Comprehensive Workflow for the Genome-wide Identification and Expression Meta-analysis of the ATL E3 Ubiquitin Ligase Gene Family in Grapevine

Abstract

Classification and nomenclature of genes in a family can significantly contribute to the description of the diversity of encoded proteins and to the prediction of family functions based on several features, such as the presence of sequence motifs or of particular sites for post-translational modification and the expression profile of family members in different conditions. This work describes a detailed protocol for gene family characterization. Here, the procedure is applied to the characterization of the Arabidopsis Tóxicos in Levadura (ATL) E3 ubiquitin ligase family in grapevine. The methods include the genome-wide identification of family members, the characterization of gene localization, structure, and duplication, the analysis of conserved protein motifs, the prediction of protein localization and phosphorylation sites as well as gene expression profiling across the family in different datasets. Such procedure, which could be extended to further analyses depending on experimental purposes, could be applied to any gene family in any plant species for which genomic data are available, and it provides valuable information to identify interesting candidates for functional studies, giving insights into the molecular mechanisms of plant adaptation to their environment.

Expression Patterns and Functional Analysis of 11 E3 Ubiquitin Ligase Genes in Rice

“…E3 ubiquitin ligases have been reported to function in several processes, including the responses to biotic and abiotic stresses ( Ariani et al, 2017 ; Sun et al, 2019 , 2022 ; Zhang et al, 2019 ; Du et al, 2021 ; Sharma et al, 2021 ). First, E3 ubiquitin ligases are involved in response to biotic stresses.…”

The Grapevine E3 Ubiquitin Ligase VriATL156 Confers Resistance against the Downy Mildew Pathogen Plasmopara viticola

“…We previously described a small group of grapevine genes encoding RING-H2 E3 ubiquitin ligases that were more strongly or specifically expressed in the resistant species Vitis riparia than its susceptible relative V. vinifera following infection with P. viticola [ 17 ]. All these genes belong to the ATL subfamily, associated with defense in Arabidopsis thaliana and other species [ 18 , 19 , 20 , 21 , 22 ]. Following extensive characterization of the grapevine ATL gene family and meta-analysis of the transcriptome datasets, we found that the expression of these genes is induced in response to a range of pathogens [ 20 ] and co-regulated together with key components of the resistance signaling cascade [ 22 ].…”