoded integrases, though some prophages insert randomly.^[3] In this lysogenic state, the prophage is maintained by a repressor protein that prevents expression of lytic genes, ensuring stable inheritance to daughter cells during bacterial division.^[2] Prophages play a crucial role in bacterial biology by conferring advantages such as immunity to superinfection by similar phages and modulating host fitness through encoded genes that enhance virulence, stress resistance, or metabolic capabilities.^[4] For instance, many bacterial pathogens, including Vibrio cholerae and Corynebacterium diphtheriae, acquire toxin genes from prophages, which are essential for disease causation.^[2] Environmental stressors like DNA damage from ultraviolet light or chemicals can trigger prophage induction, involving the host's RecA protein to cleave the repressor, leading to excision, lytic replication, and host cell lysis that releases new phages.^[5] Beyond pathogenesis, prophages drive bacterial evolution by facilitating horizontal gene transfer, including antimicrobial resistance determinants, and are present in approximately 70% of sequenced bacterial genomes, underscoring their ubiquity in microbial ecosystems.^[6] Studies have highlighted "active lysogeny," where prophages dynamically regulate host gene expression rather than remaining entirely passive, influencing processes like biofilm formation and inter-prophage interactions in polylysogenic bacteria.^[7]

Introduction and Basics

Definition

A prophage is the genome of a temperate bacteriophage that integrates into the host bacterium's chromosome or, in some cases, persists as a low-copy plasmid, establishing a stable, dormant lysogenic state in which the viral DNA replicates passively with the bacterial genome.^[8]^[9] This integration allows the prophage to remain latent without producing new virions or lysing the host cell, distinguishing it from the active replication seen in other viral forms.^[8] In contrast to virulent phages, which exclusively follow a lytic cycle that culminates in host cell destruction, temperate phages capable of lysogeny form prophages that confer no immediate harm to the bacterium while potentially providing long-term benefits such as enhanced fitness or defense against superinfection. The classic example is the lambda phage (λ), a temperate bacteriophage that integrates into the chromosome of Escherichia coli, serving as a foundational model for understanding lysogeny and prophage behavior.^[10] Prophages are ubiquitous in bacterial genomes, with studies indicating they can account for up to 10-20% of the total DNA content, contributing significantly to genetic diversity and evolution across bacterial species.^[11]

Discovery and History

The concept of lysogeny emerged in the 1940s through the work of André Lwoff at the Pasteur Institute, who described "lysogenic bacteria" as strains capable of spontaneously producing bacteriophages without external infection, attributing this to an inherent bacterial property rather than a free virus.^[12] Lwoff's studies on Bacillus megatherium demonstrated that these bacteria maintained a stable association with phage particles, laying the groundwork for understanding temperate phages.^[13] This period marked the shift from viewing phages solely as lytic agents to recognizing a dormant state within the host. The discovery of the prophage as integrated viral DNA was advanced in 1950 by Esther Lederberg, who isolated bacteriophage lambda (λ) from Escherichia coli K-12 during experiments on bacterial resistance, revealing the lysogenic cycle in this model organism. Lederberg's isolation showed that lambda could exist in a non-lytic form, integrated into the bacterial genome, challenging earlier views of phages as purely destructive.^[14] In 1951, she further demonstrated that lysogenic bacteria exhibit immunity to superinfection by homologous phages, as the integrated prophage confers resistance through repression of incoming viral replication. Concurrently, Lwoff and colleagues in the early 1950s elucidated the induction process, showing that ultraviolet (UV) light could trigger prophage excision and lytic cycle activation in lysogenic bacteria by damaging host DNA and derepressing the prophage. This work, detailed in their 1950 paper, established UV as a key inducer and solidified the prophage as a heritable genetic element responsive to environmental stress. By the 1960s, molecular characterization of lambda integration advanced significantly, with Allan Campbell proposing in 1962 that the prophage inserts site-specifically into the E. coli chromosome between gal and bio genes via recombination at attachment sites, providing a mechanistic model for lysogeny maintenance. The 1980s brought further clarity through the complete sequencing of the lambda genome by Frederick Sanger and colleagues in 1982, which revealed the cI repressor gene responsible for maintaining lysogeny by binding operators and preventing lytic gene expression. This sequencing confirmed the prophage as a linear segment of viral DNA integrated into the host genome, evolving the concept from a vague "lysogenic state" in the 1940s to a precisely defined integrated viral element by the mid-20th century.^[15]

Molecular Biology

Lysogenic Cycle

The lysogenic cycle represents a dormant phase in the life cycle of temperate bacteriophages, where the phage genome integrates into the host bacterium's chromosome as a prophage, avoiding immediate cell lysis and enabling long-term persistence.^[16] This cycle begins with phage adsorption to specific receptors on the bacterial cell surface, followed by the injection of the phage DNA into the host cytoplasm.^[17] Once inside, the linear phage DNA anneals at its cohesive ends and is ligated by host enzymes to form a stable circular molecule that serves as the precursor for integration.^[16] Following circularization, site-specific recombination mediated by phage-encoded integrases inserts the prophage into the bacterial chromosome at attachment sites (attP on the phage and attB on the host), establishing lysogeny.^[16] Concurrently, early gene expression determines the cycle's outcome: in lysogeny, the cI repressor protein (as in phage lambda) dominates over the cro protein, binding to operator sites to repress lytic genes and promote prophage maintenance, whereas cro dominance favors the lytic cycle by activating late genes for virion production.^[17] This decision point is influenced by host physiological conditions and phage multiplicity of infection.^[16] Once integrated, the prophage replicates passively with the host chromosome during bacterial cell division, ensuring vertical transmission to daughter cells without disrupting host viability.^[17] This maintenance relies on the cI repressor's continuous expression from the prophage, forming a positive feedback loop to sustain repression of lytic functions.^[16] Prophages are highly prevalent in bacterial populations, detected in approximately 75% of prokaryotic genomes, with many bacteria, including strains of Vibrio cholerae, harboring multiple prophages that contribute to genomic diversity.^[6]

