The banana E2 gene family: Genomic identification, characterization, expression profiling analysis

Chen, Dong; Hu, Huigang; Jue, Dengwei; Zhao, Qin; Chen, Hongliang; Xie, Jianghui; Jia, Liqiang

doi:10.1016/j.plantsci.2016.01.003

Cited by 18 publications

(35 citation statements)

References 58 publications

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“…The segmental duplication was dominant in tomato E2 genes than in banana, maize and rice. The class I motifs were the majority among banana 14 , maize 10 , papaya 35 and tomato which serve as a primary catalytic domain for ubiquitination activity. Arabidopsis UBC 1 and 2 orthologs in tomato SlUBC31 and SlUBC12 were expressed in roots and leaves as reported in Arabidopsis, but in tomato highly expressed in fruits as well, indicating a major role in fruit and root development.…”

Section: Discussionmentioning

confidence: 99%

“…The active-site cysteine (Cys) is located in a shallow groove between helix-2 and helix-3 8 . The previous reports on the identification of E2 enzymes members are 48 in rice 9 , 75 in maize 10 , 37 in Arabidopsis thaliana 11 , 20 in Caenorhabditis elegans 12 , 37 in human 5 , 13 in Saccharomyces cerevisiae 13 , and 72 in banana 14 . The evolution of eukaryotic genome is predicted to be associated with a number of E3 ligase enzymes and DUB 15 but as evident by previous reports 11 , 16 , extension of E2 ubiquitin conjugating enzymes are also seem to be linked with genome evolution.…”

Section: Introductionmentioning

confidence: 97%

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Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

Sharma

Bhatt

2017

Sci Rep

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The ubiquitin-proteasomal degradation mechanism has gained the attention over the past decade. The E2 ubiquitin conjugating enzymes are the crucial part of ubiquitination mechanism and they are believed to hold imperative association for plant development. It accepts ubiquitin from the E1 enzyme and interacts with the E3 ligase to transfer ubiquitin or directly transfers ubiquitin to the substrate. The functional aspects of E2 ubiquitin enzymes in plant systems are unclear. Tomato is being used as a model plant and rarely explored to study E2 ubiquitin enzyme. We have utilized in-silico methods to analyze E2 enzymes in Solanum lycopersicum and 59 genes were identified with UBC family domains. The physio-chemical properties, chromosomal localization, structural organization, gene duplication, promoter analysis, gene ontology and conserved motifs were investigated along with phylogenetic analysis of tomato E2 genes exploring evolutionary relations. The gene expression analysis of RNA sequencing data revealed expression profile of tomato E2 genes in seedling, root, leaf, seed, fruit, and flower tissues. Our study aid in the understanding of distribution, expansion, evolutionary relation and probable participation in plant biological processes of tomato E2 enzymes that will facilitate strong base for future research on ubiquitin-mediated regulations in tomato and other plant systems.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 97%

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

Sharma

Bhatt

2017

Sci Rep

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“…E2 enzymes belong to the polygenic family, and the number of members varies from a dozen to dozens in different species. 20 E2 enzymes have been found in Caenorhabditis elegans [77], 40 in A. thaliana [68], 14 in Saccharomyces cerevisiae [78], 37 in human [67], 48 in rice [79], 75 in maize [80], 72 in banana [81], 43 in Vitis vinifera [82], 34 in Carica papaya [83], 59 in tomato [84], 40 in Dimocarpus longan Lour. [85], and 57 in potato [86].…”

Section: The Family Of E2 Enzymesmentioning

confidence: 99%

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

Liu

Tang

et al. 2020

IJMS

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Owing to a sessile lifestyle in nature, plants are routinely faced with diverse hostile environments such as various abiotic and biotic stresses, which lead to accumulation of free radicals in cells, cell damage, protein denaturation, etc., causing adverse effects to cells. During the evolution process, plants formed defense systems composed of numerous complex gene regulatory networks and signal transduction pathways to regulate and maintain the cell homeostasis. Among them, ubiquitin-proteasome pathway (UPP) is the most versatile cellular signal system as well as a powerful mechanism for regulating many aspects of the cell physiology because it removes most of the abnormal and short-lived peptides and proteins. In this system, the ubiquitin-conjugating enzyme (E2) plays a critical role in transporting ubiquitin from the ubiquitin-activating enzyme (E1) to the ubiquitin-ligase enzyme (E3) and substrate. Nevertheless, the comprehensive study regarding the role of E2 enzymes in plants remains unexplored. In this review, the ubiquitination process and the regulatory role that E2 enzymes play in plants are primarily discussed, with the focus particularly put on E2 s regulation of biological functions of the cell. especially E3s (more than 1400 potential E3s are encoded in A. thaliana genome) and E2s (37 E2s are encoded in A. thaliana genome) [8,21]. Therefore, it will be an important task for future research to uncover the role of these enzymes. UbiquitinUbiquitin, a small protein of 76 amino acids acting as a tag in post-translational modification of proteins, is absolutely conserved in vertebrates and higher plants, and only two or three amino acid residues are different even among animals, plants, and fungi [22]. The high conservatism renders ubiquitin interchangeable and universal in different species [23]. Ubiquitin is a β-grasp fold protein consisting of a 3.5-turn α-helix, a short 3 10 helix against a five-strand mixed β-sheet and seven reverse turns [24]. Ubiquitin possesses two hydrophobic surfaces. One surface consists of Ile44, Leu8, Val70, and His68 [25], and the other focuses on Ile36 that can be recognized by HECT (Homology to E6-AP C terminus) E3s, DUBs (Deubiquitinating enzymes), and UBDs (Ubiquitin binding domains) [26][27][28]. Ubiquitin contains seven lysine residues, including Lys-6, Lys-11, Lys-27, Lys-29, Lys-33, Lys-48, Lys-63 (K6, K11, K27, K29, K33, K48, and K63, respectively) [29,30]. Six of the seven Lys linkages (with a preference for Lys-48>Lys-63>Lys-11>>>Lys-33/Lys-29/Lys-6) were detected in A. thaliana [31,32]. Any one of the seven lysine residues or N-terminal Met1 residues in ubiquitin is likely to be involved in ubiquitin chain formation in vivo, and different ubiquitin linkages lead to the formation of different types of ubiquitin chains and induce diverse molecular signals in the cell [29,[33][34][35][36]. Different ways of linking ubiquitin chains and substrates result in distinct fates of the substrates. It is well-known that K48-linked chains are mediators signaling proteasom...

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“…Class I E2s only contain the UBC domain; class II E2s contain the UBC domain and the N-terminal extensions; class III E2s contain the UBC domain and the C-terminal extensions; and class IV E2s contain the UBC domain and both N- and C-terminal extensions [ 4 , 6 ]. The UBC protein family is very different from the ancestral eukaryotes that possess fewer members (e.g., ≤20 in algae), to the multicellular plants and animals that possess more diverse proteins (e.g., ≥70 in banana and maize) [ 7 , 8 ]. In addition, the ubiquitin-like conjugating enzymes (UBLs), which include the related ubiquitin- (RUB) conjugating enzymes and the SUMO-conjugating enzymes, as well as the ubiquitin-conjugating enzyme variants (UEVs), were also found among the E2 classes.…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2018

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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.

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The banana E2 gene family: Genomic identification, characterization, expression profiling analysis

Cited by 18 publications

References 58 publications

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato

The Ubiquitin Conjugating Enzyme: An Important Ubiquitin Transfer Platform in Ubiquitin-Proteasome System

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

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