The lysogenic cycle is a non-destructive reproductive strategy employed by temperate bacteriophages, in which the viral genome integrates into the host bacterium's chromosome as a prophage, replicating passively alongside the host's DNA without producing new virions or lysing the cell.[1] This latent phase allows the phage to persist within the bacterial population across generations, contrasting with the virulent lytic cycle that immediately hijacks host machinery for rapid virion production and host destruction.[2] Temperate phages capable of lysogeny are estimated to infect 40–50% of microbial genomes, highlighting the cycle's prevalence in natural ecosystems.[1]The mechanism begins with phage attachment to the bacterial surface and injection of its linear DNA, which then circularizes and integrates into the host genome through site-specific recombination, often at specific attachment sites.[3] Once integrated, the prophage is maintained by regulatory proteins, such as the CI repressor in lambda phage, which suppresses lytic genes and promotes prophage stability.[1] Environmental stressors, including ultraviolet radiation or DNA-damaging agents, can trigger induction via the host's SOS response, excising the prophage and shifting to the lytic cycle for virion release.[2] In some cases, the prophage may remain extrachromosomal as a plasmid-like element, still replicating with the host.[1]Lysogeny plays a critical ecological and evolutionary role, enhancing phage survival in nutrient-poor or high-host-density environments while conferring benefits or costs to the host bacterium.[1] Through lysogenic conversion, prophages can introduce genes that alter host traits, such as toxin production in pathogens like Vibrio cholerae or Corynebacterium diphtheriae, thereby influencing bacterial virulence and microbial community dynamics.[3] Prophages also facilitate horizontal gene transfer via transduction, accelerating bacterial evolution.[1] Lysogeny was first elucidated in the mid-20th century by André Lwoff and colleagues at the Pasteur Institute; their work on inducible prophages, including in Bacillus megaterium, contributed to the 1965 Nobel Prize in Physiology or Medicine, shared with François Jacob and Jacques Monod.[4][5]
Overview
Definition and process
The lysogenic cycle represents one of the two principal reproductive strategies utilized by temperate bacteriophages, in which the phage genome integrates into the host bacterium's chromosome to form a prophage that replicates passively alongside the host DNA, avoiding immediate lysis of the infected cell.[1] This dormant phase enables the phage to persist within the bacterial population without producing viral particles, contrasting with the actively destructive lytic cycle.[3]The process initiates with the adsorption of the temperate phage to specific receptors on the bacterial cell surface, followed by the injection of the phage's linear DNA into the host cytoplasm.[1] Inside the cell, the injected DNA circularizes and undergoes site-specific recombination, mediated by phage-encoded integrase enzymes, to insert into the bacterial chromosome at defined attachment sites (attP and attB), establishing the prophage state.[6] Lytic genes are then repressed by dedicated proteins, such as the CI repressor in bacteriophage lambda, which binds to operator sequences to inhibit transcription from early promoters and maintain dormancy.[7] The integrated prophage is subsequently replicated and segregated during host cell divisions, ensuring its stable inheritance by daughter cells.[8]Distinct from latency mechanisms in eukaryotic viruses, which often involve episomal persistence without genomic integration, the lysogenic cycle is a prokaryote-specific form of viral dormancy confined to bacteriophage infections in bacteria.[8] The prophage remains quiescent in this integrated form until triggered by environmental stressors, such as DNA-damaging agents that activate the host's SOS response, prompting prophage excision and a shift to the lytic cycle.[1]
Comparison to lytic cycle
The lytic cycle begins with the bacteriophage attaching to and injecting its genome into a susceptible host bacterium, commandeering the host's metabolic machinery for immediate viral genome replication, assembly of new virions, and synthesis of lytic enzymes that rupture the cell membrane, releasing 100-200 progeny phages to infect neighboring cells.[9] This process typically completes within 20-60 minutes, depending on the phage and host conditions, resulting in the destruction of the infected cell and propagation of the virus through exponential amplification.[8]In key contrast, the lysogenic cycle postpones these destructive steps by integrating the phage genome into the host chromosome as a prophage, which replicates passively alongside the host DNA during cell division, ensuring long-term phage persistence without immediate host lysis.