Integration and Maintenance

The integration of a prophage into the host bacterial genome is achieved through site-specific recombination, a precise process that inserts the phage DNA as a linear segment into the bacterial chromosome. This recombination occurs between the phage attachment site (attP), a relatively long sequence on the phage genome, and the bacterial attachment site (attB), a shorter core sequence on the host DNA. The reaction is catalyzed by the phage-encoded integrase enzyme (Int), a member of the tyrosine recombinase family, which forms a synaptic complex with the att sites and executes strand cleavage and rejoining to generate the integrated prophage flanked by hybrid attL and attR sites.^[18]^[19] In the case of bacteriophage lambda, a model temperate phage, the attB site in Escherichia coli is located between the gal and bio operons, ensuring stable insertion without disrupting essential host genes.^[20] This mechanism, first elucidated through in vitro studies, requires additional host factors like integration host factor (IHF) to bend the DNA and facilitate Int binding, highlighting the coordinated interplay between phage and bacterial proteins.^[21] Once integrated, the prophage is maintained in a dormant lysogenic state through transcriptional repression of lytic genes, primarily mediated by phage-encoded repressor proteins. In lambda phage, the cI repressor binds cooperatively to operator sites (O_R and O_L) in the phage genome's right and left operators, blocking the promoters for early lytic genes such as N and cro while activating its own transcription from the p_RM promoter to sustain steady-state levels.^[22] This autoregulatory loop ensures robust repression, with cI dimers forming octamers via DNA looping to enhance binding affinity and stability, preventing accidental activation of the lytic cycle during host replication.^[23] In rare cases, certain prophages adopt a plasmid-like maintenance strategy rather than chromosomal integration. For instance, bacteriophage P1 persists as a low-copy-number (1-2 per cell) autonomous plasmid in E. coli lysogens, replicating via a phage-encoded RepA initiator protein that ensures partition during cell division without integrating into the host genome.^[24] This extrachromosomal form, stabilized by addiction systems like the phd-doc toxin-antitoxin module, represents an alternative to site-specific integration and is observed in other P1-like elements, allowing the prophage to evade some host restriction mechanisms while remaining heritable.^[25]

Induction Processes

Prophage Induction

Prophage induction marks the switch from the lysogenic state to the lytic cycle in temperate bacteriophages, such as lambda (λ) phage in Escherichia coli, where the integrated prophage excises from the bacterial chromosome, replicates its genome, and produces infectious particles that lyse the host cell. This process is typically initiated by environmental stresses, particularly DNA damage signals that activate the host's RecA protein. RecA forms a coprotease complex that facilitates the autocleavage of the phage-encoded CI repressor, which normally maintains lysogeny by suppressing lytic gene expression.^[26] The inactivation of CI leads to derepression of early lytic genes, including those involved in excision and replication.^[26] Excision occurs through site-specific recombination between the prophage attachment sites attL and attR, reforming the phage attP site and the bacterial attB site, mediated by the phage integrase (Int) protein along with the excisionase (Xis) protein. Int catalyzes the strand cleavage and exchange at the attachment sites, while Xis enhances the directionality toward excision by binding cooperatively to specific DNA sequences (X1 and X2 sites), bending the DNA, and interacting with Int to assemble the excisive intasome complex.^[27] This reverse recombination precisely liberates the circularized prophage DNA, which then undergoes replication and late gene expression for virion assembly. Specific triggers for RecA activation, such as UV irradiation or chemical mutagens, are explored in detail elsewhere.^[26] The biological outcomes of prophage induction include the release of 20–100 new phage particles per infected cell, known as the burst size, which varies with host physiology and induction conditions.^[28] This lytic burst contributes to bacterial population die-off, amplifying phage spread and potentially clearing susceptible lysogens in a microbial community. A classic example is UV-induced lysis in lysogenic E. coli, where irradiation triggers RecA-mediated CI cleavage, leading to coordinated prophage excision and host cell death within hours.^[26]

