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John H Paul - One of the best experts on this subject based on the ideXlab platform.
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Lysogeny and sporulation in bacillus isolates from the gulf of mexico
Applied and Environmental Microbiology, 2010Co-Authors: Jennifer M Mobberley, Robert Edwards, Nathan R Authement, Anca M Segall, R A Slepecky, John H PaulAbstract:Eleven Bacillus isolates from the surface and subsurface waters of the Gulf of Mexico were examined for their capacity to sporulate and harbor prophages. Occurrence of sporulation in each isolate was assessed through decoyinine induction, and putative lysogens were identified by prophage induction by mitomycin C treatment. No obvious correlation between ability to sporulate and prophage induction was found. Four strains that contained inducible virus-like particles (VLPs) were shown to sporulate. Four strains did not produce spores upon induction by decoyinine but contained inducible VLPs. Two of the strains did not produce virus-like particles or sporulate significantly upon induction. Isolate B14905 had a high level of virus-like particle production and a high occurrence of sporulation and was further examined by genomic sequencing in an attempt to shed light on the relationship between sporulation and Lysogeny. In silico analysis of the B14905 genome revealed four prophage-like regions, one of which was independently sequenced from a mitomycin C-induced lysate. Based on PCR and transmission electron microscopy (TEM) analysis of an induced phage lysate, one is a noninducible phage remnant, one may be a defective phage-like bacteriocin, and two were inducible prophages. One of the inducible phages contained four putative transcriptional regulators, one of which was a SinR-like regulator that may be involved in the regulation of host sporulation. Isolates that both possess the capacity to sporulate and contain temperate phage may be well adapted for survival in the oligotrophic ocean.
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Comparison of Lysogeny (prophage induction) in heterotrophic bacterial and Synechococcus populations in the Gulf of Mexico and Mississippi river plume
The ISME Journal, 2008Co-Authors: Amy Long, Lauren D Mcdaniel, Jennifer Mobberley, John H PaulAbstract:Lysogeny has been documented as a fundamental process occurring in natural marine communities of heterotrophic and autotrophic bacteria. Prophage induction has been observed to be prevalent during conditions of low host abundance, but factors controlling the process are poorly understood. A research cruise was undertaken to the Gulf of Mexico during July 2005 to explore environmental factors associated with Lysogeny. Ambient physical and microbial parameters were measured and prophage induction experiments were performed in contrasting oligotrophic Gulf and eutrophic Mississippi plume areas. Three of 11 prophage induction experiments in heterotrophic bacteria (27%) demonstrated significant induction in response to Mitomycin C. In contrast, there was significant Synechococcus cyanophage induction in seven of nine experiments (77.8%). A strong negative correlation was observed between Lysogeny and log-transformed activity measurements for both heterotrophic and autotrophic populations ( r =−0.876, P =0.002 and r =−0.815, P =0.025, respectively), indicating that bacterioplankton with low host growth favor Lysogeny. Multivariate statistical analyses indicated that ambient level of viral abundance and productivity were inversely related to heterotrophic prophage induction and both factors combined were most predictive of Lysogeny (ρ=0.899, P =0.001). For Synechococcus , low ambient cyanophage abundance was most predictive of Lysogeny (ρ=0.862, P =0.005). Abundance and productivity of heterotrophic bacteria was strongly inversely correlated with salinity, while Synechococcus was not. This indicated that heterotrophic bacterial populations were well adapted to the river plume environments, thus providing a possible explanation for differences in prevalence of Lysogeny observed between the two populations.
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Interaction of the ΦHSIC Virus with Its Host: Lysogeny or PseudoLysogeny?
