A Temperate Sinorhizobium Phage, AP-16-3, Closely Related to Phage 16-3: Mosaic Genome and Prophage Analysis

Abstract

Soil Sinorhizobium phage AP-16-3, a strain phylogenetically close to Rhizobium phage 16-3, was isolated in a mountainous region of Dagestan, belonging to the origin of cultivated plants in the Caucasus, according to Vavilov N.I. The genome of phage AP-16-3 is 61 kbp in size and contains 62 ORFs, of which 42 ORFs have homologues in the genome of Rhizobium phage 16-3, which was studied in the 1960s–1980s. A search for Rhizobium phage 16-3-related sequences was performed in the genomes of modern strains of root nodule bacteria belonging to different species, genera, and families. A total of 43 prophages of interest were identified out of 437 prophages found in the genomes of 42 strains, of which 31 belonged to Sinorhizobium meliloti species. However, almost all of the mentioned prophages contained single ORFs, and only two prophages contained 51 and 39 ORFs homologous to phages related to 16-3. These prophages were detected in S. meliloti NV1.1.1 and Rh. leguminosarum OyaliB strains belonging to different genera; however, the similarity level of these two prophages did not exceed 14.7%. Analysis of the orphan genes in these prophages showed that they encoded predominantly virion structural elements, but also enzymes and an extensive group of hypothetical proteins belonging to the L, S, and E regions of viral genes of phage 16-3. The data obtained indicate that temperate phages related to 16-3 had high infectivity against nodule bacteria and participated in intragenomic recombination events involving other phages, and in horizontal gene transfer between rhizobia of different genera. According to the data obtained, it is assumed that the repetitive lysogenic cycle of temperate bacteriophages promotes the dissolution of the phage genetic material in the host bacterial genome, and radical updating of phage and host bacterial genomes takes place.

Identification and genomic analysis of a novel temperate bacteriophage infecting Labrenzia aggregata isolated from the Mariana Trench

“…However, when searching for the R-M system in the host genome using rmsFinder, none R-M system was detected (Roberts et al, 2015), leading us to reconsider the reasoning behind the presence of methyltransferases in vB_LagS-V1. Recent analysis revealed that temperate phages are more prone to encoding methyltransferases compared to virulent phages (Kozlova et al, 2023), consistent with the observed prevalence of methyltransferases in the temperate phage, vB_LagS-V1. The over-representation of methyltransferases in temperate phages implies that methyltransferases more likely help the temperate phage to sustain the lysogenic state, and potentially provide protection to the host against infection by other phages (Oliveira et al, 2014;Kozlova et al, 2023).…”

“…The hosts of these three phages belong to the Labrenzia and have been isolated from marine environments. Whereas, other members such as Rhizobium phage RHph_TM3_3_14B, Rhizobium phage RHph_Y3_1, Sinorhizobium phage AP-16-3 and Rhizobium phage 16-3 originate from rhizobia isolated from soil environments (Ordogh and Szende, 1961;Santamarıá et al, 2022;Kozlova et al, 2023). This divergence in host and corresponding environments highlights a significant ecological distinction of vB_LagS-V1 and its associated new genus.…”