Genome-wide identification of Receptor-like Protein in Capsicum annuum

DongKue Yun,BoSeu Park,JuneSung Lee,Won-Hee Kang,Seungill Kim,Myung-Shin Kim,Doil Choi,Seon-In Yeom 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Sessile organism, plants constitutively challenged with pathogens have been developed various strategies for protection, such as preformed and inducible defense mechanisms. Receptor-like Proteins(RLPs) play critical roles in defense response as well as in plant development and growth. The domain structure of RLPs consists of extracellular leucine–rich repeats, a transmembrane domain, and a short cytoplasmic tail. Here, we identified putative 170 RLP genes from pepper genome using in-house bioinformatics pipeline. The distribution of RLPs on pepper pseudomolecule showed uneven spread and a number of RLPs were physically clustered by tandem array in the specific chromosome. Motifs analysis of pepper RLPs showed conserved LRR sequences (LxxLxxLDLxxNxxxGxIP). To understand further functional and evolutionary characteristics, evolutional relationship and gene profiling analysis are on progress.

Development of Clustered Resistance Gene Analogs-Based Markers of Resistance to <i> Phytophthora capsici</i> in Chili Pepper

Kim, Nayoung,Kang, Won-Hee,Lee, Jundae,Yeom, Seon-In Hindawi 2019 BioMed research international Vol.2019 No.-

<P>The soil-borne pathogen<I> Phytophthora capsici</I> causes severe destruction of<I> Capsicum</I> spp. Resistance in<I> Capsicum</I> against<I> P. capsici </I>is controlled by numerous minor quantitative trait loci (QTLs) and a consistent major QTL on chromosome 5. Molecular markers on<I> Capsicum</I> chromosome 5 have been developed to identify the predominant genetic contributor to resistance but have achieved little success. In this study, previously reported molecular markers were used to reanalyze the major QTL region on chromosome 5 (6.2 Mbp to 139.2 Mbp). Candidate resistance gene analogs (RGAs) were identified in the extended major QTL region including 14 nucleotide binding site leucine-rich repeats, 3 receptor-like kinases, and 1 receptor-like protein. Sequence comparison of the candidate RGAs was performed between two<I> Capsicum</I> germplasms that are resistant and susceptible, respectively, to<I> P. capsici. </I>11 novel RGA-based markers were developed through high-resolution melting analysis which were closely linked to the major QTL for<I> P. capsici</I> resistance. Among the markers, CaNB-5480 showed the highest cosegregation rate at 86.9% and can be applied to genotyping of the germplasms that were not amenable by previous markers. With combination of three markers such as CaNB-5480, CaRP-5130 and CaNB-5330 increased genotyping accuracy for 61<I> Capsicum</I> accessions. These could be useful to facilitate high-throughput germplasm screening and further characterize resistance genes against<I> P. capsici </I>in pepper.</P>

A common plant cell‐wall protein HyPRP1 has dual roles as a positive regulator of cell death and a negative regulator of basal defense against pathogens

Yeom, Seon‐,In,Seo, Eunyoung,Oh, Sang‐,Keun,Kim, Ki Woo,Choi, Doil Blackwell Publishing Ltd 2012 The Plant journal Vol.69 No.5

<P><B>Summary</B></P><P>Although hybrid proline‐rich proteins (HyPRPs) are ubiquitous in plants, little is known about their roles other than as cell‐wall structural proteins. We identified the gene <I>HyPRP1</I> in <I>Capsicum annuum</I> and <I>Nicotiana benthamiana</I>, which encodes a protein containing proline‐rich domain and eight‐cysteine motif (8CM) that is constitutively expressed in various organs, mostly in the root, but is down‐regulated upon inoculation with either incompatible or compatible pathogens. Ectopic expression of <I>HyPRP1</I> in plants accelerated cell death, showing developmental abnormality with down‐regulation of ROS‐scavenging genes, and enhanced pathogen susceptibility suppressing expression of defense‐related genes. Conversely, silencing of <I>HyPRP1</I> suppressed pathogen‐induced cell death, but enhanced disease resistance, with up‐regulation of defense‐related genes and inhibition of <I>in planta</I> growth of bacterial pathogens independently of signal molecule‐mediated pathways. Furthermore, the secreted 8CM was sufficient for these HyPRP1 functions. Together, our results suggest that a common plant cell‐wall structural protein, HyPRP1, performs distinct dual roles in positive regulation of cell death and negative regulation of basal defense against pathogen.</P>

Use of a Secretion Trap Screen in Pepper Following Phytophthora capsici Infection Reveals Novel Functions of Secreted Plant Proteins in Modulating Cell Death.

