Genome wide analysis of rice blast pathogen, Magnaporthe oryzae, in Korea

Yoonhee KIM,Hyejeong KIM,Jinsoo KIM,Miyeon JEONG,Soyoung PARK,Suyoung KIM,Jongsun Park,Soonok KIM,Yong-Hwan LEE,Seong Sook HAN,Jae Hwan ROH,Woobong CHOI 한국작물학회 2007 한국작물학회 학술발표대회 논문집 Vol.2007 No.11

Magnaporthe oryzae is a causal pathogen of the rice blast, the most destructive disease of rice worldwide. This ascomycete fungus has been intensively studied as a model organism in plant-pathogen interactions. Recently, the genome sequence of M. oryzae 70-15 was published by International Rice Blast Consortium. This led us to investigate comparative and functional analysis of this pathogen at genome-wide level. As a first step, sequencing project of M. oryzae Korean strain KJ201 was launched to face practical interests on diversity of plant pathogens. We constructed a fosmid library with a copy number controllable pCC1 vector. Over 13,000 end reads from 6637 fosmid clones were generated and anchored on genome sequence of the strain 70-15. Currently, 9,793 end reads, in which 2.684, clones with both ends and 1,757 clones with on end matched, are aligned to the sequence of strain 70-15. In the next step, shotgun sequencing of fosmid clones was conducted for fine scale comparative analysis of chromosome 7 that is well defined in genome sequencing of 70-15. Totally 119 fosmid clones were pooled in region and analyzed. For reasonable intra-species comparison in genome of M. oryzae, two strains, KJ201 and Guy11, were chosen for whole genome shotgun sequencing analysis with GS454 FLX system. About 8X genome coverage sequences were obtained for each strain and being merged for comparative analysis. Genome information of other strains is being also available from China and Japanese research groups and could be joined together for extended comparative analysis and the results give more detail in genome diversity in species level.

국화과 고유식물 10종 종자의 형태적 특성 및 온도별 발아조건

김수진(Su-jin Kim),김유리(Yu-ri Kim),김순미(Sun-mi Kim),조성현(Seong-hyeon Cho),염진화(Jinhwoa Yeom),김순옥(Soonok Kim),김원희(Won-hee Kim) 한국원예학회 2023 한국원예학회 학술발표요지 Vol.2023 No.10

<i>MHP1</i>, a <i>Magnaporthe grisea</i> hydrophobin gene, is required for fungal development and plant colonization

Kim, Soonok,Ahn, Il‐,Pyung,Rho, Hee‐,Sool,Lee, Yong‐,Hwan Blackwell Science Ltd 2005 Molecular microbiology Vol.57 No.5

<P><B>Summary</B></P><P>Fungal hydrophobins are implicated in cell morphogenesis and pathogenicity in several plant pathogenic fungi including the rice blast fungus <I>Magnaporthe grisea</I>. A cDNA clone encoding a hydrophobin (magnaporin, <I>MHP1</I>) was isolated from a cDNA library constructed from rice leaves infected by <I>M. grisea</I>. The <I>MHP1</I> codes for a typical fungal hydrophobin of 102 amino acids containing eight cysteine residues spaced in a conserved pattern. Hydropathy analysis of amino acids revealed that MHP1 belongs to the class II group of hydrophobins. The amino acid sequence of MHP1 exhibited about 20% similarity to MPG1, an <I>M. grisea</I> class I hydrophobin. Expression of <I>MHP1</I> was highly induced during plant colonization and conidiation, but could hardly be detected during mycelial growth. Transformants in which <I>MHP1</I> was inactivated by targeted gene replacement showed a detergent wettable phenotype, but were not altered in wettability with water. <I>mhp1</I> mutants also exhibited pleiotropic effects on fungal morphogenesis, including reduction in conidiation, conidial germination, appressorium development and infectious growth in host cells. Furthermore, conidia of <I>mhp1</I> mutants were defective in their cellular organelles and rapidly lose viability. As a result, <I>mhp1</I> mutants exhibited a reduced ability to infect and colonize a susceptible rice cultivar. These phenotypes were recovered by re‐introduction of an intact copy of <I>MHP1</I>. Taken together, these results indicate that <I>MHP1</I> has essential roles in surface hydrophobicity and infection‐related fungal development, and is required for pathogenicity of <I>M. grisea</I>.</P>