Applied and environmental microbiology, 2001Co-Authors: S. J. Williamson, Molly R. Mclaughlin, John H PaulAbstract:The study of marine virus-host interactions is essential in order to understand the role that viruses play in the marine environment. Viruses can interact with bacterial host cells in at least three distinct ways, resulting in lytic, lysogenic, and pseudolysogenic relationships. The majority of the research on virus-host interactions has focused on lytic infection, although studies of lysogenic and pseudolysogenic interactions are becoming more prevalent (4, 5, 9, 10, 11, 12, 18, 22, 23, 25). A lysogenic infection occurs when the viral genome becomes integrated into one of the host cellular replicons (chromosome, plasmid, or another phage genome). The prophages replicate along with the host cell and are passed onto daughter cells. Freifelder (7) claimed that greater than 90% of known bacteriophages are temperate, while Ackermann and Dubow (1) suggested that 50% of 1,200 bacterial strains contained inducible prophages. Prophages remain dormant until the lytic cycle is induced by any number of physical or chemical agents, such as mitomycin C, hydrogen peroxide, polyaromatic hydrocarbons, UV radiation, temperature, and pressure (9, 22, 25). The expression of lytic genes following damage to the host DNA by any of the above mechanisms is a viral strategy that has evolved to ensure viral propagation when conditions for host survival are compromised (16). Little is known about induction mechanisms in marine lysogens. In coliphage lambda, induction activates the RecA protein, which subsequently cleaves and inactivates the repressor to initiate the lytic process (8). It is hypothesized that the RecA protein is activated by binding to damaged DNA during DNA repair (1). The introduction of an inducing agent to a population of lysogens may result in the activation of the RecA protein, ultimately resulting in the active replication of the viral genome and the subsequent release of viral particles through lysis of the host cell. Lysogens gain specific advantages from their relationship with phage that improve their overall fitness. These effects may occur through unspecified mechanisms or the process of conversion, whereby prophage genes are expressed in the lysogens. Conversion can result in expanded metabolic capabilities, antibiotic resistance, and toxin production, but usually always in homoimmunity (13). Homoimmunity provides the resistance to superinfection by the same or similar strains of phage. Immunity observed in the halophilic archaebacterium Halobacterium salinarium to its phage ΦH is mediated by a phage repressor gene, rep (20). In order for virulent phage to replicate and persist in the environment, the rate of host-phage encounters and production must exceed the rate of virus destruction and inactivation. Conversely, the persistence of temperate phages in the environment is dependent not on host cell density but on a certain percentage of sensitive host cells and the occasional induction and lysis of host cells (28). Freifelder (6) suggested that Lysogeny might be a viral survival strategy to endure periods of low host density during nutrient starvation. Wilson and Mann (27) presented evidence that low nutrient concentrations coupled with a high virus/host cell ratio tended to favor Lysogeny. This strategy would ensure that the genetic material of the temperate phage is passed on through host cell replication and division. The prevalence of Lysogeny in the marine environment is a topic of considerable debate. Jiang and Paul (9) found that 43% of the bacterial population from a series of different marine environments contained prophage that were inducible by mitomycin C and UV light. Cochran et al. (5) found that two-thirds of the marine environments sampled in the Gulf of Mexico contained inducible prophage. A seasonal investigation into the abundance of lysogens in Tampa Bay, Fla., revealed that 52.2% of the samples displayed prophage induction (4). On the other side of the debate, evidence provided by Weinbauer and Suttle (24) and Wilcox and Fuhrman (26) indicated that Lysogeny is not an important source of phage production or bacterial mortality in coastal waters. Weinbauer and Suttle (24) found that an average of only 3% of total bacterial mortality resulted from the induction of lysogenic cells. Further evidence has suggested that Lysogeny is more prevalent in oligotrophic waters than in coastal waters (22, 24, 26). Another poorly studied interaction between bacteria and viruses that may be important in the marine environment is pseudoLysogeny. PseudoLysogeny has been described by Ackermann and Dubow (1) as a phenomenon where there is a constant production of phage in the presence of high host cell abundance. That is, phage lysis results not in culture death but rather in a state whereby a high abundance of phage coexists with exponential host growth. This might be the result of a mixture of sensitive and resistant host cells and/or a mixture of temperate and virulent phages. Following infection, bacteriophage can either enter a dormant intracellular phase or proceed with lytic infection (28). In this respect, pseudoLysogeny resembles true Lysogeny. Unlike in true Lysogeny, however, the phage genome does not integrate into host cellular replicons. Ripp and Miller (17, 18) suggested that pseudoLysogeny was an environmental condition in which starved bacterial cells coexist in an unstable relationship with infective viruses. Under these conditions, host cells do not provide enough energy in order for phage to enter into a true lysogenic or lytic condition. Phage become either virulent or temperate upon the addition of sufficient nutrient concentrations (18). Although this hypothesis for pseudolysogenic existence appears to be a plausible explanation for the sustained production of viroplankton under conditions of low host density and nutrient depletion, Moebus (14) did not find that the release of phage in starving bacteria was delayed until sufficient nutrients became available. We have investigated the relationship between ΦHSIC and its host, HSIC, a marine bacterium isolated from Mamala Bay, Oahu, Hawaii, in order to determine if the phage enters into a lysogenic or pseudolysogenic state with its host. HSIC is most closely related to Listonella pelagia, and the phage belongs to the Siphoviridae family. We reported previously that the interaction between ΦHSIC and its host could be described as lysogenic due to the confirmation of homoimmunity and phage production in the presence of mitomycin C (12). However, this original lysogen was unstable and was lost. Attempts to reestablish this interaction resulted in a pseudolysogen-like relationship. This relationship is inherently unstable and is characterized by high host abundance concurrent with a high level of spontaneous induction.
