Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses

Moon Young Ryu, Seok Keun Cho, Yourae Hong, Jinho Kim, Jong Hum Kim, Gu Min Kim, Yan Jun Chen, Eva Knoch, Birger Lindberg Møller, Woo Taek Kim, Michael Foged Lyngkjær, Seong Wook Yang

Research output: Contribution to journalArticle

1 Citation (Scopus)

Abstract

Background: Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results: In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion: This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.

Original languageEnglish
Article number326
JournalBMC Genomics
Volume20
Issue number1
DOIs
Publication statusPublished - 2019 Apr 29

Fingerprint

Ubiquitin-Protein Ligases
Droughts
Hordeum
Genes
Proteasome Endopeptidase Complex
Ubiquitin
Arabidopsis
Proteins
Mycoses
Expressed Sequence Tags
Ligases
Infection
Hydrolysis

All Science Journal Classification (ASJC) codes

  • Biotechnology
  • Genetics

Cite this

Ryu, Moon Young ; Cho, Seok Keun ; Hong, Yourae ; Kim, Jinho ; Kim, Jong Hum ; Kim, Gu Min ; Chen, Yan Jun ; Knoch, Eva ; Møller, Birger Lindberg ; Kim, Woo Taek ; Lyngkjær, Michael Foged ; Yang, Seong Wook. / Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses. In: BMC Genomics. 2019 ; Vol. 20, No. 1.
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abstract = "Background: Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results: In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion: This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.",
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Ryu, MY, Cho, SK, Hong, Y, Kim, J, Kim, JH, Kim, GM, Chen, YJ, Knoch, E, Møller, BL, Kim, WT, Lyngkjær, MF & Yang, SW 2019, 'Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses', BMC Genomics, vol. 20, no. 1, 326. https://doi.org/10.1186/s12864-019-5696-z

Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses. / Ryu, Moon Young; Cho, Seok Keun; Hong, Yourae; Kim, Jinho; Kim, Jong Hum; Kim, Gu Min; Chen, Yan Jun; Knoch, Eva; Møller, Birger Lindberg; Kim, Woo Taek; Lyngkjær, Michael Foged; Yang, Seong Wook.

In: BMC Genomics, Vol. 20, No. 1, 326, 29.04.2019.

Research output: Contribution to journalArticle

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T1 - Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses

AU - Ryu, Moon Young

AU - Cho, Seok Keun

AU - Hong, Yourae

AU - Kim, Jinho

AU - Kim, Jong Hum

AU - Kim, Gu Min

AU - Chen, Yan Jun

AU - Knoch, Eva

AU - Møller, Birger Lindberg

AU - Kim, Woo Taek

AU - Lyngkjær, Michael Foged

AU - Yang, Seong Wook

PY - 2019/4/29

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N2 - Background: Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results: In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion: This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.

AB - Background: Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. E3 ligases play a central role in subjecting proteins to hydrolysis by the UPS. Recently, it has been demonstrated that a specific class of E3 ligases termed the U-box ligases are directly associated with the defense mechanisms against abiotic and biotic stresses in several plants. However, no studies on U-box E3 ligases have been performed in one of the important staple crops, barley. Results: In this study, we identified 67 putative U-box E3 ligases from the barley genome and expressed sequence tags (ESTs). Similar to Arabidopsis and rice U-box E3 ligases, most of barley U-box E3 ligases possess evolutionary well-conserved domain organizations. Based on the domain compositions and arrangements, the barley U-box proteins were classified into eight different classes. Along with this new classification, we refined the previously reported classifications of U-box E3 ligase genes in Arabidopsis and rice. Furthermore, we investigated the expression profile of 67 U-box E3 ligase genes in response to drought stress and pathogen infection. We observed that many U-box E3 ligase genes were specifically up-and-down regulated by drought stress or by fungal infection, implying their possible roles of some U-box E3 ligase genes in the stress responses. Conclusion: This study reports the classification of U-box E3 ligases in barley and their expression profiles against drought stress and pathogen infection. Therefore, the classification and expression profiling of barley U-box genes can be used as a platform to functionally define the stress-related E3 ligases in barley.

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