[10] While the lytic cycle prioritizes rapid, aggressive replication at the expense of the host, the lysogenic cycle promotes survival during unfavorable environments by avoiding detection and lysis; lysogeny is particularly favored when the multiplicity of infection (MOI) exceeds 1, as multiple phages co-infecting a cell signal high viral density and promote integration over lysis, whereas low MOI (typically <1) drives the lytic pathway to maximize immediate progeny production.[11] Outcomes differ markedly: lytic infections form clear plaques on bacterial lawns due to complete host cell clearance, whereas lysogenic infections yield turbid plaques, as surviving lysogenic bacteria regrow within the plaque area.[12]The choice between cycles in temperate phages is governed by regulatory genes that sense environmental cues, such as the cII protein in lambda phage, which acts as a transcriptional activator to establish lysogeny by promoting expression of integration and repression genes under conditions like nutrient scarcity or host stress, with lysogeny occurring in approximately 30-40% of infections at MOI=1, increasing to near 100% at high MOI (e.g., >5).[13] Temperate bacteriophages possess the genetic machinery for both lytic and lysogenic pathways, allowing adaptive switching, whereas obligatory lytic phages, such as T4, lack lysogeny genes and commit exclusively to the destructive cycle.[3]
Molecular mechanisms
Phage entry and integration
The lysogenic cycle begins with phage adsorption to the bacterial host surface, a process mediated by specific interactions between the phage's tail fibers and host cell receptors. In the case of bacteriophage lambda infecting Escherichia coli, the tail fiber protein gpJ on the phage binds to the outer membrane protein LamB (maltoporin), a trimeric receptor involved in maltose transport.[14] This attachment is highly specific and irreversible, positioning the phage tail for subsequent steps, with the C-terminal domain of gpJ responsible for receptor recognition.[15]Following adsorption, the phage injects its linear double-stranded DNA genome into the bacterial cytoplasm. The lambda phage tail undergoes conformational changes upon LamB binding, leading to ejection of the DNA through the tail tube, involving host factors.[16] The injected DNA, approximately 48.5 kilobase pairs long, enters as a linear molecule with cohesive ends, avoiding degradation by host nucleases during transit.[17]Once in the cytoplasm, the linear phage DNA rapidly circularizes to form a stable intermediate suitable for integration or replication. This occurs through the annealing of 12-base-pair cohesive (cos) sites at the DNA termini, facilitated by host DNA ligase, which seals the nicks to produce a covalently closed circular molecule.[18]Integration of the circular phage DNA into the bacterial chromosome is achieved via site-specific recombination, ensuring stable lysogeny. The phage attachment site (attP) recombines with the bacterial attachment site (attB) at a specific locus between the gal and bio operons in E. coli, catalyzed by the phage-encoded integrase enzyme (Int protein), a tyrosine recombinase.[19] This reaction generates hybrid attachment sites (attL and attR) flanking the integrated prophage, with the process requiring additional host factors like integration host factor (IHF) for bending the attP DNA.[17] As a result, the prophage becomes part of the host chromosome and co-replicates with it during cell division, maintaining approximately one copy per bacterial cell.[18]
Gene repression and prophage maintenance
Following the integration of the phage genome into the bacterial chromosome, the lysogenic state is established through the action of the CI repressor protein, which binds cooperatively to operator sites in the right (oR) and left (oL) operator regions of the lambda phage genome. These operators flank the promoters pR and pL, respectively, and CI binding occludes these promoters, thereby repressing transcription of early lytic genes such as those encoding the Cro protein, which would otherwise promote the lytic pathway. In lambda phage, the initial synthesis of CI is facilitated by the CII protein, but once sufficient CI accumulates, it rapidly dominates to enforce repression and block Cro-mediated antagonism.[20]The maintenance of the prophage in a dormant state relies on the autoregulation of CI expression via a positive feedback loop. At low concentrations, CI dimers bind preferentially to the highest-affinity sites (oR1 and oL1), repressing pR and pL; as levels rise, CI binds to oR2, activating its own transcription from the maintenance promoter pRM while still repressing lytic genes.[21] This cooperative binding and octamerization of CI molecules further stabilizes repression by forming DNA loops between oL and oR, enhancing the inhibition of lytic promoters and ensuring CI levels remain sufficient without overproduction.[22] Prophage genes are expressed at basal levels during this phase, integrated as part of the host genome and replicated passively with bacterial DNA during cell division.[23]In the prophage configuration, the integrated lambda DNA behaves as a bacterial chromosomal segment, segregating equally to daughter cells via the host's binary fission machinery, which preserves the lysogenic state across generations.[23] The robust repression mediated by CI binding prevents stochastic derepression or accidental activation of lytic functions, allowing stable lysogeny to endure even under varying environmental conditions.[24]
