Characterization of the Ubiquitin-Conjugating Enzyme Gene Family in Rice and Evaluation of Expression Profiles under Abiotic Stresses and Hormone Treatments.

Zhiguo E,Yuping Zhang,Tingting Li,Lei Wang,Heming Zhao,Girdhar K Pandey

doi:10.1371/journal.pone.0122621

Zhiguo E, Yuping Zhang + Show 4 more

Open Access

https://doi.org/10.1371/journal.pone.0122621

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Journal: PloS one	Publication Date: Apr 22, 2015
Citations: 53	License type: CC BY 4.0

Affiliation: China National Rice Research Institute

Abstract

Ubiquitin-conjugating enzyme E2s (UBCs), which catalyze the transfer of ubiquitin to substrate or E3 ligases, are key enzymes in ubiquitination modifications of target proteins. However, little is known about the knowledge of UBC gene family in rice. In this study, a total of 39 UBC encoding genes, which all contained an UBC domain with a cysteine active site, were identified in the rice genome. These were classified into fifteen distinct subfamilies based upon their sequence similarity and phylogenetic relationships. A subset of 19 OsUBC genes exhibited chromosomal duplication; 4 and 15 OsUBC genes were tandemly and segmentally duplicated, respectively. Comprehensive analyses were performed to investigate the expression profiles of OsUBC genes in various stages of vegetative and reproductive development using data from EST, Microarrays, MPSS, and real-time PCR. Many OsUBC genes exhibited abundant and tissue-specific expression patterns. Moreover, 14 OsUBCs were found to be differentially expressed under treatments with drought, or salt stresses. The expression analysis after treatments with IAA, 6-BA, GA and ABA indicated that almost all OsUBC genes were responsive to at least two of the four hormones. Several genes were significantly down-regulated under all of the hormone treatments, and most of the genes reduced by 6-BA were also reduced by GA. This study will facilitate further studies of the OsUBC gene family and provide useful clues for functional validation of OsUBCs in rice.

Highlights

Ubiquitination is the crucial regulatory step for the selective protein degradation mechanism in the ubiquitin-26S proteasome pathway in plants [1,2,3]
We used multiple bioinformatics resources in our efforts to comprehensively explore the entire Ubiquitin-conjugating enzyme E2s (UBCs) gene family in rice. 49 protein sequences were obtained through UBC domain searching with the MSU-RGAP (MSU-Rice Genome Annotation Project) database. 90 protein sequences of OsUBCs from japonica were deposited in InterPro of the European Bioinformatics Institute database
Considering the potential functional significance of UBC members and the fact that only a few UBC family members have been described in higher plants, it was timely and quite relevant for us to characterize the UBC gene family in rice

Summary

Introduction

Ubiquitination is the crucial regulatory step for the selective protein degradation mechanism in the ubiquitin-26S proteasome pathway in plants [1,2,3]. Ubiquitination is known to regulate important functions in a wide variety of plant growth and developmental processes including photomorphogenesis, vascular differentiation, flower development, both phytohormone and light signaling, as well as biotic and abiotic stress responses [4,5,6,7]. The key enzymes involved in PLOS ONE | DOI:10.1371/journal.pone.0122621. Ltd. Life Science and Technology Center, China National Seed Group Co., Ltd. provided support in the form of salary for author HZ, but did not have any additional role in the study design, data collection and analysis, decision to publish, or preparation of the manuscript. The specific role of this author is articulated in the ‘author contributions’ section

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