Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein

Li, Ping; Yong, Shanghai; Zhou, Xin; Shen, Jiayin

doi:10.3390/pathogens11121445

Cited by 4 publications

(4 citation statements)

References 89 publications

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“…This gene is present in the genomes of all Epsilon crAss-like phages and has been shown to be involved in Red recombination of phage Lambda [ 44 ]. In addition, genes encoding a transcriptional repressor, and two prophage anti-repressors were detected in the crAssE-Sib genome ( Figure 1 and Table S1 ) [ 45 , 46 ]. A repressor was found using HHblits with a probability of 99.17% and an e-value of 1.2 × 10 −13 , whereas BLASTP identified it with an e-value of 3 × 10 −15 .…”

Section: Resultsmentioning

confidence: 99%

“…Surprisingly, genes encoding prophage repressor and anti-repressors were found in some Epsilonunovirus genomes. It has been previously shown that the anti-repression system is associated with the switching of the life cycle in temperate phages [ 45 , 46 , 55 , 56 ]. Analysis of other crAss-like phage genomes showed that these genes are absent in other crAss-like phages.…”

Section: Discussionmentioning

confidence: 99%

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Genome Analysis of Epsilon CrAss-like Phages

Babkin,

Tikunov,

Baykov

et al. 2024

Viruses

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CrAss-like phages play an important role in maintaining ecological balance in the human intestinal microbiome. However, their genetic diversity and lifestyle are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon crAss-like phage genomes was found. Comparative analysis indicated that epsilon crAss-like phages are divided into two putative genera, which were proposed to be named Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the former. The crAssE-Sib genome contains a diversity-generating retroelement (DGR) cassette with all essential elements, including the reverse transcriptase (RT) and receptor binding protein (RBP) genes. However, this RT contains the GxxxSP motif in its fourth domain instead of the usual GxxxSQ motif found in all known phage and bacterial DGRs. RBP encoded by CrAssE-Sib and other Epsilonunoviruses has an unusual structure, and no similar phage proteins were found. In addition, crAssE-Sib and other Epsilonunoviruses encode conserved prophage repressor and anti-repressors that could be involved in lysogenic-to-lytic cycle switches. Notably, DNA primase sequences of epsilon crAss-like phages are not included in the monophyletic group formed by the DNA primases of all other crAss-like phages. Therefore, epsilon crAss-like phage substantially differ from other crAss-like phages, indicating the need to classify these phages into a separate family.

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Section: Resultsmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Genome Analysis of Epsilon CrAss-like Phages

Babkin,

Tikunov,

Baykov

et al. 2024

Viruses

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show abstract

“…Surprisingly, the genes encoding prophage repressors and anti-repressors absent in crAss-like phages were found in the epsilon crAss-like genomes. It has been previously shown that antirepression system is associated with the switching of the life cycle in the temperate podoviridae phages [27,28]. There are two prophage anti-repressor genes and one transcription repressor gene in the crAssE-Sib phage genome (Figure 1).…”

Section: Discussionmentioning

confidence: 95%

Genome Analysis of Epsilon Crass-like Phages Revealed That Some of Them Can Be Temperate Phages Encoding Atypical Diversity-Generating Retroelements

Babkin,

Tikunov,

Baykov

et al. 2023

Preprint

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СrAss-like phages play an important role in maintaining ecological balance in the human intestine microbiome. However, their lifestyle and genetic diversity are still insufficiently studied. In this study, a novel CrAssE-Sib phage genome belonging to the epsilon сrAss-like phage genomes was found. Detailed analysis indicated that CrAssE-Sib encodes unusual proteins – DNA primase, virion RNA polymerase, prophage antirepressor, and transcriptional repressor, as well as reverse transcriptase (RT) and receptor binding protein (RBP) that are part of diversity-generating retroelement (DGR). Comparative analysis showed that all epsilon сrAss-like phages are divided into two putative genera, which were proposed to name Epsilonunovirus and Epsilonduovirus; CrAssE-Sib belongs to the first of them. RT from CrAssE-Sib and several Epsilonunoviruses contains a specific motif in its fourth domain that was not previously found in RTs from phage and bacterial DGRs. In addition, RBP from CrAssE-Sib and all Epsilonunoviruses has a unique structure. The presence of the conservative prophage repressor and anti–repressors that belong to the lysogenic-to-lytic cycle switches indicate that CrAssE-Sib and other Epsilonunoviruses could be temperate. Epsilon сrAss-like phage substantially differ from other crAss-like phages, including zeta сrAss-like phages. This fact indicates the need to isolate these phages into a separate family.

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“…[ 146a ] Moreover, the immunity to double infection can be weakened by increasing the expression of antirepressor proteins or decreasing the production of suppressor proteins, which is conducive to the preparation of phages. [ 144 ] In conclusion, the influence of superinfection immunity effect on phage preparation should be taken into consideration when designing the phages as carriers, so as to maximize the advantage of phage nanomaterials. The PSs are concentrated at the tumor site taking advantage of the tumor‐targeting capacity of phage nanocarriers, thereby avoiding damage to other normal tissues and reducing side effects.…”

Section: Phage Nanovectors For Tumor Therapy Based On Different Pathwaysmentioning

confidence: 99%

Recent Progress in Phage‐Based Nanoplatforms for Tumor Therapy

Li,

Peng,

Feng

et al. 2023

Small

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Nanodrug delivery systems have demonstrated a great potential for tumor therapy with the development of nanotechnology. Nonetheless, traditional drug delivery systems are faced with issues such as complex synthetic procedures, low reproducibility, nonspecific distribution, impenetrability of biological barrier, systemic toxicity, etc. In recent years, phage‐based nanoplatforms have attracted increasing attention in tumor treatment for their regular structure, fantastic carrying property, high transduction efficiency and biosafety. Notably, therapeutic or targeting peptides can be expressed on the surface of the phages through phage display technology, enabling the phage vectors to possess multifunctions. As a result, the drug delivery efficiency on tumor will be vastly improved, thereby enhancing the therapeutic efficacy while reducing the side effects on normal tissues. Moreover, phages can overcome the hindrance of biofilm barrier to elicit antitumor effects, which exhibit great advantages compared with traditional synthetic drug delivery systems. Herein, this review not only summarizes the structure and biology of the phages, but also presents their potential as prominent nanoplatforms against tumor in different pathways to inspire the development of effective nanomedicine.

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Characterization of a New Temperate Escherichia coli Phage vB_EcoP_ZX5 and Its Regulatory Protein

Cited by 4 publications

References 89 publications

Genome Analysis of Epsilon CrAss-like Phages

Genome Analysis of Epsilon CrAss-like Phages

Genome Analysis of Epsilon Crass-like Phages Revealed That Some of Them Can Be Temperate Phages Encoding Atypical Diversity-Generating Retroelements

Recent Progress in Phage‐Based Nanoplatforms for Tumor Therapy

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