Local Atomic Structure and Amorphization of Tungsten Doped Ceria/Titania

Kim, Soonok,Jo, Seung-Hyeon,Cho, Dae-Seung,Lee, Heesoo American Scientific Publishers 2018 Nanoscience and nanotechnology letters Vol.10 No.5

The complete chloroplast genome of <i>Eleutherococcus gracilistylus</i> (W.W.Sm.) S.Y.Hu (Araliaceae)

Kim, Kyunghee,Lee, Junki,Lee, Sang-Choon,Kim, Nam-Hoon,Jang, Woojong,Kim, Soonok,Sung, Sangmin,Lee, Jungho,Yang, Tae-Jin Informa UK (Informa Healthcare) 2016 Mitochondrial DNA. Part A Vol.27 No.5

Combining ChIP-chip and Expression Profiling to Model the MoCRZ1 Mediated Circuit for Ca ²⁺ /Calcineurin Signaling in the Rice Blast Fungus

Kim, Soonok,Hu, Jinnan,Oh, Yeonyee,Park, Jongsun,Choi, Jinhee,Lee, Yong-Hwan,Dean, Ralph A.,Mitchell, Thomas K. Public Library of Science 2010 PLoS pathogens Vol.6 No.5

<▼1><P>Significant progress has been made in defining the central signaling networks in many organisms, but collectively we know little about the downstream targets of these networks and the genes they regulate. To reconstruct the regulatory circuit of calcineurin signal transduction via <I>MoCRZ1</I>, a <I>Magnaporthe oryzae</I> C2H2 transcription factor activated by calcineurin dephosphorylation, we used a combined approach of chromatin immunoprecipitation - chip (ChIP-chip), coupled with microarray expression studies. One hundred forty genes were identified as being both a direct target of MoCRZ1 and having expression concurrently differentially regulated in a calcium/calcineurin/MoCRZ1 dependent manner. Highly represented were genes involved in calcium signaling, small molecule transport, ion homeostasis, cell wall synthesis/maintenance, and fungal virulence. Of particular note, genes involved in vesicle mediated secretion necessary for establishing host associations, were also found. <I>MoCRZ1</I> itself was a target, suggesting a previously unreported autoregulation control point. The data also implicated a previously unreported feedback regulation mechanism of calcineurin activity. We propose that calcium/calcineurin regulated signal transduction circuits controlling development and pathogenicity manifest through multiple layers of regulation. We present results from the ChIP-chip and expression analysis along with a refined model of calcium/calcineurin signaling in this important plant pathogen.</P></▼1><▼2><P><B>Author Summary</B></P><P>All organisms have the innate ability to perceive their environment and respond to it, largely through controlling gene expression. Tailored specificity of a response is primarily achieved through signal cascades involving unique receptors, downstream transcription factors (proteins that bind to DNA to regulate gene expression), and the genes these transcription factors regulate. For fungal plant pathogens, signal transduction cascades are involved in perception of hosts, transgression of physical barriers, suppression or elicitation of host defenses, <I>in vivo</I> nutrient acquisition, and completion of their life cycle. We know that the Ca<SUP>2+</SUP>/calcineurin signaling pathway is a central conduit regulating these aspects of the life cycle for fungal pathogens of plants and animals. In this study, we used advanced ChIP-chip and microarray gene expression technologies to identify the genes that the Ca<SUP>2+</SUP>/calcineurin responsive transcription factor MoCRZ1 directly binds to and regulates the expression of. Our findings show conservations and divergence in this pathway within the fungal kingdom. It also identifies points of control in the pathway that were previously unidentified. Most importantly, this study implicates this pathway in the establishment of host associations and virulence for the causal agent of rice blast disease, <I>Magnaporthe oryzae</I>, the most important disease of rice worldwide.</P></▼2>

우리나라 직물의 상품명을 중심으로 한 조사

김애리,오순실,최경희,박영신,현순옥,김명수,김옥섭,유희옥 연세대학교 생활과학대학 1975 婦學 Vol.8 No.-

Improvement of Storage Stability of Meatballs Using Propolis

SoonOk Woo,Sung-Kuk Kim,Sangmi Han,Se Gun Kim,Kyung Won Bang,Hye Ri Jang,Hyo Jung Moon,Hyun Ji Kim 한국식품영양과학회 2018 한국식품영양과학회 학술대회발표집 Vol.2018 No.10

