Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection

Lin, Zihan; Nie, Hongtao; Zhang, Yanming; Yin, Zhihui; Yan, Xiwu

doi:10.1016/j.cbd.2022.101012

Cited by 7 publications

(5 citation statements)

References 106 publications

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“…The U-box type E3 family contains 79 members in maize ( Li et al., 2022 ), 68 in sorghum ( Fang et al., 2022 ) and 62 in tomato ( Sharma and Taganna, 2020 ); this family is slightly larger in size than the E2 family. Furthermore, the E3 genes are involved in plant development, growth and abiotic stress response, which is consistent with the functions of E2 genes reported previously ( Sharma and Taganna, 2020 ; Wang et al., 2021 ; Fang et al., 2022 ; Li et al., 2022 ; Lin et al., 2022 ).…”

Section: Discussionsupporting

confidence: 91%

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Yao

Xie

et al. 2023

Front. Plant Sci.

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Ubiquitin-conjugating enzyme (UBC) is a critical part of the ubiquitin–proteasome pathway and plays crucial roles in growth, development and abiotic stress response in plants. Although UBC genes have been detected in several plant species, characterization of this gene family at the whole-genome level has not been conducted in Brassica napus. In the present study, 200 putative BnUBCs were identified in B. napus, which were clustered into 18 subgroups based on phylogenetic analysis. BnUBCs within each subgroup showed relatively conserved gene architectures and motifs. Moreover, the gene expression patterns in various tissues as well as the identification of cis-acting regulatory elements in BnUBC promoters suggested further investigation of their potential functions in plant growth and development. Furthermore, three BnUBCs were predicted as candidate genes for regulating agronomic traits related to oil content and yield through association mapping. In conclusion, this study provided a wealth of information on the UBC family in B. napus and revealed their effects on oil content and yield, which will aid future functional research and genetic breeding of B. napus.

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Section: Discussionsupporting

confidence: 91%

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Yao

Xie

et al. 2023

Front. Plant Sci.

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“…Changes in the expression of SjHECTs in response to heat stress indicated that SjHECTs play an important role during heat shock. The similar result was reported in the Ruditapes philippinarum HECT involved in heat shock stress, wherein a part of the gene expression was signi cantly up-regulated (Lin et al 2022). Under heat stress, misfolded and damaged proteins accumulate in cells (Dikic 2017), which required the UPS system to function and greatly increases the requirement of HECT ligase.…”

Section: Expression Characteristic Ofsjhect Genes At Different Develo...supporting

confidence: 78%

Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Saccharina japonica and a comparative analysis with five other algae

Huang

Liu

et al. 2023

Preprint

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Homologous to E6-associated protein Carboxyl Terminus (HECT) is one important family of E3 ubiquitin ligase superfamily involved in the ubiquitin-proteasome pathway. This gene family plays widely roles in the regulation of growth, development and signaling pathways in different organisms, as a specific key molecule in ubiquitin signal transduction. Large number of studies have focused on the identification and characterization of HECT E3 ligase in plants and animals, but studies in Ochrophyta, a phylogenetic lineage that is distantly related to terrestrial plants and animals, are very scarce. This study comprehensively analyzed the HECT E3 ligase gene family in algae Saccharina japonica with significant economic and ecological value. Eighteen HECT E3 ligase members were identified in S. japonica genome, and the physicochemical parameters, phylogenetic relationships, structural mechanisms, functional annotations, and gene expression of these E3 ligases were analyzed and characterized. Additionally, the HECT E3 genes were also identified from other five algae genomes. A total of 90 HECT E3 from the six algae species were used to elucidate the evolutionary relatedness of the HECT gene family in algae. The resulted phylogenetic tree revealed that the HECT family was mainly divided into six branches. Protein structure analysis revealed the conservation of the HECT domain in the entire gene family, showing the substrate binding and structure-function relationships. A large number of regulatory elements involved in stress, hormone regulation, light response, growth and development were identified in the promoter region of SjHECT E3 genes. Expression analysis indicated that members in different SjHECT gene subfamilies might play specific roles in the growth and heat stress response of S. japonica. Overall, the identification and analysis of the HECT E3 gene family in S. japonica laid the foundation for further study on the function and regulatory pathways of HECT in Ochrophyta species.

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“…Previous studies have reported significant upregulation of genes encoding proteasome and antioxidant enzymes in Chlamys opercularis when exposed to the toxin domoic acid ( Ventoso et al, 2019 ). Similarly, genes involved in the ubiquitin-proteasome pathway were found to be significantly upregulated after R. philippinarum infection with Vibrio anguillarum ( Lin et al, 2022 ). Among the identified key DEGs in the present study, PSMCs and PSMDs belong to the 26s proteasome, which consists of a 20s core granule and two 19s regulatory granules.…”

Section: Discussionmentioning

confidence: 99%

Exploration of anti-stress mechanisms in high temperature exposed juvenile golden cuttlefish (Sepia esculenta) based on transcriptome profiling

Wang

Bao

et al. 2023

Front. Physiol.

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Sepia esculenta is a cephalopod widely distributed in the Western Pacific Ocean, and there has been growing research interest due to its high economic and nutritional value. The limited anti-stress capacity of larvae renders challenges for their adaptation to high ambient temperatures. Exposure to high temperatures produces intense stress responses, thereby affecting survival, metabolism, immunity, and other life activities. Notably, the molecular mechanisms by which larval cuttlefish cope with high temperatures are not well understood. As such, in the present study, transcriptome sequencing of S. esculenta larvae was performed and 1,927 differentially expressed genes (DEGs) were identified. DEGs were subjected to functional enrichment analyses using the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases. The top 20 terms of biological processes in GO and 20 high-temperature stress-related pathways in KEGG functional enrichment analysis were identified. A protein-protein interaction network was constructed to investigate the interaction between temperature stress-related genes. A total of 30 key genes with a high degree of participation in KEGG signaling pathways or protein-protein interactions were identified and subsequently validated using quantitative RT-PCR. Through a comprehensive analysis of the protein-protein interaction network and KEGG signaling pathway, the functions of three hub genes (HSP90AA1, PSMD6, and PSMA5), which belong to the heat shock protein family and proteasome, were explored. The present results can facilitate further understanding of the mechanism of high temperature resistance in invertebrates and provide a reference for the S. esculenta industry in the context of global warming.

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Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Ruditapes philippinarum and their involvement in the response to heat stress and Vibrio anguillarum infection

Cited by 7 publications

References 106 publications

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Genome-wide characterization of ubiquitin-conjugating enzyme gene family explores its genetic effects on the oil content and yield of Brassica napus

Genome-wide identification and analysis of HECT E3 ubiquitin ligase gene family in Saccharina japonica and a comparative analysis with five other algae

Exploration of anti-stress mechanisms in high temperature exposed juvenile golden cuttlefish (Sepia esculenta) based on transcriptome profiling

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