Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses
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 demonst...
| Main Authors: | , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2019-04-01
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| Series: | BMC Genomics |
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| Online Access: | http://link.springer.com/article/10.1186/s12864-019-5696-z |
| _version_ | 1818303796792524800 |
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| author | 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 |
| author_facet | 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 |
| author_sort | Moon Young Ryu |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-12-13T06:00:30Z |
| format | Article |
| id | doaj.art-da799c351d28475681f100b947c731ff |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-12-13T06:00:30Z |
| publishDate | 2019-04-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-da799c351d28475681f100b947c731ff2022-12-21T23:57:21ZengBMCBMC Genomics1471-21642019-04-0120111510.1186/s12864-019-5696-zClassification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stressesMoon Young Ryu0Seok Keun Cho1Yourae Hong2Jinho Kim3Jong Hum Kim4Gu Min Kim5Yan-Jun Chen6Eva Knoch7Birger Lindberg Møller8Woo Taek Kim9Michael Foged Lyngkjær10Seong Wook Yang11Department of Systems Biology, College of Life Science and Biotechnology, Yonsei UniversityDepartment of Systems Biology, College of Life Science and Biotechnology, Yonsei UniversitySamsung Medical CenterSamsung Medical CenterDepartment of Systems Biology, College of Life Science and Biotechnology, Yonsei UniversityDepartment of Systems Biology, College of Life Science and Biotechnology, Yonsei UniversityPlant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of CopenhagenPlant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of CopenhagenPlant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of CopenhagenDepartment of Systems Biology, College of Life Science and Biotechnology, Yonsei UniversityPlant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of CopenhagenPlant Biochemistry Laboratory, Department of Plant and Environmental Sciences, University of CopenhagenAbstract 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.http://link.springer.com/article/10.1186/s12864-019-5696-zBarleyHordeum vulgareUbiquitin proteasome system (UPS)Biotic stressAbiotic stress |
| spellingShingle | 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 Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses BMC Genomics Barley Hordeum vulgare Ubiquitin proteasome system (UPS) Biotic stress Abiotic stress |
| title | Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses |
| title_full | Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses |
| title_fullStr | Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses |
| title_full_unstemmed | Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses |
| title_short | Classification of barley U-box E3 ligases and their expression patterns in response to drought and pathogen stresses |
| title_sort | classification of barley u box e3 ligases and their expression patterns in response to drought and pathogen stresses |
| topic | Barley Hordeum vulgare Ubiquitin proteasome system (UPS) Biotic stress Abiotic stress |
| url | http://link.springer.com/article/10.1186/s12864-019-5696-z |
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