Structure and Expression of OsUBP6, an Ubiquitin-Specific Protease 6 Homolog in Rice (Oryza sativa L.)

Moon, Yea Kyung; Hong, Jong Pil; Cho, Young Chan; Yang, Sang-Jin; An, Gynheung; Kim, Woo Taek

doi:10.1007/s10059-009-0138-4

Cited by 19 publications

(15 citation statements)

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“…Two of them already have known functions, including Os2-CysPrxA, which interacts with h-type thioredoxin 1 (OsTRXh1) and is involved in ABA sensitivity during seed germination and the early seedling stage (Zhang et al 2011). This PRX also interacts with EPSPS, which participates in tolerance to drought and salinity (Tuteja et al 2013); RPN10, which is related to canavanine resistance as a subunit of 26S proteasome (Takase et al 2004), and the ubiquitin specific protease 6 (OsUBP6), which is related to growth rates during the seedling stage as well as the transport of iron into the mitochondria (Moon et al 2009). These linkages suggest potential roles for Os2-CysPrxA in regulating ABA sensitivity, abiotic stress tolerance, normal plant development, and ubiquitin-dependent proteolysis at the cellular and molecular levels.…”

Section: Discussionmentioning

confidence: 99%

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Gho

Park

Kim

et al. 2017

Rice

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BackgroundPeroxiredoxins (PRXs) have recently been identified as plant antioxidants. Completion of various genome sequencing projects has provided genome-wide information about PRX genes in major plant species. Two of these -- Oryza sativa (rice) and Arabidopsis -- each have 10 PRX members. Although significant progress has been made in understanding their biological roles in Arabidopsis, those functions in rice, a model crop plant, have not been well studied.ResultsWe performed a comparative expression analysis of rice and Arabidopsis PRXs. Our phylogenetic analysis revealed that one subgroup contains three rice and three Arabidopsis Type-II PRXs that are expressed ubiquitously. This suggests that they are involved in housekeeping functions to process reactive oxygen species (ROS). Within the second subgroup, expression of Os1-CysPrxA (LOC_Os7g44430) and AtOs1-CysPrx is conserved in seeds while Os1-CysPrxB (LOC_Os7g44440) shows a root-preferential pattern of expression. We used transgenic plants expressing the GUS reporter gene under the control of the promoters of these two tandem duplicates to confirm their meta-expression patterns. Our GUS expression data from developing seeds and those that were germinating indicated that Os1-CysPrxB is involved in root development, as initiated from the embryo, while Os1-CysPrxA has roles in regulating endosperm development near the aleurone layer. For the third and fourth subgroups, the rice PRXs are more likely to show leaf/shoot-preferential expression, while those from Arabidopsis are significantly expressed in the flowers and seeds in addition to the leaf/shoot. To determine the biological meaning of those expression patterns that were dominantly identified in rice PRXs, we analyzed three rice genes showing leaf/shoot-preferential expression in a mutant of the light-responsive 1-deoxy-D-xylulose 5-phosphate reductoisomerase (dxr) gene and found that two of them were significantly down-regulated in the mutant.ConclusionA global expression analysis of the PRX family in rice identified tandem duplicates, Os1-CysPrxA and Os1-CysPrxB, in the 1-CysPrx subgroup that are differentially expressed in developing seeds and germinating seeds. Analysis of the cis-acting regulatory elements (CREs) revealed unique CREs responsible for embryo and root or endosperm-preferential expression. In addition, the presence of leaf/shoot-preferential PRXs in rice suggests that they are required in that crop because those plants must tolerate a higher light intensity in their normal growth environment when compared with that of Arabidopsis. Downregulation of two PRXs in the dxr mutant causing an albino phenotype, implying that those genes have roles in processing ROS produced during photosynthesis. Network analysis of four PRXs allowed us to model regulatory pathways that explain the underlying protein interaction network. This will be a useful hypothetical model for further study.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-017-0170-5) contains suppleme...

