Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice (Oryza sativa)

Wang, Donghui; Song, Wei; Wei, Shaowei; Zheng, Yafeng; Chen, Zhi-Shan; Han, Jing-Dan; Zhang, Hongtao; Luo, Jianxun; Qin, Yong-Mei; Xu, Zhi-Hong; Bai, Shu-Nong

doi:10.3389/fpls.2018.01636

Cited by 26 publications

(31 citation statements)

References 56 publications

(77 reference statements)

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“…To analyze the phylogenetic relationship of the UBPs among different species and study the potential functions of PeUBPs, a Neighbor-joining phylogenetic tree was constructed based on the alignments of 132 full-length UBP protein sequences from moso bamboo (48), rice (25) [28], A. thaliana (27) [13], and purple false brome ( Brachypodium distachyon ) (29). The detailed characteristics of the UBP genes from A. thaliana (Dicotyledonous subfamily), rice ( Oryza sativa ; Poaceae subfamily), and B. distachyon (close relationship with moso bamboo; Monocotyledons ) are listed in supplementary Table S1.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

Shi

Zhang

et al. 2019

IJMS

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The largest group of deubiquitinases—ubiquitin-specific proteases (UBPs)—perform extensive and significant roles in plants, including the regulation of development and stress responses. A comprehensive analysis of UBP genes has been performed in Arabidopsis thaliana, but no systematic study has been conducted in moso bamboo (Phyllostachys edulis). In this study, the genome-wide identification, classification, gene, protein, promoter region characterization, divergence time, and expression pattern analyses of the UBPs in moso bamboo were conducted. In total, 48 putative UBP genes were identified in moso bamboo, which were divided into 14 distinct subfamilies in accordance with a comparative phylogenetic analysis using 132 full-length protein sequences, including 48, 27, 25, and 32 sequences from moso bamboo, A. thaliana, rice (Oryza sativa), and purple false brome (Brachypodium distachyon), respectively. Analyses of the evolutionary patterns and divergence levels revealed that the PeUBP genes experienced a duplication event approximately 15 million years ago and that the divergence between PeUBP and OsUBP occurred approximately 27 million years ago. Additionally, several PeUBP members were significantly upregulated under abscisic acid, methyl jasmonate, and salicylic acid treatments, indicating their potential roles in abiotic stress responses in plants.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

Shi

Zhang

et al. 2019

IJMS

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“…The eukaryotic-specific UBP family is one of the largest families of DUBs, and it acts in plant growth and development. UBP families have been identified and characterized in several organisms, including A. thaliana (Yan et al, 2000), rice (Wang et al, 2018a) , Moso Bamboo (Wu et al, 2019), yeast (Wilkinson, 1997) and M. oryzae (Cai et al, 2020).…”

Section: Discussionmentioning

confidence: 99%

“…Three data sets were used for phylogenetic analysis, including identified TaUBP protein sequences, 27 AtUBP protein sequences (Liu et al, 2008) downloaded from TAIR (https://www.arabidopsis.org/), and 25 UBP protein sequences in O. sativa (OsUBPs) (Wang et al, 2018a) downloaded from the Rice Genome Annotation Project (http://rice.plantbiology.msu.edu/downloads_gad.shtml). Multiple sequence alignments were performed through MEGA-X software using MUSCLE function.…”

Section: Multiple Sequence Alignments and Phylogenetic Analysismentioning

confidence: 99%

“…The stability of the E3 ubiquitin ligase MARCH6 is regulated by USP19 (Nakamura et al, 2014). Currently, 16 Ubp genes in yeast (Wilkinson, 1997), 27 UBP genes in A. thaliana (Yan et al, 2000) and 25 UBP genes in rice (Wang et al, 2018a) have been identified. Studies in yeast have revealed several Ubps-controlled processes, such as stress responses, energy metabolism, nutrient utilization and sexual reproduction (Auesukaree et al, 2009;Dudley et al, 2005;Kahana, 2001).…”

Section: Introductionmentioning

confidence: 99%

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Genome-wide identification and characterization of UBP gene family in wheat (Triticum aestivum L.)

