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Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato.
Sci Rep. 2020 06 12; 10(1):9581.SR

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.

Authors+Show Affiliations

TERI School of Advanced Studies, 10 Institutional Area, Vasant Kunj, New Delhi, Delhi, 110070, India. bs211190@yahoo.com. School of Life and Environmental Sciences, Faculty of Science, Engineering, and Built Environment, Deakin University, Geelong, VIC-3220, Australia. bs211190@yahoo.com.SciBiz Informatics, 2/F Unit 3 CFI Building, Maharlika Highway, Brgy. Guindapunan, Palo, Leyte, 6501, Philippines.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

32533036

Citation

Sharma, Bhaskar, and Joemar Taganna. "Genome-wide Analysis of the U-box E3 Ubiquitin Ligase Enzyme Gene Family in Tomato." Scientific Reports, vol. 10, no. 1, 2020, p. 9581.
Sharma B, Taganna J. Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. Sci Rep. 2020;10(1):9581.
Sharma, B., & Taganna, J. (2020). Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. Scientific Reports, 10(1), 9581. https://doi.org/10.1038/s41598-020-66553-1
Sharma B, Taganna J. Genome-wide Analysis of the U-box E3 Ubiquitin Ligase Enzyme Gene Family in Tomato. Sci Rep. 2020 06 12;10(1):9581. PubMed PMID: 32533036.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome-wide analysis of the U-box E3 ubiquitin ligase enzyme gene family in tomato. AU - Sharma,Bhaskar, AU - Taganna,Joemar, Y1 - 2020/06/12/ PY - 2020/01/14/received PY - 2020/05/18/accepted PY - 2020/6/14/entrez PY - 2020/6/14/pubmed PY - 2020/12/15/medline SP - 9581 EP - 9581 JF - Scientific reports JO - Sci Rep VL - 10 IS - 1 N2 - 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. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/32533036/Genome_wide_analysis_of_the_U_box_E3_ubiquitin_ligase_enzyme_gene_family_in_tomato_ L2 - https://doi.org/10.1038/s41598-020-66553-1 DB - PRIME DP - Unbound Medicine ER -