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Complete genome sequence of soybean dwarf virus infecting soybean (Glycine max L.)
Yeonhwa Jo(조연화),Hoseong Choi(최호성),Bong Choon Lee(이봉춘),Jin-Sung Hong(홍진성),Won Kyong Cho(조원경) 한국미생물학회 2022 미생물학회지 Vol.58 No.2
We found a soybean plant displaying severe viral disease symptoms, such as stunting, rugosity, and yellowing. To reveal the viral agent, we extracted total RNA from the leaf sample and prepared a ribosome-deleted library followed by RNAsequencing. Raw data were de novo assembled, and the assembled contigs were used in a BLASTX search against a viral protein database. We identified four contigs associated with Soybean dwarf virus (SbDV) belonging to the genus Luteovirus in the family Luteoviridae. We obtained the complete genome of SbDV isolate HS with 5,686 nucleotides (nt), encoding five open reading frames (ORFs). The phylogenetic analysis showed that SbDV isolate HS belongs to Group A containing isolates from the USA and the Czech Republic. Here, we report the complete genome sequence of SbDV isolate HS infecting soybean in Korea obtained by RNA-sequencing.
Pyrroloquinoline quinone is a plant growth promotion factor produced by Pseudomonas fluorescens B16.
Choi, Okhee,Kim, Jinwoo,Kim, Jung-Gun,Jeong, Yeonhwa,Moon, Jae Sun,Park, Chang Seuk,Hwang, Ingyu American Society of Plant Physiologists 2008 Plant Physiology Vol.146 No.2
<P>Pseudomonas fluorescens B16 is a plant growth-promoting rhizobacterium. To determine the factors involved in plant growth promotion by this organism, we mutagenized wild-type strain B16 using OmegaKm elements and isolated one mutant, K818, which is defective in plant growth promotion, in a rockwool culture system. A cosmid clone, pOK40, which complements the mutant K818, was isolated from a genomic library of the parent strain. Tn3-gusA mutagenesis of pOK40 revealed that the genes responsible for plant growth promotion reside in a 13.3-kb BamHI fragment. Analysis of the DNA sequence of the fragment identified 11 putative open reading frames, consisting of seven known and four previously unidentified pyrroloquinoline quinone (PQQ) biosynthetic genes. All of the pqq genes showed expression only in nutrient-limiting conditions in a PqqH-dependent manner. Electrospray ionization-mass spectrometry analysis of culture filtrates confirmed that wild-type B16 produces PQQ, whereas mutants defective in plant growth promotion do not. Application of wild-type B16 on tomato (Solanum lycopersicum) plants cultivated in a hydroponic culture system significantly increased the height, flower number, fruit number, and total fruit weight, whereas none of the strains that did not produce PQQ promoted tomato growth. Furthermore, 5 to 1,000 nm of synthetic PQQ conferred a significant increase in the fresh weight of cucumber (Cucumis sativus) seedlings, confirming that PQQ is a plant growth promotion factor. Treatment of cucumber leaf discs with PQQ and wild-type B16 resulted in the scavenging of reactive oxygen species and hydrogen peroxide, suggesting that PQQ acts as an antioxidant in plants.</P>
Antioxidant Activity of Water Extract from Black Raspberry on C2C12 Muscle Cells
Yeonhwa Lee,Yunji Park,Jihye Choi,Jeongjin Park,Kyungmi Kim,Woojin Jun 한국식품영양과학회 2021 한국식품영양과학회 학술대회발표집 Vol.2021 No.10
Black raspberry (Rubus occidentalis) is black-fruited raspberry native to north america and known to have various activities. This study investigated the antioxidant activities and intracellular ROS level of water extract from black raspberry (ROW) on C2C12 cells. Antioxidant activity was evaluated by 2,2"-azinobis-(3-ethylbenzothiazoline-6-sulfonic acid) (ABTs) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activities. Total phenolic and flavonoid contents also measured. Intracellular ROS level was evaluated using DCF-DA method at concentrations of 200-500 μg/mL on H₂O₂-induced C2C12 myoblast cell. Intracellular ROS production showed higher level in the H₂O₂ treated group than control group and dose-dependent decrease in the sample group. These results suggest black raspberry water extract have antioxidant activity and effect against oxidative stress.
