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Choi Wonho,Kim Jae-hui,Lee Ju Seok,Park Jung-Ho 대한독성 유전단백체 학회 2023 Molecular & cellular toxicology Vol.19 No.3
Backgrounds Almost all bacteria harbor toxin–antitoxin (TA) systems on their chromosomes, which are associated with diverse biological roles such as stress response, cell physiology, biofi lm formation, and programmed cell death. Pseudomonas cichorii JBC1 has a diverse host range and can cause disease in a wide range of plant species. Under favorable environmental conditions, the bacterium can cause severe disease in nearly all of the crops that have been described. However, TA systems have not been determined. Objective This study aimed to identify the TA system of P. cichorii JBC1 genome based on the cell toxicity of Escherichia coli regulated by TA systems and to evaluate the mRNA expression levels under various stressful growth conditions. Results Among 11 putative TA pairs predicted from the P. cichorii JBC1 genome by in silico analysis, two toxins, PCH70- 01,410 and − 16,540, caused cell growth arrest and cell death in E. coli , and the toxicity of PCH70-01,410 and − 16,540 was neutralized by its cognate antitoxin candidates, PCH70-01,400 and − 16,550 in PCH70-01,400/01410 and PCH70- 16,550/16540 TA complexes, respectively. Moreover, mRNA expression levels of PCH70-01,400/01410 and PCH70- 16,550/16540 diff ered under various stresses (i.e., oxidative, acidic, and heat shocks). Conclusion Two TA systems, PCH70-01,400/01410 and PCH70-16,550/16540, were identifi ed in P. cichorii JBC 1. These TA systems show diff erent toxin and antitoxin mRNA expression levels according to stressful growth conditions, including oxidative, acidic, and heat shocks in E. coli .
( Wonho Choi ),( Min-ho Yoon ),( Jung-ho Park ) 한국미생물생명공학회(구 한국산업미생물학회) 2018 Journal of microbiology and biotechnology Vol.28 No.6
Bacterial programmed cell death is regulated by the toxin-antitoxin (TA) system. YhaV (toxin) and Pr1F (antitoxin) have been recently identified as a type II TA system in Escherichia coli. YhaV homologs have conserved active residues within the C-terminus, and to characterize the function of this region, we purified native YhaV protein (without denaturing) and constructed YhaV proteins of varying lengths. Here, we report a new low-temperature method of purifying native YhaV, which is notable given the existing challenges of purifying this highly toxic protein. The secondary structures and thermostability of the purified native protein were characterized and no significant structural destruction was observed, suggesting that the observed inhibition of cell growth in vivo was not the result of structural protein damage. However, it has been reported that excessive levels of protein expression may result in protein misfolding and changes in cell growth and mRNA stability. To exclude this possibility, we used an [<sup>35</sup>S]-methionine prokaryotic cell-free protein synthesis system in vitro in the presence of purified YhaV, and two C-terminal truncated forms of this protein (YhaV-L and YhaV-S). Our results suggest that the YhaV C-terminal region is essential for mRNA interferase activity, and the W143 or H154 residues may play an analogous role to Y87 of RelE.
Choi, Byoung-Ju,Lee, Jung A,Choi, Jae-Sung,Park, Jong-Gyu,Lee, Sang-Ho,Yih, Wonho Pergamon Press 2017 Chemosphere Vol.173 No.-
<P><B>Abstract</B></P> <P>Hydrographic observation and biological samplings were conducted to assess the distribution of phytoplankton community over the sloping shelf of the eastern Yellow Sea in May 2012. The concentration of chlorophyll <I>a</I> was determined and phytoplankton was microscopically examined to conduct quantitative and cluster analyses. A cluster analysis of the phytoplankton species and abundance along four observation lines revealed the three-dimensional structure of the phytoplankton community distribution: the coastal group in the mixed region, the offshore upper layer group preferring stable water column, and the offshore lower layer group. The subsurface maximum of phytoplankton abundance and chlorophyll <I>a</I> concentration appeared as far as 64 km away from the tidal front through the middle layer intrusion. The phytoplankton abundance was high in the shore side of tidal front during the spring tide. The phytoplankton abundance was relatively high at 10-m depth in the mixed region while the concentration of chlorophyll <I>a</I> was high below the depth. The disparity between the profiles of the phytoplankton abundance and the chlorophyll <I>a</I> concentration in the mixed region was related to the depth-dependent species change accompanied by size-fraction of the phytoplankton community.</P> <P><B>Highlights</B></P> <P> <UL> <LI> Physical environment, chlorophyll concentration and phytoplankton community were investigated in the eastern Yellow Sea. </LI> <LI> Three-dimensional structure of phytoplankton communities was identified in the tidal front region. </LI> <LI> Phytoplankton abundance and chlorophyll <I>a</I> concentration were high in the shore side of the front during the spring tide. </LI> <LI> Subsurface maximum of phytoplankton abundance appeared about 64 km away from the front through the middle layer intrusion. </LI> <LI> Profiles of phytoplankton abundance and chlorophyll <I>a</I> concentration were different due to depth-dependent species change. </LI> </UL> </P>
Translation-dependent mRNA cleavage by YhaV in <i>Escherichia coli</i>
Choi, Wonho,Yamaguchi, Yoshihiro,Lee, Jae-Woo,Jang, Kyung-Min,Inouye, Masayori,Kim, Sung-Gun,Yoon, Min-Ho,Park, Jung-Ho North-Holland Pub 2017 FEBS letters Vol. No.
