Genomic diversity of bacteriophages infecting Rhodobacter capsulatus and their relatedness to its gene transfer agent RcGTA

Abstract

The diversity of bacteriophages is likely unparalleled in the biome due to the immense variety of hosts and the multitude of viruses that infect them. Recent efforts have led to description at the genomic level of numerous bacteriophages that infect the Actinobacteria, but relatively little is known about those infecting other prokaryotic phyla, such as the purple non-sulfur photosynthetic α-proteobacterium Rhodobacter capsulatus. This species is a common inhabitant of freshwater ecosystems and has been an important model system for the study of photosynthesis. Additionally, it is notable for its utilization of a unique form of horizontal gene transfer via a bacteriophage-like element known as the gene transfer agent (RcGTA). Only three bacteriophages of R. capsulatus had been sequenced prior to this report. Isolation and characterization at the genomic level of 26 new bacteriophages infecting this host advances the understanding of bacteriophage diversity and the origins of RcGTA. These newly discovered isolates can be grouped along with three that were previously sequenced to form six clusters with four remaining as single representatives. These bacteriophages share genes with RcGTA that seem to be related to host recognition. One isolate was found to cause lysis of a marine bacterium when exposed to high-titer lysate. Although some clusters are more highly represented in the sequenced genomes, it is evident that many more bacteriophage types that infect R. capsulatus are likely to be found in the future.

Fig 1. R. capsulatus phage virion morphologies.

Representative transmission electron micrographs of virion particles from each R. capsulatus phage cluster shows the presence of Siphoviridae morphologies. Cluster designations, RcA-RcF or Singleton, are indicated above the representative phage name.

Fig 2. Network phylogeny of R. capsulatus bacteriophages.

The predicted proteins of all 29 R. capsulatus phages and those found in the 14,087 bp RcGTA structural gene region were sorted into 833 families (phams) according to shared amino acid sequence similarities using Phamerator [31]. Each genome was then assigned values reflecting the presence or absence of members of each pham; the genomes were compared and displayed using Splitstree. Clusters are indicated with colored ovals. The scale bar indicates 0.01 substitutions/site. Asterisks indicate sequences available prior to this study.

Fig 3. Gene content phamerator maps of the longest genomes for each cluster and the newly discovered singletons RcSimone-Håstad and RcZahn.

Proposed genes transcribed from left to right are presented above the central graduated line while those transcribed in the opposite direction are found below the line. Boxes filled in with color represent genes that are shared by at least one other phage in the collection. Those without color represent orphams, or predicted genes that do not have any closely related homologues in this collection. The scale is the same for all genomes presented and they are ordered by length from shortest (RcSaxon, 36,081 bp) to longest (RcZahn, 101,599 bp).

Fig 4. Evolutionary relationships of R. capsulatus bacteriophages and RcGTA.

The genome BLAST distance phylogeny (GBDP) tree generated using phage nucleotide sequences entered into the VICTOR web application under settings recommended for prokaryotic viruses and the D0 distance formula. The numbers above branches are GBDP pseudo-bootstrap support values from 100 replications. The branch lengths on the resulting VICTOR tree are scaled in terms of the respective distance formula used.

Fig 5. Genes shared with RcGTA.

Genes shared between RcGTA, RcZahn, RcSimone-Håstad, and members of the RcA and RcC clusters are indicated by shared color. The locations of several of these proteins within the tail region of RcGTA particles have recently been identified [18]. Genes sharing the same coloration have been designated by Phamerator as being members of the same pham while those that are colorless are considered to be orphams as their amino acid sequence identity with any other predicted proteins in this database does not reach the 32.5% identity CLUSTALW threshold used by Phamerator. Regions of color between genomes highlight pairwise nucleotide sequence similarities. Colors towards the red end of the spectrum represent regions with reduced levels of similarity but still above the BLASTN cut off value of 10⁻⁴ that still warrants shading.