Perspectives provided by leopard and other cat genomes: how diet determined the evolutionary history of carnivores, omnivores, and herbivores

( Soonok Kim ),( Yun Sung Cho ),( Jong Bhak ),( Stephen J. O`brian ),( Joo-hong Yeo ) 생화학분자생물학회(구 한국생화학분자생물학회) 2017 BMB Reports Vol.50 No.1

Recent advances in genome sequencing technologies have enabled humans to generate and investigate the genomes of wild species. This includes the big cat family, such as tigers, lions, and leopards. Adding the first high quality leopard genome, we have performed an in-depth comparative analysis to identify the genomic signatures in the evolution of felid to become the top predators on land. Our study focused on how the carnivore genomes, as compared to the omnivore or herbivore genomes, shared evolutionary adaptations in genes associated with nutrient metabolism, muscle strength, agility, and other traits responsible for hunting and meat digestion. We found genetic evidence that genomes represent what animals eat through modifying genes. Highly conserved genetically relevant regions were discovered in genomes at the family level. Also, the Felidae family genomes exhibited low levels of genetic diversity associated with decreased population sizes, presumably because of their strict diet, suggesting their vulnerability and critical conservation status. Our findings can be used for human health enhancement, since we share the same genes as cats with some variation. This is an example how wildlife genomes can be a critical resource for human evolution, providing key genetic marker information for disease treatment. [BMB Reports 2017; 50(1): 3-4]

중국의 반부패 조직기구와 법률체계를 통해 본 법치주의

김순옥 ( Soonok Kim ) 사단법인 아시아문화학술원 2020 인문사회 21 Vol.11 No.3

중국은 90년대 후반 이후 줄곧 법치주의를 표방해오면서 반부패법에도 이를 적용시키는 제도화의 노력을 하고 있다. 이 연구에서는 당정의 반부패 조직기구 운영과 법률체계를 통해 중국의 법치주의 단계를 파악하고자 한다. 본 연구는 세 가지 분석을 시도한다. 첫째, 당정 및 사법기관의 반부패 조직기구를 살펴보고 둘째, 기율위원회와 검찰원 법원의 관계를 파악하고 셋째, 반부패법의 법률체계를 분석할 것이다. 연구결과에 의하면 반부패 기구는 당정과 사법권에 포진돼 있으며 중국공산당의 기율위원회가 최상위 기관의 기능을 수행하고 있다. 기율위원회와 검찰원 법원의 관계에서 사법권의 독립성이 제대로 확보되지 못하고 의존적인 관계가 지속되고 있다. 반부패법은 다른 법체계로 대체되고 있으며 당의 규율이 최상위법에 위치해 있다. 현재의 중국 반부패 법치주의 정도는 당의 통치와 제도가 혼합된 형태라고 판단된다. 중국당국이 추구하는 법치주의 실현을 통한 민주사회 달성을 위해서 광범위한 법치체계의 개혁이 지속적으로 필요하다. Since the late 1990’s China has made efforts to keep up with the rule of law by trying to institutionalize anti-corruption laws. This study intends to investigate the stage of Chinese rule of law through the operation of the anti-corruption organization and the legal system run by the government and its ruling party. For the specific content of analysis the paper focuses on three aspects; (1) the anti-corruption organizations of the government-ruling party and judicial institutions; (2) understanding the relation between the Discipline Committee and the prosecution; (3) looking into the legal system of anti-corruption laws. Research results indicate that the anti-corruption organization is controlled under the government-ruling party and the judicial branch while the Discipline Committee of the Chinese Communist Party is at the top. The relationship between the Discipline Committee and the provincial council and the prosecutor’s court forms a dependable relationship. The anti-corruption laws are replaced by other legal systems, and the ruling party’s rules have the highest authority. Accordingly, what is acknowledged through the level of the rule of law of China’s anti-corruption legal system is that it represents a combination of the ruling party’s rule and system. Therefore, in order to achieve a democratic society through the realization of the rule of law, expansive progress of reforming the legal system seems to be in demand.