Triggers and Molecular Regulation

Prophage induction is primarily triggered by environmental stresses that signal potential threats to the bacterial host's survival, such as DNA-damaging agents including ultraviolet (UV) radiation, the alkylating agent mitomycin C, and oxidative stressors like hydrogen peroxide. UV radiation causes thymine dimers in DNA, activating repair pathways that lead to prophage excision, as demonstrated in studies of lambdoid prophages where exposure to UV light significantly increases phage release. Similarly, mitomycin C crosslinks DNA strands, mimicking replication stress and promoting induction in Shiga-toxin-encoding prophages with high efficiency at concentrations around 0.2-2 μg/mL. Hydrogen peroxide induces oxidative damage, particularly in Escherichia coli lysogens, where it elevates reactive oxygen species levels and triggers λ prophage excision through OxyR-dependent pathways, with induction observed at 0.5-2 mM concentrations. Certain antibiotics, such as quinolones, can also trigger induction by inhibiting DNA gyrase and activating the SOS response.^[29] Additional triggers include quorum-sensing signals and nutrient limitations, which provide context-dependent cues for prophage activation. Quorum sensing, mediated by autoinducer molecules like acyl-homoserine lactones or cyclic di-GMP, can synchronize induction across bacterial populations; for instance, in Vibrio cholerae, host quorum-sensing pathways regulate CTX prophage-encoded cholera toxin production at high cell densities. Nutrient stress, such as phosphate starvation, also modulates induction via sensing mechanisms; in E. coli, cryptic prophages interact with the Pho regulon to regulate phosphate uptake under low phosphate availability (below 10 μM), delaying exit from dormancy and enhancing persister cell resuscitation under starvation. A specific example is the PhoB-PhoR system in phosphate-limited conditions phosphorylating PhoB, which can indirectly influence prophage operators in cryptic elements, promoting induction under nutrient stress without SOS involvement. At the molecular level, these triggers converge on regulatory pathways that disrupt prophage maintenance, with the SOS response serving as the canonical mechanism in many systems. DNA damage activates RecA protein, which forms filaments on single-stranded DNA and facilitates autocleavage of the λ cI repressor at a specific Ala-Gly bond, reducing cI levels below a critical threshold (approximately 10-20% of steady-state concentration) and derepressing lytic genes; this process requires RecA concentrations exceeding 10 μM for efficient filament formation. Quantitative models of λ prophage induction reveal a sharp threshold, where DNA damage equivalent to a cleavage rate of about 2.0 × 10^{-3} s^{-1} achieves 50% induction probability, ensuring bistable switching from lysogeny. In some phages, alternative regulation involves two-component systems; for example, the PhoB-PhoR system in phosphate-limited conditions phosphorylates PhoB, which can indirectly influence prophage operators in cryptic elements, promoting induction under nutrient stress without SOS involvement.

Specialized Phenomena

Zygotic Induction

Zygotic induction refers to the activation of a prophage into the lytic cycle immediately upon its transfer to a non-lysogenic recipient cell during bacterial conjugation. This process was first observed in experiments with Escherichia coli lysogenic for bacteriophage lambda, where conjugation between a lysogenic Hfr donor and a non-lysogenic F⁻ recipient led to unexpected cell lysis and phage release in the zygote.^[30]^[31] The mechanism involves the transfer of prophage DNA as part of the donor chromosome during conjugation, but the recipient cell lacks the cytoplasmic repressor proteins (such as CI in lambda) that maintain lysogeny in the donor. Without these repressors, or due to their rapid dilution during cell division in the zygote, the prophage becomes derepressed, triggering expression of early lytic genes, site-specific excision from the chromosome, and replication leading to virion assembly and host cell lysis.^[32]^[14] This contrasts with standard prophage induction in established lysogens, which requires external triggers like DNA damage to inactivate the repressor. Key experiments in the 1950s demonstrated that zygotic induction occurs specifically in lambda lysogens during Hfr-mediated conjugation, with over 50% of zygotes lysing and producing phage particles shortly after transfer, far exceeding lysis rates in stable lysogenic cultures.^[30] These findings, reported by Wollman and Jacob, highlighted the role of diffusible repressors in lysogeny and provided early evidence for gene regulation mechanisms in bacteria.^[31] Zygotic induction imposes a significant barrier to the horizontal transfer of lysogeny, as the recipient cell often lyses before the prophage can reintegrate and restore the repressed state, thereby preventing stable propagation of the lysogenic genome in new hosts.^[33] This selective disadvantage creates evolutionary pressure against maintaining lysogeny in bacterial populations prone to conjugation, potentially favoring lytic phage lifestyles or alternative gene transfer strategies in dynamic environments.^[14]

Prophage Reactivation

Prophage reactivation is a DNA repair phenomenon in which the survival of ultraviolet (UV)-irradiated bacteriophage lambda is enhanced when it infects a bacterial host lysogenic for a homologous but heteroimmune prophage, such as λimm434. This process, distinct from standard prophage induction and Weigle (UV) reactivation, relies on homologous recombination between the damaged infecting phage DNA and the resident prophage DNA to repair UV-induced lesions, including pyrimidine dimers and double-strand breaks (DSBs).^[34] The mechanism is initiated when the UV-damaged infecting phage triggers the host's SOS response, leading to activation of RecA protein, which facilitates recombination. In recA+ hosts, the RecA-mediated strand invasion allows the damaged phage DNA to use the intact prophage DNA as a template for repair. The phage-encoded Red recombination system (Redα and Redβ genes) can partially substitute for RecA in recombination-deficient hosts, promoting DSB repair through homologous sequences. This system is expressed following SOS induction of the prophage, enhancing efficiency in polylysogenic cells with multiple homologous prophages. Mutations in recA severely reduce reactivation, while red+ prophages provide an alternative pathway.^[35]^[34] Unlike Weigle reactivation, which occurs in UV-irradiated non-lysogenic hosts and involves error-prone mutagenesis, prophage reactivation is primarily recombination-based and does not significantly increase mutation rates. It provides up to 100-fold increase in survival of UV-damaged phages compared to non-lysogenic hosts, demonstrating the prophage's role in facilitating propagation of related phages under stress. This phenomenon underscores the evolutionary advantage of lysogeny in enabling repair assistance to incoming phages.^[34]^[36]