Induction to lytic cycle
The induction from the lysogenic to the lytic cycle in temperate bacteriophages, such as lambda phage, is primarily triggered by DNA damage to the host bacterium, including exposure to ultraviolet (UV) radiation or genotoxic agents like mitomycin C. This damage activates the host's SOS response, where the RecA protein binds to regions of single-stranded DNA generated during DNA repair, adopting a coprotease form that promotes the autocleavage of the CI repressor protein. The resulting inactivation of CI disrupts the repression of lytic promoters p<sub>R</sub> and p<sub>L</sub>, initiating the regulatory cascade toward lysis.[25][26]With CI levels diminished, transcription from p<sub>R</sub> and p<sub>L</sub> proceeds unchecked, enabling expression of early lytic genes, notably the cro gene. The Cro protein binds preferentially to the O<sub>R3</sub> operator site, repressing the maintenance promoter p<sub>RM</sub> to prevent CI resynthesis and further favoring lytic gene activation, including those for DNA replication and virion assembly. Concurrently, derepression activates the int and xis genes from the p<sub>L</sub> operon; the Int integrase and Xis excisionase proteins then catalyze site-specific recombination between the prophage attachment sites (attL and attR), excising the integrated phage genome as a circular DNA molecule to enable autonomous replication.[26][27]The excised phage genome then undergoes theta and rolling-circle replication, followed by expression of late genes encoding structural proteins and holins/lysins, leading to the production of approximately 100 new virions per cell and subsequent hostlysis to release them. This process ensures phage propagation under conditions where the host's viability is threatened.[25]Induction frequency escalates with additional host stressors beyond DNA damage, such as antibiotics (e.g., fluoroquinolones) that indirectly activate the SOS response or nutrientstarvation that signals environmental adversity; these cues serve as a "bet-hedging" strategy for the phage, enhancing its survival odds by timing lysis to coincide with host decline.[28][29]
Discovery and evidence
Historical background
The discovery of bacteriophages began in 1915 when Frederick Twort observed translucent areas on bacterial cultures, interpreting them as an infectious agent destroying bacteria, followed by Félix d'Hérelle's independent identification in 1917 of a similar lytic agent in dysentery patients' feces, which he termed "bacteriophage."[30][30]In the 1920s, researchers began suspecting a non-lytic form of bacteriophage infection, termed lysogeny, based on observations of bacterial strains that carried phages without immediate cell destruction or plaque formation, though these ideas faced skepticism and were often dismissed as contamination or heresies against the prevailing lytic model.[31][32]A pivotal advancement occurred in the 1950s when André Lwoff at the Pasteur Institute demonstrated lysogeny experimentally using Bacillus megaterium; in 1950, he showed that lysogenic bacteria could divide multiple times without releasing phages, and by 1951–1952, ultraviolet irradiation induced phage release from each cell—yielding about 100 phages—without prior lysis, establishing the prophage as integrated, non-infectious bacterial DNA.[30][30]In 1951, Esther Lederberg isolated the temperate lambda phage (λ) from Escherichia coli K-12 during her PhD work, providing a key model system for studying lysogeny as the phage integrated into the host genome without killing it immediately.[33] In the 1960s, François Jacob and Jacques Monod advanced understanding through genetic mapping of lambda phage, revealing regulatory mechanisms that maintained the prophage state and controlled induction, integrating lysogeny into broader models of gene expression.[34]These contributions culminated in the 1965 Nobel Prize in Physiology or Medicine awarded jointly to Lwoff, Jacob, and Monod for discoveries on genetic control of enzyme and virus synthesis, with lysogeny studies providing foundational insights into regulatory genetics.[4]
Key experiments demonstrating lysogeny
