Bacteria and bacteriophages
S. marcescens CV/rc3 (HER 1311) and phage η were obtained from the Centre de Référence pour les Virus Bactériens Félix d’Hérelle (Université Laval, QC, Canada). The host was grown in Difco Luria-Bertani broth (LB; Fisher Scientific, Toronto, ON, Canada) at 30°C with shaking at 180 rpm or on LB agar plates (LB with 1.5% [wt/vol] agar) at 30°C. The bacteriophage titer was determined using the double agar overlay method [
48]. Phage particles were partially purified by PEG precipitation and continuous CsCl purification [
49]. Purified phage was dialyzed using a Pierce 10 K Slide-A-Lyzer cassette (Thermo Fisher Scientific, Rockford, IL, USA) against 10 mM Tris-0.1 mM EDTA (pH 8.0) (TE) buffer to remove CsCl. Purified phage was stored at 4°C.
Electron microscopy
Purified phages were sedimented by centrifugation at 25,000 g for 60 min, using a Beckman Coulter J-E (Palo Alto, CA) centrifuge and a JA19.1 fixed angle rotor. The pellet was washed twice under the same conditions in neutral ammonium acetate (0.1 M). Phages were deposited on copper grids with carbon-coated Formvar films, stained with 2% uranyl acetate (pH 4.5) and examined using a Philips EM 300 electron microscope.
DNA isolation, digestion and HPLC analysis: Phage
DNA was extracted by standard phenol chloroform extraction and ethanol precipitation [
50]. The purified phage η genomic DNA was digested to the nucleoside level in preparation for HPLC analysis according to the protocol described by [
30] using DNase I, phosphodiesterase I and alkaline phosphatase (Worthington Biochemical Corp. Vassar, NJ, USA). The number of units of phosphodiesterase I were increased from 0.01 units in the protocol to 0.1 units. The phosphodiesterase I and alkaline phosphatase digestions were done in a water bath at 25°C. The digested DNA was filtered using an Ultrafree–MC membrane with a pore size of 0.1 μm (Millipore Corp, Billerica, MA, USA) to remove particles in preparation for loading onto the HLPC column. Standard nucleosides were purchased from Sigma-Aldrich (Sigma-Aldrich, Oakville, Canada).
The protocol developed was based on the method outlined by [
30]. The analysis was performed on an Agilent 1100 series LC/MSD_SL Trap system. Samples (100 μl) were injected into the LC/MSD system through an Agilent 1100 series thermostated auto-sampler. Separations were carried out on a 5 μm Agilent ZORBAX SB C-18 column (4.6 × 150 mm) at a flow rate of 0.75 ml/min. Two mobile phase solvents were used; Solvent A was 0.1% formic acid in deionized water; Solvent B was 100% HPLC grade acetonitrile. Dimethyl sulfoxide (DMSO) was used to dissolve the concentrated nucleosides. HPLC method: 98/2 A/B for five minutes then increasing to 95/5 A/B at ten minutes, 80/20 A/B at 12 minutes then returning to 100% A.
DNA sequencing and annotation
Phage DNA was digested, ligated and treated with Bal31 exonuclease according to manufacturer’s specifications (NEB) and resolved using a 1% agarose gel. Genome end determination was carried out following protocols published by Loessner
et al., [
32] and Casjens
et al., [
51]. Pulsed-field gel analysis was carried out following the protocol of Lingohr
et al., [
52].
The genome sequence was determined using 454 sequencing technology at the McGill University and Genome Quebec Innovation Centre (Montreal, QC, Canada) with 49.1 fold coverage. The genome was annotated using Kodon (Applied Maths, Austin, TX, USA) with the proteins screened for homologs using the BLASTP feature of Geneious Pro 6.2 (Biomatters Ld., Auckland, New Zealand). Their molecular mass and pI were calculated using the Batch MW and pI Finder server at
http://greengene.uml.edu/programs/FindMW.html. Potential protein motifs were identified using the NCBI Batch CD-Search tool at
http://www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi? with an E-value threshold of 0.0001. Transmembrane domains were screened for using TMHMM [
53] and Phobius [
54]. In certain cases HHpred [
55,
56] was employed to analyze the protein sequences. The annotated sequence was deposited with GenBank under accession number KC460990 (GI:511624446). RNA secondary structure prediction was used to support the identification of rho-independent terminators [
57]. The oriC was identified using Ori-Finder [
58]. The gene diagram was constructed using Genome Vx [
59].
Structural protein analysis
Phage particles which had been purified through CsCl twice were used for SDS-PAGE structural protein analysis. Purified whole phages were denatured at 100°C for 5 min. in Laemmli Sample Buffer supplemented with 100 mM 2-mercaptoethanol. The structural proteins were resolved in a Bio-Rad Ready 5-15% Tris-HCl gel, in Running Buffer (25 mM Tris, 192 mM glycine, 0.1% SDS, pH 8.3 (Bio-Rad)) at 150 V for an hour. Visible bands were excised, and then digested in-gel by sequencing-grade trypsin. The cleaved peptide fragments of the proteins were extracted using acentonitrile/0.1% trifluoroacetic acid (TFA) (v/v, 60:40), then dried by a Savant vacuum centrifuge (Thermo Fisher Scientific, Nepean, Ontario). In the subsequent mass spectrometric analyses, the peptides were reconstituted in 8 μl of 0.2% formic acid (FA) and identified using a nanoAcquity ultra-performance liquid chromatograph (UPLC, Waters, Milford, MA) – linear ion-trap Fourier transform ion cyclotron resonance (LTQ-FT ICR, Thermo Fisher, San Jose, CA) mass spectrometer. The sample was normally trapped by a reverse-phase (RP) Symmetry C18 column (180 μm i.d. × 20 mm length, 5 μm) at 5 μl/min of solvent A (0.1% FA) for 3 minutes, and then separated through a C18 analytical column (100 μm i.d. × 100 mm, 1.7 μm, BEH 130) at 400 nl/min for 65 minutes. UPLC gradient was set up to a linear gradient from 5% to 30% solvent B (0.1% FA in acetonitrile), followed by to 85% solvent B over 10 min. for peptide elution. FT-MS scans were acquired with high resolution (100,000) MS from m/z 300 to 2000, and MS/MS measurements in linear ion-trap mode by data-dependent scans of the top eight intense precursor ions at multiply charged states of 2+, 3+ and 4+. Dynamic exclusion was set to a period of time at 180 s.
Protein identification was performed using Mascot Server (version 2.3.0, Matrix Science, London, UK), and UPLC MS/MS raw data were searched against the in-house database of the protein sequence derived from the annotated genome of phage η. The search parameters were restricted to tryptic peptides for a maximum of 2 missed cleavages. Cysteine carbamidomethylation was designated as a fixed modification, and deamidation of asparagine and glutamine, methionine oxidation were considered as variable modifications. Mass tolerances were set up to 10 ppm for the FT-MS ions and 1 Da for ion trap MS/MS fragment ions. Peptide assignments were filtered by an ion score cut off at 20, and the identified MS/MS spectra were also verified manually.