Phage T4 endonuclease SegD that is similar to group I intron endonucleases does not initiate homing of its own gene

Соколов, А.С.; Latypov, O. R.; Kolosov, P. M.; Shlyapnikov, M. G.; Bezlepkina, Tamara A.; Kholod, Natalia; Kadyrov, Farid A.; Granovsky, Igor

doi:10.1016/j.virol.2017.12.031

Cited by 3 publications

(2 citation statements)

References 33 publications

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“…ORF17 and ORF81 are both annotated as homing endonucleases, which are site-specific endonucleases that initiate homing, a nonreciprocal transfer of its own gene into a new allele that lacks this gene (Wilson and Edgell, 2009). However, the phage T4 endonuclease SegD, which is similar to group I intron endonucleases, did not initiate homing of its own gene or genetic recombination between phages in its site inserted into the rII locus (Sokolov et al, 2018). ORF18 is annotated as a single-strand binding protein.…”

Section: Characteristics and Annotations Of The Complete Genome Of Ph...mentioning

confidence: 99%

Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae

Han

et al. 2022

Front. Microbiol.

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Section: Characteristics and Annotations Of The Complete Genome Of Ph...mentioning

confidence: 99%

Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae

Han

et al. 2022

Front. Microbiol.

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“…HEGs have been extensively characterized in T4 and related phages (11)(12)(13)(14)(15), but interest in HEGs has not kept pace with the massive expansion of bacteriophage genomic research (16).T4-like phages have been noted as having a particularly high density of HEGs, and T4 itself stands out even among its relatives. 11% of T4's coding sequence is occupied by HEGs (6).…”

Section: Introductionmentioning

confidence: 99%

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Barth

Seed

2023

Preprint

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Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.

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Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Barth,

Dunham,

Seed

2023

NAR Genomics and Bioinformatics

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Homing endonuclease genes (HEGs) are ubiquitous selfish elements that generate targeted double-stranded DNA breaks, facilitating the recombination of the HEG DNA sequence into the break site and contributing to the evolutionary dynamics of HEG-encoding genomes. Bacteriophages (phages) are well-documented to carry HEGs, with the paramount characterization of HEGs being focused on those encoded by coliphage T4. Recently, it has been observed that the highly sampled vibriophage, ICP1, is similarly enriched with HEGs distinct from T4’s. Here, we examined the HEGs encoded by ICP1 and diverse phages, proposing HEG-driven mechanisms that contribute to phage evolution. Relative to ICP1 and T4, we found a variable distribution of HEGs across phages, with HEGs frequently encoded proximal to or within essential genes. We identified large regions (> 10kb) of high nucleotide identity flanked by HEGs, deemed HEG islands, which we hypothesize to be mobilized by the activity of flanking HEGs. Finally, we found examples of domain swapping between phage-encoded HEGs and genes encoded by other phages and phage satellites. We anticipate that HEGs have a larger impact on the evolutionary trajectory of phages than previously appreciated and that future work investigating the role of HEGs in phage evolution will continue to highlight these observations.

show abstract

Phage T4 endonuclease SegD that is similar to group I intron endonucleases does not initiate homing of its own gene

Cited by 3 publications

References 33 publications

Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae

Genomic characterization of a new phage BUCT541 against Klebsiella pneumoniae K1-ST23 and efficacy assessment in mouse and Galleria mellonella larvae

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

Nuclease genes occupy boundaries of genetic exchange between bacteriophages

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