Negative roles of MAPK signaling cascades for itrogen-fixing nodule formation in Medicago truncatula

Wonsil Bae,Jinsoo Lee,Hojin Ryu 한국육종학회 2015 한국육종학회 심포지엄 Vol.2015 No.07

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events including abiotic/biotic stress responses, innate immunity, hormone signaling and cell specificity in plants. The MAPK-mediated stress and ethylene signaling are recently known to be involved in nitogen-fixing symbiotic interactions; however, the biological role of MAPK for nodule development in legume plants is largely unknown. We here elucidated that MtMKK5-MtMPK3/6 cascade negatively regulate the nitrogen fixing nodule formation in Medicago truncatula. MtMKK5, an ortholog of SIMKK, overexpression significantly reduces the nodule formation in M. truncatula roots. MtMKK5 directly activates MtMPK3/6 by phosphorylation on the TEY motif within the activation loop in the cytoplasm, which might link to EFD as a negative regulator for nodule formation. EFD has a putative MAPK phosphorylation Thr residue and could be a target of the activated MtMPK3/6 in the nucleus. Consistently, a MAPK specific inhibitor U0126 enhances nodule formation and confers similar nodule phenotypes to the efd-1 mutant such as lower proliferation and differentiation to symbiotic tissues. Our works thus reveal a key negative signaling module mediated by MtMKK5-MtMPK3/6-EFD for symbiotic nitrogen fixing nodule organogenesis.

비료처리와 시설재배 고추 근권에서의 미생물 군집구조 변화분석

Wonsil Bae,Ye-Jin Lee,Hojin Ryu 한국토양비료학회 2020 한국토양비료학회 학술발표회 초록집 Vol.2020 No.10

AKR2A-mediated import of chloroplast outer membrane proteins is essential for chloroplast biogenesis

Bae, Wonsil,Lee, Yong Jik,Kim, Dae Heon,Lee, Junho,Kim, Soojin,Sohn, Eun Ju,Hwang, Inhwan Nature Publishing Group 2008 Nature cell biology Vol.10 No.2

In plant cells, chloroplasts have essential roles in many biochemical reactions and physiological responses. Chloroplasts require numerous protein components, but only a fraction of these proteins are encoded by the chloroplast genome. Instead, most are encoded by the nuclear genome and imported into chloroplasts from the cytoplasm post-translationally. Membrane proteins located in the chloroplast outer envelope membrane (OEM) have a critical function in the import of proteins into the chloroplast. However, the biogenesis of chloroplast OEM proteins remains poorly understood. Here, we report that an Arabidopsis ankyrin repeat protein, AKR2A, plays an essential role in the biogenesis of the chloroplast OEM proteins. AKR2A binds to chloroplast OEM protein targeting signals, as well as to chloroplasts. It also displays chaperone activity towards chloroplast OEM proteins, and facilitates the targeting of OEP7 to chloroplasts in vitro. AKR2A RNAi in plants with an akr2b knockout background showed greatly reduced levels of chloroplast proteins, including OEM proteins, and chloroplast biogenesis was also defective. Thus, AKR2A functions as a cytosolic mediator for sorting and targeting of nascent chloroplast OEM proteins to the chloroplast.

The crosstalk mechanism of Brassinosteroids and ABA in early seedling development

Hojin Ryu,Wonsil Bae,Ildoo Hwang 한국육종학회 2013 한국육종학회 심포지엄 Vol.2013 No.07

Seed germination and the establishment of young seedlings are critical phases in the plant’s life cycle. To control these processes, plants have evolved diverse hormonal signaling networks in which brassinosteroids (BRs) attenuate abscisic acid (ABA) responses; however, the underlying regulatory mechanism remains elusive. Here, we reveal that epigenetic silencing of the ABA signaling regulator ABI3 via the BR-related transcription factor BES1 is essential for the inhibitory effect of BRs on ABA signaling during early seedling development. BR-activated BES1 forms a transcriptional repressor complex with TPL via its EAR motif that recruits the histone deacetylase HDA19. This facilitates the histone H3-mediated deacetylation of ABI3 chromatin, leading to the suppression of ABI3 and its downstream target ABI5, which results in reduced ABA sensitivity. We propose that the BR-activated BES1-TPL-HDA19 repressor complex controls epigenetic silencing of ABI3 and thereby suppresses the ABA response during early seedling development.

Negative roles of MAPK signaling cascades for nitrogen-fixing nodule formation in Medicago truncatula

Hojin Ryu,Wonsil Bae,Hyunsook Kim,Kwangryul Back,Hyunwoo Cho,Ildoo Hwang 한국육종학회 2012 한국육종학회 심포지엄 Vol.2012 No.07