Yeom, Seon-In,Baek, Hyang-Ku,Oh, Sang-Keun,Kang, Won-Hee,Lee, Sang Jik,Lee, Je Min,Seo, Eunyoung,Rose, Jocelyn K C,Kim, Byung-Dong,Choi, Doil APS Press 2011 Molecular plant-microbe interactions Vol.24 No.6

<P>In plants, the primary defense against pathogens is mostly inducible and associated with cell wall modification and defense-related gene expression, including many secreted proteins. To study the role of secreted proteins, a yeast-based signal-sequence trap screening was conducted with the RNA from Phytophthora capsici-inoculated root of Capsicum annuum 'Criollo de Morelos 334' (CM334). In total, 101 Capsicum annuum secretome (CaS) clones were isolated and identified, of which 92 were predicted to have a secretory signal sequence at their N-terminus. To identify differences in expressed CaS genes between resistant and susceptible cultivars of pepper, reverse Northern blots and real-time reverse-transcription polymerase chain reaction were performed with RNA samples isolated at different time points following P. capsici inoculation. In an attempt to assign biological functions to CaS genes, we performed in planta knock-down assays using the Tobacco rattle virus-based gene-silencing method. Silencing of eight CaS genes in pepper resulted in suppression of the cell death induced by the non-host bacterial pathogen (Pseudomonas syringae pv. tomato T1). Three CaS genes induced phenotypic abnormalities in silenced plants and one, CaS259 (PR4-l), caused both cell death suppression and perturbed phenotypes. These results provide evidence that the CaS genes may play important roles in pathogen defense as well as developmental processes.</P>

Genome-wide identification of pepper NB-LRR gene family and their evolutionary history in Solanaceae

Eunyoung Seo,Seon-In Yeom,Seungill Kim,Joohyun Lee,Saet-Byul Kim,Eunbi Choi,Eun Hye Choi,Doil Choi 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Plants have evolved elaborate innate immune systems against invading pathogens, such as bacteria, fungi, oomycetes, viruses and insects. Among them, intracellular immune receptors known as nucleotide-binding site and leucine-rich repeat (NB-LRR) play critical roles in effector-triggered immunity (ETI) regarding to plant defense. Here, we identified potential NB-LRR coding sequences from pepper genome using bioinformatics analysis and performed comparative analysis with Solanaceae plants. As a result, we identified 267, 443, and 755 NBS-encoding genes in the genome of tomato, potato, and pepper, respectively. These may indicate that the Solanaceae NB-LRRs were evolved through species-specific unequal-duplication event. Further phylogenetic and clustering analyses revealed that Solanaceae NB-LRRs were classified into the 14 subgroups with 1 TNL and 13 CNL types. We found that the genes in CNL-G1 and CNL-G2 subgroup were highly expanded compared to other subgroup showing a large portion of NB-LRR in pepper genome. Among 755 NB-LRRs in pepper genome, 623 were physically mapped on all 12 pepper chromosome pseudomolecules. Furthermore, a number of NB-LRRs in the same group were physically clustered by tandem array in the specific chromosome. Genome-wide identification of pepper NB-LRR family and their evolutionary analysis could provide an important resource for identification and characterization of genes for breeding of disease resistance crops.

