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Na Et Al Characterization of LysPBC4 PDF
Na Et Al Characterization of LysPBC4 PDF
doi: 10.1093/femsle/fnw092
Advance Access Publication Date: 11 April 2016
Research Letter
ABSTRACT
Bacillus cereus is a spore-forming, Gram-positive bacterium and is a major food-borne pathogen. A B. cereus-specific
bacteriophage PBC4 was isolated from the soil of a stock farm, and its genome was analyzed. PBC4 belongs to the
Siphoviridae family and has a genome consisting of 80 647-bp-long double-stranded DNA, including 123 genes and two
tRNAs. LysPBC4, the endolysin of PBC4, has an enzymatically active domain (EAD) on its N-terminal region and a putative
cell wall-binding domain (CBD) on its C-terminal region, respectively. Although the phage PBC4 showed a very limited host
range, LysPBC4 could lyse all of the B. cereus strains tested. However, LysPBC4 did not kill other bacteria such as B. subtilis or
Listeria, indicating that the endolysin has specific lytic activity against the B. cereus group species. Furthermore,
LysPBC4 CBD fused with enhanced green fluorescent protein (EGFP) could decorate limited strains of B. cereus group,
suggesting that the LysPBC4 CBD may be a promising material for specific detection of B. cereus.
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2 FEMS Microbiology Letters, 2016, Vol. 363, No. 12
Table 1. Lytic activity of phage PBC4 and its endolysin LysPBC4, and Bacteriophage isolation and propagation
the binding activity of LysPBC4 CBD.
PBC4 was isolated from soil samples obtained from the National
Species PBC4 LysPBC4 PBC4 CBD Academy of Agricultural Science in Suwon, South Korea. To
isolate a bacteriophage, we applied the same method as in the
B. cereus ATCC 27348 – + +
previous study (Kong and Ryu 2015). Isolated phages were ampli-
B. cereus ATCC 21768 – + –
Figure 1. Genomic analysis of phage PBC4. (a) The genome map of bacteriophage PBC4. At least two genes, endolysin and holin, involved in host lysis were confirmed.
Each color of ORF indicates its function: yellow, packaging; blue, structural genes; green, host lysis; red, DNA manipulation; purple, additional functions; and black,
hypothetical genes. The inner circle with the red line indicates the G + C content. The scale unit is a base pair. (b) Comparative genomic analysis between phage PBC4
and Basilisk on the nucleotide sequence level. Both phages are B. cereus-targeting Siphoviridae. Their genomes have high similarities at the nucleotide or protein level.
However, some of the genes, like those for the tail fiber, differ, indicating that these two phages may have different host ranges or lytic activities.
4 FEMS Microbiology Letters, 2016, Vol. 363, No. 12
the N-terminal region of the EGFP-CBD fusion proteins, respec- fluorescent microscopy (Carl Zeiss, Oberkochen, Germany) was
tively. The expression of proteins was induced by treating the used in the assay.
E. coli BL21(DE3) strains containing recombinant plasmids with
1 mM of isopropyl β-D-1-thiogalactopyranoside (IPTG) (Sigma-
GenBank accession numbers
Aldrich, St. Louis, MO). The LysPBC4 and EGFP CBD fusion pro-
teins were expressed by incubating the cells at 37◦ C for 6 h and at The GenBank accession numbers of PBC4 and LysPBC4 are
Figure 2. Phylogenetic tree of various phages having (a) related major capsid proteins (MCPs) and (b) TerLs. Each host bacterium is shown in the parentheses after the
name of the phage. The numbers at the nodes represent the bootstrap probabilities.
Na et al. 5
integrase of Bacillus phage Staley (59% amino acid sequence sim- tity (41%). Specifically, a putative chitinase, which was found ad-
ilarity; GenBank accession No. NC 022767) (Hastings et al. 2013), jacent to the tail fiber protein of Basilisk, is absent in PBC4. Con-
suggests that PBC4 is a temperate phage having both lytic and sidering that the tail fiber proteins of phages have been known
lysogenic life cycles. Although no MCP was identified by se- to determine the host range of phages (Scholl et al. 2001), the
quence analysis, the protein PBC4 006 could be predicted to be host specificities of the two B. cereus phages might differ.
