• Journal of Microbiology and Biotechnology
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• v.26 no.9
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• pp.1629-1635
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• 2016

A novel bacteriophage, PBES 02, infecting Cronobacter sakazakii was isolated and characterized. It has a spherical head of 90 nm in diameter and a tail of 130 nm in length, and belongs to Myoviridae as observed under a transmission electron microscope. The major virion protein appears to be 38 kilodaltons (kDa) in size. The latent period of PBES 02 is 30 min and the burst size is 250. Infectivity of the phage remained intact after exposure to temperatures ranging from 4℃ to 55℃ for 1 h. It was also stable after exposure to pHs ranging from 6 to 10 for 1 h. The phage effectively removed contaminating Cronobacter sakazakii from broth infant formula. PBES 02 has a double-stranded DNA genome of 149,732 bases. Its GC ratio is 50.7%. Sequence analysis revealed that PBES 02 has 299 open reading frames (ORFs) and 14 tRNA genes. Thirty-nine ORFs were annotated, including 24 related to replication and regulation functions, 10 related to structural proteins, and 5 related to DNA packaging. The genome of PBES 02 is closely related to that of two other C. sakazakii phages, CR3 and CR8. Comparison of DNA sequences of genes encoding the major capsid protein revealed a wide geographical distribution of related phages over Asia, Europe, and America.

• Journal of Microbiology and Biotechnology
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• v.24 no.6
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• pp.725-731
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• 2014

The classical biotype strains of the Vibrio cholerae O1 serogroup harbor the biotype-specific cholera-toxin encoding phage (CTX) $CTX^{cla}$, and the El Tor biotype strains contain CTX-1. Although the classical biotype strains have become extinct, a remnant of classical CTX phage is transferred to the El Tor biotype strains. The prototype El Tor strains, which produce the biotype-specific cholera toxin, are now being replaced by atypical El Tor variant strains producing classical biotype cholera toxin. The genome sequences of the CTX phages in atypical El Tor strains indicate that the CTX phages in atypical El Tor strains are a mosaic of $CTX^{cla}$ and CTX-1. Before the emergence of atypical El Tor stains in the early 1990s, unusual pre-seventh pandemic strains were isolated in the US Gulf Coast between 1973 and 1986. These strains have characteristics of atypical El Tor strains since they are El Tor biotype strains containing $CTX^{cla}$, yet the genome sequence of this CTX phage indicates that it is different from $CTX^{cla}$ and is therefore classified separately as $CTX^{US\;Gulf}$.

• Journal of Microbiology and Biotechnology
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• v.23 no.8
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• pp.1147-1153
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• 2013

Pectobacterium carotovorum subsp. carotovorum (formerly Erwinia carotovora subsp. carotovora) is a plant pathogen that causes soft rot and stem rot diseases in several crops, including Chinese cabbage, potato, and tomato. To control this bacterium, we isolated a bacteriophage, PP1, with lytic activity against P. carotovorum subsp. carotovorum. Transmission electron microscopy revealed that the PP1 phage belongs to the Podoviridae family of the order Caudovirales, which exhibit icosahedral heads and short non-contractile tails. PP1 phage showed high specificity for P. carotovorum subsp. carotovorum, and several bacteria belonging to different species and phyla were resistant to PP1. This phage showed rapid and strong lytic activity against its host bacteria in liquid medium and was stable over a broad range of pH values. Disease caused by P. carotovorum subsp. carotovorum was significantly reduced by PP1 treatment. Overall, PP1 bacteriophage effectively controls P. carotovorum subsp. carotovorum.

• Journal of Microbiology and Biotechnology
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• v.18 no.2
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• pp.328-333
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• 2008

A series of pep tides binding to the HCV NS5B polymerase was selected from phage display peptide libraries. A conserved motif of Ser-Arg-X-Arg/Leu was identified among the selected peptides, and Pep2 (Trp-Ser-Arg-Pro-Arg-Ser-Leu) was chosen for further characterization. The binding of Pep2 to HCV NS5B in vivo was shown by a yeast two-hybrid assay and by subcellular colocalization analysis using immunofluorescence confocal microscopy. The in vitro interaction was also confirmed by GST pulldown assay. The replication of the HCV 1b subgenomic replicon was efficiently inhibited by the presence of the peptide. By using a subtractive biopanning against Pep2, the binding site of the peptide was mapped at the pocket of Pro388 to Pro391 in the thumb subdomain of the polymerase. A yeast two-hybrid analysis using Pro388Ala and Pro391Ala mutants of NS5B confirmed the binding.