<P>Many bacteria have toxin-antitoxin (TA) systems, where toxin gene expression inhibits their own cell growth. mRNA is one of the well-known targets of the toxins in the type II toxin-antitoxin systems. Here, we examined the ribosome dependency of the endoribonuclease activity of YhaV, one of the toxins in type II TA systems, on mRNA in vitro and in vivo. A polysome profiling assay revealed that YhaV is bound to the 70S ribosomes and 50S ribosomal subunits. Moreover, we found that while YhaV cleaves ompF and lpp mRNAs in a translation-dependent manner, they did not cleave the 5' untranslated region in primer extension experiments. From these results, we conclude that YhaV is a ribosome-dependent toxin that cleaves mRNA in a translation-dependent manner.</P>
Choi Wonho,Maharjan Anoth,Im Hae Gang,Park Ji-Young,Park Jong-Tae,Park Jung-Ho 한국미생물학회 2023 The journal of microbiology Vol.61 No.4
Toxin-antitoxin (TA) systems are widespread in bacteria and archaea plasmids and genomes to regulate DNA replication, gene transcription, or protein translation. Higher eukaryotic and prokaryotic nucleotide-binding (HEPN) and minimal nucleotidyltransferase (MNT) domains are prevalent in prokaryotic genomes and constitute TA pairs. However, three gene pairs (MTH304/305, 408/409, and 463/464) of Methanothermobacter thermautotropicus ΔH HEPN-MNT family have not been studied as TA systems. Among these candidates, our study characterizes the MTH463/MTH464 TA system. MTH463 expression inhibited Escherichia coli growth, whereas MTH464 did not and blocked MTH463 instead. Using site-directed MTH463 mutagenesis, we determined that amino acids R99G, H104A, and Y106A from the R[ɸX]4-6H motif are involved with MTH463 cell toxicity. Furthermore, we established that purified MTH463 could degrade MS2 phage RNA, whereas purified MTH464 neutralized MTH463 activity in vitro. Our results indicate that the endonuclease toxin MTH463 (encoding a HEPN domain) and its cognate antitoxin MTH464 (encoding the MNT domain) may act as a type II TA system in M. thermautotropicus ΔH. This study provides initial and essential information studying TA system functions, primarily archaea HEPN-MNT family.
Reference Evapotranspiration Calculator Software를 이용한 기상관측소 기준증발산 추정
최원호(Choi Wonho),최민하(Choi Minha),오현제(Oh Hyunje),박주양(Park Jooyang) 대한토목학회 2010 대한토목학회논문집 B Vol.30 No.2B
Reference Evapotranspiration Calculator Software (REF-ET)는 ASCE 및 FAO 기준증발산량을 포함한 총 17개의 FAO Penman-Monteith (PM) 방정식의 연산을 동시에 수행할 수 있는 프로그램으로서, 본 연구에서는 REF-ET에 대한 상세한 소개와 함께 기상관측소의 관측지료를 이용하여 REF-ET의 효용성을 논하였다. REF-ET는 각종 PM 방정식들에 대한 시일 월 단위 모의와 지역적 특성의 반영 및 결측자료에 대한 보정 등이 가능하다. REF-ET를 이용하여 서울 기상관측소의 29년간 증발산량을 모의한 결과, 일복사량에 주로 좌우되는 FAO24-Rd 식과 1957-Makk 식의 상관계수가 각각 0.89와 0.88로 높게 나타났으며, 이는 소형증발접시를 이용한 기준증발산량 관측값이 공기 동력학적 증발량만을 주로 반영하기 때문인 것으로 사료된다. 또한 RMSE/bias 분석을 통해 기준증발산 방정식들에 의한 계산값이 증발접시로부터의 기준증발산량에 비해 다소 과대평가되는 현상을 나타내었으나, 이 경우에도 1957-Makk 식이 가장 정확한 것으로 나타났다. 일단위 시계열 분석시 1957-Makk 식은 여름철의 증발산량을 저평가하는 경향을 나타내었으나, 전체적으로 1.06 ㎜/day의 오차로 증발산량을 모의 가능하였다. 차후 기상관측자료의 정확도를 높이는 연구들과 REF-ET를 병행한다면, 해당 지역 및 기간에 대한 증발산량 모의 및 관련 특성인자를 파악하는 연구에 활용도가 높을 것으로 기대된다. The Reference Evapotranspiration Calculator Software (REF-ET) supports computational guidelines for the reference evapotranspiration using seventeen FAO Penman-Monteith (PM) equations simultaneously such as the ASCE and FAO standardized forms. The REF-ET can conveniently consider missing data predictions and regional site characterizations, when reference ET is computed on monthly, daily, and hourly time steps. The applicability of the REF-ET was estimated to simulate the reference ET using hourly weather data from Seoul weather station for 29 years. The result found that the FAO24-Rd and 1957-Makk equations closely concerned with solar radiation parameter which were the most highly correlated to reference ET computed by pan coefficient. In addition, the 1957-Makk equation was identified as the most correct computational method for reference ET by analysis of bias and root mean square error. The 1957-Makk equation could predict the reference ET within the error of less than 1.06 ㎜/day, though all the other equations tended toward overestimation of predicting the reference ET in comparison with refecence ET of pan. The results of this study suggest that the REF-ET will be applicable to support reference ET estimation for a variety of field condition and time-scale.