an MCP, because it showed high sequence identity (71%) with
that (gp36) of the B. cereus phage Basilisk, whose MCP was exper-
imentally proven (Grose et al. 2014a,b). A putative TerL belong- Identification of endolysin from PBC4 and its domain
ing to the terminase 1 superfamily was identified, but a small
composition
subunit of terminase-encoding gene was not found. Among the
predicted phage’s structural proteins, a putative tail fiber protein We identified an N-acetylmuramoyl-L-alanine amidase
(PBC4 021) corresponds to the short tail fiber observed in a TEM (PBC4 025), which has lytic activity against peptidoglycan
image (Fig. 1 and Fig. S1, Supporting Information). cell walls (Young 1992; Young, Wang and Roof 2000), and anno-
The comparative analysis of genomes between PBC4 and tated it as an endolysin. The endolysin of phage PBC4 (LysPBC4)
Basilisk revealed that they share an 83.3% nucleotide identity has two distinct domains. On the N-terminal region, the domain
over the entire genome with the same architectures (Fig. 1b). ‘amidase 3’ (PF01520), generally functioning as an enzymat-
This is also evident from phylogenetic trees based on MCP and ically active domain (EAD) (Ghuysen et al. 1969; Herbold and
TerL, which are common targets for phage taxonomy (Brüssow Glaser 1975), was predicted, while the “amidase02 C” domain
and Frank 2001; Comeau and Henry 2008) (Fig. 2). Both MCP and (PF12123), a putative cell wall-binding domain (CBD) (Yuan, Peng
TerL of PBC4 have high similarities to those of Basilisk, with 71% and Gao 2012; Kong et al. 2015), was found from the C-terminal
and 82% amino acid sequence identity, respectively. These data region (Fig. 3a). These two distinct domains appeared to be
indicate that the phage PBC4 and Basilisk are closely related connected by a flexible linker region, since the region from the
phages. Interestingly, although the late gene products, such as 170th to 185th amino acid is rich in glycine, alanine having
the terminase, structural proteins and lysis-related proteins of short side chains, serine, threonine and asparagine having polar
PBC4 and Basilisk, demonstrated high sequence homology, their side chains, all of which are predicted to form random coils and
putative tail fiber proteins showed relatively low sequence iden- are usually found in many linker proteins (Schmitz, Schuch and
6 FEMS Microbiology Letters, 2016, Vol. 363, No. 12
Fischetti 2010; Schmelcher, Tchang and Loessner 2011). The bidity reduction assay revealed that the endolysin LysPBC4
active site residues His10, Glu24, His80 and Glu142 were found showed broader lytic activity than the host range of bacterio-
to be conserved in EAD; three of these residues (His10, Glu24 phage PBC4, but it was still specific for B. cereus group strains (Ta-
and His80) were predicted to be zinc-binding sites. ble 1). LysPBC4 could kill all of the B. cereus strains tested, and it
BLASTP analysis revealed many proteins having sequence could also lyse the B. thuringiensis and B. mycoides strains, which
homology with LysPBC4. Most were autolysins, cell wall- belong to the B. cereus group. Meanwhile, other Bacilli, including
hydrolyzing enzymes (Shockman and Höltje 1994) required for B. subtilis, were resistant to LysPBC4. Other Gram-positive and
bacterial cell growth, peptidoglycan maturation, and various Gram-negative bacteria were also insensitive to LysPBC4, mean-
other cellular functions (Blackman, Smith and Foster 1998; ing that the endolysin specifically kills the B. cereus group at
Smith, Blackman and Foster 2000). Additional comparative anal- the species level (Table 1, Fig. 4). Considering that some Bacillus
ysis revealed that the N-terminal EAD of LysPBC4 is more con- species, such as B. subtilis, have been granted GRAS status (West-
served than the C-terminal CBD. For instance, the N-terminal ers, Westers and Quax 2004) and are widely used as the starter
regions of two endolysins from phage PBC4 and Basilisk showed strain for fermented foods (Cladera-Olivera, Caron and Brandelli
69% sequence identity, whereas the C-terminal regions showed 2004), the B. cereus-specific lytic activity could render LysPBC4 a
only 33% sequence homology. Due to the conserved EAD, promising tool for controlling pathogenic Bacilli.
