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

Abstract 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 e...

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Autores principales:	Bhaskar Sharma, Tarun Kumar Bhatt
Formato:	article
Lenguaje:	EN
Publicado:	Nature Portfolio 2017
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/6399d8d3e1e443ae8396fb22c23d9606
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spelling	oai:doaj.org-article:6399d8d3e1e443ae8396fb22c23d96062021-12-02T11:52:39ZGenome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato10.1038/s41598-017-09121-42045-2322https://doaj.org/article/6399d8d3e1e443ae8396fb22c23d96062017-08-01T00:00:00Zhttps://doi.org/10.1038/s41598-017-09121-4https://doaj.org/toc/2045-2322Abstract 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.Bhaskar SharmaTarun Kumar BhattNature PortfolioarticleMedicineRScienceQENScientific Reports, Vol 7, Iss 1, Pp 1-12 (2017)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Bhaskar Sharma Tarun Kumar Bhatt Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
description	Abstract 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.
format	article
author	Bhaskar Sharma Tarun Kumar Bhatt
author_facet	Bhaskar Sharma Tarun Kumar Bhatt
author_sort	Bhaskar Sharma
title	Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
title_short	Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
title_full	Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
title_fullStr	Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
title_full_unstemmed	Genome-wide identification and expression analysis of E2 ubiquitin-conjugating enzymes in tomato
title_sort	genome-wide identification and expression analysis of e2 ubiquitin-conjugating enzymes in tomato
publisher	Nature Portfolio
publishDate	2017
url	https://doaj.org/article/6399d8d3e1e443ae8396fb22c23d9606
work_keys_str_mv	AT bhaskarsharma genomewideidentificationandexpressionanalysisofe2ubiquitinconjugatingenzymesintomato AT tarunkumarbhatt genomewideidentificationandexpressionanalysisofe2ubiquitinconjugatingenzymesintomato
_version_	1718394988795002880

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

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