CRP·cAMP-dependent Transcription Activation of the Escherichia coli pts PO Promoter by the Heat shock RNA Polymerase(Eσ³²) in Vitro

Ryu, Sangryeol Korean Society of Molecular Biology 1998 Molecules and cells Vol.8 No.5

Roles of the superoxide dismutase SodB and the catalase KatA in the antibiotic resistance of Campylobacter jejuni.

Hwang, Sunyoung,Ryu, Sangryeol,Jeon, Byeonghwa Japan Antibiotics Research Association 2013 Journal of antibiotics Vol.66 No.6

Bacteriophage PBC1 and Its Endolysin as an Antimicrobial Agent against <i>Bacillus cereus</i>

Kong, Minsuk,Ryu, Sangryeol American Society for Microbiology 2015 Applied and environmental microbiology Vol.81 No.7

<P><I>Bacillus cereus</I> is an opportunistic human pathogen responsible for food poisoning and other, nongastrointestinal infections. Due to the emergence of multidrug-resistant <I>B. cereus</I> strains, the demand for alternative therapeutic options is increasing. To address these problems, we isolated and characterized a <I>Siphoviridae</I> virulent phage, PBC1, and its lytic enzymes. PBC1 showed a very narrow host range, infecting only 1 of 22 <I>B. cereus</I> strains. Phylogenetic analysis based on the major capsid protein revealed that PBC1 is more closely related to the <I>Bacillus clarkii</I> phage BCJA1c and phages of lactic acid bacteria than to the phages infecting <I>B. cereus</I>. Whole-genome comparison showed that the late-gene region, including the terminase gene, structural genes, and holin gene of PBC1, is similar to that from <I>B. cereus</I> temperate phage 250, whereas their endolysins are different. Compared to the extreme host specificity of PBC1, its endolysin, LysPBC1, showed a much broader lytic spectrum, albeit limited to the genus <I>Bacillus</I>. The catalytic domain of LysPBC1 when expressed alone also showed <I>Bacillus</I>-specific lytic activity, which was lower against the <I>B. cereus</I> group but higher against the <I>Bacillus subtilis</I> group than the full-length protein. Taken together, these results suggest that the virulent phage PBC1 is a useful component of a phage cocktail to control <I>B. cereus</I>, even with its exceptionally narrow host range, as it can kill a strain of <I>B. cereus</I> that is not killed by other phages, and that LysPBC1 is an alternative biocontrol agent against <I>B. cereus</I>.</P>

Antirepression System Associated with the Life Cycle Switch in the Temperate <i>Podoviridae</i> Phage SPC32H

Kim, Minsik,Ryu, Sangryeol American Society for Microbiology 2013 Journal of virology Vol.87 No.21

<P>Prophages switch from lysogenic to lytic mode in response to the host SOS response. The primary factor that governs this switch is a phage repressor, which is typically a host RecA-dependent autocleavable protein. Here, in an effort to reveal the mechanism underlying the phenotypic differences between the <I>Salmonella</I> temperate phages SPC32H and SPC32N, whose genome sequences differ by only two nucleotides, we identified a new class of <I>Podoviridae</I> phage lytic switch antirepressor that is structurally distinct from the previously reported <I>Sipho</I>- and <I>Myoviridae</I> phage antirepressors. The SPC32H repressor (Rep) is not cleaved by the SOS response but instead is inactivated by a small antirepressor (Ant), the expression of which is negatively controlled by host LexA. A single nucleotide mutation in the consensus sequence of the LexA-binding site, which overlaps with the <I>ant</I> promoter, results in constitutive Ant synthesis and consequently induces SPC32N to enter the lytic cycle. Numerous potential Ant homologues were identified in a variety of putative prophages and temperate <I>Podoviridae</I> phages, indicating that antirepressors may be widespread among temperate phages in the order <I>Caudovirales</I> to mediate a prudent prophage induction.</P>

Characterization of a novel cell wall binding domain-containing Staphylococcus aureus endolysin LysSA97

Chang, Yoonjee,Ryu, Sangryeol Springer International 2017 Applied microbiology and biotechnology Vol.101 No.1

<P>Endolysin from Staphylococcus aureus phage SA97 (LysSA97) was cloned and investigated. LysSA97 specifically lyse the staphylococcal strains and effectively disrupted staphylococcal biofilms. Bioinformatic analysis of LysSA97 revealed a novel putative cell wall binding domain (CBD) as well as two enzymatically active domains (EADs) containing cysteine, histidine-dependent amidohydrolases/peptidases (CHAP, PF05257) and N-acetylmuramoyl-L-alanine amidase (Amidase-3, PF01520) domains. Comparison of 98 endolysin genes of S. aureus phages deposited in GenBank showed that they can be classified into six groups based on their domain composition. Interestingly, approximately 80.61 % of the staphylococcal endolysins have a src-homology 3 (SH3, PF08460) domain as CBD, but the remaining 19.39 %, including LysSA97, has a putative C-terminal CBD with no homology to the known CBD. The fusion protein containing green fluorescent protein and the putative CBD of LysSA97 showed a specific binding spectrum against staphylococcal cells comparable to SH3 domain (PF08460), suggesting that the C-terminal domain of LysSA97 is a novel CBD of staphylococcal endolysins.</P>

Effective inhibition of <i>Salmonella</i> Typhimurium in fresh produce by a phage cocktail targeting multiple host receptors

Bai, Jaewoo,Jeon, Byeonghwa,Ryu, Sangryeol Elsevier 2019 Food microbiology Vol.77 No.-