One of the pivotal experiments demonstrating lysogeny was conducted by André Lwoff and colleagues in 1950, where they exposed lysogenic cultures of Bacillus megaterium to ultraviolet (UV) irradiation. This treatment triggered the release of up to 100 bacteriophages per bacterium without lysing all cells immediately, indicating that the phage genome existed in a dormant, integrated form within the bacterial chromosome rather than as free infectious particles. The experiment established that lysogeny represents a stable, heritable state where the prophage could be induced to enter the lytic cycle under stress conditions like UV light, providing direct evidence for the prophage hypothesis.[30]In 1951, Esther Lederberg developed a plaque assay using the newly isolated lambda phage on Escherichia coli K-12, revealing distinct plaque morphologies that supported lysogeny. Lytic phages produced clear plaques by killing all host cells in the infection zone, whereas temperate phages like lambda formed turbid plaques due to the survival and growth of lysogenized bacteria within the plaque center, which were immune to superinfection. This visual distinction in plaque appearance confirmed the existence of a lysogenic pathway where infected bacteria could propagate the prophage without immediate lysis, distinguishing temperate phages from obligately lytic ones.Further evidence for prophage integration came from conjugation experiments in the mid-1950s by François Jacob and Élie Wollman, who crossed lysogenic Hfr strains of E. coli K-12 with non-lysogenic F- recipients. The prophage was transferred along with chromosomal markers at a specific locus, and recombinants inheriting the prophage became lysogenic, demonstrating that the viral genome was stably inserted into the bacterial chromosome and segregated with it during genetic exchange.[35] This transfer occurred with high frequency when the prophage was proximal to the origin of transfer, mapping its position between the pro and lac genes and solidifying the concept of the prophage as a chromosomal element.
Temperate bacteriophages
Characteristics and decision-making
Temperate bacteriophages possess a dual lifecycle capability, allowing them to either replicate lytically, leading to host cell destruction and virion release, or enter lysogeny by integrating their genome into the bacterial chromosome as a stable prophage. This contrasts with virulent phages, which lack the genetic machinery for integration and are confined to the lytic cycle, invariably lysing the host upon infection. In well-studied temperate phages such as lambda, essential genes enabling lysogeny include int, encoding integrase for site-specific recombination with the host genome; cI, a repressor that binds operators to silence lytic genes and maintain the prophage state; and cII, a transcriptional activator that promotes cI expression during initial infection.[36][37]While the lambda phage provides a paradigmatic model, decision-making mechanisms vary across temperate phages, including quorum-sensing communication in some Bacillus-infecting phages.[38] In phages like lambda, the decision between lysogeny and lysis is regulated by a bistable molecular switch centered on the antagonistic interplay between the cII and cro proteins. The cII protein, when accumulated sufficiently, activates promoters for cI and integrase, tipping the balance toward lysogeny by establishing repression of lytic functions. In opposition, cro binds to the same operator region, repressing cI transcription and favoring lytic gene expression, ensuring commitment to progeny production and host lysis. This double-negative feedback loop creates epigenetic stability, where the prevailing state reinforces itself.[39]Infection parameters and host physiology heavily influence this cII-cro balance in lambda-like phages. In phages like lambda, a high multiplicity of infection (MOI), involving multiple phages per cell, elevates cII levels by overwhelming host proteases that degrade it, thereby promoting lysogeny to propagate the phage genome vertically through bacterial division rather than risking host extinction via lysis. Similarly, suboptimal host conditions, such as nutrient scarcity, stabilize cII and favor lysogeny, as they signal limited opportunities for horizontal transmission in a sparse susceptible population.[13]Environmental cues further modulate the lysis-lysogeny choice, often aligning with bacterial population dynamics. Nutrient limitation represses lytic gene expression and extends the commitment window for lysogeny, particularly in low-density microbial communities where host encounters are rare. High phage density, akin to quorum sensing, can also bias toward lysogeny by increasing coinfection probability and reducing the risk of overexploiting available hosts.[40][38]The ubiquity of lysogeny is evident from the prevalence of prophages, with at least 50% of bacterial genomes harboring integrated elements, highlighting its role in bacterial evolution and ecology.[41]
Examples of temperate phages