Host Interactions

Costs to the Host

Harboring a prophage imposes a metabolic burden on the bacterial host, as the prophage DNA must be replicated alongside the host genome during cell division, diverting cellular resources. For instance, prophage sequences can constitute up to 5% of the bacterial genome, requiring additional energy for DNA synthesis and maintenance, which reduces overall host fitness.^[37] This burden is exacerbated in resource-limited environments, potentially slowing bacterial growth rates.^[38] A significant risk associated with lysogeny is spontaneous prophage induction, which occurs at rates around $10^{-4} per hour in bacteriophage λ lysogens, leading to cell lysis and potential population-level crashes in bacterial communities.^[39] This stochastic process releases free phages that can infect nearby susceptible cells, but it directly diminishes the lysogenic population by causing host death without compensatory benefits in the absence of external stressors.^[40] Prophage-encoded virulence factors, such as Shiga toxin in Escherichia coli O157:H7, enhance host pathogenicity by enabling toxin production that damages eukaryotic cells, but this comes at the trade-off of increased self-lysis risk during prophage induction.^[41] The temperate Stx-converting phages integrate into the host genome to confer this advantage, yet their activation under stress conditions can trigger lytic cycles, sacrificing the bacterial carrier for phage propagation.^[42] In λ-lysogenic E. coli, the prophage presence often results in slower replication rates under environmental stress, such as nutrient limitation or high population densities, where the added metabolic load hinders recovery compared to non-lysogenic strains.^[43] This fitness decrement highlights the inherent costs of lysogeny, balancing potential long-term survival strategies against immediate growth impairments.^[44]

Benefits to the Host

Prophages confer superinfection immunity to their bacterial hosts by expressing repressor proteins that inhibit the replication of related incoming phages, thereby protecting the lysogenic bacterium from subsequent infections. In the case of bacteriophage lambda integrated into Escherichia coli, the cI repressor protein binds to operator sites on the prophage genome, preventing the expression of lytic genes in superinfecting lambda phages and ensuring the stability of the lysogenic state.^[45] This mechanism not only preserves the host's viability but also allows the prophage to propagate vertically through host cell division without competition from similar viruses.^[46] Prophages can enhance bacterial virulence by encoding genes for toxins and other pathogenicity factors that improve the host's ability to colonize and survive within eukaryotic hosts. A prominent example is the CTXφ prophage in Vibrio cholerae, which carries the ctxAB genes responsible for producing cholera toxin, the primary virulence determinant that causes severe diarrhea during infection.^[47] Similarly, prophages in other pathogens contribute adhesins or effectors that facilitate tissue invasion and immune evasion, thereby increasing the bacterium's pathogenic potential.^[48] Certain prophages promote stress resistance in bacterial hosts by aiding in biofilm formation and conferring tolerance to antibiotics and environmental pressures. Filamentous prophages, such as Pf4 in Pseudomonas aeruginosa, integrate into the host genome and promote the assembly of structured biofilms that shield bacteria from antimicrobial agents and host defenses, enhancing survival in chronic infections.^[49] Additionally, prophage-encoded genes can transfer antibiotic resistance elements, providing a selective advantage in antibiotic-exposed environments.^[50]

Evolutionary and Ecological Roles

Gene Transfer and Virulence Factors

Prophages play a central role in horizontal gene transfer among bacteria through transduction mechanisms activated during prophage induction. Generalized transduction occurs when the phage's packaging machinery mistakenly encapsidates random segments of the host chromosome into phage heads during the lytic cycle, allowing transfer of any bacterial DNA to a recipient cell upon infection. This process typically packages host DNA in 1–6% of virions, with about 10–15% successfully injecting into new hosts, facilitating the spread of diverse genetic material without specificity to prophage location.^[51] Specialized transduction, in contrast, involves imprecise excision of the integrated prophage from the bacterial chromosome, incorporating adjacent host genes into the phage genome for targeted transfer. This rare event, occurring in approximately 1 in 10^4–10^6 particles, is limited to genes flanking the prophage attachment site and exemplifies how lysogeny enables precise gene mobility.^[51] A classic example of specialized transduction is provided by bacteriophage lambda (λ) in Escherichia coli, where aberrant excision leads to the packaging and transfer of the gal operon genes adjacent to the prophage integration site. This mechanism, elucidated in early genetic studies, demonstrated how prophage excision errors create hybrid phage particles capable of transducing specific bacterial markers, influencing bacterial adaptability.^[52] Similarly, bacteriophage P1 functions as a plasmid-like prophage in E. coli, maintained at 1–2 copies per cell through autonomous replication and partitioning systems, which supports efficient generalized transduction of chromosomal DNA fragments up to 100 kb. P1's stable extrachromosomal state allows it to serve as a natural vector for gene transfer, with applications in cloning and genetic mapping due to its high transduction efficiency.^[53] Prophages significantly contribute to bacterial pathogenicity by encoding virulence factors, including toxins and resistance elements, which are integrated into the host genome during lysogeny. For instance, the β-prophage in Corynebacterium diphtheriae carries the gene for diphtheria toxin, an ADP-ribosylating exotoxin that halts eukaryotic protein synthesis and causes systemic tissue damage in diphtheria infections.^[54] In Vibrio cholerae, the CTXφ filamentous prophage encodes cholera toxin, which disrupts intestinal ion transport to induce massive fluid loss, driving cholera pandemics that have affected millions historically.^[54] Prophages also harbor antibiotic resistance cassettes, such as those conferring beta-lactamase production, enabling bacteria to acquire survival advantages through phage-mediated dissemination. These virulence genes, often expressed without lysis, enhance host fitness in pathogenic niches.^[51] Overall, prophages account for 10–20% of the bacterial accessory genome—the flexible, non-core portion varying between strains—serving as key reservoirs for transferable elements that drive pathogenicity and adaptation. In pathogens like V. cholerae, prophage-encoded toxins have been pivotal in epidemic outbreaks, underscoring their ecological impact.^[55]

