Pseudomonas Phage PaBG—A Jumbo Member of an Old Parasite Family

Evseev, Peter; Сыкилинда, Н. Н.; Gorshkova, Anna; Kurochkina, Lidia P.; Ziganshin, Rustam H.; Drucker, Valentin; Miroshnikov, Konstantin A.

doi:10.3390/v12070721

Cited by 13 publications

(11 citation statements)

References 85 publications

(111 reference statements)

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“…Jumbo phages encoding their own RNAPs likely rely on a common transcriptional strategy during the infection. Jumbo phages that do not encode their own RNAPs are evolutionarily unrelated to jumbo phages with RNAPs and usually encode clearly recognizable homologs of bacterial σ factors likely interacting with the host RNAP core and directing it to phage promoters [ 63 , 64 , 65 , 66 , 67 ].…”

Section: Jumbo Phages Encoding Rna Polymerases and Their Featuresmentioning

confidence: 99%

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Sokolova

Misovetc

Severinov

2020

Viruses

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Prokaryotic viruses with DNA genome longer than 200 kb are collectively referred to as “jumbo phages”. Some representatives of this phylogenetically diverse group encode two DNA-dependent RNA polymerases (RNAPs)—a virion RNAP and a non-virion RNAP. In contrast to most other phage-encoded RNAPs, the jumbo phage RNAPs are multisubunit enzymes related to RNAPs of cellular organisms. Unlike all previously characterized multisubunit enzymes, jumbo phage RNAPs lack the universally conserved alpha subunits required for enzyme assembly. The mechanism of promoter recognition is also different from those used by cellular enzymes. For example, the AR9 phage non-virion RNAP requires uracils in its promoter and is able to initiate promoter-specific transcription from single-stranded DNA. Jumbo phages encoding multisubunit RNAPs likely have a common ancestor allowing making them a separate subgroup within the very diverse group of jumbo phages. In this review, we describe transcriptional strategies used by RNAP-encoding jumbo phages and describe the properties of characterized jumbo phage RNAPs.

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Section: Jumbo Phages Encoding Rna Polymerases and Their Featuresmentioning

confidence: 99%

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Sokolova

Misovetc

Severinov

2020

Viruses

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“…Pseudomonas virus PaBG was also detected in the investigated kitchen sponges. It specifically infects Pseudomonas aeruginosa , which is often known as antibiotic-resistant pathogen causing nosocomial infections, but also occurs in many other wet habitats (Evseev et al 2020 ; Robert Koch-Institut 2017 ). Pseudomonas aeruginosa was indeed present in the sponge samples.…”

Section: Discussionmentioning

confidence: 99%

Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota

et al. 2022

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Kitchen sponges are particularly well known to harbor a high number and diversity of bacteria, including pathogens. Viruses, archaea, and eukaryotes in kitchen sponges, however, have not been examined in detail so far. To increase knowledge on the non-bacterial kitchen sponge microbiota and its potential hygienic relevance, we investigated five used kitchen sponges by means of metagenomic shot-gun sequencing. Viral particles were sought to be enriched by a filter step during DNA extraction from the sponges. Data analysis revealed that ~ 2% of the sequences could be assigned to non-bacterial taxa. Each sponge harbored different virus (phage) species, while the present archaea were predominantly affiliated with halophilic taxa. Among the eukaryotic taxa, besides harmless algae, or amoebas, mainly DNA from food-left-overs was found. The presented work offers new insights into the complex microbiota of used kitchen sponges and contributes to a better understanding of their hygienic relevance.

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“…are present in all habitats, but some species such as P. aeruginosa tend to be present in areas closely associated with human activities [79]. Representatives of the genus Pseudomonas and their viruses were isolated previously from Lake Baikal [80,81]. For eukaryotic viruses, there was the greatest overlap of scaffolds with Yellowstone Lake virophage 5 and Melanoplus sanguinipes entomopoxvirus also isolated from the geographically distant and distinctive environments [82,83].…”

Section: The Diversity Of Viral Communities In the B Bacilliferamentioning

confidence: 99%

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

et al. 2022

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Sponges (type Porifera) are multicellular organisms that give shelter to a variety of microorganisms: fungi, algae, archaea, bacteria, and viruses. The studies concerning the composition of viral communities in sponges have appeared rather recently, and the diversity and role of viruses in sponge holobionts remain largely undisclosed. In this study, we assessed the diversity of DNA viruses in the associated community of the Baikal endemic sponge, Baikalospongia bacillifera, using a metagenomic approach, and compared the virome data from samples of sponges and Baikal water (control sample). Significant differences in terms of taxonomy, putative host range of identified scaffolds, and functional annotation of predicted viral proteins were revealed in viromes of sponge B. bacillifera and the Baikal water. This is the evidence in favor of specificity of viral communities in sponges. The diversity shift of viral communities in a diseased specimen, in comparison with a visually healthy sponge, probably reflects the changes in the composition of microbial communities in affected sponges. We identified many viral genes encoding the proteins with metabolic functions; therefore, viruses in Baikal sponges regulate the number and diversity of their associated community, and also take a part in the vital activity of the holobiont, and this is especially significant in the case of damage (or disease) of these organisms in unfavorable conditions. When comparing the Baikal viromes with similar datasets of marine sponge (Ianthella basta), in addition to significant differences in the taxonomic and functional composition of viral communities, we revealed common scaffolds/virotypes in the cross-assembly of reads, which may indicate the presence of some closely related sponge-specific viruses in marine and freshwater sponges.

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Pseudomonas Phage PaBG—A Jumbo Member of an Old Parasite Family

Cited by 13 publications

References 85 publications

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Multisubunit RNA Polymerases of Jumbo Bacteriophages

Minority report: small-scale metagenomic analysis of the non-bacterial kitchen sponge microbiota

Metagenomic Assessment of DNA Viral Diversity in Freshwater Sponges, Baikalospongia bacillifera

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