One prominent example of a temperate bacteriophage is the lambda phage (λ), which primarily infects Escherichia coli and integrates its genome into the host chromosome at the specific attachment site attB during lysogeny, serving as a foundational model for studies on genetic repression mechanisms in prophage maintenance.[42][43]Another well-characterized temperate phage is bacteriophage Mu, which exhibits transposon-like behavior by integrating its genome at random sites within the host bacterial chromosome, often leading to insertional mutations that have made it a valuable tool in genetic mapping.[44][45]In contrast, bacteriophage P1 maintains its lysogenic state as a low-copy-number plasmid prophage in E. coli and related enteric bacteria, replicating autonomously without chromosomal integration, which distinguishes it from site-specific integrators like lambda.[46]Lambda phage remains the most extensively studied temperate phage, forming the basis for the majority of foundational research on lysogeny, with 2023 analyses highlighting its role in enhancing E. coli pathogenicity through prophage-encoded factors such as toxin delivery systems in pathogenic strains.[47][48]
Biological implications
Fitness tradeoffs for bacteria
The lysogenic state provides bacteria with notable fitness benefits, primarily through superinfection immunity, where the prophage-encoded repressor protein prevents infection by similar phages, thereby protecting the host from lysis by incoming viruses.[49] Additionally, occasional expression of prophage genes can enhance bacterial resistance to environmental stresses, such as oxidative damage or nutrient limitation, by providing accessory functions that improve host survival under adverse conditions.[50]Despite these advantages, lysogeny imposes significant costs on the bacterial host. The maintenance of the prophage requires replication alongside the bacterial genome, representing an energetic burden as additional genetic cargo that diverts resources from core cellular processes.[51] Furthermore, the risk of spontaneous or stress-induced prophage induction can lead to host cell death, as the lytic cycle lyses the bacterium to release new phages, potentially decimating lysogenic populations.[52] Studies indicate that lysogens often exhibit reduced growth rates compared to non-lysogenic counterparts, typically 10-20% slower, due to these metabolic overheads.The persistence of lysogeny reflects a dynamic tradeoff, where the stable integration of the prophage is favored in nutrient-rich, low-stress environments that support bacterial proliferation without frequent phage encounters.[53] However, under stressful conditions like DNA damage or high population density, induction becomes more likely, allowing phage propagation at the expense of individual hosts but potentially benefiting the broader bacterial population through density regulation. In phage-abundant settings, lysogens gain a competitive edge over non-lysogens by virtue of their immunity, enabling them to outcompete susceptible strains and maintain higher relative abundances.[52]
Lysogenic conversion effects
Lysogenic conversion refers to the process by which integrated prophages express genes that alter the phenotype of the bacterial host, often conferring new traits that enhance survival or pathogenicity. These prophage-encoded genes, sometimes termed morons or accessory genes, are typically not essential for the phage lifecycle but provide fitness advantages to the lysogenized bacterium. For instance, in enterohemorrhagic Escherichia coli O157:H7, lambdoid prophages encode the Shiga toxin genes (stx1 and stx2), which are expressed from the host genome and contribute to the bacterium's ability to cause severe disease.[54] Similarly, the filamentous phage CTXφ integrates into the genome of Vibrio cholerae and encodes the cholera toxin (ctxAB), a key virulence determinant that enables the bacterium to produce the potent enterotoxin responsible for epidemic cholera.[55]Prophage genes can significantly improve bacterial survival in hostile environments. In Bacillus anthracis, lysogenic infection by temperate phages promotes biofilm formation, allowing the bacteria to adhere to surfaces and resist environmental stresses such as desiccation or host immune responses; notably, prophage-cured strains exhibit reduced biofilm assembly compared to lysogens.[56] Additionally, prophage morons frequently encode antibiotic resistance genes, facilitating adaptation to antimicrobial pressures. For example, prophages in multidrug-resistant bacteria often carry genes conferring resistance to classes like beta-lactams and aminoglycosides, with such elements enriched in clinical isolates of pathogens like Pseudomonas aeruginosa and Staphylococcus aureus.[57]These modifications extend to enhanced virulence, where prophage-expressed effectors amplify the host's pathogenic potential. The Shiga toxin from lambdoid phages in E. coli O157:H7 damages vascular endothelium, leading to hemorrhagic colitis and hemolytic uremic syndrome, while CTXφ-mediated cholera toxin in V. cholerae disrupts intestinal ion transport, causing massive fluid loss.[58] Prophage-driven lysogenic conversion accounts for many bacterial virulence factors, with prophages constituting up to 10-20% of a bacterial genome, including toxin and effector genes critical for infection in pathogens.[59] This phenomenon underscores the role of temperate phages in transforming avirulent strains into dangerous pathogens.