Role in Bacterial Evolution

Prophages and their remnants, known as cryptic prophages, significantly contribute to genome mosaicism in bacteria by integrating viral sequences that fragment and rearrange host DNA, leading to diverse genomic architectures across strains. These elements can constitute 10–20% of a bacterium's genome, serving as hotspots for genetic variation through mechanisms such as inversions, deletions, and insertions.^[55] Cryptic prophages, in particular, act as permanent reservoirs of genes that persist without active replication, influencing long-term genomic stability and adaptability.^[56] In adaptive evolution, prophages drive bacterial speciation by facilitating horizontal gene transfer (HGT) of beneficial genes, including those that enhance fitness in new environments. For instance, bacteria acquire CRISPR spacers targeting prophage sequences, which not only provides immunity against viral reinfection but also promotes genetic diversification by selecting for variants with altered prophage integrations. This process accelerates evolutionary divergence, as prophages encode genes that can confer novel traits, such as metabolic capabilities or stress resistance, thereby shaping species boundaries over time.^[57]^[58] Prophages also regulate bacterial population dynamics through induction-mediated lysis, which curbs excessive growth and prevents population blooms in dense communities. At high cell densities, signaling molecules like autoinducer-2 trigger prophage excision and lysis, reducing host numbers and maintaining ecological balance within microbial consortia. This density-dependent control influences community structure, favoring lysogenic states in sparse populations while promoting lytic cycles to alleviate resource competition.^[59] Over evolutionary timescales, fossilized prophage sequences preserved in ancient bacterial genomes reveal their ancient origins and persistent role in adaptation. For example, ultra-conserved bacteriophage genomes have been identified in samples dating back over 1,300 years, indicating that prophage integrations have long contributed to genomic evolution. Recent studies from the 2020s further highlight prophages' involvement in spreading antibiotic resistance genes via HGT, enhancing bacterial survival in selective pressures like antimicrobial environments and underscoring their ongoing impact on evolutionary trajectories.^[60]^[61]

Applications and Impacts

Biotechnology and Medical Uses

Prophages have been instrumental in biotechnology as research tools, particularly through the use of bacteriophage lambda (λ) as a cloning vector for recombinant DNA technology. Lambda phage, which integrates as a prophage in its lysogenic state, was first adapted in the 1970s for inserting foreign DNA fragments into its genome, enabling efficient packaging and propagation in Escherichia coli hosts.^[62] This vector system revolutionized molecular cloning by allowing the stable maintenance and amplification of eukaryotic and prokaryotic genes, with insertion sites like the non-essential att region facilitating up to 20 kb of foreign DNA without disrupting essential phage functions.^[63] Its site-specific recombination machinery, including the integrase enzyme, further supports in vitro shuffling of genetic elements for constructing gene libraries.^[15] Prophage sequencing has emerged as a valuable method for bacterial typing and epidemiological surveillance. By analyzing the diversity of prophage integrase genes or full prophage sequences in bacterial genomes, researchers can distinguish strains with high resolution, as prophages often vary in insertion sites and genetic content across isolates.^[64] For instance, prophage integrase typing schemes have been developed for pathogens like group B Streptococcus (GBS), enabling the classification of clinical isolates based on prophage profiles and correlating them with virulence or antibiotic resistance patterns.^[65] This approach complements multilocus sequence typing by providing additional markers from mobile genetic elements, aiding in outbreak tracking and source attribution.^[44] In phage therapy, engineered prophages offer targeted lysis of multidrug-resistant (MDR) bacteria, leveraging their lysogenic integration for precise delivery followed by controlled induction. Temperate phages like lambda have been modified to incorporate CRISPR-Cas systems, allowing initial lysogenization in target cells and subsequent activation of Cas nucleases to cleave bacterial chromosomes, ensuring selective killing of MDR strains such as E. coli or Pseudomonas aeruginosa.^[66] Studies from 2023 to 2025 have explored such hybrids for selective bacterial killing in mixed cultures.^[66] These constructs address limitations of obligately lytic phages by minimizing resistance evolution through dual lytic and gene-editing mechanisms.^[67] Prophage-based vectors facilitate gene delivery for bacterial transformation, exploiting lysogenic cycles to stably insert payloads into host genomes. Lambda-derived vectors enable homologous recombination for targeted gene knock-ins or edits in E. coli and related species, with efficiencies exceeding 10^5 transformants per microgram of DNA.^[68] This has applications in synthetic biology, such as engineering metabolic pathways for biofuel production. In microbiome editing, prophage vectors show promise for in situ modifications; for example, CRISPR-equipped phages can base-edit specific genes in gut bacteria like Bacteroides thetaiotaomicron within complex communities, altering carbohydrate metabolism without disrupting overall diversity.^[69] Such approaches enable precise tuning of microbial functions for therapeutic outcomes, like enhancing short-chain fatty acid production to combat dysbiosis.^[70] Recent advances include AI-optimized prophage designs to combat antimicrobial resistance (AMR). Machine learning models trained on phage-host interaction data predict optimal temperate phage genomes for broad-spectrum lysis of MDR pathogens, incorporating features like receptor-binding proteins and induction triggers.^[71] Synthetic lysogeny systems support stable gene expression in bacterial hosts. For instance, engineering lambda prophages into E. coli enables controlled switching between lysogenic and lytic states.^[10] Phage-based platforms aid vaccine production by displaying antigens on bacterial surfaces, enhancing immunogenicity in preclinical models.^[72]