Peng

Liu

et al. 2021

PeerJ

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Ubiquitination is essential for plant growth and development. Deubiquitination cooperates with ubiquitination to regulate the ubiquitination levels of target proteins. The ubiquitin-specific protease (UBP) family is the largest group of deubiquitinases (DUBs), which perform extensive and significant roles in eukaryotic organisms. However, the UBP genes in wheat (TaUBPs) are not identified, and the functions of TaUBPs are unknown. The present study identified 97 UBP genes in the whole genome of T. aestivum. These genes were divided into 15 groups and non-randomly distributed on chromosomes of T. aestivum. Analyses of evolutionary patterns revealed that TaUBPs mainly underwent purification selection. The studies of cis-acting regulatory elements indicated that they might be involved in response to hormones. Quantitative real-time PCR (qRT-PCR) results showed that TaUBPs were differentially expressed in different tissues. Besides, several TaUBPs were significantly up-regulated when plants were treated with salicylic acid (SA), implying that these DUBs may play a role in abiotic stress responses in plants and few TaUBPs displayed differential expression after viral infection. Furthermore, TaUBP1A.1 (TraesCS1A02G432600.1) silenced by virus-induced gene silencing (VIGS) facilitates Chinese wheat mosaic virus (CWMV) infection in wheat, indicating that TaUBP1A.1 may be involved in a defense mechanism against viruses. This study comprehensively analyzed the UBP gene family in wheat and provided a basis for further research of TaUBPs functions in wheat plant response to viral infection.

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“…Additionally, there were also some other domains appeared in the PtrJAMM proteins. To analyze the phylogenetic relationship of the DUB proteins among different species including Arabidopsis thaliana, rice, and Populus trichocarpa, five Neighbor-joining phylogenetic trees were constructed based on the alignments of full-length DUB protein sequences from Arabidopsis thaliana (27 UBPs, 12 OTUs, 3 MJDs, 3 UCHs, and 8 JAMM), rice (44 UBPs, 22OTUs, 2 MJDs, 5 UCHs, and 9 JAMM)[33], Populus trichocarpa(44 UBPs, 23 OTUs, 4 MJDs,3…”

mentioning

confidence: 99%

The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns

Zheng

2020

Preprint

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Background: The deubiquitinases (DUB) family are a class of enzymes that regulate the stability or reverse the ubiquitination modification of many proteins in the cell, participating in cell cycle regulation, cell division and differentiation, various physiological activities such as DNA damage repair, growth and development, and response to stress. However, little is known about these genes in the woody plants. Results: In the present study, 88 DUB genes were identified in woody model plant Populus trichocarpa, including 44 PtrUBP, 3 PtrUCH, 23 PtrOTU, 4 PtrMJD, and 14 PtrJAMM with similar domains. According to the phylogenetic analysis, the 44 PtrUBP genes were classified into 14 subfamily, three PtrUCHs were classified into two groups, 23 PtrOTUs had six groups, four PtrMJDs had two groups, and 14 PtrJAMMs had six groups. The structure and motif analysis indicated that the same subfamily had similar genome structure and motif distribution characteristics. Ks/Ka analysis showed that the segmental duplication events played a major role in the expansion of Populus DUB genes. Synteny analysis of Populus DUB genes and four other species provided deep perception into the evolutionary traits of DUB genes. Expression profiles derived from transcriptome data exhibited distinct expression patterns of DUB genes in various tissues. Based on the result of promoter cis-regulatory elements analysis, we selected 16 representative PtrUBP genes to test their response to different hormonal treatments. The results showed that most of PtrUBPs were upregulated in the ABA, SA, and MeJA treatments, implying that their potential roles in abiotic stress response in Populus. Conclusion: The results in this study broaden our understanding of the DUB gene family in plants, and the analysis of the structure, conserved elements, and expression patterns of the DUBs provide a solid foundation for exploring their specific functions in Populus as well as indicate potential role of PtrUBP gene in abiotic stress.

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Characterization of the Ubiquitin C-Terminal Hydrolase and Ubiquitin-Specific Protease Families in Rice (Oryza sativa)

Cited by 26 publications

References 56 publications

Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

Genome-Wide Identification and Characterization of the UBP Gene Family in Moso Bamboo (Phyllostachys edulis)

Genome-wide identification and characterization of UBP gene family in wheat (Triticum aestivum L.)

The DUBs Family in Populus: Identification, Characterization, Evolution and Expression Patterns

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