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Section: Discussionmentioning

confidence: 99%

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Gho

Park

Kim

et al. 2017

Rice

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“…We took a more stringent criterion and propose that there are 44 OsUBP genes in the rice genome (Supplementary Table S2 ). This dataset contains all OsUBP genes reported by Moon et al (2009) , except for Os08g41640 which contains neither a C12 nor a C19 domain.…”

Section: Resultsmentioning

confidence: 99%

“…Western blotting was carried out as described by Gu et al (2011) with modifications: primary antibody in a 1:1000 dilution (SantaCruz) and the secondary antibody (Promega) was added at concentration of 1:2000. The rice OsUBP6 (Os01g36930) protein was a positive control ( Moon et al, 2009 ).…”

Section: Methodsmentioning

confidence: 99%

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

et al. 2018

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The ubiquitin C-terminal hydrolase (UCH) and ubiquitin-specific processing protease (UBP) protein families both function in protein deubiquitination, playing important roles in a wide range of biological processes in animals, fungi, and plants. Little is known about the functions of these proteins in rice (Oryza sativa), and the numbers of genes reported for these families have not been consistent between different rice database resources. To further explore their functions, it is necessary to first clarify the basic molecular and biochemical nature of these two gene families. Using a database similarity search, we clarified the numbers of genes in these two families in the rice genome, examined the enzyme activities of their corresponding proteins, and characterized the expression patterns of all OsUCH and representative OsUBP genes. Five OsUCH and 44 OsUBP genes were identified in the rice genome, with four OsUCH proteins and 10 of 16 tested representative OsUBP proteins showing enzymatic activities. Two OsUCHs and five OsUBPs were found to be preferentially expressed in the early development of rice stamens. This work thus lays down a reliable bioinformatic foundation for future investigations of genes in these two families, particularly for exploring their potential roles in rice stamen development.

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“…So far, the second plant species with the most information on this family is rice, another angiosperm, where the preliminary characterisation of DUBs is emerging. OsUBP6 is involved in rice plant growth and is a member of the putative OsUBP family with another 20 members ( Moon et al, 2009 ). WTG1, which shows high sequence similarity to the human OTUB1 and controls kernel size and shape ( Huang et al, 2017 ).…”

Section: Remarks and Future Perspectivesmentioning

confidence: 99%

Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones

March

Farrona

2018

Front. Plant Sci.

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Selective degradation of proteins in the cell occurs through ubiquitination, which consists of post-translational deposition of ubiquitin on proteins to target them for degradation by proteases. However, ubiquitination does not only impact on protein stability, but promotes changes in their functions. Whereas the deposition of ubiquitin has been amply studied and discussed, the antagonistic activity, deubiquitination, is just emerging and the full model and players involved in this mechanism are far from being completely understood. Nevertheless, it is the dynamic balance between ubiquitination and deubiquitination that is essential for the development and homeostasis of organisms. In this review, we present a detailed analysis of the members of the deubiquitinase (DUB) superfamily in plants and its division in different clades. We describe current knowledge in the molecular and functional characterisation of DUB proteins, focusing primarily on Arabidopsis thaliana. In addition, the striking function of the duality between ubiquitination and deubiquitination in the control of gene expression through the modification of chromatin is discussed and, using the available information of the activities of the DUB superfamily in yeast and animals as scaffold, we propose possible scenarios for the role of these proteins in plants.

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Structure and Expression of OsUBP6, an Ubiquitin-Specific Protease 6 Homolog in Rice (Oryza sativa L.)

Cited by 19 publications

References 40 publications

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

Comparative Expression Analysis of Rice and Arabidopsis Peroxiredoxin Genes Suggests Conserved or Diversified Roles Between the Two Species and Leads to the Identification of Tandemly Duplicated Rice Peroxiredoxin Genes Differentially Expressed in Seeds

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

Plant Deubiquitinases and Their Role in the Control of Gene Expression Through Modification of Histones

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