• Korean Journal of Microbiology
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• v.24 no.4
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• pp.400-405
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• 1986

We have constructed a phylogenetic tree for eleven species by comparing their tRNA sequences. The tree suggests that prokaryotes diverged very early before the emergence of animals. The fact that H. volcano, an archaebacterium, clusters with eukaryotes implied that eukaryotes did not diverge directly from thier common ancestor with eubacteria. The branching order of phage $T_{4}$ and phage $T_{5}$ indicates that they have diverged separately from thier hosts and they might have evolved independently. A correlation between nucleotide substitution in tRNAs and paleontological record was observed. We verified that our phylogenetic tree fits very well with traditional ones very well by imposing the molecular clock on the tree.

• Journal of Microbiology and Biotechnology
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• v.16 no.2
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• pp.303-307
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• 2006

We have screened phage display peptide libraries to select for peptides binding to various sized $TiO_2$ nanoparticles. Phage libraries displaying random 7mer, 12mer, and C-7-Cmer peptides were used for screening. The size of target $TiO_2$ particles used were 7 nm, 15 nm, and 25 nm in diameter. We could select peptides binding each nanoparticles from all 3 libraries. Their binding was confirmed by transmission electron microscopy (TEM). Each peptide investigated was also shown to bind the other sized particles, meaning that the binding was specific for the nature of the particle rather than for the size of it. One of the 7mer peptides (PEP9, SVSPISH) was chosen for further analysis. The binding was shown to be in a dose-dependent manner, suggesting a specific interaction.

• The Plant Pathology Journal
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• v.32 no.6
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• pp.584-588
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• 2016

Several Bacillus species were isolated from rice field soils, and 16S rRNA gene sequence analysis showed that Bacillus cereus was the most abundant. A strain named BC1 showed antifungal activity against Rhizoctonia solani. Bacteriophages infecting strain BC1 were isolated from the same soil sample. The isolated phage PK16 had an icosahedral head of $100{\pm}5nm$ and tail of $200{\pm}5nm$, indicating that it belonged to the family Myoviridae. Analysis of the complete linear dsDNA genome revealed a 158,127-bp genome with G + C content of 39.9% comprising 235 open reading frames as well as 19 tRNA genes (including 1 pseudogene). Blastp analysis showed that the proteins encoded by the PK16 genome had the closest hits to proteins of seven different bacteriophages. A neighbor-joining phylogenetic tree based on the major capsid protein showed a robust clustering of phage PK16 with phage JBP901 and BCP8-2 isolated from Korean fermented food.

• Journal of the Korean Society of Food Science and Nutrition
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• v.24 no.3
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• pp.466-469
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• 1995

The effect of lithium-ascorbate derivatives on viruses was investigated using a wide variety of bacterial viruses(phage). Lithium-ascorbate derivatives exerted an inactivating effect on all phages examined. Lithium-ascorbate derivatives have antiviral effects. The antiviral effect of lithium 2-o-octadecyl ascorbate was stronger than that of lithium ascorbate. Even at 10∼20 times lower concentration, the lithium 2-o-octadecyl ascorbate showed very much similar phage inactivating effect to that of ascorbate and lithium ascorbate.

• Journal of Microbiology
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• v.40 no.2
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• pp.134-139
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• 2002

Effects of GTP on the inhibition of self-splicing of primary transcripts of the phage T4 thymidylate synthase gene (td) by thiamine pyrophosphate and its analogs have been investigated. The order of the inhibitory efficiency for compounds tested was as follows: thiamine pyrophosphate > thiamine monophosphate > thiamine. of all compounds examined, thiamine pyrophosphate was the most potent inhibitor, Increasing GTP concentration in splicing reaction tended to overcome the suppressive effects of self-splicing by thiamine pyrophosphate and its analogs. The inhibition by thiamine pyrophosphate was most sensitized to a higher concentration of GTP, It has been speculated that the key structural features in thiamine pyrophosphate and its analogs responsible for the inhibition of splicing may be a thiamine moiety in which the phosphorylation of 2-hydroxylethyl group on 5-position of thiazolium ring rendered further stimulation of inhibition in self-splicing reaction..

• Genomics & Informatics
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• v.15 no.2
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• pp.69-80
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• 2017

In this study, cytolethal distending toxin (CDT) producer isolates genome were compared with genome of pathogenic and commensal Escherichia coli strains. Conserved genomic signatures among different types of CDT producer E. coli strains were assessed. It was shown that they could be used as biomarkers for research purposes and clinical diagnosis by polymerase chain reaction, or in vaccine development. cdt genes and several other genetic biomarkers were identified as signature sequences in CDT producer strains. The identified signatures include several individual phage proteins (holins, nucleases, and terminases, and transferases) and multiple members of different protein families (the lambda family, phage-integrase family, phage-tail tape protein family, putative membrane proteins, regulatory proteins, restriction-modification system proteins, tail fiber-assembly proteins, base plate-assembly proteins, and other prophage tail-related proteins). In this study, a sporadic phylogenic pattern was demonstrated in the CDT-producing strains. In conclusion, conserved signature proteins in a wide range of pathogenic bacterial strains can potentially be used in modern vaccine-design strategies.