The Ubiquitin-Conjugating Enzyme Gene Family in Longan (Dimocarpus longan Lour.): Genome-Wide Identification and Gene Expression during Flower Induction and Abiotic Stress Responses.

Dengwei Jue,Bo Shu,Jianghui Xie,Chengming Liu,Yicheng Wang,Liqin Liu,Shengyou Shi,Xuelian Sang

doi:10.3390/molecules23030662

Abstract

Ubiquitin-conjugating enzymes (E2s or UBC enzymes) play vital roles in plant development and combat various biotic and abiotic stresses. Longan (Dimocarpus longan Lour.) is an important fruit tree in the subtropical region of Southeast Asia and Australia; however the characteristics of the UBC gene family in longan remain unknown. In this study, 40 D. longan UBC genes (DlUBCs), which were classified into 15 groups, were identified in the longan genome. An RNA-seq based analysis showed that DlUBCs showed distinct expression in nine longan tissues. Genome-wide RNA-seq and qRT-PCR based gene expression analysis revealed that 11 DlUBCs were up- or down-regualted in the cultivar “Sijimi” (SJ), suggesting that these genes may be important for flower induction. Finally, qRT-PCR analysis showed that the mRNA levels of 13 DlUBCs under SA (salicylic acid) treatment, seven under methyl jasmonate (MeJA) treatment, 27 under heat treatment, and 16 under cold treatment were up- or down-regulated, respectively. These results indicated that the DlUBCs may play important roles in responses to abiotic stresses. Taken together, our results provide a comprehensive insight into the organization, phylogeny, and expression patterns of the longan UBC genes, and therefore contribute to the greater understanding of their biological roles in longan.

Highlights

IntroductionUbiquitylation ( called ubiquitinylation or ubiquitination) is the covalent attachment of ubiqutin (Ub) to substrate proteins
Ubiquitylation is the covalent attachment of ubiqutin (Ub) to substrate proteins
The expression levels measured by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR) for Six D. longan UBC genes (DlUBCs) genes (DlUBC11, 16, 19, 20, 30 and 31) randomly selected were similar to the results obtained from the RNA-seq data (Figure 5)

Summary

Introduction

Ubiquitylation ( called ubiquitinylation or ubiquitination) is the covalent attachment of ubiqutin (Ub) to substrate proteins. Ubiquitin is a small protein containing 76 amino acids that is highly conserved in eukaryotes; only three residues differ between yeast, human, and plant species [1,2]. The process of protein ubiquitination (ubiquitin-proteasome system, UPS) is mediated through the action of three enzymes, E1 (Ub-activating enzyme, UBA), E2 (Ub-conjugating enzyme, UBC), and E3. Ub is first linked to E1 through an ATP-dependent reaction that creates a thioester bond between the C-terminus of Ub and the cysteine in the active site of E1. The activated Ub is transferred via a thioester bond from E1 to a cysteine residue of E2, before ubiquitin is transferred either to a substrate directly aided by E3 or to a cysteine of an alternative ubiquitin protein ligase (E3s) by a second transthiolation reaction to the target substrate.

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