Jo, Yeonhwa,Song, Myung-Kyu,Choi, Hoseong,Park, Jae-Seong,Lee, Jae-Wung,Cho, Won Kyong,Kim, Kook-Hyung Springer-Verlag 2018 Journal of plant pathology Vol.100 No.1
<P>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.</P>
JEONG, YEONHWA,CHEONG, HOON,CHOI, OKHEE,KIM, JUNG KYU,KANG, YONGSUNG,KIM, JINWOO,LEE, SEUNGDON,KOH, SERRY,MOON, JAE SUN,HWANG, INGYU Blackwell Publishing Ltd 2011 Molecular plant pathology Vol.12 No.4
<P><B>SUMMARY</B></P><P>The host specificity of <I>Ralstonia solanacearum</I>, the causal organism of bacterial wilt on many solanaceous crops, is poorly understood. To identify a gene conferring host specificity of the bacterium, SL341 (virulent to hot pepper but avirulent to potato) and SL2029 (virulent to potato but avirulent to hot pepper) were chosen as representative strains. We identified a gene, <I>rsa1</I>, from SL2029 that confers avirulence to SL341 in hot pepper. The <I>rsa1</I> gene encoding an 11.8‐kDa protein possessed the perfect consensus hrp<SUB>II</SUB> box motif upstream of the gene. Although the expression of <I>rsa1</I> was activated by HrpB, a transcriptional activator for <I>hrp</I> gene expression, Rsa1 protein was secreted in an Hrp type III secretion‐independent manner. Rsa1 exhibited weak homology with an aspartic protease, cathepsin D, and possessed protease activity. Two specific aspartic protease inhibitors, pepstatin A and diazoacetyl‐<SMALL>d</SMALL>,<SMALL>l</SMALL>‐norleucine methyl ester, inhibited the protease activity of Rsa1. Substitution of two aspartic acid residues with alanine at positions 54 and 59 abolished protease activity. The SL2029 <I>rsa1</I> mutant was much less virulent than the wild‐type strain, but did not induce disease symptoms in hot pepper. These data indicate that Rsa1 is an extracellular aspartic protease and plays an important role for the virulence of SL2029 in potato.</P>
Jo, Yeonhwa,Choi, Hoseong,Bae, Miah,Kim, Sang-Min,Kim, Sun-Lim,Lee, Bong Choon,Cho, Won Kyong,Kim, Kook-Hyung The Korean Society of Plant Pathology 2017 Plant Pathology Journal Vol.33 No.5
Soybean is the most important legume crop in the world. Several diseases in soybean lead to serious yield losses in major soybean-producing countries. Moreover, soybean can be infected by diverse viruses. Recently, we carried out a large-scale screening to identify viruses infecting soybean using available soybean transcriptome data. Of the screened transcriptomes, a soybean transcriptome for soybean seed development analysis contains several virus-associated sequences. In this study, we identified five viruses, including soybean mosaic virus (SMV), infecting soybean by de novo transcriptome assembly followed by blast search. We assembled a nearly complete consensus genome sequence of SMV China using transcriptome data. Based on phylogenetic analysis, the consensus genome sequence of SMV China was closely related to SMV isolates from South Korea. We examined single nucleotide variations (SNVs) for SMVs in the soybean seed transcriptome revealing 780 SNVs, which were evenly distributed on the SMV genome. Four SNVs, C-U, U-C, A-G, and G-A, were frequently identified. This result demonstrated the quasispecies variation of the SMV genome. Taken together, this study carried out bioinformatics analyses to identify viruses using soybean transcriptome data. In addition, we demonstrated the application of soybean transcriptome data for virus genome assembly and SNV analysis.