ANNOTATED SEQUENCE RECORD
Sequence analysis of the Lactobacillus temperate phage Sha1
Bo Hyun Yoon
Se Hwan Jang
Received: 16 March 2011 / Accepted: 10 May 2011 / Published online: 24 June 2011
Ó Springer-Verlag 2011
Abstract Bacteriophage Sha1, a newly isolated temper-
ate phage from a mitomycin-C-induced lysate of Lacto-
bacillus plantarum isolated from Kimchi, has an isometric
head (58 nm 9 60 nm) and a long tail (259 nm 9 11 nm).
The double-strand DNA genome of the phage Sha1 was
41,726 base pairs (bp) long, with a G?C content of
40.61%. Bioinformatic analysis of Sha1 shows that this
phage contains 58 putative open reading frames (ORFs).
Sha1 can be classiﬁed as a member of the large family
Siphoviridae by genomic structure and morphology. To our
knowledge, this is the ﬁrst report of genomic sequencing
and characterization of temperate phage Sha1 from wild-
type L. plantarum isolated from kimchi in Korea.
Kimchi is the most famous traditional food in Korea, made
by fermentation of vegetables by various lactic acid bac-
teria, such as Leuconostoc mesenteroides, Lacotococcus
lactis and varied Lactobacilli . L. plantarum are gram-
positive facultatively anaerobic bacteria that are commonly
found in many fermented food products . Due to their
high acid tolerance compared to other lactic acid bacteria,
L. plantarum bacteria control the ﬁnal stage of kimchi
fermentation [8, 17]. L. plantarum was isolated from fer-
mented kimchi and identiﬁed by 16S rRNA-based PCR
analysis . Bacteriophages of L. plantarum have been
reported frequently, but this study is the ﬁrst report of
genomic sequencing and characterization of a temperate
phage of L. plantarum isolated from kimchi.
The phage Sha1 was isolated from a mitomycin C
(MMC C)-induced lysate of L. plantarum by polyethylene
glycol (PEG) precipitation and puriﬁed in a CsCl gradient
. CsCl-puriﬁed phage samples were negatively stained
with 2% (w/v) aqueous uranyl acetate (pH 4.0) on copper
grids covered with a ﬁlm of carbon-formvar, ionized, and
examined by transmission electron microscopy (Hitachi
H-7500, Japan) at an accelerating voltage of 80 kV.
According to morphology analysis by TEM, Sha1 has an
isometric head (58 nm 9 60 nm) and a long tail
(259 nm 9 11 nm) and belongs to the family Siphoviridae
The phage DNA was isolated from puriﬁed phage par-
ticles by the phenol extraction method . DNase I
(10 lg/ml) and RNase A (20 lg/ml) were added to the
phage lysate. After incubation at room temperature for
15 min, 0.5 M EDTA (pH 8.0) and proteinase K (1 mg/ml)
were added, followed by incubation at 65°C for 30 min.
After incubation, the DNA was extracted with phenol-
chloroform-isoamylalcohol. The phage DNA was precipi-
tated with ethanol and dissolved in sterile distilled water.
The genome sequence was generated by ultra-high-
throughput GS FLX sequencing to 20-fold redundancy on
average. Putative open reading frames (ORFs) were ana-
lyzed with GeneMark.hmm for Prokaryotes, version 2.4
. Amino acid sequences were comparatively analyzed
with the protein Basic Local Alignment Search Tool
Nucleotide sequence accession number: The complete genome
sequence of Sha1 was deposited in the GenBank database under
accession number HQ141411.
Electronic supplementary material The online version of this
article (doi:10.1007/s00705-011-1048-2) contains supplementary
material, which is available to authorized users.
B. H. Yoon Á S. H. Jang Á H.-I. Chang (&)
College of Life Sciences and Biotechnology, Korea University,
5-1 Anam-Dong, Sungbuk-Gu, Seoul, Korea
Arch Virol (2011) 156:1681–1684