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Complete genome sequence of a marine roseophage provides evidence into the evolution of gene transfer agents in alphaproteobacteria

Sijun Huang12, Yongyu Zhang13, Feng Chen2 and Nianzhi Jiao1*

  • * Corresponding author: Nianzhi Jiao jiao@xmu.edu.cn

  • † Equal contributors

Author Affiliations

1 State Key Laboratory of Marine Environmental Science, Xiamen University, Xiamen 361005, PR China

2 Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA

3 Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen 361012, PR China

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Virology Journal 2011, 8:124  doi:10.1186/1743-422X-8-124

Published: 17 March 2011

Abstract

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.