Genome-Wide Distribution, Expression and Function Analysis of the U-Box Gene Family in Brassica oleracea L.

Hu, Dengke; Xie, Qinqin; Liu, Qianying; Zuo, Tonghong; Zhang, Hecui; Zhang, Yizhong; Lian, Xiaoping; Zhu, Liquan

doi:10.3390/genes10121000

Cited by 18 publications

(16 citation statements)

References 73 publications

(66 reference statements)

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“…Most members of the U-box gene family are ligases, mediating the ubiquitination modification of protein, which enables ubiquitin to be combined with substrates to manipulate various protein activities ( Azevedo et al, 2001 ; Monaghan et al, 2009 ; Wang et al, 2015 ; You and He, 2016 ; Qin et al, 2020 ). It has been reported that the expression of U-box genes can affect their functions both in plant development and stress conditions ( Hu et al, 2018 , 2019 ; Lu et al, 2020 ; Sharma and Taganna, 2020 ; Wang J. et al, 2020 ; Wang N. et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

“…AtPUB11 degrades AtLRR1 (LEUCINE RICH REPEAT PROTEIN 1) and Atkin7 (KINASE 7), and negatively regulates ABA-mediated drought tolerance in Arabidopsis thaliana ( Chen X. X. et al, 2020 ). However, U-box genes have important value for plant resistance, and they have been identified in rice ( Oryza sativa ), tomato ( Solanum lycopersicum ), apple ( Malus domestica ), banana ( Musa nana ), soybean ( Glycine max ), Chinese cabbage ( Brassica rapa ), cotton ( Gossypium hirsutum ), and cabbage ( Brassica oleracea ) ( Azevedo et al, 2001 ; Li et al, 2009 ; Wang et al, 2015 , Wang J. et al, 2020 ; Wang K. L. et al, 2020 ; Hu et al, 2018 , 2019 ; Sharma and Taganna, 2020 ). However, comprehensive genome-wide identification of U-box genes in sorghum has not been performed, and expression characteristics have not been analyzed.…”

Section: Introductionmentioning

confidence: 99%

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Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Fang

Yang

et al. 2022

Front. Microbiol.

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The U-box family is one of the main E3 ubiquitin ligase families in plants. The U-box family has been characterized in several species. However, genome-wide gene identification and expression profiling of the U-box family in response to abiotic stress in Sorghum bicolor remain unclear. In this study, we broadly identified 68 U-box genes in the sorghum genome, including 2 CHIP genes, and 1 typical UFD2 (Ub fusion degradation 2) gene. The U-box gene family was divided into eight subclasses based on homology and conserved domain characteristics. Evolutionary analysis identified 14, 66, and 82 U-box collinear gene pairs in sorghum compared with arabidopsis, rice, and maize, respectively, and a unique tandem repeat pair (SbPUB26/SbPUB27) is present in the sorghum genome. Gene Ontology (GO) enrichment analysis showed that U-box proteins were mainly related to ubiquitination and modification, and various stress responses. Comprehensive analysis of promoters, expression profiling, and gene co-regulation networks also revealed that many sorghum U-box genes may be correlated with multiple stress responses. In summary, our results showed that sorghum contains 68 U-box genes, which may be involved in multiple abiotic stress responses. The findings will support future gene functional studies related to ubiquitination in sorghum.

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Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Fang

Yang

et al. 2022

Front. Microbiol.

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“…ARC1 is a typical E3 ubiquitin ligase in B. oleracea self-incompatibility, which plays an important role in the signal process of selfincompatibility. At the same time, PUB protein and ARC1 belong to E3 ubiquitin ligase, which may lead to self-incompatibility by negative regulation of pollen germination or interaction with SRK during B. oleracea self-incompatibility [53][54][55]. E3 ubiquitin ligase plays an important role in B. oleracea self-incompatibility, and BoGAPC may be involved in B. oleracea self-incompatibility by interacting with E3 ubiquitin ligase or producing other biological stress responses.…”

Section: Replication and Evolution Of Gapdh Gene In B Oleraceamentioning

confidence: 99%

Analysis of SI-Related BoGAPDH Family Genes and Response of BoGAPC to SI Signal in Brassica oleracea L.

