Genomic, proteomic and bioinformatic analysis of two temperate phages in Roseobacter clade bacteria isolated from the deep-sea water

Abstract

BackgroundMarine phages are spectacularly diverse in nature. Dozens of roseophages infecting members of Roseobacter clade bacteria were isolated and characterized, exhibiting a very high degree of genetic diversity. In the present study, the induction of two temperate bacteriophages, namely, vB_ThpS-P1 and vB_PeaS-P1, was performed in Roseobacter clade bacteria isolated from the deep-sea water, Thiobacimonas profunda JLT2016 and Pelagibaca abyssi JLT2014, respectively. Two novel phages in morphological, genomic and proteomic features were presented, and their phylogeny and evolutionary relationships were explored by bioinformatic analysis.ResultsElectron microscopy showed that the morphology of the two phages were similar to that of siphoviruses. Genome sequencing indicated that the two phages were similar in size, organization, and content, thereby suggesting that these shared a common ancestor. Despite the presence of Mu-like phage head genes, the phages are more closely related to Rhodobacter phage RC1 than Mu phages in terms of gene content and sequence similarity. Based on comparative genomic and phylogenetic analysis, we propose a Mu-like head phage group to allow for the inclusion of Mu-like phages and two newly phages. The sequences of the Mu-like head phage group were widespread, occurring in each investigated metagenomes. Furthermore, the horizontal exchange of genetic material within the Mu-like head phage group might have involved a gene that was associated with phage phenotypic characteristics.ConclusionsThis study is the first report on the complete genome sequences of temperate phages that infect deep-sea roseobacters, belonging to the Mu-like head phage group. The Mu-like head phage group might represent a small but ubiquitous fraction of marine viral diversity.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3886-0) contains supplementary material, which is available to authorized users.

Genome Study of a Novel Virulent Phage vB_SspS_KASIA and Mu-like Prophages of Shewanella sp. M16 Provides Insights into the Genetic Diversity of the Shewanella Virome

“…Nevertheless, there is an increasing number of reports of mitomycin-induced Mu-like viruses, for example vB_CibM-P1 of Citromicrobium bathyomarinum JL354 [77], prophages of Porphyrobacter sp.YT40 [78], vB_RhkS_P1 of Rhodovulum sp. P5 [79], vB_ThpS-P1 Thiobacimonas profunda JLT2016 [80], vB_PeaS-P1 Pelagibaca abyssi JLT2014 [80], fF4 Flavobacterium columnare ATCC 23,463 [81], and, in this study, MuM16-1 of Shewanella sp. M16.…”

The genomic content and context of auxiliary metabolic genes in roseophages

“…The repressor LexA regulates the induction of the SOS response in host cells and may also play a role in controlling the host life cycle than accelerating the host metabolic rate (Sanchez‐Alberola et al ., 2015). More deep sea isolates are needed to determine whether their unique AMG feature is indicative of a divergent life strategy or just a result of their mosaic relationship with the other phages (Tang et al ., 2017). More evidence is also needed to illustrate how the roseophage geological distribution and phage lifestyle impact on the AMG content of roseophages.…”

Prophage Genomics and Ecology in the Family Rhodobacteraceae

“…These phages were isolated by plaque assay or Mitomycin C induction from Roseovarius nubinhibens , Thiobacimonas profunda , Pelagibacter abyssi , and Sulfitobacter sp. Strain 2047 [ 40 , 44 , 54 , 55 , 56 ]. Among the isolated roseophages identified as lytic in their original description, 75% contain an integrase or lytic repressor gene that are characteristic of temperate phages, suggesting that they may have the ability to integrate, although this has not been observed in laboratory conditions [ 40 ].…”