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Lysogeny and transduction
Methods in Microbiology, 2001Co-Authors: John H Paul, Sunny C JiangAbstract:Publisher Summary Lysogeny and transduction describes a type of phage/host interaction and a method of bacterial gene transfer (procaryotic sex), respectively. This chapter describes methods that have been found useful in studying Lysogeny and transduction in the marine environment. Lysogeny occurs when a phage enters into a stable symbiosis with its host. The host (bacterium or algal cell) and phage capable of entering into such a relationship are termed a “lysogen and temperate phage,” respectively. The temperate phage genome becomes integrated into one of the replicons of the cell (chromosome, plasmid, or another temperate phage genome) and is termed a “prophage.” In transduction, the genes are originated in a bacterial host and are not a normal part of the phage genome. The detection of Lysogeny in cultures or natural populations is usually through prophage induction by use of a mutagenic agent, usually mitomycin C. The methods described are all based on some derivative of this procedure. Bacteriophage-mediated transduction is one of three well-known mechanisms, along with conjugation and transformation, of horizontal gene transfer among prokaryotic organisms. In transduction, bacterial DNA or plasmid DNA is encapsulated into phage particles during lytic replication of the phage in the donor cell and is transferred to the recipient cell by infection. This donor DNA either undergoes recombination with the host chromosome to produce a stable transductant or remains extrachromosomal as a plasmid.
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Significance of Lysogeny in the Marine Environment: Studies with Isolates and a Model of Lysogenic Phage Production
Microbial Ecology, 1998Co-Authors: Sunny C Jiang, John H PaulAbstract:The importance of Lysogeny in marine microbial populations is just beginning to be understood. To determine the abundance of lysogens in bacterial populations, we studied the occurrence of lysogenic bacteria among bacterial isolates from a variety of marine environments. More than 116 bacteria isolated on artificial seawater nutrient agar plates were tested for the presence of inducible prophage by mitomycin C and UV radiation. Induction was determined as a decrease in culture absorbance at 600 nm, after treatment with inducing agents. Samples in which optical density decreased or remained the same after induction were further examined by transmission electron microscopy, for the presence of virus-like particles. More than 40% of the bacterial isolates contained inducible prophage, as determined by mitomycin C induction. A higher percentage of lysogenic bacteria was found in isolates from oligotrophic environments, compared to coastal or estuarine environments. These studies suggest that lysogenic bacteria are important components in marine microbial populations. However, a mathematical model based on viral and bacterial abundance and production rates suggests that, under normal conditions, lysogenic viral production contributes less than 0.02% of total viral production. Therefore, lysogens in the marine environment may serve as a source of viruses and only contribute significantly to viral production during natural induction events.
Hideo Takahashi - One of the best experts on this subject based on the ideXlab platform.
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the site specific recombination system of actinophage tg1
Fems Microbiology Letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-lysogen and nonlysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
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The site‐specific recombination system of actinophage TG1
FEMS microbiology letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-lysogen and nonlysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
Keith E. Shearwin - One of the best experts on this subject based on the ideXlab platform.
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instability of cii is needed for efficient switching between lytic and lysogenic development in bacteriophage 186
Nucleic Acids Research, 2020Co-Authors: Iain Murchland, Ian B Dodd, Alexandra Ahlgrenberg, Julian M J Pietsch, Alejandra Isabel, Keith E. ShearwinAbstract:The CII protein of temperate coliphage 186, like the unrelated CII protein of phage λ, is a transcriptional activator that primes expression of the CI immunity repressor and is critical for efficient establishment of Lysogeny. 186-CII is also highly unstable, and we show that in vivo degradation is mediated by both FtsH and RseP. We investigated the role of CII instability by constructing a 186 phage encoding a protease resistant CII. The stabilised-CII phage was defective in the lysis-Lysogeny decision: choosing Lysogeny with close to 100% frequency after infection, and forming prophages that were defective in entering lytic development after UV treatment. While lysogenic CI concentration was unaffected by CII stabilisation, lysogenic transcription and CI expression was elevated after UV. A stochastic model of the 186 network after infection indicated that an unstable CII allowed a rapid increase in CI expression without a large overshoot of the lysogenic level, suggesting that instability enables a decisive commitment to Lysogeny with a rapid attainment of sensitivity to prophage induction.
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Cro's role in the CI-Cro bistable switch is critical for λ's transition from Lysogeny to lytic development
Genes and Development, 2007Co-Authors: Rachel A. Schubert, J. Barry Egan, Ian B Dodd, Keith E. ShearwinAbstract:CI represses cro; Cro represses cI. This double negative feedback loop is the core of the classical CI-Cro epigenetic switch of bacteriophage lambda. Despite the classical status of this switch, the role in lambda development of Cro repression of the P(RM) promoter for CI has remained unclear. To address this, we created binding site mutations that strongly impaired Cro repression of P(RM) with only minimal effects on CI regulation of P(RM). These mutations had little impact on lambda development after infection but strongly inhibited the transition from Lysogeny to the lytic pathway. We demonstrate that following inactivation of CI by ultraviolet treatment of lysogens, repression of P(RM) by Cro is needed to prevent synthesis of new CI that would otherwise significantly impede lytic development. Thus a bistable CI-Cro circuit reinforces the commitment to a developmental transition.
