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Article ; Online: Effects of Abscisic Acid and Salicylic Acid on Gene Expression in the Antiviral RNA Silencing Pathway in Arabidopsis

Mazen Alazem / Kook-Hyung Kim / Na-Sheng Lin

International Journal of Molecular Sciences, Vol 20, Iss 10, p

2019 Volume 2538

Abstract: The RNA silencing pathways modulate responses to certain stresses, and can be partially tuned by several hormones such as salicylic acid (SA) and abscisic acid (ABA). Although SA and ABA are often antagonistic and often modulate different stress ... ...

Abstract	The RNA silencing pathways modulate responses to certain stresses, and can be partially tuned by several hormones such as salicylic acid (SA) and abscisic acid (ABA). Although SA and ABA are often antagonistic and often modulate different stress responses, they have similar effects on virus resistance, which are partially achieved through the antiviral RNA silencing pathway. Whether they play similar roles in regulating the RNA silencing pathway is unclear. By employing coexpression and promoter analyses, we found that some ABA- and SA-related transcription factors (TFs) are coexpressed with several AGO , DCL , and RDR genes, and have multiple binding sites for the identified TFs in the queried promoters. ABA and SA are antagonistic with respect to the expression of AGO1 and RDRs because ABA was able to induce these genes only in the SA mutant. Nevertheless, both hormones showed similarities in the regulation of other genes, for example, the induction of AGO2 by ABA was SA-dependent, indicating that ABA acts upstream of SA in this regulation. We inferred that the similar effects of ABA and SA on some genes resulted in the redundancy of their roles in resistance to bamboo mosaic virus, but that the two hormones are antagonistic with respect to other genes unrelated to their biosynthesis pathways.
Keywords	abscisic acid ; salicylic acid ; crosstalk ; RNA silencing pathway ; bamboo mosaic virus ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	570
Language	English
Publishing date	2019-05-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Comparative Study of Metagenomics and Metatranscriptomics to Reveal Microbiomes in Overwintering Pepper Fruits

Yeonhwa Jo / Chang-Gi Back / Kook-Hyung Kim / Hyosub Chu / Jeong Hun Lee / Sang Hyun Moh / Won Kyong Cho

International Journal of Molecular Sciences, Vol 22, Iss 6202, p

2021 Volume 6202

Abstract: Red pepper ( Capsicum annuum , L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA ... ...

Abstract	Red pepper ( Capsicum annuum , L.), is one of the most important spice plants in Korea. Overwintering pepper fruits are a reservoir of various microbial pepper diseases. Here, we conducted metagenomics (DNA sequencing) and metatranscriptomics (RNA sequencing) using samples collected from three different fields. We compared two different library types and three different analytical methods for the identification of microbiomes in overwintering pepper fruits. Our results demonstrated that DNA sequencing might be useful for the identification of bacteria and DNA viruses such as bacteriophages, while mRNA sequencing might be beneficial for the identification of fungi and RNA viruses. Among three analytical methods, KRAKEN2 with raw data reads (KRAKEN2_R) might be superior for the identification of microbial species to other analytical methods. However, some microbial species with a low number of reads were wrongly assigned at the species level by KRAKEN2_R. Moreover, we found that the databases for bacteria and viruses were better established as compared to the fungal database with limited genome data. In summary, we carefully suggest that different library types and analytical methods with proper databases should be applied for the purpose of microbiome study.
Keywords	pepper ; fruit ; microbiome ; bacteria ; fungi ; viruses ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using RNA-Sequencing Data to Examine Tissue-Specific Garlic Microbiomes

Yeonhwa Jo / Chang-Gi Back / Kook-Hyung Kim / Hyosub Chu / Jeong Hun Lee / Sang Hyun Moh / Won Kyong Cho

International Journal of Molecular Sciences, Vol 22, Iss 6791, p

2021 Volume 6791

Abstract: Garlic ( Allium sativum ) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in ... ...

