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Open Access Research

The genome and proteome of Serratia bacteriophage η which forms unstable lysogens

Jenna M Denyes16, Peter J Krell1, Richard A Manderville2, Hans-Wolfgang Ackermann3, Yi-Min She4 and Andrew M Kropinski15*

Author Affiliations

1 Department of Molecular & Cellular Biology, University of Guelph, Guelph, ON N1G 2W1, Canada

2 Department of Chemistry, University of Guelph, Guelph, ON N1G 2W1, Canada

3 Department of Microbiology, Immunology, and Infectiology, Faculty of Medicine, Laval University, Quebec, QC G1X 4C6, Canada

4 Shanghai Center for Plant Stress Biology, Chinese Academy of Sciences, 3888 Chenhua Road, Shanghai 201602, China

5 Laboratory for Foodborne Zoonoses, Public Health Agency of Canada, 110 Stone Road West, Guelph, Ontario N1G 3W4, Canada

6 Current address: ETH Zurich, Institute of Food, Nutrition and Health, Schmelzbergstrasse 7, 8092 Zurich, Switzerland

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Virology Journal 2014, 11:6  doi:10.1186/1743-422X-11-6

Published: 16 January 2014

Abstract

Background

Serratia marcescens phage η is a temperate unclassified member of the Siphoviridae which had been reported as containing hypermodified guanine residues.

Methods

The DNA was characterized by enzymatic digestion followed by HPLC analysis of the nucleoside composition, and by DNA sequencing and proteomic analysis. Its ability to form stable lysogens and integrate was also investigated.

Results

Enzymatic digestion and HPLC analysis revealed phage η DNA did not contain modified bases. The genome sequence of this virus, determined using pyrosequencing, is 42,724 nucleotides in length with a mol% GC of 49.9 and is circularly permuted. Sixty-nine putative CDSs were identified of which 19 encode novel proteins. While seven close genetic relatives were identified, they shared sequence similarity with only genes 40 to 69 of the phage η genome, while gp1 to gp39 shared no conserved relationship. The structural proteome, determined by SDS-PAGE and mass spectrometry, revealed seven unique proteins. This phage forms very unstable lysogens with its host S. marcescens.

Keywords:
Serratia marcescens; Phage evolution; Genome; Proteome; Bioinformatics; Lysogeny; Unstable lysogeny; Modified nucleosides; Siphoviridae