Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity

Sharma, Vikas; Hünnefeld, Max; Luthe, Tom; Frunzke, Julia

doi:10.1038/s41598-023-30829-z

Cited by 7 publications

(1 citation statement)

References 73 publications

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“…[ 40 , 41 ]. Six prophages (27087P2, 27087P3, KS1P4, KS1P5, B43P4 and B43P5) include an integrase, a terminase and several structural conserved protein domains in the correct order (terminase – portal – protease – scaffold – major head shell (coat) protein – head/tail joining proteins – tail shaft protein – tape measure protein – tail tip/baseplate proteins – tail fibre) and so have the potential be intact [ 9 , 42 ]. However, CheckV results indicated only 27087P3, B43P4 and B43P5 as high quality, at 91% complete and 73kb in length, while prophages 27087P2, KS1P4 and KS1P5 are shorter (66-67kb) and were considered medium quality.…”

Section: Resultsmentioning

confidence: 99%

Genomic and taxonomic evaluation of 38 Treponema prophage sequences

Ridgway,

Lu,

Blower

et al. 2024

BMC Genomics

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Background Despite Spirochetales being a ubiquitous and medically important order of bacteria infecting both humans and animals, there is extremely limited information regarding their bacteriophages. Of the genus Treponema, there is just a single reported characterised prophage. Results We applied a bioinformatic approach on 24 previously published Treponema genomes to identify and characterise putative treponemal prophages. Thirteen of the genomes did not contain any detectable prophage regions. The remaining eleven contained 38 prophage sequences, with between one and eight putative prophages in each bacterial genome. The prophage regions ranged from 12.4 to 75.1 kb, with between 27 and 171 protein coding sequences. Phylogenetic analysis revealed that 24 of the prophages formed three distinct sequence clusters, identifying putative myoviral and siphoviral morphology. ViPTree analysis demonstrated that the identified sequences were novel when compared to known double stranded DNA bacteriophage genomes. Conclusions In this study, we have started to address the knowledge gap on treponeme bacteriophages by characterising 38 prophage sequences in 24 treponeme genomes. Using bioinformatic approaches, we have been able to identify and compare the prophage-like elements with respect to other bacteriophages, their gene content, and their potential to be a functional and inducible bacteriophage, which in turn can help focus our attention on specific prophages to investigate further.

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Section: Resultsmentioning

confidence: 99%

Genomic and taxonomic evaluation of 38 Treponema prophage sequences

Ridgway,

Lu,

Blower

et al. 2024

BMC Genomics

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The impacts of phage-actinobacterial interactions on the ecological functions of actinobacteria

Nwokolo,

Enebe,

Chigor

et al. 2024

The Microbe

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Tailless and filamentous prophages are predominant in marine Vibrio

Steensen,

Séneca,

Bartlau

et al. 2024

The ISME Journal

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Although tailed bacteriophages (phages) of the class Caudoviricetes are thought to constitute the most abundant and ecologically relevant group of phages that can integrate their genome into the host chromosome, it is becoming increasingly clear that other prophages are widespread. Here, we show that prophages derived from filamentous and tailless phages with genome sizes below 16 kb make up the majority of prophages in marine bacteria of the genus Vibrio. To estimate prophage prevalence unaffected by database biases, we combined comparative genomics and chemical induction of 58 diverse Vibrio cyclitrophicus isolates, resulting in 107 well-curated prophages. Complemented with computationally predicted prophages, we obtained 1,158 prophages from 931 naturally co-existing strains of the family Vibrionaceae. Prophages resembling tailless and filamentous phages predominated, accounting for 80% of all prophages in V. cyclitrophicus and 60% across the Vibrionaceae. In our experimental model, prophages of all three viral realms actively replicated upon induction indicating their ability to transfer to new hosts. Indeed, prophages were rapidly gained and lost, as suggested by variable prophage content between closely related V. cyclitrophicus. Prophages related to filamentous and tailless phages were integrated into only three genomic locations and restored the function of their integration site. Despite their small size, they contained highly diverse accessory genes that may contribute to host fitness, such as phage defense systems. We propose that, like their well-studied tailed equivalent, tailless and filamentous temperate phages are active and highly abundant drivers of host ecology and evolution in marine Vibrio, which have been largely overlooked.

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Systematic analysis of prophage elements in actinobacterial genomes reveals a remarkable phylogenetic diversity

Cited by 7 publications

References 73 publications

Genomic and taxonomic evaluation of 38 Treponema prophage sequences

Genomic and taxonomic evaluation of 38 Treponema prophage sequences

The impacts of phage-actinobacterial interactions on the ecological functions of actinobacteria

Tailless and filamentous prophages are predominant in marine Vibrio

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