Characterization of Streptomyces plasmid-phage pFP4 and its evolutionary implications

Chen, Zhenhua; Zhong, Li; Shen, Meijuan; Fang, Ping; Qin, Zhongjun

doi:10.1016/j.plasmid.2012.05.004

Cited by 8 publications

(5 citation statements)

References 37 publications

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“…Of these, 110 were recognized as plasmids by MOB-suite or keywords but also contained virusrelated COG or Pfam functions as indicated by the keywords 'virus', 'viral', or 'phage'. These predictions carry both plasmid and viral features, a phenomenon that has previously been reported (36)(37)(38)(39), and thus they blur the traditional categories of mobile elements. Surprisingly, 808 predictions that matched a known chromosome were also circular-associated and recognized by MOB-suite or plasmid keywords.…”

Section: Plasx Unveils a Large Database Of New Plasmids From The Human Gut Microbiomementioning

confidence: 79%

The genetic and ecological landscape of plasmids in the human gut

Fogarty

Eren

2020

Preprint

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Plasmids play a critical role in rapid bacterial adaptation by encoding accessory functions that may increase the host's fitness. However, the diversity and ecology of plasmids is poorly understood due to computational and experimental challenges in plasmid identification. Here, we report the Plasmid Classification System (PCS), a machine learning classifier that recognizes plasmid sequences based on gene functions. To train PCS, we performed a large-scale discovery and comparison of gene functions in a reference set of >16,000 plasmids and >14,000 chromosomes. PCS accurately recognizes a diverse range of plasmid subtypes, and it outperforms the previous state-of-the-art approach based on k-mer decomposition of sequences. Armed with this model, we conducted, to our knowledge, the largest search for naturally occurring human gut plasmids in 406 publicly available metagenomes representing 5 countries. This search yielded 6,257 high-confidence predicted plasmids, of which 576 had evidence of a circular conformation based on pair-end mapping. These predicted plasmids were found to be highly prevalent across the metagenomes compared to the reference set of known plasmids, suggesting there is extensive and uncharacterized plasmid diversity in the human gut microbiome.

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Section: Plasx Unveils a Large Database Of New Plasmids From The Human Gut Microbiomementioning

confidence: 79%

The genetic and ecological landscape of plasmids in the human gut

Fogarty

Eren

2020

Preprint

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“…These results suggest that Streptomyces phages WheeHeim and Forthebois are temperate phages. Alternatively, they might be plasmid-phages with an unusually long carrier state capable of exhibiting superinfection exclusion after more than 100 generations [75,76]. In both cases, the absence of homologs for conventional lysogeny-related genes or plasmid-associated rep genes puts forward the hypothesis that these phages might utilize a novel mechanism for determining phage replication and cell fate.…”

Section: Virion Stability Lifestyle and Determination Of The Membranmentioning

confidence: 99%

A Novel Genus of Actinobacterial Tectiviridae

Caruso

deCarvalho

Huynh

et al. 2019

Viruses

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Streptomyces phages WheeHeim and Forthebois are two novel members of the Tectiviridae family. These phages were isolated on cultures of the plant pathogen Streptomyces scabiei, known for its worldwide economic impact on potato crops. Transmission electron microscopy showed viral particles with double-layered icosahedral capsids, and frequent instances of protruding nanotubes harboring a collar-like structure. Mass-spectrometry confirmed the presence of lipids in the virion, and serial purification of colonies from turbid plaques and immunity testing revealed that both phages are temperate. Streptomyces phages WheeHeim and Forthebois have linear dsDNA chromosomes (18,266 bp and 18,251 bp long, respectively) with the characteristic two-segment architecture of the Tectiviridae. Both genomes encode homologs of the canonical tectiviral proteins (major capsid protein, packaging ATPase and DNA polymerase), as well as PRD1-type virion-associated transglycosylase and membrane DNA delivery proteins. Comparative genomics and phylogenetic analyses firmly establish that these two phages, together with Rhodococcus phage Toil, form a new genus within the Tectiviridae, which we have tentatively named Deltatectivirus. The identification of a cohesive clade of Actinobacteria-infecting tectiviruses with conserved genome structure but with scant sequence similarity to members of other tectiviral genera confirms that the Tectiviridae are an ancient lineage infecting a broad range of bacterial hosts.

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“…Persisting as a linear plasmid inside the bacteria could mean an advantage for this type of phage since they would not be subjected to the restrictions that have prophages integrated into bacterial chromosomes. Furthermore, plasmidial prophages could be transferred horizontally by conjugation, as has been observed in other types of plasmidial phages [ 39 ].…”

Section: Discussionmentioning

confidence: 99%

Valp1, a Newly Identified Temperate Phage Facilitating Coexistence of Lysogenic and Non-Lysogenic Populations of Vibrio anguillarum

Arce,

Venegas,

Paez

et al. 2024

Pathogens

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Vibrio anguillarum is a pathogen for several fish and shellfish species. Its ecology is influenced by diverse factors, including bacteriophages. Here, we identify and characterize a new temperate bacteriophage (Valp1) of V. anguillarum. Valp1 is a myovirus with a 60 nm head and a 90 nm contractile tail. Its double-stranded DNA genome of 42,988 bp contains 68 genes, including a protelomerase gene, typical of telomeric phages. Valp1 inhibits the growth of the virulent strain of V. anguillarum PF4, while the derived lysogenic strain P1.1 presents a slight reduction in its growth but is not affected by the presence of Valp1. Both strains present similar virulence in a larval zebrafish (Danio rerio) model, and only slight differences have been observed in their biochemical profile. Co-culture assays reveal that PF4 and P1.1 can coexist for 10 hours in the presence of naturally induced Valp1, with the proportion of PF4 ranging between 28% and 1.6%. By the end of the assay, the phage reached a concentration of ~108 PFU/mL, and all the non-lysogenic PF4 strains were resistant to Valp1. This equilibrium was maintained even after five successive subcultures, suggesting the existence of a coexistence mechanism between the lysogenic and non-lysogenic populations of V. anguillarum in conjunction with the phage Valp1.

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Characterization of Streptomyces plasmid-phage pFP4 and its evolutionary implications

Cited by 8 publications

References 37 publications

The genetic and ecological landscape of plasmids in the human gut

The genetic and ecological landscape of plasmids in the human gut

A Novel Genus of Actinobacterial Tectiviridae

Valp1, a Newly Identified Temperate Phage Facilitating Coexistence of Lysogenic and Non-Lysogenic Populations of Vibrio anguillarum

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