Abstract	Garlic ( Allium sativum ) is a perennial bulbous plant. Due to its clonal propagation, various diseases threaten the yield and quality of garlic. In this study, we conducted in silico analysis to identify microorganisms, bacteria, fungi, and viruses in six different tissues using garlic RNA-sequencing data. The number of identified microbial species was the highest in inflorescences, followed by flowers and bulb cloves. With the Kraken2 tool, 57% of identified microbial reads were assigned to bacteria and 41% were assigned to viruses. Fungi only made up 1% of microbial reads. At the species level, Streptomyces lividans was the most dominant bacteria while Fusarium pseudograminearum was the most abundant fungi. Several allexiviruses were identified. Of them, the most abundant virus was garlic virus C followed by shallot virus X. We obtained a total of 14 viral genome sequences for four allexiviruses. As we expected, the microbial community varied depending on the tissue types, although there was a dominant microorganism in each tissue. In addition, we found that Kraken2 was a very powerful and efficient tool for the bacteria using RNA-sequencing data with some limitations for virome study.
Keywords	pepper ; fruit ; microbiome ; bacteria ; fungi ; viruses ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Five Questions about Mycoviruses.

Moonil Son / Jisuk Yu / Kook-Hyung Kim

PLoS Pathogens, Vol 11, Iss 11, p e

2015 Volume 1005172

Keywords	Immunologic diseases. Allergy ; RC581-607 ; Biology (General) ; QH301-705.5
Language	English
Publishing date	2015-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: A plant intron enhances the performance of an infectious clone in planta

Tran, Phu-Tri / Miao Fang / Kristin Widyasari / Kook-Hyung Kim

Journal of virological methods. 2019 Mar., v. 265

2019

Abstract: Although infectious clones are fundamental tools in virology and plant pathology, their efficacy is often reduced by the instability of viral sequences in Escherichia coli. In this study, we constructed an infectious clone of PepMoV (pPepMoV) in a ... ...

Abstract	Although infectious clones are fundamental tools in virology and plant pathology, their efficacy is often reduced by the instability of viral sequences in Escherichia coli. In this study, we constructed an infectious clone of PepMoV (pPepMoV) in a bacterial binary vector (pSNU1); the clone induces symptoms of PepMoV in agroinfiltrated plants. During its modification and maintenance in E. coli, however, the pPepMoV infectious clone was instable in the bacteria. Manipulation of this unstable clone in the bacterial strain DH10B led to the spontaneous formation of a recombined clone with high stability in the bacteria but with reduced infectivity due to an unwanted insertion of an E. coli sequence in the NIa-protease coding region. Replacement of this sequence with a plant intron restored infectivity and maintained plasmid stability. In addition to restoring plasmid growth in both E. coli and Agrobacterium, the presence of the intron in the PepMoV sequence enhanced the accumulation of PepMoV in agroinfiltrated leaves and resulted in symptom induction in upper systemic leaves that was nearly as strong as with PepMoV sap-inoculation. Plant introns have been previously used to stabilize plasmids in E. coli without any effect or with an unexpected lag in symptom development. In contrast, the current results demonstrated the in vivo enhancement of an infectious clone by a plant intron.
Keywords	Agrobacterium ; Escherichia coli ; bacteria ; clones ; enzymes ; introns ; leaves ; pathogenicity ; plant pathology ; plasmids ; virology
Language	English
Dates of publication	2019-03
Size	p. 26-34.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2018.12.012
Database	NAL-Catalogue (AGRICOLA)

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Article: Identification of residues or motif(s) of the rice stripe virus NS3 protein required for self-interaction and for silencing suppressor activity

Kim, Hangil / Won Kyong Cho / Sen Lian / Kook-Hyung Kim

Virus research. 2017 May 02, v. 235

2017

Abstract: Rice stripe virus (RSV) is an important pathogen of rice. The RSV genome consists of four single-stranded RNA segments that encode seven viral proteins. A previous report found that NS3 is a viral suppressor of RNA silencing and self interacts. Using a ... ...

Abstract	Rice stripe virus (RSV) is an important pathogen of rice. The RSV genome consists of four single-stranded RNA segments that encode seven viral proteins. A previous report found that NS3 is a viral suppressor of RNA silencing and self interacts. Using a model that predicts protein structure, we identified amino acid residues or motifs, including four Î±-helix motifs, required for NS3 self-interaction. We then used yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays to study the interactions between full-length NS3 and its truncated and alanine substitution mutants. Y2H and BiFC results showed that the N-terminal region of NS3 is essential for self-interaction. All Î±-helix deletion mutants and substitution mutants lost the ability to self-interact. To identify the relationship between NS3 self-interaction and silencing suppressor activity, we used a GFP silencing system in Nicotiana benthamiana with Agrobacterium-mediated transient overexpression of each mutated NS3 protein. All of the deletion and the Î±-helix substitution mutants that had lost the ability to self-interact also lost their silencing suppressor ability. The substitution of amino acids with alanine at positions 70â75, 76â83, and 173â177, however, resulted in mutants that were able to self-interact but were unable to function as silencing suppressors. These results suggest that RSV requires NS3 self-interaction to suppress RNA silencing and to thereby counter host defenses.
Keywords	Nicotiana benthamiana ; RNA ; RNA interference ; Rice stripe virus ; alanine ; fluorescence ; genome ; models ; mutants ; pathogens ; protein structure ; rice ; two hybrid system techniques ; viral proteins
Language	English
Dates of publication	2017-0502
Size	p. 14-23.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2017.03.022
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Time-Course Small RNA Profiling Reveals Rice miRNAs and Their Target Genes in Response to Rice Stripe Virus Infection.