LysPBC4 showed an overall 63% amino acid sequence identity
with an endolysin of Basilisk (Grose et al. 2014a,b), 51% with an
endolysin of BCP78 (GenBank accession no. JN797797) and 49%
Binding spectrum of LysPBC4 CBD
with PlyM19 (GenBank accession no. HM011607.1) (Schmitz et al. To confirm the binding activity of the C-terminal amidase 02
2010) (Fig. 3b). LysPBC4 also showed close relatedness (30% iden- domain, two different length variants (one with a puta-
tity) to LysPBC1, as they have similar domain structures (ami- tive linker and one without) were tested (Fig. 5). Both con-
dase 3 and amidase02 C) (Kong et al. 2015). However, the CBDs of structs were tagged with EGFP at the N-terminus and named
these endolysins showed only marginal sequence identity (23%) EGFP PBC4 CBD1 and EGFP PBC4 CBD2, respectively. As shown
(Fig. 3c). This result implies that some key residues or motifs in in Fig. 5, the EGFP PBC4 CBD1, which includes a putative linker
both CBDs are conserved (which is why they are predicted as sequence, displayed a strong cell wall-binding activity, whereas
same amidase02 C domain), whereas their overall structures or the EGFP PBC4 CBD2, which devoid of the putative linker,
binding targets may differ. showed no binding activity. These results indicate the impor-
tance of a putative linker region for cell wall-binding capacity
of EGFP-tagged LysPBC4 CBD. It could be that the putative linker
Antibacterial activity of LysPBC4
region is critical for proper folding of the LysPBC4 CBD. It is also
The LysPBC4 was expressed and purified from a recombinant possible that the linker itself plays an important role in bind-
E. coli BL21(DE3) strain (Fig. S2, Supporting Information). A tur- ing cell wall of the B. cereus. Further, study would be necessary
Na et al. 7
to elucidate the exact role of the linker region of LysPBC4. Bind- crobial genomes. Implications for finding sequence
ing spectrum of EGFP PBC4 CBD showed that LysPBC4 CBD could motifs in regulatory regions. Nucleic Acids Res 2001;29:
bind to four of nine strains of B. cereus and two other B. cereus 2607–18.
group species tested (Table 1). Other bacteria, such as B. subtilis Blackman SA, Smith TJ, Foster SJ. The role of autolysins dur-
and other bacterial species, could not be bound by LysPBC4 CBD ing vegetative growth of Bacillus subtilis 168. Microbiology
(Fig. S3, Supporting Information). These results suggest that 1998;144:73–82.
B. cereus group-specific cell wall moieties are the most likely Bottone EJ. Bacillus cereus, a volatile human pathogen. Clin Micro-
binding target of LysPBC4 CBD. Also, the inability of binding of biol Rev 2010;23:382–98.
LysPBC4 CBD toward certain B. cereus strains proposes the differ- Brüssow H, Frank D. Comparative phage genomics and the evo-
ence of cell wall structure among the B. cereus group strains. The lution of Siphoviridae: insights from dairy phages. Mol Micro-
specific binding activity of LysPBC4 CBD could be useful for the biol 2001;39:213–23.
development of efficient bioprobes against B. cereus. Cladera-Olivera F, Caron G, Brandelli A. Bacteriocin-like sub-
stance production by Bacillus licheniformis strain P40. Lett Appl
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SUPPLEMENTARY DATA Comeau AM, Henry MK. The capsid of the T4 phage super-
Supplementary data are available at FEMSLE online. family: the evolution, diversity, and structure of some of
the most prevalent proteins in the biosphere. Mol Biol Evol
2008;25:1321–32.
FUNDING Delcher AL, Bratke KA, Powers EC et al. Identifying bacterial
This work was supported by the National Research Foundation genes and endosymbiont DNA with Glimmer. Bioinformatics
of Korea (NRF) grant (NRF-2014R1A2A1A10051563) and the Pub- 2007;23:673–9.
lic Welfare & Safety research program (NRF-2012M3A2A1051684) Dunne M, Mertens HD, Garefalaki V et al. Bacteriophage en-
funded by the Ministry of Science, ICT and Future Planning, dolysins: a novel anti-infective to control Gram-positive
Republic of Korea. pathogens. Int J Med Microbiol 2010;300:357–62.
Fischetti VA. Bacteriophage endolysins: a novel anti-infective
Conflict of interest. None declared. to control Gram-positive pathogens. Int J Med Microbiol
2010;300:357–62.
Ghuysen JM, Dierickx L, Coyette J et al. Technique for the prepa-
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