Isolation of New Stenotrophomonas Bacteriophages and Genomic Characterization of Temperate Phage S1

Abstract

Twenty-two phages that infect Stenotrophomonas species were isolated through sewage enrichment and prophage induction. Of them, S1, S3, and S4 were selected due to their wide host ranges compared to those of the other phages. S1 and S4 are temperate siphoviruses, while S3 is a virulent myovirus. The genomes of S3 and S4, about 33 and 200 kb, were resistant to restriction digestion. The lytic cycles lasted 30 min for S3 and about 75 min for S1 and S4. The burst size for S3 was 100 virions/cell, while S1 and S4 produced about 75 virus particles/cell. The frequency of bacteriophage-insensitive host mutants, calculated by dividing the number of surviving colonies by the bacterial titer of a parallel, uninfected culture, ranged between 10 ؊5 and 10 ؊6 for S3 and 10 ؊3 and 10 ؊4 for S1 and S4. The 40,287-bp genome of S1 contains 48 open reading frames (ORFs) and 12-bp 5 protruding cohesive ends. By using a combination of bioinformatics and experimental evidence, functions were ascribed to 21 ORFs. The morphogenetic and lysis modules are well-conserved, but no lysislysogeny switch or DNA replication gene clusters were recognized. Two major clusters of genes with respect to transcriptional orientation were observed. Interspersed among them were lysogenic conversion genes encoding phosphoadenosine phosphosulfate reductase and GspM, a protein involved in the general secretion system II. The attP site of S1 may be located within a gene that presents over 75% homology to a Stenotrophomonas chromosomal determinant.

Functional Genomic Analysis of Two Staphylococcus aureus Phages Isolated from the Dairy Environment

“…The major capsid protein of Pseudomonas aeruginosa bacteriophage PAJU2 is thought to be synthesized as a protein fused to a prohead protease and is autocatalytically cleaved (53). Similar domain architecture is found in the capsid protein from Stenotrophomonas bacteriophage S1 (19). This protein matches three types of proteins in the databases: proteases, scaffold protein, and major head proteins.…”

Complete Genome Sequence of IME13, a Stenotrophomonas maltophilia Bacteriophage with Large Burst Size and Unique Plaque Polymorphism

“…The one-step growth curve showed it had a very big burst size which exceeded 3,000 (data not shown). A Stenotrophomonas maltophilia phage of such a big burst size had not yet been reported (3)(4)(5)7). Meantime, the phage appeared as at least three obviously different sizes of plaques on a double-layer Luria broth agar plate, a phenomenon that we had never observed on other phages.…”

Genomic and Biological Analysis of Phage Xfas53 and Related Prophages of Xylella fastidiosa

“…At 624 residues, the predicted major capsid protein of these phages (corresponding to PD1106 in Xpd1) is larger than that from typical phages. The major capsid proteins from several phages, for example, Stenotrophomonas phage S1, are synthesized from similarly sized precursors (23). Like S1 and lactococcal bacteriophage c2, the Xpd1 major capsid protein contains a prohead protease domain, suggesting that the protein is self-processed and could also contain a scaffolding domain (15,23).…”

“…The major capsid proteins from several phages, for example, Stenotrophomonas phage S1, are synthesized from similarly sized precursors (23). Like S1 and lactococcal bacteriophage c2, the Xpd1 major capsid protein contains a prohead protease domain, suggesting that the protein is self-processed and could also contain a scaffolding domain (15,23). The Xfp1-like phages possess homologues of lambda nu1, A, and B, encoding the lambda TerS, TerL, and portal proteins, respectively.…”