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

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.

Figure 1

Electron micrograph of phage η negatively stained with 2% uranyl acetate. The bar indicates 100 nm.

Figure 2

Determination of the nature of the termini in phage η DNA. A. Bal31 exonuclease treated phage λ DNA with subsequent EcoRI restriction digestion, Lanes are labeled according to the number of minutes the DNA was incubated with the Bal31 before EcoRI digestion with the bands which decrease are boxed. B. phage η DNA was digested with exonuclease and subsequently digested with EcoRI. All lanes labeled L in both 2A and 2B are loaded with Ultra Ranger DNA Ladder ™ with size markers indicated in kb.

Figure 3

Genetic map of η. The genes are color coded according to function with red: novel, light green: prophage or bacterial related, dark green: phage related, black: lysis cassette, orange: recombination, brown: replication, yellow: packaging related, dark blue; confirmed structural, light blue: hypothetical, white: morons, grey: possible DNA binding and Kil. Promoters (P), terminators (T), direct repeats (R) and the ori are also included. Promoters are indicated with black arrows on stalks, while rho-independent terminators are indicated . The GenomeVx software package was used to construct this figure.