Sen Lian / Won Kyong Cho / Sang-Min Kim / Hoseong Choi / Kook-Hyung Kim

PLoS ONE, Vol 11, Iss 9, p e

2016 Volume 0162319

Abstract: It has been known that many microRNAs (miRNAs) are involved in the regulation for the plant development and defense mechanism by regulating the expression of the target gene. Several previous studies has demonstrated functional roles of miRNAs in ... ...

Abstract	It has been known that many microRNAs (miRNAs) are involved in the regulation for the plant development and defense mechanism by regulating the expression of the target gene. Several previous studies has demonstrated functional roles of miRNAs in antiviral defense mechanisms. In this study, we employed high-throughput sequencing technology to identify rice miRNAs upon rice stripe virus (RSV) infection at three different time points. Six libraries from mock and RSV-infected samples were subjected for small RNA sequencing. Bioinformatic analyses revealed 374 known miRNAs and 19 novel miRNAs. Expression of most identified miRNAs was not dramatically changed at 3 days post infection (dpi) and 7 dpi by RSV infection. However, many numbers of miRNAs were up-regulated in mock and RSV-infected samples at 15 dpi by RSV infection. Moreover, expression profiles of identified miRNAs revealed that only few numbers of miRNAs were strongly regulated by RSV infection. In addition, 15 resistance genes were targets of six miRNAs suggesting that those identified miRNAs and 15 NBS-LRR resistance genes might be involved in RSV infection. Taken together, our results provide novel insight into the dynamic expression profiles of rice miRNAs upon RSV infection and clues for the understanding of the regulatory roles of miRNAs via time-course.
Keywords	Medicine ; R ; Science ; Q
Subject code	500 ; 570
Language	English
Publishing date	2016-01-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Identification of Viruses and Viroids Infecting Tomato and Pepper Plants in Vietnam by Metatranscriptomics

Hoseong Choi / Yeonhwa Jo / Won Kyong Cho / Jisuk Yu / Phu-Tri Tran / Lakha Salaipeth / Hae-Ryun Kwak / Hong-Soo Choi / Kook-Hyung Kim

International Journal of Molecular Sciences, Vol 21, Iss 7565, p

2020 Volume 7565

Abstract: Tomato ( Lycopersicum esculentum L.) and pepper ( Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and ... ...

Abstract	Tomato ( Lycopersicum esculentum L.) and pepper ( Capsicum annuum L.) plants belonging to the family Solanaceae are cultivated worldwide. The rapid development of next-generation sequencing (NGS) technology facilitates the identification of viruses and viroids infecting plants. In this study, we carried out metatranscriptomics using RNA sequencing followed by bioinformatics analyses to identify viruses and viroids infecting tomato and pepper plants in Vietnam. We prepared a total of 16 libraries, including eight tomato and eight pepper libraries derived from different geographical regions in Vietnam. We identified a total of 602 virus-associated contigs, which were assigned to 18 different virus species belonging to nine different viral genera. We identified 13 different viruses and two viroids infecting tomato plants and 12 viruses and two viroids infecting pepper plants with viruses as dominantly observed pathogens. Our results showed that multiple infection of different viral pathogens was common in both plants. Moreover, geographical region and host plant were two major factors to determine viral populations. Taken together, our results provide the comprehensive overview of viral pathogens infecting two important plants in the family Solanaceae grown in Vietnam.
Keywords	metatranscriptomics ; pepper ; tomato ; Vietnam ; virus ; Biology (General) ; QH301-705.5 ; Chemistry ; QD1-999
Subject code	580
Language	English
Publishing date	2020-10-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: In silico identification of viruses and viroids infecting grapevine cultivar cabernet sauvignon using a grapevine transcriptome

Jo, Yeonhwa / Hoseong Choi / Jae-Seong Park / Jae-Wung Lee / Kook-Hyung Kim / Myung-Kyu Song / Wong Kyong Cho

Journal of plant pathology. 2018 Apr., v. 100, no. 1

2018

Abstract: Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine ... ...

