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Genome and proteome analysis of 7-7-1, a flagellotropic phage infecting Agrobacterium sp H13-3

Andrew M Kropinski12*, An Van den Bossche3, Rob Lavigne3, Jean-Paul Noben4, Patrick Babinger5 and Rüdiger Schmitt6

Author Affiliations

1 Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, Guelph, ON, NIG 3W4, Canada

2 Department of Molecular & Cellular Biology, University of Guelph, Guelph, NIG 2W1, ON, Canada

3 Division of Gene Technology, Katholieke Universiteit Leuven, Kasteelpark Arenberg 21, 3001, Heverlee, Belgium

4 Biomedical Research Institute and Transnational University Limburg, School of Life Sciences, Hasselt University, Diepenbeek, Belgium

5 Institut für Biophysik und physikalische Biochemie, Universität Regensburg, D-93040, Regensburg, Germany

6 Institut für Biochemie, Genetik und Mikrobiologie, Universität Regensburg, D-93040, Regensburg, Germany

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Virology Journal 2012, 9:102  doi:10.1186/1743-422X-9-102

Published: 31 May 2012

Abstract

Background

The flagellotropic phage 7-7-1 infects motile cells of Agrobacterium sp H13-3 by attaching to and traveling along the rotating flagellar filament to the secondary receptor at the base, where it injects its DNA into the host cell. Here we describe the complete genomic sequence of 69,391 base pairs of this unusual bacteriophage.

Methods

The sequence of the 7-7-1 genome was determined by pyro(454)sequencing to a coverage of 378-fold. It was annotated using MyRAST and a variety of internet resources. The structural proteome was analyzed by SDS-PAGE coupled electrospray ionization-tandem mass spectrometry (MS/MS).

Results

Sequence annotation and a structural proteome analysis revealed 127 open reading frames, 84 of which are unique. In six cases 7-7-1 proteins showed sequence similarity to proteins from the virulent Burkholderia myovirus BcepB1A. Unique features of the 7-7-1 genome are the physical separation of the genes encoding the small (orf100) and large (orf112) subunits of the DNA packaging complex and the apparent lack of a holin-lysin cassette. Proteomic analysis revealed the presence of 24 structural proteins, five of which were identified as baseplate (orf7), putative tail fibre (orf102), portal (orf113), major capsid (orf115) and tail sheath (orf126) proteins. In the latter case, the N-terminus was removed during capsid maturation, probably by a putative prohead protease (orf114).

Keywords:
Agrobacterium; Phage evolution; Phage ecology; Genome; Proteome; Complex flagellum; Bioinformatics; Posttranslational modification