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

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 l...

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Main Authors:	Bhaskar Sharma, Joemar Taganna
Format:	article
Language:	EN
Published:	Nature Portfolio 2020
Subjects:	Medicine R Science Q
Online Access:	https://doaj.org/article/76b7e3708c99428a858c9b019fc733f9
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spelling	oai:doaj.org-article:76b7e3708c99428a858c9b019fc733f92021-12-02T17:52:33ZGenome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato10.1038/s41598-020-66553-12045-2322https://doaj.org/article/76b7e3708c99428a858c9b019fc733f92020-06-01T00:00:00Zhttps://doi.org/10.1038/s41598-020-66553-1https://doaj.org/toc/2045-2322Abstract 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.Bhaskar SharmaJoemar TagannaNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 10, Iss 1, Pp 1-15 (2020)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bhaskar Sharma Joemar Taganna Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
description	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.
format	article
author	Bhaskar Sharma Joemar Taganna
author_facet	Bhaskar Sharma Joemar Taganna
author_sort	Bhaskar Sharma
title	Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
title_short	Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
title_full	Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
title_fullStr	Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
title_full_unstemmed	Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato
title_sort	genome-wide analysis of the u-box e3 ubiquitin ligase enzyme gene family in tomato
publisher	Nature Portfolio
publishDate	2020
url	https://doaj.org/article/76b7e3708c99428a858c9b019fc733f9
work_keys_str_mv	AT bhaskarsharma genomewideanalysisoftheuboxe3ubiquitinligaseenzymegenefamilyintomato AT joemartaganna genomewideanalysisoftheuboxe3ubiquitinligaseenzymegenefamilyintomato
_version_	1718379174795673600

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

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