Bloodstream Infections and Clinical Significance of Healthcare-associated Bacteremia: A Multicenter Surveillance Study in Korean Hospitals

Son, Jun Seong,Song, Jae-Hoon,Ko, Kwan Soo,Yeom, Joon Sup,Ki, Hyun Kyun,Kim, Shin-Woo,Chang, Hyun-Ha,Ryu, Seong Yeol,Kim, Yeon-Sook,Jung, Sook-In,Shin, Sang Yop,Oh, Hee Bok,Lee, Yeong Seon,Chung, Doo The Korean Academy of Medical Sciences 2010 JOURNAL OF KOREAN MEDICAL SCIENCE Vol.25 No.7

<P>Recent changes in healthcare systems have changed the epidemiologic paradigms in many infectious fields including bloodstream infection (BSI). We compared clinical characteristics of community-acquired (CA), hospital-acquired (HA), and healthcare-associated (HCA) BSI. We performed a prospective nationwide multicenter surveillance study from 9 university hospitals in Korea. Total 1,605 blood isolates were collected from 2006 to 2007, and 1,144 isolates were considered true pathogens. HA-BSI accounted for 48.8%, CA-BSI for 33.2%, and HCA-BSI for 18.0%. HA-BSI and HCA-BSI were more likely to have severe comorbidities. <I>Escherichia coli</I> was the most common isolate in CA-BSI (47.1%) and HCA-BSI (27.2%). In contrast, <I>Staphylococcus aureus</I> (15.2%), coagulase-negative <I>Staphylococcus</I> (15.1%) were the common isolates in HA-BSI. The rate of appropriate empiric antimicrobial therapy was the highest in CA-BSI (89.0%) followed by HCA-BSI (76.4%), and HA-BSI (75.0%). The 30-day mortality rate was the highest in HA-BSI (23.0%) followed by HCA-BSI (18.4%), and CA-BSI (10.2%). High Pitt score and inappropriate empirical antibiotic therapy were the independent risk factors for mortality by multivariate analysis. In conclusion, the present data suggest that clinical features, outcome, and microbiologic features of causative pathogens vary by origin of BSI. Especially, HCA-BSI shows unique clinical characteristics, which should be considered a distinct category for more appropriate antibiotic treatment.</P>

Isolation of putative pepper defense-related genes against the pathogen Phytophthora capsici using suppression subtractive hybridization/macroarray and RNA-sequencing analyses

김동환,강원희,Seon-In Yeom,Byung-Dong Kim 한국원예학회 2019 Horticulture, Environment, and Biotechnology Vol.60 No.5

The oomycete Phytophthora capsici Leonian is one of the most economically important pathogens limiting pepper ( Capsicumannuum ) production in many regions around the world. Insights into the defense mechanisms of pepper against P. capsiciwould be helpful in the breeding of resistant cultivars. However, little is still known about the defense system in pepperagainst P. capsici . We used suppression subtractive hybridization (SSH) followed by macro-array screening to isolate theputative candidate defense genes (PSH, Phytophthora Subtractive Hybridization) in pepper that are diff erentially expressedbetween the resistant cultivar ( CM334 ) and the susceptible cultivar ( Chilsungcho ) following P. capsici infection. A total of72 PSH genes were identifi ed and categorized based on their putative functions. Semi-quantitative RT-PCR analyses using11 selected genes confi rmed their diff erential expressions between the resistant and susceptible cultivars along the timecourse of infection with P. capsici . Furthermore, RNA-seq analyses were performed to understand the possible roles of PSHgenes in the defense response to P. capsici as well as three viruses, including two tobacco mosaic virus strains and one PepperMottle Virus strain. We found that 37 genes out of 72 displayed diff erential expression in our RNA-seq-based heatmapbetween ‘ CM334 ’ and ‘ Chilsungcho ’ upon pathogen infection. In particular, two genes, CA00g99220 and CA00g96010,and one gene, CA12g16620, were shown to be strongly and uniquely expressed in the resistant cultivar, CM334, against P. capsici and two viruses, respectively. Thus, we consider that this combined approach using SSH/macro-array screening andRNA-seq analyses is a relevant tool for isolation of candidate defense-related genes upon pathogen infection. Data in thisstudy provide a good source for further study on the defense mechanisms against pathogens in chili pepper.

Genome-wide comparative analysis in Solanaceous species reveals evolution of microRNAs targeting defense genes in <i>Capsicum</i> spp.