Evolutionary role and pathogenicity
The lysogenic cycle plays a pivotal role in bacterial evolution by facilitating horizontal gene transfer (HGT) through prophages, which integrate viral DNA into the bacterial genome and enable the exchange of genetic material across bacterial populations.[60] This process promotes genome plasticity, allowing bacteria to acquire new traits such as metabolic capabilities or stress resistance, thereby driving adaptive evolution and diversification.[1] Prophages contribute to bacterial speciation by mediating lysogenic conversion, where integrated phage genes alter host phenotypes in ways that enhance niche specialization and reproductive isolation among bacterial lineages.[61] Notably, prophage sequences are present in a majority (around 70-80%) of sequenced bacterial genomes, underscoring their widespread influence on evolutionary trajectories.[62]In terms of pathogenicity, temperate phages enhance bacterial virulence by disseminating toxin and adhesin genes via HGT, enabling the spread of pathogenic traits within and across species.[48] For instance, studies from 2023 highlight how temperate phages in foodborne pathogens like Salmonella and Staphylococcus carry virulence factors that amplify infection severity and host colonization.[48] Recent research also implicates prophages in the propagation of antibiotic resistance genes (ARGs) among clinical isolates, with prophage-encoded ARGs enriched in multidrug-resistant strains, complicating treatment of infections caused by pathogens such as Escherichia coli and Acinetobacter baumannii.[57] This dissemination fosters the emergence of hypervirulent, resistant bacterial populations in clinical and environmental settings.[63]Bacteria have evolved strategies to mitigate the risks of prophage induction and subsequent lysis, including modulation of the SOS response—a DNA damage repair pathway that typically triggers the switch from lysogeny to the lytic cycle.[53] By regulating RecA protein activity, hosts can suppress SOS activation to maintain prophage dormancy under stress conditions.[28] Additionally, CRISPR-Cas systems target prophage sequences directly, cleaving integrated viral DNA to prevent auto-induction and preserve host integrity, as observed in systems that exhibit auto-immunity against endogenous prophages.[64] Type III-A CRISPR variants further exemplify this by permitting lysogeny while restricting lytic replication, balancing viral persistence with host survival.[65]Post-2020 research has illuminated lysogeny's integration into broader ecological contexts, revealing its role in shaping microbiome dynamics through prophage-mediated gene flow that influences community stability and resilience.[66] In human gut microbiomes, for example, prophages in ~88% of bacterial species (and over 90% of genomes) contribute to interspecies interactions that can either promote or disrupt symbiotic balances.[66] As of 2025, studies show that around 24% of prophages in human gut bacterial isolates are inducible under various conditions, further influencing community interactions.[67] These advances also link lysogeny to challenges in phage therapy, where temperate phages confer resistance to therapeutic lytic phages by altering bacterial susceptibility or inducing protective states within microbial consortia.[68] Evolutionary models further demonstrate that lysogeny stabilizes long-term phage-bacteria coexistence by enabling population-level persistence amid fluctuating environmental pressures, as seen in chaotic dynamics where lytic and temperate strategies equilibrate naturally.[69]