Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria
© Huang et al; licensee BioMed Central Ltd. 2011
Received: 9 August 2010
Accepted: 17 March 2011
Published: 17 March 2011
Roseophage RDJLΦ1 is a siphovirus isolated from South China Sea on Roseobacter denitrificans OCh114. Its virion encapsulates 62.7 kb genome that encodes 87 gene products. RDJLΦ1 shares similar genome organization and gene content with the marine bacteriophage ΦJL001 and Pseudomonas phages YuA and M6, which are different from those of typical λ- or Mu-like phages. Four hallmark genes (ORFs 81 to 84) of RDJLΦ1 were highly homologous to RcGTA-like genes 12 to 15. The largest gene (ORF 84) was predicted to encode a tail fibre protein that could be involved in host recognition. Extended phylogenetic and comparative genomic analyses based on 77 RcGTA-like element-containing bacterial genomes revealed that RcGTA-like genes 12 to 15 together appear to be a conserved modular element that could also be found in some phage or prophage genomes. Our study suggests that RcGTA-like genes-containing phages and prophages and complete RcGTAs possibly descended from a same prophage ancestor that had diverged and then evolved vertically. The complete genome of RDJLΦ1 provides evidence into the hypothesis that extant RcGTA may be a prophage remnant.
Viruses are the most abundant entities of the world's oceans, ranging from ~3×106 to ~108 viruses per ml . Bacteriophages (viruses that infect bacteria) are known to play an important role in regulating the species composition of bacteria [1–4] and in the host evolution through phage-mediated horizontal gene transfer [5–7]. Bacteria in the Roseobacter clade (roseobacter hereafter) are abundant, and typically comprise 10-20% of marine bacterial communities [8, 9]. More than 30 genomes of representative roseobacters have been sequenced , and the genomics studies also showed that nearly all roseobacter genomes carry a conserved gene transfer agent (GTA) gene cluster of RcGTA (GTA producted by Rhodobacter capsulatus) type [10–14] which could assemble a phage-like particle that transfers random pieces of genome DNA from producing cells to recipient cells through a generalized transduction-like process . The widespread occurrence of RcGTA was hypothesized to be a potential efficient mechanism for horizontal gene transfer .
Up to date, only a limited number of roseophage (phage that infects roseobacter) genomes have been reported [16–18], which were all in Podoviridae family. In this study, we presented the genome sequence of Roseophage RDJLΦ1 that infects Roseobacter denitrificans OCh114. RDJLΦ1 was isolated from the South China Sea surface water (17.597°N, 116.029°E) collected in September 2007 as previously described . RDJLΦ1 was characterized as a host-specific siphovirus, which has an isometric head and a long, flexible, non-contractile tail, and belongs to Siphoviridae family, Caudovirales order . RDJLΦ1 is a lytic phage with burst size of ca. 203 and latent period of ca. 80 min . This is the first presented genome of a siphovirus infecting marine Roseobacter.
Phage RDJLΦ1 structural protein assignment based on the previously reported SDS-PAGE analysis 
tail tape measure protein
major tail protein
unknown structural protein
major capsid protein
The RDJLΦ1 genome can be divided into three modules: (i) DNA metabolism and replication, (ii) phage-host interaction, (iii) DNA packaging and structure formation (Figure 1). This type of genome organization is similar to those of ΦJL001, YuA and M6, but differs from those of λ- and Mu-like phages . RDJLΦ1, ΦJL001, YuA and M6 also share the similar gene contents in the three modules. No lysis genes were predicted in RDJLΦ1 genome, whereas lysis cassettes including four genes (endopeptidase Rz, embedded Rz1, holing and endolysin) were found in YuA and M6 genomes . Phylogenetic analysis based on terminase large subunit (TerL) protein showed that RDJLΦ1 fell into the "P22-like headful" cluster and was closely related to Salmonella phages ES18, E1 and Listonella phage ΦHSIC (Additional file 2). Despite the factor that RDJLΦ1, YuA, M6 and ΦJL001 share certain genomic similarity, temperate phages YuA, M6 and ΦJL001 clustered closely together but distantly to RDJLΦ1. Phages that infect marine, even aquatic, bacteria are isolated and characterized less frequently than terrestrial phages, resulting in the difficulty in their taxonomic classifications.
The RcGTA-like gene cluster appears to consist of two modular components: (i) head-to-tail module (gene 1 to 11); (ii) tail fibre and host recognition module (gene 12 to 15). It is interesting that up to date RcGTA-like genes in a (pro)phage have been found either from region (i) or region (ii), but not from both. Likely, the juncture between regions (i) and (ii) is a hotspot for genetic recombination. The last four RcGTA-like genes seem to be a conserved element as a unit. The vertical descent inside the RcGTA-like gene clusters appears to be unbalanced that losing or keeping some element could be under certain selective pressure. However, the reason why some (pro)phages tend to retain gene module (ii) that is associated with the putative host recognition function is not clear.
We thank Rui Zhang for providing discussion and suggestions in this work. This work was supported by the research programs of MOST (2007CB815904), NSFC (40632013, 40841023) and SOA (200805068) to NJ and Xiamen University 111 Program to FC. YZ was supported by MEL Visiting Fellowship Program (MELRS0931) and NSFC project (41006087).
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