Mitogen-activated protein kinase (MAPK) signaling cascades play critical roles in various cellular events including abiotic/biotic stress responses, innate immunity, hormone signaling and cell specificity in plants. The MAPK-mediated stress and ethylene signaling are recently known to be involved in nitogen-fixing symbiotic interactions; however, the biological role of MAPK for nodule development in legume plants is largely unknown. We here elucidated that MtMKK5-MtMPK3/6 cascade negatively regulate the nitrogen fixing nodule formation in Medicago truncatula. MtMKK5, an ortholog of SIMKK, overexpression significantly reduces the nodule formation in M. truncatula roots. MtMKK5 directly activates MtMPK3/6 by phosphorylation on the TEY motif within the activation loop in the cytoplasm, which might link to EFD as a negative regulator for nodule formation. EFD has a putative MAPK phosphorylation Thr residue and could be a target of the activated MtMPK3/6 in the nucleus. Consistently, a MAPK specific inhibitor U0126 enhances nodule formation and confers similar nodule phenotypes to the efd-1 mutant such as lower proliferation and differentiation to symbiotic tissues. Our works thus reveal a key negative signaling module mediated by MtMKK5-MtMPK3/6-EFD for symbiotic nitrogen fixing nodule organogenesis.

Cytokinin signaling promotes root secondary growth and bud formation in Panax ginseng

Kyoung Rok Geem,Yookyung Lim,Jeongeui Hong,Wonsil Bae,Jinsu Lee,Soeun Han,Jinsu Gil,Hyunwoo Cho,Hojin Ryu The Korean Society of Ginseng 2024 Journal of Ginseng Research Vol.48 No.2

Background: Panax ginseng, one of the valuable perennial medicinal plants, stores numerous pharmacological substrates in its storage roots. Given its perennial growth habit, organ regeneration occurs each year, and cambium stem cell activity is necessary for secondary growth and storage root formation. Cytokinin (CK) is a phytohormone involved in the maintenance of meristematic cells for the development of storage organs; however, its physiological role in storage-root secondary growth remains unknown. Methods: Exogenous CK was repeatedly applied to P. ginseng, and morphological and histological changes were observed. RNA-seq analysis was used to elucidate the transcriptional network of CK that regulates P. ginseng growth and development. The HISTIDINE KINASE 3 (PgHK3) and RESPONSE REGULATOR 2 (PgRR2) genes were cloned in P. ginseng and functionally analyzed in Arabidopsis as a two-component system involved in CK signaling. Results: Phenotypic and histological analyses showed that CK increased cambium activity and dormant axillary bud formation in P. ginseng, thus promoting storage-root secondary growth and bud formation. The evolutionarily conserved two-component signaling pathways in P. ginseng were sufficient to restore CK signaling in the Arabidopsis ahk2/3 double mutant and rescue its growth defects. Finally, RNA-seq analysis of CK-treated P. ginseng roots revealed that plant-type cell wall biogenesis-related genes are tightly connected with mitotic cell division, cytokinesis, and auxin signaling to regulate CK-mediated P. ginseng development. Conclusion: Overall, we identified the CK signaling-related two-component systems and their physiological role in P. ginseng. This scientific information has the potential to significantly improve the field-cultivation and biotechnology-based breeding of ginseng.

Nitrate enhances the secondary growth of storage roots in Panax ginseng

Kyoung Rok Geem,Jaewook Kim,Wonsil Bae,Moo-Geun Jee,Jin Yu,Inbae Jang,Dong-Yun Lee,Chang Pyo Hong,Donghwan Shim,Hojin Ryu The Korean Society of Ginseng 2023 Journal of Ginseng Research Vol.47 No.3

Background: Nitrogen (N) is an essential macronutrient for plant growth and development. To support agricultural production and enhance crop yield, two major N sources, nitrate and ammonium, are applied as fertilizers to the soil. Although many studies have been conducted on N uptake and signal transduction, the molecular genetic mechanisms of N-mediated physiological roles, such as the secondary growth of storage roots, remain largely unknown. Methods: One-year-old P. ginseng seedlings treated with KNO₃ were analyzed for the secondary growth of storage roots. The histological paraffin sections were subjected to bright and polarized light microscopic analysis. Genome-wide RNA-seq and network analysis were carried out to dissect the molecular mechanism of nitrate-mediated promotion of ginseng storage root thickening. Results: Here, we report the positive effects of nitrate on storage root secondary growth in Panax ginseng. Exogenous nitrate supply to ginseng seedlings significantly increased the root secondary growth. Histological analysis indicated that the enhancement of root secondary growth could be attributed to the increase in cambium stem cell activity and the subsequent differentiation of cambium-derived storage parenchymal cells. RNA-seq and gene set enrichment analysis (GSEA) revealed that the formation of a transcriptional network comprising auxin, brassinosteroid (BR)-, ethylene-, and jasmonic acid (JA)-related genes mainly contributed to the secondary growth of ginseng storage roots. In addition, increased proliferation of cambium stem cells by a N-rich source inhibited the accumulation of starch granules in storage parenchymal cells. Conclusion: Thus, through the integration of bioinformatic and histological tissue analyses, we demonstrate that nitrate assimilation and signaling pathways are integrated into key biological processes that promote the secondary growth of P. ginseng storage roots.