<P><B>Abstract</B></P> <P> <I>Salmonella</I> contamination of fresh produce is the primary bacterial cause of a significant number of foodborne outbreaks and infections. Bacteriophages can be used as natural antibacterial agents to control foodborne pathogens. However, the rapid development of bacterial resistance to phage infection is a significant barrier to practical phage application. To overcome this problem, we developed a novel phage cocktail consisting of the three phages (BSPM4, BSP101 and BSP22A) that target different host receptors, including flagella, O-antigen and BtuB, respectively. Whole genome sequence analysis of the phages revealed that three phages do not harbor genes involved in lysogen formation or toxin production, suggesting they are safe for use as biocontrol agents in foods. <I>In vitro</I> treatment of the phage cocktail resulted in a significant reduction in the development of bacterial resistance. Phage cocktail treatments achieved 4.7–5.5 log CFU/cm<SUP>2</SUP> reduction of viable cell number in iceberg lettuce and 4.8–5.8 log CFU/cm<SUP>2</SUP> reduction in cucumber after 12 h at room temperature (25 °C). The phage cocktail exhibited good antimicrobial efficiency, suggesting that it could reduce <I>S</I>. Typhimurium contamination of fresh produce. The strategy of developing cocktails of phages that target multiple host receptors can be used to develop novel biocontrol agents of <I>S</I>. Typhimurium.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Receptors of <I>Salmonella</I> Typhimurium-targeting bacteriophages were identified. </LI> <LI> A three-phage cocktail targeting different receptors was developed. </LI> <LI> Simultaneous targeting of three different receptors reduced the development of resistance. </LI> <LI> Phage cocktails represent promising biocontrol agents. </LI> </UL> </P>

Development of an Engineered Bioluminescent Reporter Phage for the Sensitive Detection of Viable <i>Salmonella</i> Typhimurium

Kim, Seongmi,Kim, Minsik,Ryu, Sangryeol American Chemical Society 2014 ANALYTICAL CHEMISTRY - Vol.86 No.12

<P>Because foodborne illnesses continuously threaten public health, rapid and sensitive detection of pathogens in food has become an important issue. As an alternative to time-consuming and laborious conventional detection methods, a technique using recombinant reporter phages has been developed. Here, we developed an advanced bioluminescent reporter phage SPC32H-CDABE by inserting a bacterial <I>luxCDABE</I> operon into the <I>Salmonella</I> temperate phage SPC32H genome. Whole SPC32H genome sequencing enabled the selection of nonessential genes, which can be replaced with approximately 6-kb <I>luxCDABE</I> operon, which provides both luciferase (LuxAB) and its substrate, fatty aldehyde, as generated by fatty acid reductase (LuxCDE). Thus, the SPC32H-CDABE detection assay is simpler and more efficient compared to the <I>luxAB</I>-based assay because the substrate addition step is excluded. At least 20 CFU/mL of pure <I>S.</I> Typhimurium culture was detectable using SPC32H-CDABE within 2 h, and the signals increased proportionally to the number of cells contaminated in lettuce, sliced pork, and milk. These results thereby demonstrate that this phage successfully detects live <I>Salmonella</I> without appreciable interference from food components. Furthermore, the presented data suggest that SPC32H-CDABE represents a promising easy-to-use diagnostic tool for the detection of <I>Salmonella</I> contamination in food.</P><P><B>Graphic Abstract</B> <IMG SRC='http://pubs.acs.org/appl/literatum/publisher/achs/journals/content/ancham/2014/ancham.2014.86.issue-12/ac500645c/production/images/medium/ac-2014-00645c_0005.gif'></P><P><A href='http://pubs.acs.org/doi/suppl/10.1021/ac500645c'>ACS Electronic Supporting Info</A></P>

A Comparative Evaluation of Radiation-Induced DNA Damage using Real-Time PCR: Influence of Base Composition

Lim, Sangyong,Yoon, Hyunjin,Ryu, Sangryeol,Jung, Jinwoo,Lee, Myungchul,Kim, Dongho Academic Press 2006 Radiation research Vol.165 No.4

Lim, S., Yoon, H., Ryu, S., Jung, J., Lee, M. and Kim, D. A Comparative Evaluation of Radiation-Induced DNA Damage using Real-Time PCR: Influence of Base Composition. Radiat. Res. 165, 430??437 (2006).To study the radiosensitivity of DNA segments at the open reading frame (gene) level, real-time PCR was used to analyze DNA damages induced by ionizing radiation. After irradiation (1, 3 and 5 kGy) of genomic DNA purified from Salmonella typhimurium, real-time PCR based on SYBR Green fluorescence and melting temperature was performed using various primer sets targeting the rfbJ, rfaJ, rfaB, hilD, ssrB, pipB, sopD, pduQ, eutG, oadB, ccmB and ccmA genes. The ccmA and ccmB genes, which existed as two copies on the chromosome and had a high GC content (??0%), showed much lower radiosensitivities than the other genes tested, particularly at 5 kGy; this distinctive feature was seen only when the genes were located on the chromosome, regardless of copy number. Our results reinforce the concept that gene sensitivity to ionizing radiation depends on the base composition and/or the spatial localization of the gene on the chromosome.

Characterization of LysPBC4, a novel<i>Bacillus cereus</i>-specific endolysin of bacteriophage PBC4

Na, Hongjun,Kong, Minsuk,Ryu, Sangryeol,Millard, Andrew Oxford University Press 2016 FEMS microbiology letters Vol.363 No.12

Complete genome sequence of enterobacteria phage 4MG, a new member of the subgroup “PVP-SE1-like phage” of the “rV5-like viruses”

Kim, Minsik,Heu, Sunggi,Ryu, Sangryeol Springer-Verlag 2014 Archives of virology Vol.159 No.11