A Novel Podophage StenR_269 Suggests a New Family in the Class Caudoviricetes

Stenotrophomonas rhizophila was first discovered in soil; it is associated with the rhizosphere and capable of both protecting roots and stimulating plant growth. Therefore, it has a great potential to be used in biocontrol. The study of S. rhizophila phages is important for a further evaluation of...

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Published in:Viruses Vol. 15; no. 12; p. 2437
Main Authors: Yakubovskij, Vyacheslav I., Morozova, Vera V., Kozlova, Yuliya N., Tikunov, Artem Y., Babkin, Igor V., Bardasheva, Alevtina V., Zhirakovskaya, Elena V., Baykov, Ivan K., Kaverina, Galina B., Tikunova, Nina V.
Format: Journal Article
Language:English
Published: Switzerland MDPI AG 15.12.2023
Subjects:
Adsorption
Bacteria
bacteriophages
Biological control
capsid
Caudoviricetes
coal
Comparative analysis
comparative genomics
data analysis
Electron microscopy
genome
Genomes
Microscopy
Morphology
morphs
new family
nucleotide sequences
phage
Phages
plant growth
Podoviridae
podovirus morphotype
remediation
Rhizosphere
soil
Soil remediation
Stenotrophomonas
Stenotrophomonas rhizophila
Xanthomonas
Zobellviridae
Madrid Spain
Russia
Spain
Caudoviricetes
Stenotrophomonas rhizophila
Zobellviridae
N4-like capsid protein
phage
comparative genomics
podovirus morphotype
ISSN:1999-4915, 1999-4915
Online Access:Get full text
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Summary:Stenotrophomonas rhizophila was first discovered in soil; it is associated with the rhizosphere and capable of both protecting roots and stimulating plant growth. Therefore, it has a great potential to be used in biocontrol. The study of S. rhizophila phages is important for a further evaluation of their effect on the fitness and properties of host bacteria. A novel phage StenR_269 and its bacterial host S. rhizophila were isolated from a soil sample in the remediation area of a coal mine. Electron microscopy revealed a large capsid (~Ø80 nm) connected with a short tail, which corresponds to the podovirus morphotype. The length of the genomic sequence of the StenR_269 was 66,322 bp and it contained 103 putative genes; 40 of them encoded proteins with predicted functions, 3 corresponded to tRNAs, and the remaining 60 were identified as hypothetical ones. Comparative analysis indicated that the StenR_269 phage had a similar genome organization to that of the unclassified Xanthomonas phage DES1, despite their low protein similarity. In addition, the signature proteins of StenR_269 and DES1 had low similarity and these proteins clustered far from the corresponding proteins of classified phages. Thus, the StenR_269 genome is orphan and the analyzed data suggest a new family in the class Caudoviricetes.
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ISSN:1999-4915
1999-4915
DOI:10.3390/v15122437