Economic and Societal Implications

Prophages in Vibrio species encode virulence factors, including exotoxins, that enhance bacterial pathogenicity and contribute to vibriosis outbreaks in aquaculture, leading to substantial stock mortality and economic losses estimated at over $1 billion annually in global fish farming.^[48]^[73] These lysogenic elements amplify toxin production upon induction, exacerbating infections in species like shrimp and finfish, where disease control measures further strain industry profitability.^[74] In human health economics, prophage-encoded Shiga toxins in Escherichia coli O157:H7 drive severe outbreaks, imposing annual costs of approximately $405 million (in 2003 dollars) in the United States for medical care, premature deaths, and productivity losses.^[75]^[76] Conversely, the growing recognition of prophage dynamics has spurred phage therapy development as an alternative to antibiotics, with the global market projected to reach $1.65 billion by 2030, potentially offsetting treatment costs amid rising antimicrobial resistance.^[77] Environmentally, prophages aid bioremediation by carrying auxiliary metabolic genes that enhance bacterial degradation of pollutants like hydrocarbons, facilitating microbial adaptation in contaminated sites such as oil spills.^[78] However, in wastewater systems, prophage-encoded antibiotic resistance genes pose risks by promoting horizontal transfer to environmental bacteria, potentially disseminating resistance beyond treatment facilities.^[79]^[80] As of 2025, prophage-mediated spread of antimicrobial resistance genes exacerbates the U.S. healthcare crisis, contributing to direct costs exceeding $4.6 billion annually for key resistance threats through prolonged hospitalizations and ineffective treatments for resistant infections.^[81]^[82] This economic burden underscores the societal need for integrated surveillance of lysogenic elements in public health and environmental management.^[83]