Abstract	Next-generation sequencing (NGS)-based studies have reported a large amount of transcriptome data. In fact, plant transcriptome data sometimes contain sequence reads associated with viruses and viroids. Recently, we screened several grapevine transcriptomes to identify viruses and viroids that infect grapevine and we selected a transcriptome of the grapevine cultivar Cabernet Sauvignon for an in silico data analysis. After de novo assembly of raw data, the obtained contigs were blasted against a virus reference database. We identified five viruses and two viroids that infected the grapevine. We discovered that 2.16% of the transcriptome was comprised of viral RNAs, with more than half of the viral reads deriving from grapevine rupestris stem pitting-associated virus. However, the RNA populations of the two viroids were more than half of the total viral population based on the viral RNA copy number. Moreover, we identified single nucleotide polymorphisms for each virus and viroid and performed phylogenetic analyses. Taken together, we report the successful application of plant transcriptome data using bioinformatics analyses in the identification of five viruses and two viroids in the grapevine cultivar Cabernet Sauvignon, which is one of the most important grapevine cultivars in the world.
Keywords	bioinformatics ; cultivars ; databases ; Grapevine rupestris stem pitting-associated virus ; high-throughput nucleotide sequencing ; phylogeny ; plant diseases and disorders ; plant viruses ; RNA ; single nucleotide polymorphism ; transcriptome ; viroids ; viruses ; Vitis
Language	English
Dates of publication	2018-04
Size	p. 91-96.
Publishing place	Edizioni ETS
Document type	Article
ZDB-ID	1378427-4
ISSN	2239-7264 ; 1125-4653
ISSN (online)	2239-7264
ISSN	1125-4653
DOI	10.1007/s42161-018-0009-y
Database	NAL-Catalogue (AGRICOLA)

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Z 6602: Show issues

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Article: Interaction study of rice stripe virus proteins reveals a region of the nucleocapsid protein (NP) required for NP self-interaction and nuclear localization

Lian, Sen / Kook-Hyung Kim / Sang-Min Kim / Won Kyong Cho / Yeonhwa Jo

Virus research. 2014 Apr. 21, v. 183

2014

Abstract: Rice stripe virus (RSV), which belongs to the genus Tenuivirus, is an emergent virus problem. The RSV genome is composed of four single-strand RNAs (RNA1–RNA4) and encodes seven proteins. We investigated interactions between six of the RSV proteins by ... ...

Abstract	Rice stripe virus (RSV), which belongs to the genus Tenuivirus, is an emergent virus problem. The RSV genome is composed of four single-strand RNAs (RNA1–RNA4) and encodes seven proteins. We investigated interactions between six of the RSV proteins by yeast-two hybrid (Y2H) assay in vitro and by bimolecular fluorescence complementation (BiFC) in planta. Y2H identified self-interaction of the nucleocapsid protein (NP) and NS3, while BiFC revealed self-interaction of NP, NS3, and NCP. To identify regions(s) and/or crucial amino acid (aa) residues required for NP self-interaction, we generated various truncated and aa substitution mutants. Y2H assay showed that the N-terminal region of NP (aa 1–56) is necessary for NP self-interaction. Further analysis with substitution mutants demonstrated that additional aa residues located at 42–47 affected their interaction with full-length NP. These results indicate that the N-terminal region (aa 1–36 and 42–47) is required for NP self-interaction. BiFC and co-localization studies showed that the region required for NP self-interaction is also required for NP localization at the nucleus. Overall, our results indicate that the N-terminal region (aa 1–47) of the NP is important for NP self-interaction and that six aa residues (42–47) are essential for both NP self-interaction and nuclear localization.
Keywords	amino acids ; fluorescence ; genome ; mutants ; nucleocapsid proteins ; Rice stripe virus ; RNA
Language	English
Dates of publication	2014-0421
Size	p. 6-14.
Publishing place	Elsevier B.V.
Document type	Article
ZDB-ID	605780-9
ISSN	1872-7492 ; 0168-1702
ISSN (online)	1872-7492
ISSN	0168-1702
DOI	10.1016/j.virusres.2014.01.011
Database	NAL-Catalogue (AGRICOLA)

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Zs.A 1965: Show issues

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