Functional and comparative genome analysis of novel virulent actinophages belonging to Streptomyces flavovirens

Abstract

BackgroundNext Generation Sequencing (NGS) technologies provide exciting possibilities for whole genome sequencing of a plethora of organisms including bacterial strains and phages, with many possible applications in research and diagnostics. No Streptomyces flavovirens phages have been sequenced to date; there is therefore a lack in available information about S. flavovirens phage genomics. We report biological and physiochemical features and use NGS to provide the complete annotated genomes for two new strains (Sf1 and Sf3) of the virulent phage Streptomyces flavovirens, isolated from Egyptian soil samples.ResultsThe S. flavovirens phages (Sf1 and Sf3) examined in this study show higher adsorption rates (82 and 85%, respectively) than other actinophages, indicating a strong specificity to their host, and latent periods (15 and 30 min.), followed by rise periods of 45 and 30 min. As expected for actinophages, their burst sizes were 1.95 and 2.49 virions per mL. Both phages were stable and, as reported in previous experiments, showed a significant increase in their activity after sodium chloride (NaCl) and magnesium chloride (MgCl2.6H2O) treatments, whereas after zinc chloride (ZnCl2) application both phages showed a significant decrease in infection.The sequenced phage genomes are parts of a singleton cluster with sizes of 43,150 bp and 60,934 bp, respectively. Bioinformatics analyses and functional characterizations enabled the assignment of possible functions to 19 and 28 putative identified ORFs, which included phage structural proteins, lysis components and metabolic proteins.Thirty phams were identified in both phages, 10 (33.3%) of them with known function, which can be used in cluster prediction. Comparative genomic analysis revealed significant homology between the two phages, showing the highest hits among Sf1, Sf3 and the closest Streptomyces phage (VWB phages) in a specific 13Kb region. However, the phylogenetic analysis using the Major Capsid Protein (MCP) sequences highlighted that the isolated phages belong to the BG Streptomyces phage group but are clearly separated, representing a novel sub-cluster.ConclusionThe results of this study provide the first physiological and genomic information for S. flavovirens phages and will be useful for pharmaceutical industries based on S. flavovirens and future phage evolution studies.

The Isolation and Characterization of Kronos, a Novel Caulobacter Rhizosphere Phage that is Similar to Lambdoid Phages

“…3). This adsorption rate was consistent with that of other rhizosphere phages [31], but was in stark contrast to the adsorption rate of the transducing phage Cr30, which was previously shown to adsorb at a rate that was 2.3-fold slower [11]. In addition, Kronos exhibited an eclipse period of 55 min with a burst size of 28 PFU per adsorbed phage (Fig.…”

Genome Sequences of Five Streptomyces Bacteriophages Forming Cluster BG

“…The genus Streptomyces is very diverse, with more than 576 validly published species names ( 1 ). Nevertheless, bacteriophages that infect Streptomyces have been described for only a few of these species ( 2 – 5 ). Streptomyces phages are currently grouped into 10 clusters (BA to BJ) within the actinobacteriophages based on nucleotide sequence similarity as well as their gene content ( http://www.phagesdb.org ) ( 6 ).…”

Characterization of a novel temperate phage facilitatingin vitrodispersal of multicellular bacteria

“…The last few years have been marked by a sustained effort in the isolation and sequencing of Streptomyces phages from environmental samples (17–19, 10, 20, 21). Moreover, the Streptomyces genome can constitute per se a viral genetic reservoir, through the genomes of temperate prophages that they may host.…”

“…The last few years have been marked by a sustained effort in the isolation and sequencing of Streptomyces phages from environmental samples (17)(18)(19)10,20,21).…”