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

Wu, Ruihua; Shi, Yanrong; Zhang, Qian; Zheng, Wenqing; Chen, Shao Liang; Du, Liqing; Lu, Cunfu

doi:10.3390/ijms20174309

Cited by 18 publications

(25 citation statements)

References 62 publications

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“…Full-length cDNA clones of CWMV and WYMV RNAs have previously been constructed (Yang et al, 2016;Zhang et al, 2019). 'cv Yangmai 158 plants at the three leaf-stage were inoculated with inoculation buffer (as controls), CWMV or WYMV.…”

Section: Plant Growth Sa Treatment and Inoculation Of Virusmentioning

confidence: 99%

“…It is predicted that CWMV RNA2 encodes four proteins, including a coat protein (CP), two minor CP-related proteins (N-CP and CP-RT), and a cysteine-rich protein (CRP) (Andika et al, 2013;Diao et al, 1999;Sun et al, 2013a;Sun et al, 2013b). WYMV belongs to the genus Bymovirus, family Potyviridae, and has a genome containing two positive single RNA strands (Zhang et al, 2019). Both WYMV RNA1 and WYMV RNA2 encode a polyprotein, respectively.…”

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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Section: Plant Growth Sa Treatment and Inoculation Of Virusmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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

Peng

Liu

et al. 2021

PeerJ

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“…Homologous pairs of UGDH genes were obtained with Clustal X2.1 and used to calculate the non-synonymous substitution (Ka) and synonymous substitution (Ks) rates with KaKs Calculator 2.0. The Ks value can be used to calculate the divergence time (T) 50 . Specifically, because the special synonymous substitution rate (λ) for moso bamboo is 6.5 × 10 −9 , the divergence time was calculated with the following equation: T = Ks/2λ 51 .…”

Section: Peugdh Protein Alignment and Phylogenetic Analysismentioning

confidence: 99%

Genome-wide identification and characterization of UDP-glucose dehydrogenase family genes in moso bamboo and functional analysis of PeUGDH4 in hemicellulose synthesis

Yang

Kang

et al. 2020

Sci Rep

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Uridine diphosphate glucose dehydrogenases (UGDHs) are critical for synthesizing many nucleotide sugars and help promote the carbohydrate metabolism related to cell wall synthesis. In plants, UGDHs are encoded by a small gene family. Genome-wide analyses of these genes have been conducted in Glycine max and Arabidopsis thaliana, however, the UGDH gene family has not been comprehensively and systematically investigated in moso bamboo (Phyllostachys edulis), which is a special woody grass monocotyledonous species. In this study, we identified nine putative PeUGDH genes. Furthermore, analysis of gene duplication events and divergences revealed that the expansion of the PeUGDH family was mainly due to segmental and tandem duplications approximately 4.76-83.16 million years ago. An examination of tissue-specific PeUGDH expression indicated that more than 77% of the genes were predominantly expressed in the stem. Based on relative expression levels among PeUGDH members in different tissues in moso bamboo, PeUGDH4 was selected for detailed analysis. The results of subcellular localization indicated that PeUGDH4-GFP fusion proteins was observed to be localized in the cytoplasm. The ectopic overexpression of PeUGDH4 in Arabidopsis significantly increased the contents of hemicellulose and soluble sugar, suggesting that PeUGDH4 acts as a key enzyme involved in bamboo cell wall synthesis. The presence of a cell wall, which provides rigidity and flexibility, is one of the main characteristics that differentiates plant cells from animal cells. The cell wall, comprised mainly of complex polysaccharides (cellulose, hemicellulose, and pectin) and some structural proteins, is critical for plant growth 1-3. Additionally, UDP-glucose (UDP-Glc) is the chief form of activated sugar, representing a branch point of glucose metabolism 4 and a major substrate in many glycosylation reactions. For example, UDP-Glc is the substrate used by sucrose phosphate synthase to synthetize sucrose-6-phosphate in the cytosol. Moreover, in plastids, UDP-Glc is essential for the direct or indirect (via ADP-glucose) production of starch 5. Therefore, UDP-Glc is indispensable for the synthesis of sucrose, cellulose, and callose, which contribute to cell wall formation. The UDP-glucose dehydrogenases (UGDHs) are involved in the synthesis of matrix polysaccharides and can convert UDP-glucose into UDP-glucuronate (UDP-GlcA) and produce two NAD + molecules. Furthermore, UDP-GlcA is not only the intermediate pivot of polysaccharide metabolism, it is also an important glucuronic acid donor during cell wall polysaccharide synthesis. Previous studies revealed that UDP-GlcA continues to be glycosylated to form UDP-galacturonic acid, UDP-xylose, UDP-apiose, and other nucleoside sugars participating in the biosynthesis of hemicellulose and pectin, which represent over half of the cell wall biomass in Arabidopsis

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“…Andrade et al [53] described the role that the JRL domain plays in conjunction with the dirigent domain (dirigent-jacalin, or DJ) in drought tolerance, thus demonstrating the role of chimeric lectin in abiotic stress. Thus far, genome-wide analysis of SBP-like [53], ARF [54], MADS-box [55], UBP [56], MYB [57] and other gene families has been performed in Moso bamboo, but there is little known about the occurrence of different D-J lectins within bamboo species, despite the sequencing of its genome several years ago [58]. The new assembly of the Moso bamboo genome offers an opportunity to improve our understanding of the abundance, distribution and expansion of bamboo lectins [59].…”

Section: Introductionmentioning

confidence: 99%

Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis)

Huang

Chen

et al. 2021

PLoS ONE

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Dirigent-jacalin (D-J) genes belong to the plant chimeric lectin family, and play vital roles in plant growth and resistance to abiotic and biotic stresses. To explore the functions of the D-J family in the growth and development of Moso bamboo (Phyllostachys edulis), their physicochemical properties, phylogenetic relationships, gene and protein structures, and expression patterns were analyzed in detail. Four putative PeD-J genes were identified in the Moso bamboo genome, and microsynteny and phylogenetic analyses indicated that they represent a new branch in the evolution of plant lectins. PeD-J proteins were found to be composed of a dirigent domain and a jacalin-related lectin domain, each of which contained two different motifs. Multiple sequence alignment and homologous modeling analysis indicated that the three-dimensional structure of the PeD-J proteins was significantly different compared to other plant lectins, primarily due to the tandem dirigent and jacalin domains. We surveyed the upstream putative promoter regions of the PeD-Js and found that they mainly contained cis-acting elements related to hormone and abiotic stress response. An analysis of the expression patterns of root, leaf, rhizome and panicle revealed that four PeD-J genes were highly expressed in the panicle, indicating that they may be required during the formation and development of several different tissue types in Moso bamboo. Moreover, PeD-J genes were shown to be involved in the rapid growth and development of bamboo shoots. Quantitative Real-time PCR (qRT PCR) assays further verified that D-J family genes were responsive to hormones and stresses. The results of this study will help to elucidate the biological functions of PeD-Js during bamboo growth, development and stress response.

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

Cited by 18 publications

References 62 publications

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

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

Genome-wide identification and characterization of UDP-glucose dehydrogenase family genes in moso bamboo and functional analysis of PeUGDH4 in hemicellulose synthesis

Genome-wide identification and expression analysis of dirigent-jacalin genes from plant chimeric lectins in Moso bamboo (Phyllostachys edulis)

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