Characterization of the Rosellinia necatrix Transcriptome and Genes Related to Pathogenesis by Single-Molecule mRNA Sequencing

Kim, Hyeongmin,Lee, Seung Jae,Jo, Ick-Hyun,Lee, Jinsu,Bae, Wonsil,Kim, Hyemin,Won, Kyungho,Hyun, Tae Kyung,Ryu, Hojin The Korean Society of Plant Pathology 2017 Plant Pathology Journal Vol.33 No.4

White root rot disease, caused by the pathogen Rosellinia necatrix, is one of the world's most devastating plant fungal diseases and affects several commercially important species of fruit trees and crops. Recent global outbreaks of R. necatrix and advances in molecular techniques have both increased interest in this pathogen. However, the lack of information regarding the genomic structure and transcriptome of R. necatrix has been a barrier to the progress of functional genomic research and the control of this harmful pathogen. Here, we identified 10,616 novel full-length transcripts from the filamentous hyphal tissue of R. necatrix (KACC 40445 strain) using PacBio single-molecule sequencing technology. After annotation of the unigene sets, we selected 14 cell cycle-related genes, which are likely either positively or negatively involved in hyphal growth by cell cycle control. The expression of the selected genes was further compared between two strains that displayed different growth rates on nutritional media. Furthermore, we predicted pathogen-related effector genes and cell wall-degrading enzymes from the annotated gene sets. These results provide the most comprehensive transcriptomal resources for R. necatrix, and could facilitate functional genomics and further analyses of this important phytopathogen.

Bacillus thuringiensis C25의 흰날개무늬병 Rosellinia necatrix에 대한 항진균 활성에 관여하는 유전자 특성 및 기능 유전체학적 연구

김강민 ( Kangmin Kim ),이화용 ( Hwa-yong Lee ),배원실 ( Wonsil Bae ),조민 ( Min Cho ),류호진 ( Hojin Ryu ) 한국균학회 2019 韓國菌學會誌 Vol.47 No.4

Biocontrol agents (BCAs) are widely used to protect plants from diverse biotic and abiotic stresses in agricultural and ecological fields. Among the various microbes, many subspecies of the gram-positive genus, Bacillus, have been successfully industrialized as eco-friendly biological pesticides and fertilizers. In the current study, we demonstrated that Bacillus thuringiensis C25 exhibited antagonistic effects on the mycelial growth of Rosellinia necatrix, a fungal phytopathogen. Scanning electron microscopy analysis revealed that B. thuringiensis C25 degraded the cell wall structures of R. necatrix mycelia. In the functional genomic analysis of B. thuringiensis C25, we annotated 5,683 genes and selected the gene sets that potentially encoded fungal cell wall degrading enzymes (CWDEs). The growth inhibition effects on R. necatrix were highly correlated with the transcriptional activity of the mycelial cell wall degrading genes of B. thuringiensis C25. The transcript levels of CWDEs, including CshiA, B, and Glycos_transf_2 genes in B. thuringiensis C25, were enhanced following co-cultivation with R. necatrix. In conclusion, our study suggested that B. thuringiensis C25 could serve as a suitable candidate for controlling R. necatrix and could facilitate elucidating the mechanisms underlying the antifungal activities of BCAs against phytopathogens.

Genome-wide transcriptomic analysis of BR-deficient Micro-Tom reveals correlations between drought stress tolerance and brassinosteroid signaling in tomato

Lee, Jinsu,Shim, Donghwan,Moon, Suyun,Kim, Hyemin,Bae, Wonsil,Kim, Kyunghwan,Kim, Yang-Hoon,Rhee, Sung-Keun,Hong, Chang Pyo,Hong, Suk-Young,Lee, Ye-Jin,Sung, Jwakyung,Ryu, Hojin Elsevier 2018 Plant physiology and biochemistry Vol.127 No.-

<P><B>Abstract</B></P> <P>Brassinosteroids (BRs) are plant steroid hormones that play crucial roles in a range of growth and developmental processes. Although BR signal transduction and biosynthetic pathways have been well characterized in model plants, their biological roles in an important crop, tomato (<I>Solanum lycopersicum</I>), remain unknown. Here, cultivated tomato (WT) and a BR synthesis mutant, Micro-Tom (MT), were compared using physiological and transcriptomic approaches. The cultivated tomato showed higher tolerance to drought and osmotic stresses than the MT tomato. However, BR-defective phenotypes of MT, including plant growth and stomatal closure defects, were completely recovered by application of exogenous BR or complementation with a <I>SlDWARF</I> gene. Using genome-wide transcriptome analysis, 619 significantly differentially expressed genes (DEGs) were identified between WT and MT plants. Several DEGs were linked to known signaling networks, including those related to biotic/abiotic stress responses, lignification, cell wall development, and hormone responses. Consistent with the higher susceptibility of MT to drought stress, several gene sets involved in responses to drought and osmotic stress were differentially regulated between the WT and MT tomato plants. Our data suggest that BR signaling pathways are involved in mediating the response to abiotic stress via fine-tuning of abiotic stress-related gene networks in tomato plants.</P> <P><B>Highlights</B></P> <P> <UL> <LI> BR-deficient Micro-Tom showed lower drought and osmotic stress tolerance. </LI> <LI> Complementation of BR activity completely restored stress and developmental defects in Micro-Tom. </LI> <LI> BR signaling is tightly connected with gene networks related to abiotic stress and development. </LI> </UL> </P>