Complete Genomic and Lysis-Cassette Characterization of the Novel Phage, KBNP1315, which Infects Avian Pathogenic Escherichia coli (APEC)

Abstract

Avian pathogenic Escherichia coli (APEC) is a major pathogen that causes avian colibacillosis and is associated with severe economic losses in the chicken-farming industry. Here, bacteriophage KBNP1315, infecting APEC strain KBP1315, was genomically and functionally characterized. The evolutionary relationships of KBNP1315 were analyzed at the genomic level using gene (protein)-sharing networks, the Markov clustering (MCL) algorithm, and comparative genomics. Our network analysis showed that KBNP1315 was connected to 30 members of the Autographivirinae subfamily, which comprises the SP6-, T7-, P60-, phiKMV-, GAP227- and KP34-related groups. Network decomposition suggested that KBNP1315 belongs to the SP6-like phages, but our comparison of putative encoded proteins revealed that key proteins of KBNP1315, including the tail spike protein and endolysin, had relative low levels of amino acid sequence similarity with other members of the SP6-like phages. Thus KBNP1315 may only be distantly related to the SP6-like phages, and (based on the difference in endolysin) its lysis mechanism may differ from theirs. To characterize the lytic functions of the holin and endolysin proteins from KBNP1315, we expressed these proteins individually or simultaneously in E. coli BL21 (DE3) competent cell. Interestingly, the expressed endolysin was secreted into the periplasm and caused a high degree of host cell lysis that was dose-dependently delayed/blocked by NaN3-mediated inhibition of the SecA pathway. The expressed holin triggered only a moderate inhibition of cell growth, whereas coexpression of holin and endolysin enhanced the lytic effect of endolysin. Together, these results revealed that KBNP1315 appears to use a pin-holin/signal-arrest-release (SAR) endolysin pathway to trigger host cell lysis.

Application of a Novel Phage LPSEYT for Biological Control of Salmonella in Foods

“…The holin is nominally a class III holin but the topology of the transmembrane domain (TMD) of this holin is predicted to be different to the prototype class III holin of bacteriophage T4 [47,48]. Although previously not evident in Salmonella phages, the topology of LPSEYT's holin is similar to that reported for Escherichia coli phage KBNP1315 and mycobacteriophage Ms6 [49,50]. The endolysin of LPSEYT's lysis cassette was predicted to have a transmembrane helix in the N-terminal region as the terminal signal-anchor-release (SAR) domain.…”

Phage biocontrol to combat Pseudomonas syringae pathogens causing disease in cherry

“…As such, we posit that phages MR1 and MR2 may also be classified within this genus of phage and consideration should be given to assigning them to a new species within this genus according to the guidelines of the ICTV (Adriaenssens and Brister, 2017). Phage MR4 represents a new species of phage within the Zindervirus ( Autographivirinae subfamily; Lee et al , 2015). The collection of similar phages (MR5, MR6, MR7, MR8, MR12, MR16 and MR18) had low similarity to other phage genomes in the database, with the best hit being against Pseudomonas phage phi‐2, a member of the Autographivirinae subfamily, belonging to the genus Phikmvvirus .…”

Haemophilus influenzae HP1 Bacteriophage Encodes a Lytic Cassette with a Pinholin and a Signal-Arrest-Release Endolysin

“…The most studied is the lytic cassette encoded by lambdoid phage 21 specific for E. coli, composed of pinholin, antiholin, and SAR-endolysin [2]. In addition, other studies described the existence of lytic cassettes, composed of pinholin and SAR-endolysin, encoded by different phages as ΦKMV, that infects Pseudomonas aeruginosa [13], Xfas53 phage infecting Xylella fastidiosa [14], coliphage P1 [12] or KBNP1315 phage that infects Avian Pathogenic E. coli (APEC) [15]. The regulation of SAR-endolysin release seems to be complex but associated with pinholin.…”