Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya

Jue, Dengwei; Sang, Xuelian; Shu, Bo; Liu, Liqin; Wang, Yicheng; Jia, Zhiwei; Zeng, Yu; Shi, Shengyou

doi:10.1371/journal.pone.0171357

Cited by 13 publications

(21 citation statements)

References 55 publications

(84 reference statements)

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“…It is well understood that the gene organization on the genome is also responsible for their diversity among species 34 . Although a large variation in the distribution of introns was observed but majority comprises similar structural organization containing 4 to 6 introns, compared to E2 genes in maize with 3–4 10 and 5 introns in Carica papaya 35 . The structural insights of E2 genes reveal strong structural integrity.…”

Section: Discussionmentioning

confidence: 91%

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: 91%

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%

“…Therefore, this will be the direction for research in this field shortly. 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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“…The B. rapa sequences were downloaded from the database ( http://brassicadb.org/brad/ ), while for other species rice [ 9 ] ( http://rice.plantbiology.msu.edu/ ), tomato [ 8 ] ( https://solgenomics.net/organism/Solanum_lycopersicum/ genome ), Maize [ 10 ] ( https://www.maizegdb.org/ ), Vitis vinifera [ 7 ], and Carica papaya [ 11 ] sequences were downloaded based on the reported studies. From Pfam database ( https://pfam.sanger.ac.uk/ ) the E2 UBC domains (PF00179) were first downloaded and Hidden Markov Model (HMM) search was carried out in Brassica genome with default parameters.…”

Section: Methodsmentioning

confidence: 99%

“…Some of the recent studies highlighted that involvement of E2 genes family exited as multifunctional and playing key parts in various physiological activities. In several crops, such as in grapes 43 [ 7 ], tomato 59 [ 8 ], rice 39 [ 9 ], maize 75 [ 10 ], Carica papaya 34 [ 11 ], and Arabidopsis 41 [ 12 ], genes were identified, respectively, as during the process of evolution the number of genes of E2 increases with the complex nature and the development of organism [ 13 ]. For example, fewer genes ≤ 20 in algae were found in ancestral eukaryotes compared to certain plants and animals > 40 [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses inBrassica rapa

Khan

et al. 2018

BioMed Research International

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To understand ubiquitination mechanism, E2s (ubiquitin conjugating enzymes) have crucial part as they play a major role in regulating many biological processes in plants. Meanwhile, Brassica rapa is an important leafy vegetable crop and therefore its characterization along with the expression pattern of E2s under various stresses is imperative. In this study, a total of 83 genes were identified in B. rapa and were classified into four different classes based on domain information. Here, we analyzed phylogenetic relationships, collinear correlation, gene duplication, interacting network, and expression patterns of E2 genes in B. rapa. Furthermore, RT-PCR analysis for 8 multiple abiotic and hormone treatments (namely, ABA, GA, JA, BR, PEG, NaCl, and heat and cold stress) illustrated striking expression pattern under one or more treatments, speculating that these might be stress-responsive genes. The cis-elements and interaction network analyses implicate valuable clues of important function of E2 genes in development and multiple stress responses in B. rapa. This study will further facilitate functional analysis of E2s for improving stress resistance mechanism in B. rapa.

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Characterization and expression analysis of genes encoding ubiquitin conjugating domain-containing enzymes in Carica papaya

Cited by 13 publications

References 55 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

Evolution and Expression Divergence of E2 Gene Family under Multiple Abiotic and Phytohormones Stresses inBrassica rapa

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