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

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

doi:10.1186/s12864-019-5696-z

Moon Young Ryu, Gu Min Kim + Show 10 more

Open Access

https://doi.org/10.1186/s12864-019-5696-z

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Abstract

BackgroundControlled 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.ResultsIn 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.ConclusionThis 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.

Highlights

Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses
We propose a re-classification of the Arabidopsis, rice and barley PLANT U-box (PUB) proteins into 10 Classes according to their functional domains using NCBI CDD and InterPro protein domain predictions
Identification of U-box E3 ligase encoding genes in the barley genome Based on the published high-quality reference genome sequence of barley (Hordeum vulgare) [36], BLAST searches using full length cDNA sequences and expressed sequence tags (ESTs) encoding U-box-type E3 ligases in Arabidopsis and rice as query sequences, 67 U-box E3 ligase encoding genes were predicted in barley (Fig. 1a, c)

Summary

Introduction

Controlled turnover of proteins as mediated by the ubiquitin proteasome system (UPS) is an important element in plant defense against environmental and pathogen stresses. Class II members (29 Arabidopsis; 28 rice) possess a variable number of Armadillo repeats (ARM) in their C-termini. These are thought to form an α-solenoid structure that might constitute a protein interaction domain [12,13,14]. Class VII members (1 Arabidopsis; 6 rice) contain a tetratrico-peptide repeat (TRP) domain, which has been shown to mediate protein-protein interactions [10]. Class VIII is rice specific and contains only one member, which in addition to the U-box domain possesses a TRP domain and a kinase domain. The U-box E3 ligase family in grapevine [15] and Medicago [16] has been separated into

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