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Maintenance of bacteriophage P1 plasmid - PMC - NIH
The fact that plasmid-linked mutations can cause prophage instability suggests that P1 codes for at least some of the functions determining its own autonomy ...
[23]
Efficient traceless modification of the P1 bacteriophage genome ...
Mar 19, 2023 · In lysogens, P1 is maintained as a unit-copy circular plasmid. P1-related prophages or plasmids are prevalent in natural isolates of E. coli, ...
[24]
Proteolytic cleavage of bacteriophage lambda repressor in induction.
Proteolytic cleavage may be the primary mechanism of repressor inactivation in this induction pathway, or it may follow a different event which causes the ...
[25]
Structure of the cooperative Xis–DNA complex reveals a ... - PNAS
Xis is the master regulator of λ recombination, stimulating phage excision in vivo >106-fold, while simultaneously inhibiting phage reintegration (8–10).
[26]
Stability and Instability in the Lysogenic State of Phage Lambda
... burst size is 100 phage per switching event. We observed ∼4 ... Bacteriophage lambda cro mutations: effects on activity and intracellular degradation.
[27]
[PDF] Francois Jacob - Nobel Lecture
This phenom- enon, termed zygotic induction, showed that the equilibrium between the prophage and the bacterium is maintained by some regulatory system ...
[28]
[Processes of conjugation and recombination in Escherichia coli. II ...
Chromosomal location of phage lambda and genetic results of zygotic induction] ... 1957 Sep;93(3):323-39. [Article in French]. Authors. E L WOLLMAN, F JACOB.
[29]
How Escherichia coli Became the Flagship Bacterium of Molecular ...
Aug 2, 2022 · In other words, when prophage DNA enters the cytoplasm of a nonlysogen, induction occurs. They termed this phenomenon zygotic induction. As we ...
[30]
Timing of integration into the chromosome is critical for the fitness of ...
Feb 13, 2023 · ... zygotic induction of phage lambda following its transfer to a new, non-lysogenic host via conjugation [38]. After transfer to a new host ...
[31]
Repair mechanisms involved in prophage reactivation and UV ...
The following results were obtained: (1) Prophage reactivation is strongly decreased in a host carrying recA mutations but quite unaffected by mutation lex-I ...Missing: SOS | Show results with:SOS
[32]
E. coli recA protein-directed cleavage of phage λ repressor ... - Nature
Jan 3, 1980 · The recA protein mediates both genetic recombination and several cellular responses to DNA damage, including the induction of temperate ...
[33]
What makes the bacteriophage λ Red system useful for genetic ...
The role of high-frequency double-strand break repair/recombination in the life cycle of the lambdoid phages is discussed. Bacteriophage λ, Homologous ...Missing: reactivation | Show results with:reactivation
[34]
λ Recombination and Recombineering | EcoSal Plus - ASM Journals
The bacteriophage λ Red homologous recombination system has been studied over the past 50 years as a model system to define the mechanistic details of how ...
[35]
Cell survival, UV-reactivation and induction of prophage λ in ...
Efficient UV-induction of prophage λ is linked to the induction of lexA-controlled host processes that repair the UV-damaged prophage. Article PDF. Download to ...Missing: radiation | Show results with:radiation
[36]
[PDF] Prophage rates in the human microbiome vary by body site and host ...
May 5, 2023 · contributes to the animal's overall thermogenic energy expenditure 4. ... The median prophage DNA content ranges from 0-5% of the bacterial genome ...Missing: cost | Show results with:cost
[37]
The Promise and Pitfalls of Prophages - PMC - PubMed Central
Although small genomes are more likely to be non-lysogenic, if they carry a prophage, they have a slightly larger average prophage density (2.6%) than larger ...
[38]
Optimality of the spontaneous prophage induction rate - PMC
Prophage induction can be triggered by various environmental factors, such as DNA damage ... However, when it is higher than some threshold then the lysogens will ...
[39]
Impact of Spontaneous Prophage Induction on the Fitness of ...
Jan 7, 2015 · It is tempting to speculate that RecA and the SOS response are responsible for the prophage induction dynamics in this system, because the ...
[40]
Insights into the genome architecture and evolution of Shiga toxin ...
May 19, 2021 · E. coli acquires Shiga toxin genes through a lambdoid prophage insertion, known as Shiga or Stx phage. Stx phages are temperate, meaning that ...
[41]
Genomic Characterization of Two Shiga Toxin–Converting ...
Feb 25, 2021 · The objectives of this study were to genomically characterize two Stx-converting phages induced from environmental STEC strains and to evaluate their ...
[42]
Prophage maintenance is determined by environment-dependent ...
Apr 22, 2024 · The expression of viral proteins during lysogenic conversion can impose a metabolic burden on the host, making the prophage costly in certain ...
[43]
Prophage Genomics - PMC - PubMed Central - NIH
One could anticipate that the prophage decreases the fitness of its lysogenic host by at least two processes: the metabolic burden to replicate extra DNA (Fig.
[44]
Bacteriophage Lambda: a Paradigm Revisited - PMC - NIH
Bacteriophage lambda has an archetypal immunity system, which prevents the superinfection of its Escherichia coli lysogens.
[45]
Prophages mediate defense against phage infection through ...
Jun 3, 2016 · In this study, we examined a wide range of Pseudomonas aeruginosa phages and found that they mediate superinfection exclusion through a variety of mechanisms.
[46]
CTX Prophages in Classical Biotype Vibrio cholerae - NIH
CTXφ is a filamentous, lysogenic bacteriophage whose genome encodes cholera toxin, the primary virulence factor produced by Vibrio cholerae.
[47]
Widespread distribution of prophage-encoded virulence factors in ...
Jul 2, 2018 · Moreover, we found that 45% of Vibrio species harbored a complete prophage-like element belonging to the Inoviridae family, which encode the ...
[48]
Bacterial viruses enable their host to acquire antibiotic resistance ...
Nov 7, 2016 · Prophages provide a competitive advantage to its host. The efficacy of autotransduction is in part attributed to virulent phages propagating on ...
[49]
Prophage terminase with tRNase activity sensitizes Salmonella ...
Apr 4, 2024 · In this study, we describe a lysogenic prophage that represses translation in Salmonella exposed to oxidative stress generated by the phagocyte NADPH oxidase.
[50]
Phage-mediated horizontal gene transfer and its implications ... - NIH
Apr 13, 2022 · Phage transduction is a type of HGT event in which a bacteriophage transfers non-viral DNA from one bacterial host cell to another.Missing: zygotic | Show results with:zygotic
[51]
Genetic transduction by phages and chromosomal islands: The new ...
Aug 8, 2019 · Since their discovery in the 1950s, generalized and specialized transduction stood as the only mechanisms of phage transduction—until now.
[52]
Genome of Bacteriophage P1 | Journal of Bacteriology
As a prophage, P1 is a stable plasmid maintained at about one copy per bacterial chromosome. Several P1 genes scattered throughout the genome are expressed in ...
[53]
Why Bacteriophage Encode Exotoxins and other Virulence Factors
