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

PLoS One. 2015 Apr 22;10(4):e0122621. doi: 10.1371/journal.pone.0122621. eCollection 2015.

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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Chromosomes, Plant / genetics
  • Gene Duplication / drug effects
  • Gene Expression Profiling*
  • Genomics
  • Molecular Sequence Data
  • Oryza / drug effects
  • Oryza / enzymology
  • Oryza / genetics*
  • Oryza / physiology*
  • Phylogeny
  • Plant Growth Regulators / pharmacology*
  • Reproduction / drug effects
  • Reproduction / genetics
  • Sequence Alignment
  • Stress, Physiological / genetics*
  • Ubiquitin-Conjugating Enzymes / chemistry
  • Ubiquitin-Conjugating Enzymes / genetics*

Substances

  • Plant Growth Regulators
  • Ubiquitin-Conjugating Enzymes

Grants and funding

This research was supported by the special fund for Agro-Scientific Research in the Public Interest (201203031, 201203029, 201003016) and the Special Foundation for Basic Research and the Development of Central Level Scientific Research Institutes in China (2012RG006). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Heming Zhao is employed by Life Science and Technology Center, China National Seed Group Co., 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.