Seo, Eunyoung,Kim, Taewook,Park, June Hyun,Yeom, Seon-In,Kim, Seungill,Seo, Min-Ki,Shin, Chanseok,Choi, Doil Oxford University Press 2018 DNA research Vol.25 No.6

<P><B>Abstract</B></P><P>MicroRNAs (miRNAs) play roles in various biological processes in plants including growth, development, and disease resistance. Previous studies revealed that some plant miRNAs produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs), and they regulate a cascade of gene expression. We performed a genome-wide comparative analysis of miRNAs in Solanaceous species (pepper, tomato, and potato), from an evolutionary perspective. Microsynteny of miRNAs was analysed based on the genomic loci and their flanking genes and most of the well-conserved miRNA genes maintained microsynteny in Solanaceae. We identified target genes of the miRNAs via degradome analysis and found that several miRNAs target many genes encoding nucleotide-binding leucine-rich repeat (NLR) or receptor-like proteins (RLPs), which are known to be major players in defense responses. In addition, disease-resistance-associated miRNAs trigger phasiRNA production in pepper, indicating amplification of the regulation of disease-resistance gene families. Among these, miR-n033a-3p, whose target NLRs have been duplicated in pepper, targets more NLRs belonging to specific subgroup in pepper than those in potato. miRNAs targeting resistance genes might have evolved to regulate numerous targets in Solanaceae, following expansion of target resistance genes. This study provides an insight into evolutionary relationship between miRNAs and their target defense genes in plants.</P>

Genome-wide Identification, Classification, and Expression Analysis of the Receptor-Like Protein Family in Tomato

Kang, Won-Hee,Yeom, Seon-In The Korean Society of Plant Pathology 2018 Plant Pathology Journal Vol.34 No.5

Receptor-like proteins (RLPs) are involved in plant development and disease resistance. Only some of the RLPs in tomato (Solanum lycopersicum L.) have been functionally characterized though 176 genes encoding RLPs, which have been identified in the tomato genome. To further understand the role of RLPs in tomato, we performed genome-guided classification and transcriptome analysis of these genes. Phylogenic comparisons revealed that the tomato RLP members could be divided into eight subgroups and that the genes evolved independently compared to similar genes in Arabidopsis. Based on location and physical clustering analyses, we conclude that tomato RLPs likely expanded primarily through tandem duplication events. According to tissue specific RNA-seq data, 71 RLPs were expressed in at least one of the following tissues: root, leaf, bud, flower, or fruit. Several genes had expression patterns that were tissue specific. In addition, tomato RLP expression profiles after infection with different pathogens showed distinguish gene regulations according to disease induction and resistance response as well as infection by bacteria and virus. Notably, Some RLPs were highly and/or unique expressed in susceptible tomato to pathogen, suggesting that the RLP could be involved in disease response, possibly as a host-susceptibility factor. Our study could provide an important clues for further investigations into the function of tomato RLPs involved in developmental and response to pathogens.

Genome-wide Identification, Classification, and Expression Analysis of the Receptor-Like Protein Family in Tomato

Won-Hee Kang,Seon-In Yeom 한국식물병리학회 2018 Plant Pathology Journal Vol.34 No.5

Receptor-like proteins (RLPs) are involved in plant development and disease resistance. Only some of the RLPs in tomato (Solanum lycopersicum L.) have been functionally characterized though 176 genes encoding RLPs, which have been identified in the tomato genome. To further understand the role of RLPs in tomato, we performed genome-guided classification and transcriptome analysis of these genes. Phylogenic comparisons revealed that the tomato RLP members could be divided into eight subgroups and that the genes evolved independently compared to similar genes in Arabidopsis. Based on location and physical clustering analyses, we conclude that tomato RLPs likely expanded primarily through tandem duplication events. According to tissue specific RNA-seq data, 71 RLPs were expressed in at least one of the following tissues: root, leaf, bud, flower, or fruit. Several genes had expression patterns that were tissue specific. In addition, tomato RLP expression profiles after infection with different pathogens showed distinguish gene regulations according to disease induction and resistance response as well as infection by bacteria and virus. Notably, Some RLPs were highly and/ or unique expressed in susceptible tomato to pathogen, suggesting that the RLP could be involved in disease response, possibly as a host-susceptibility factor. Our study could provide an important clues for further investigations into the function of tomato RLPs involved in developmental and response to pathogens.