Novel Modification Sites of dPreQ 0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages
Restricted accessResearch articleFirst published online December, 2025
Novel Modification Sites of dPreQ 0 in Aminobacter niigataensis Phage Erebus Provide New Insights into the Role of 7-Deazaguanine Modifications in Bacteriophages
Bacteriophages protect themselves against host-encoded defense systems through DNA modifications. This study introduces Erebus, a newly identified phage infecting Aminobacter niigataensis, a bacterium capable of mineralizing 2,6-dichlorobenzamide- a common pesticide metabolite. The use of such bacterial degraders has been proposed for the bioremediation of contaminated groundwater. However, the presence of bacteriophages targeting these degraders poses a potential challenge to the success of such strategies.
Materials and Methods:
The Erebus phage was isolated and subjected to whole-genome sequencing. Phylogenetic analysis was performed to determine its taxonomic placement and genomic synteny. DNA modifications were identified using a combination of liquid chromatography–mass spectrometry (LC-MS) and Oxford Nanopore Technologies sequencing. Transmission electron microscopy was used to determine the phage morphology.
Results:
Phylogenetic analysis revealed that Erebus belongs to an unclassified genus, showing high synteny with Rhizobium phages of the Kleczkowskaviridae family. The phage possesses a double-stranded DNA genome of 52,229 base pairs, which includes a functional 7-deazaguanine DNA-modification system. Nanopore sequencing and LC-MS analysis confirmed the presence of PreQ0 modifications at novel GG and AG motifs, conferring resistance against multiple restriction endonucleases.
Conclusions:
This is the first report of a phage infecting the genus Aminobacter, highlighting the potential impact of bacteriophages on microbial biodegradation strategies. The findings underscore the importance of considering phage-host interactions when deploying bacterial degraders for environmental remediation.
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