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. 2017 Aug 17;7(1):8613.
doi: 10.1038/s41598-017-09121-4.

Genome-wide Identification and Expression Analysis of E2 Ubiquitin-Conjugating Enzymes in Tomato

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Free PMC article

Genome-wide Identification and Expression Analysis of E2 Ubiquitin-Conjugating Enzymes in Tomato

Bhaskar Sharma et al. Sci Rep. .
Free PMC article

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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.

Conflict of interest statement

The authors declare that they have no competing interests.

Figures

Figure 1
Figure 1
The diagram represents chromosomal map of tomato genome constructed by ArkMap software. All 59 E2 enzymes of tomato are localized on 12 chromosomes.
Figure 2
Figure 2
The phylogenetic tree of the Solanum lycopersicum E2 members is constructed by Neighbour-Joining method with 1000 bootstrap values. The E2 enzymes are divided into four classes and represented by different colors.
Figure 3
Figure 3
The discovered conserved motifs in all 59 sequences of tomato E2 enzymes are illustrated. A total of 10 motifs were discovered and their organization on the protein is represented by color boxes.
Figure 4
Figure 4
The exon/intron distribution of corresponding 59 identified tomato E2 enzymes was detected by comparing coding sequences (CDS) with their corresponding genomic sequences using GSDS tool online. The green box represents CDS; the blue boxes indicate upstream or downstream; the discontinuous lines refer to introns.
Figure 5
Figure 5
The word cloud image of promoter elements of 59 E2 ubiquitin conjugating enzymes. The size and intensity indicate frequency of the elements.
Figure 6
Figure 6
A gene expression profile of 59 tomato E2 enzyme sequences in seed, seedling, root, vegetative, leaf, flower and fruit tissue of Micro Tom, Heinz 1706, M82, Moneymaker, SUN1642, and Alisa Craig cultivars of tomato is illustrated. The normalized gene expression level is represented by a color scale histogram.
Figure 7
Figure 7
A gene expression profile of 59 tomato E2 enzyme sequences during hormone treatment and pathogen infection in root, leaf and fruit tissues of Micro Tom, Avigail, Hongtaiyamg, Moneymaker cultivars of tomato. The normalized gene expression level is represented by a color scale histogram.

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