TY - JOUR

T1 - A Novel Podophage StenR_269 Suggests a New Family in the Class Caudoviricetes

AU - Yakubovskij, Vyacheslav I

AU - Morozova, Vera V

AU - Kozlova, Yuliya N

AU - Tikunov, Artem Y

AU - Babkin, Igor V

AU - Bardasheva, Alevtina V

AU - Zhirakovskaya, Elena V

AU - Baykov, Ivan K

AU - Kaverina, Galina B

AU - Tikunova, Nina V

N1 - This study was supported by the Ministry of Science and Higher Education of the Russian Federation under project grant no. 075-15-2021-1085.

PY - 2023/12

Y1 - 2023/12

N2 - 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.

AB - 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.

KW - Genome, Viral

KW - Bacteriophages/genetics

KW - Genomics

KW - Capsid Proteins/genetics

KW - Soil

UR - https://www.scopus.com/record/display.uri?eid=2-s2.0-85180650842&origin=inward&txGid=e18369288019186d832a4846f94b1f7d

U2 - 10.3390/v15122437

DO - 10.3390/v15122437

M3 - Article

C2 - 38140678

VL - 15

JO - Viruses

JF - Viruses

SN - 1999-4915

IS - 12

M1 - 2437

ER -