Kentaro Morita - One of the best experts on this subject based on the ideXlab platform.
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the site specific recombination system of actinophage tg1
Fems Microbiology Letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-lysogen and nonlysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
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The site‐specific recombination system of actinophage TG1
FEMS microbiology letters, 2009Co-Authors: Kentaro Morita, Naoki Fusada, Mamoru Komatsu, Nobutaka Hirano, Tomoyuki Yamamoto, Haruo Ikeda, Hideo TakahashiAbstract:Actinophage TG1 forms stable lysogens by integrating at a unique site on chromosomes of Streptomyces strains. The phage (attPTG1) and bacterial (attBTG1) attachment sites for TG1 were deduced from comparative genomic studies on the TG1-lysogen and nonlysogen of Streptomyces avermitilis. The attBTG1 was located within the 46-bp region in the dapC gene (SAV4517) encoding the putative N-succinyldiaminopimelate aminotransferase. TG1-lysogens of S. avermitilis, however, did not demand either lysine or diaminopimelate for growth, indicating that the dapC annotation of S. avermitilis requires reconsideration. A bioinformatic survey of DNA databases using the fasta program for the attBTG1 sequence extracted possible integration sites from varied streptomycete genomes, including Streptomyces coelicolor A3(2) and Streptomyces griseus. The gene encoding the putative TG1 integrase (intTG1) was located adjacent to the attPTG1 site. TG1 integrase deduced from the intTG1 gene was a protein of 619 amino acids having a high sequence similarity to φC31 integrase, especially at the N-terminal catalytic region. By contrast, sequence similarities at the C-terminal regions crucial for the recognition of attachment sites were moderate or low. The site-specific recombination systems based on TG1 integrase were shown to work efficiently not only in Streptomyces strains but also in heterologous Escherichia coli.
Alon Savidor - One of the best experts on this subject based on the ideXlab platform.
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communication between viruses guides lysis Lysogeny decisions
Nature, 2017Co-Authors: Zohar Erez, Ida Steinbergerlevy, Maya Shamir, Shany Doron, Avigail Stokaravihail, Yoav Peleg, Sarah Melamed, Azita Leavitt, Alon SavidorAbstract:Temperate viruses can become dormant in their host cells, a process called Lysogeny. In every infection, such viruses decide between the lytic and the lysogenic cycles, that is, whether to replicate and lyse their host or to lysogenize and keep the host viable. Here we show that viruses (phages) of the SPbeta group use a small-molecule communication system to coordinate lysis-Lysogeny decisions. During infection of its Bacillus host cell, the phage produces a six amino-acids-long communication peptide that is released into the medium. In subsequent infections, progeny phages measure the concentration of this peptide and lysogenize if the concentration is sufficiently high. We found that different phages encode different versions of the communication peptide, demonstrating a phage-specific peptide communication code for Lysogeny decisions. We term this communication system the 'arbitrium' system, and further show that it is encoded by three phage genes: aimP, which produces the peptide; aimR, the intracellular peptide receptor; and aimX, a negative regulator of Lysogeny. The arbitrium system enables a descendant phage to 'communicate' with its predecessors, that is, to estimate the amount of recent previous infections and hence decide whether to employ the lytic or lysogenic cycle.
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Communication between viruses guides lysis–Lysogeny decisions
Nature, 2017Co-Authors: Zohar Erez, Maya Shamir, Shany Doron, Yoav Peleg, Sarah Melamed, Azita Leavitt, Alon Savidor, Ida Steinberger-levy, Avigail Stokar-avihail, Shira AlbeckAbstract:Temperate viruses can become dormant in their host cells, a process called Lysogeny. In every infection, such viruses decide between the lytic and the lysogenic cycles, that is, whether to replicate and lyse their host or to lysogenize and keep the host viable. Here we show that viruses (phages) of the SPbeta group use a small-molecule communication system to coordinate lysis-Lysogeny decisions. During infection of its Bacillus host cell, the phage produces a six amino-acids-long communication peptide that is released into the medium. In subsequent infections, progeny phages measure the concentration of this peptide and lysogenize if the concentration is sufficiently high. We found that different phages encode different versions of the communication peptide, demonstrating a phage-specific peptide communication code for Lysogeny decisions. We term this communication system the 'arbitrium' system, and further show that it is encoded by three phage genes: aimP, which produces the peptide; aimR, the intracellular peptide receptor; and aimX, a negative regulator of Lysogeny. The arbitrium system enables a descendant phage to 'communicate' with its predecessors, that is, to estimate the amount of recent previous infections and hence decide whether to employ the lytic or lysogenic cycle.
