A new perspective on lysogeny: prophages as active regulatory switches of bacteria

Feiner, Ron; Argov, Tal; Rabinovich, Lev; Sigal, Nadejda; Borovok, Ilya; Herskovits, Anat A.

doi:10.1038/nrmicro3527

Cited by 373 publications

(332 citation statements)

References 96 publications

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“…[51] Deactivated prophages can also act as regulatory switches -a process called "active lysogeny." [52] Here, prophages sit within the coding region of the gene disrupting gene function. Excision of the prophage restores function, but the excised phage is unable to perform lysis.…”

Section: Temperate Phages As Sources Of Genetic Variation For Evolumentioning

confidence: 99%

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

2017

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Infection by a temperate phage can lead to death of the bacterial cell, but sometimes these phages integrate into the bacterial chromosome, offering the potential for a more long-lasting relationship to be established. Here we define three major ecological and evolutionary benefits of temperate phage for bacteria: as agents of horizontal gene transfer (HGT), as sources of genetic variation for evolutionary innovation, and as weapons of bacterial competition. We suggest that a coevolutionary perspective is required to understand the roles of temperate phages in bacterial populations.

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Section: Temperate Phages As Sources Of Genetic Variation For Evolumentioning

confidence: 99%

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

2017

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“…Although no stable lysogenic isolates could be obtained for this phage , it is genetically homologous (71% sequence identity) to the temperate phage PaP3 (Tan et al, 2007). This AMG could be an artifact of its former temperate nature, where it would yield a fitness benefit to the host during lysogeny (Feiner et al, 2015). The two other AMGs, solely present in LUZ24, are involved in glutathione metabolism ( Table 2).…”

Section: Observed Correlations Between the Phage-specific Metabolic Rmentioning

confidence: 99%

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

et al. 2016

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Phage-mediated metabolic changes in bacteria are hypothesized to markedly alter global nutrient and biogeochemical cycles. Despite their theoretic importance, experimental data on the net metabolic impact of phage infection on the bacterial metabolism remains scarce. In this study, we tracked the dynamics of intracellular metabolites using untargeted high coverage metabolomics in Pseudomonas aeruginosa cells infected with lytic bacteriophages from six distinct phage genera. Analysis of the metabolomics data indicates an active interference in the host metabolism. In general, phages elicit an increase in pyrimidine and nucleotide sugar metabolism. Furthermore, clear phage-specific and infection stage-specific responses are observed, ranging from extreme metabolite depletion (for example, phage YuA) to complete reorganization of the metabolism (for example, phage phiKZ). As expected, pathways targeted by the phage-encoded auxiliary metabolic genes (AMGs) were enriched among the metabolites changing during infection. The effect on pyrimidine metabolism of phages encoding AMGs capable of host genome degradation (for example, YuA and LUZ19) was distinct from those lacking nuclease-encoding genes (for example, phiKZ), which demonstrates the link between the encoded set of AMGs of a phage and its impact on host physiology. However, a large fraction of the profound effect on host metabolism could not be attributed to the phage-encoded AMGs. We suggest a potentially crucial role for small, 'non-enzymatic' peptides in metabolism take-over and hypothesize on potential biotechnical applications for such peptides. The highly phage-specific nature of the metabolic impact emphasizes the potential importance of the 'phage diversity' parameter when studying metabolic interactions in complex communities.

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“…Lysogeny leads to a temporary alignment between the welfare of the bacteria and the phage. Active lysogeny regulates bacterial genes (Feiner et al, 2015). Most microbial genomes sequenced to date have at least one lysogen, and some have more than 20 lysogens, like Sodalis glossinidius which has 29 (Kang et al, in review).…”

Section: Ecological Speciation With Phagesmentioning

confidence: 99%

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

et al. 2018

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Phages have a major impact on microbial populations. In this work, we discuss how predation, transduction, lysogeny, and phage domestication lead to symbio-centric genomic interactions between bacteria and phages, ranging from antagonistic to mutualistic. Furthermore, these interactions influence bacterial diversification and ecotype formation. We then propose an additional consideration in the form of a symbio-centric ecological speciation framework for bacteria. Our framework builds upon classical morphological and molecular taxonomy by also considering bacteria and their phages as a unit of evolutionary selection. This framework acknowledges the considerable effect that phage interaction has on bacterial genomic content, regulation, and evolution, and will advance our understanding of bacterial evolution.

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A new perspective on lysogeny: prophages as active regulatory switches of bacteria

Cited by 373 publications

References 96 publications

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

High coverage metabolomics analysis reveals phage-specific alterations to Pseudomonas aeruginosa physiology during infection

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

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