Human diseases directly caused by prophage-encoded VFs include (but are not limited to) botulism, diphtheria, cholera, and those associated with Shiga toxigenic ...
[54]
Prophages and bacterial genomics: what have we learned so far?
Jun 17, 2003 · Prophages can constitute as much as 10–20% of a bacterium's genome and are major contributors to differences between individuals within species.Types Of Prophages And... · Virion Protein Genes As... · Prophage Evolution And...
[55]
Bacterial 'Grounded' Prophages: Hotspots for Genetic Renovation ...
Feb 11, 2019 · These grounded prophages offer several advantages to the bacterial genome evolution through propensity for genetic variations including inversions, deletions, ...
[56]
The driving force of prophages and CRISPR-Cas system in ... - Nature
Jan 6, 2017 · External DNA acquired by horizontal gene transfer (HGT) is the main driving force in the evolution of bacterial genomes. Integrated phages ( ...
[57]
Prophages are associated with extensive CRISPR–Cas auto-immunity
We propose a scenario where it is common to acquire an STS against a prophage, and this may trigger more extensive STS buildup by primed spacer acquisition.
[58]
Quorum Sensing and Metabolic State of the Host Control Lysogeny ...
Sep 10, 2019 · Lysis is further controlled by the metabolic state of the cell, mediated by the cyclic-3′,5′-AMP (cAMP) receptor protein (CRP) of the host. We ...
[59]
Ultra-conserved bacteriophage genome sequence identified in 1300 ...
Jun 1, 2023 · We carefully confirmed their ancient origin and unexpectedly found an ultraconserved genome of a virus living in at least a 1300-year-old ...
[60]
Prophages as a source of antimicrobial resistance genes in ... - NIH
Mar 20, 2025 · Prophages contribute significantly to horizontal gene transfer, including the potential spread of antimicrobial resistance (AMR) genes, because they can ...Missing: 2020s | Show results with:2020s
[61]
Bacteriophage lambda as a cloning vector - PMC - PubMed Central
Extensive research has been directed toward the development of multipurpose lambda vectors for cloning ever since the potential of using coliphage lambda as ...
[62]
Novel bacteriophage lambda cloning vector. - PNAS
A simple method for generating phage collections representing eukaryotic genomes has been developed by using a novel bacteriophage lambda vector, lambda 1059.
[63]
Development and Application of a Prophage Integrase Typing ...
Aug 30, 2020 · A typing scheme for prophages based on full-prophage sequence diversity and insertion sites has been proposed for GBS (van der Mee-Marquet et ...
[64]
Revisiting typing systems for group B Streptococcus prophages
This study provides insights into the prophage content of 365 GBS isolates collected from clinical samples in the context of an Argentinean multicentric study.
[65]
Precision targeting of genetic variations in mixed bacterial cultures ...
Jun 1, 2025 · In this study, we developed a model system by integrating CRISPR-Cas12a into the genome of temperate bacteriophage λ, enabling precise regulation of lysogeny ...
[66]
Engineered phage with antibacterial CRISPR–Cas selectively ...
May 4, 2023 · Finally, CRISPR–Cas systems can contribute to targeting efficacy as a complementary killing modality to the lytic activity of the phage. CRISPR ...
[67]
Phage engineering and phage‐assisted CRISPR‐Cas delivery to ...
In this review, we briefly explain strategies to engineer bacteriophages. Next, we highlight the literature supporting CRISPR‐Cas9‐assisted phage engineering.
[68]
Phage-based delivery of CRISPR-associated transposases ... - PNAS
Jul 29, 2025 · We engineer phage λ with CRISPR-associated transposases to enable flexible bacterial genome manipulation, including in a mixed microbial community context.
[69]
CRISPR-based engineering of phages for in situ bacterial base editing
Nov 7, 2022 · Here, we describe a phage-based approach for precision editing of an individual gene within a target host organism in a community context.
[70]
Precise microbiome engineering using natural and synthetic ... - NIH
May 2, 2024 · A novel approach for precise microbiome engineering using bacteriophages, in which virulent phages are synthesized from prophage DNA in lysogenic strains.
[71]
Optimizing phage therapy with artificial intelligence: a perspective
May 27, 2025 · We review recent advances in artificial intelligence (AI) approaches that are advancing the study of phage-host interactions in ways that might enable the ...
[72]
Phage based vaccine: A novel strategy in prevention and treatment
Phage-based vaccines elicit an effective cellular and humoral immune response with no need for adjuvants and no potential risk of infection in human cells.
[73]
Vibriophages and Their Interactions with the Fish Pathogen Vibrio ...
Vibriosis is one of the most prevalent and devastating diseases in marine aquaculture, causing substantial mortality and economic losses in both fish and ...
[74]
Recent Discovery of Diverse Prophages Located in Genomes of ...
This review underscored crucial roles of prophages in shaping Vibrio spp. genomes and their implications for food safety and public health.3.1. Prophages Contribute To... · 3.2. Prophages Amplify The... · 3.4. Prophages Promote The...
[75]
Economic cost of illness due to Escherichia coli O157 infections in ...
The annual cost of illness due to O157 STEC was $405 million (in 2003 dollars), including $370 million for premature deaths, $30 million for medical care, and ...
[76]
The Prophage and Us—Shiga Toxin Phages Revisited - MDPI
Feb 2, 2023 · Initially described in the early 1980s, Shiga toxin-converting bacteriophages (Stx-phages) have been the subject of numerous publications [2,3].Missing: cost | Show results with:cost
[77]
Bacteriophage Therapy Market Size Expected to Reach USD ...
Jan 9, 2025 · Bacteriophage Therapy Market Size Expected to Reach USD 1,651.8 Million by 2030 ; Growth Rate. Poised to grow at a CAGR of 3.7% ; Historical Data.
[78]
Unveiling the hidden role of aquatic viruses in hydrocarbon pollution ...
Oct 5, 2023 · Our findings suggest phage AMGs may contribute to alkane and aromatic hydrocarbon degradation, participating in the initial, rate-limiting ...
[79]
Prophage-encoded antibiotic resistance genes are enriched in ...
Sep 27, 2024 · Overall, 11.9% of prophages (3200 of 26,858) could be matched with 10,161 bacterial genomes using CRISPR-spacer matching (excluding the original ...
[80]
Bacteriophages in sewage: abundance, roles, and applications - PMC
The abundance of phages encoding virulence genes and ARGs increases the chances of their transduction to the resident bacteria in the sewage environment.
[81]
CDC Partners Estimate Healthcare Cost of Antimicrobial-resistant ...
Treating six of the most alarming antimicrobial resistance threats identified by CDC contribute to more than $4.6 billion in healthcare costs annually.Missing: prophage | Show results with:prophage
[82]
Bacteriophages Contribute to the Spread of Antibiotic Resistance ...
The economic impact of foodborne illness in the USA ... phage mediated spread of antibiotic resistance genes occurring in the environment cannot be discounted.
[83]
Phages connect the biological dots of antimicrobial resistance - NIH
Aug 6, 2025 · An additional challenge of phage product development is the substantial associated financial cost. ... Phage–plasmids spread antibiotic resistance ...