Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato

Bhaskar Sharma,Joemar Taganna

doi:10.1038/s41598-020-66553-1

Bhaskar Sharma, Joemar Taganna

Open Access

https://doi.org/10.1038/s41598-020-66553-1

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Abstract

E3 ubiquitin ligases are a central modifier of plant signaling pathways that act through targeting proteins to the degradation pathway. U-box E3 ubiquitin ligases are a distinct class of E3 ligases that utilize intramolecular interactions for its scaffold stabilization. U-box E3 ubiquitin ligases are prevalent in plants in comparison to animals. However, the evolutionary aspects, genetic organizations, and functional fate of the U-box E3 gene family in plant development, especially in tomato is not well understood. In the present study, we have performed in-silico genome-wide analysis of the U-box E3 ubiquitin ligase gene family in Solanum lycopersicum. We have identified 62 U-box genes with U-box/Ub Fusion Degradation 2 (UFD2) domain. The chromosomal localization, phylogenetic analysis, gene structure, motifs, gene duplication, syntenic regions, promoter, physicochemical properties, and ontology were investigated. The U-box gene family showed significant conservation of the U-box domain throughout the gene family. Duplicated genes discerned noticeable functional transitions among duplicated genes. The gene expression profiles of U-box E3 family members show involvement in abiotic and biotic stress signaling as well as hormonal pathways. We found remarkable participation of the U-box gene family in the vegetative and reproductive tissue development. It is predicted to be actively regulating flowering time and endosperm formation. Our study provides a comprehensive picture of distribution, structural features, promoter elements, evolutionary relationship, and gene expression of the U-box gene family in the tomato. We predict the crucial participation of the U-box gene family in tomato plant development and stress responses.

Highlights

Ubiquitin mediated proteasomal degradation is one of the major mechanisms for post-translational regulation of gene expression and protein quality control in eukaryotes[1,2]
U-box containing armadillo repeats were not found in root tissues of Arabidopsis thaliana, while our results exclusively show a strong pattern of SlU-box 14, 25, and 43 carrying armadillo repeats revealing the intervention of the U-box E3 ubiquitin ligase in tomato plant growth and development
E3 ubiquitin ligase is the largest family of the ubiquitin proteasomal degradation mechanism that regulates the ubiquitination of the substrates[5,59]

Summary

Introduction

Ubiquitin mediated proteasomal degradation is one of the major mechanisms for post-translational regulation of gene expression and protein quality control in eukaryotes[1,2]. The major classes of the E3 ubiquitin ligases are; RING (Really Interesting New Gene), HECT (Homologous to E6-associated protein C terminus), CRL (Cullin-RING ligase) and U-box[5] They mediate the transfer of the ubiquitin-protein to the substrate by either generating an intermediate complex (E3 and Ubiquitin) or directly[9,10,11]. The U-box gene family is an important E3 ubiquitin ligase that influences many plants signaling pathways and acts differently than other E3 enzyme classes. The identification of the U-box gene family members in the tomato will help to understand the evolutionary and functional aspects of ubiquitin proteasomal degradation system in plants and the extent of involvement of the U-box E3 ubiquitin ligase in the cellular systems and signaling pathways. It will support to develop efficient approaches for agricultural challenges and aid in our understanding on the role of ubiquitin proteasomal degradation in plant system

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