Xie

Zhang

et al. 2021

Genes

Self Cite

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Glyceraldehyde 3-phosphate dehydrogenase (GAPDH) is not only involved in carbohydrate metabolism, but also plays an important role in stress resistance. However, it has not been reported in Brassica oleracea. In this study, we performed a genome-wide identification of BoGAPDH in B. oleracea and performed cloning and expression analysis of one of the differentially expressed genes, BoGAPC. A total of 16 members of the BoGAPDH family were identified in B. oleracea, which were conserved, distributed unevenly on chromosomes and had tandem repeat genes. Most of the genes were down-regulated during self-pollination, and the highest expression was found in stigmas and sepals. Different transcriptome data showed that BoGAPDH genes were differentially expressed under stress, which was consistent with the results of qRT-PCR. We cloned and analyzed the differentially expressed gene BoGAPC and found that it was in the down-regulated mode 1 h after self-pollination, and the expression was the highest in the stigma, which was consistent with the result of GUS staining. The promoter region of the gene not only has stress response elements and plant hormone response elements, but also has a variety of specific elements for regulating floral organ development. Subcellular localization indicates that the BoGAPC protein is located in the cytoplasm and belongs to the active protein in the cytoplasm. The results of prokaryotic expression showed that the size of the BoGAPC protein was about 37 kDa, which was consistent with the expected results, indicating that the protein was induced in prokaryotic cells. The results of yeast two-hybrid and GST pull-down showed that the SRK kinase domain interacted with the BoGAPC protein. The above results suggest that the BoGAPDH family of B. oleracea plays an important role in the process of plant stress resistance, and the BoGAPC gene may be involved in the process of self-incompatibility in B. oleracea, which may respond to SI by encoding proteins directly interacting with SRK.

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“…The 2000-bp sequences of sunflower PM H + -ATPase gene promoters were extracted from the H. annuus L. genome database [29]. The promoter Cis-acting elements were detected and identified using the PLACE database [36]. The distribution of salt stress-related Cis-acting elements were visualized by GSDS 2.0 [34].…”

Section: Cis-acting Elements Analysis Of Pm H + -Atpase Genes Promotementioning

confidence: 99%

Genome-Wide Identification and Analysis of P-Type Plasma Membrane H+-ATPase Sub-Gene Family in Sunflower and the Role of HHA4 and HHA11 in the Development of Salt Stress Resistance

Marowa

Liu

et al. 2020

Genes

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The P-type plasma membrane (PM) H+-ATPase plays a major role during the growth and development of a plant. It is also involved in plant resistance to a variety of biotic and abiotic factors, including salt stress. The PM H+-ATPase gene family has been well characterized in Arabidopsis and other crop plants such as rice, cucumber, and potato; however, the same cannot be said in sunflower (Helianthus annuus). In this study, a total of thirteen PM H+-ATPase genes were screened from the recently released sunflower genome database with a comprehensive genome-wide analysis. According to a systematic phylogenetic classification with a previously reported species, the sunflower PM H+-ATPase genes (HHAs) were divided into four sub-clusters (I, II, IV, and V). In addition, systematic bioinformatics analyses such as gene structure analysis, chromosome location analysis, subcellular localization predication, conserved motifs, and Cis-acting elements of promoter identification were also done. Semi-quantitative PCR analysis data of HHAs in different sunflower tissues revealed the specificity of gene spatiotemporal expression and sub-cluster grouping. Those belonging to sub-cluster I and II exhibited wide expression in almost all of the tissues studied while sub-cluster IV and V seldom showed expression. In addition, the expression of HHA4, HHA11, and HHA13 was shown to be induced by salt stress. The transgenic plants overexpressing HHA4 and HHA11 showed higher salinity tolerance compared with wild-type plants. Further analysis showed that the Na+ content of transgenic Arabidopsis plants decreased under salt stress, which indicates that PM H+ ATPase participates in the physiological process of Na+ efflux, resulting in salt resistance of the plants. This study is the first to identify and analyze the sunflower PM H+ ATPase gene family. It does not only lay foundation for future research but also demonstrates the role played by HHAs in salt stress tolerance.

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Genome-Wide Distribution, Expression and Function Analysis of the U-Box Gene Family in Brassica oleracea L.

Cited by 18 publications

References 73 publications

Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Identification, characterization, and expression profiling of the putative U-box E3 ubiquitin ligase gene family in Sorghum bicolor

Analysis of SI-Related BoGAPDH Family Genes and Response of BoGAPC to SI Signal in Brassica oleracea L.

Genome-Wide Identification and Analysis of P-Type Plasma Membrane H+-ATPase Sub-Gene Family in Sunflower and the Role of HHA4 and HHA11 in the Development of Salt Stress Resistance

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