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. 2022 Feb 14;14(2):392.
doi: 10.3390/v14020392.

Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa

Qiannan Liu  1   2 , Tingyun Yan  1   2 , Xiaoxiang Tan  1   2 , Zhongyan Wei  2 , Yanjun Li  2 , Zongtao Sun  2 , Hehong Zhang  2 , Jianping Chen  1   2
Affiliations

Genome-Wide Identification and Gene Expression Analysis of the OTU DUB Family in Oryza sativa

Qiannan Liu et al. Viruses. .

Abstract

Ovarian tumor domain (OTU)-containing deubiquitinating enzymes (DUBs) are an essential DUB to maintain protein stability in plants and play important roles in plant growth development and stress response. However, there is little genome-wide identification and analysis of the OTU gene family in rice. In this study, we identified 20 genes of the OTU family in rice genome, which were classified into four groups based on the phylogenetic analysis. Their gene structures, conserved motifs and domains, chromosomal distribution, and cis elements in promoters were further studied. In addition, OTU gene expression patterns in response to plant hormone treatments, including SA, MeJA, NAA, BL, and ABA, were investigated by RT-qPCR analysis. The results showed that the expression profile of OsOTU genes exhibited plant hormone-specific expression. Expression levels of most of the rice OTU genes were significantly changed in response to rice stripe virus (RSV), rice black-streaked dwarf virus (RBSDV), Southern rice black-streaked dwarf virus (SRBSDV), and Rice stripe mosaic virus (RSMV). These results suggest that the rice OTU genes are involved in diverse hormone signaling pathways and in varied responses to virus infection, providing new insights for further functional study of OsOTU genes.

Keywords: OTU DUB; genome-wide; plant hormone treatment; rice; virus infection.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Phylogenetic tree, motif analysis of OTUs, and conserved domain. (A) Phylogenetic analysis of OsOTU proteins in rice. (B) Conserved motif analysis of OsOTUs using MEME tools. Motifs are shown in different colored rectangles. (C) Conserved domain distributions of the out proteins in rice. The OTU domain and The Peptudase C65 domain are indicated in red and blue rectangles, respectively.
Figure 2
Figure 2
Phylogenetic analysis of OsOTU family proteins from Arabidopsis thaliana, Oryza sativa, and Zea mays. The phylogenetic tree was constructed using MEGA6.0 software by the neighbor-joining method with 1000 bootstrap replicates.
Figure 3
Figure 3
Exon–intron structure analysis of OsOTU family proteins. Green rectangles indicate untranslated regions (UTRs) from 5′and 3’, red rectangles indicate exons, and black lines indicate introns.
Figure 4
Figure 4
Prediction and analysis of OsOTU gene cis-acting elements. The potential cis-regulatory elements in the promoter regions 2000 bp upstream of the Oryza sativa were predicted by the PlantCARE website. Different colors indicated the elements related to growth and development (seed-specific regulation and root-specific), plant hormones (methyl jasmonate, abscisic acid, salicylic acid, gibberllin acid and auxin), and stress responsiveness (light, low temperature, and drought inducibility, defense and stress responsive).
Figure 5
Figure 5
The expression pattern of OsOTU genes under different hormone treatments. Plants were treated with SA (500 μM) (A), MeJA (100 μM) (B). Samples were collected at 0, 3, 6, and 12 h. The OsUBQ5 gene was the reference gene used to calibrate the relative gene expression. Error bars represent ±SE (n = 3). One-way analysis of variance was conducted by Duncan’s new multiple-range test, n = 3. * indicates significant differences from the mock control at p ≤ 0.05 by Fisher’s least significant difference tests.
Figure 6
Figure 6
The expression pattern of OsOTU genes under different hormone treatments. Plants were treated with NAA (50 μM). Samples were collected at 0, 3, 6, and 12 h. The OsUBQ5 gene was the reference gene used to calibrate the relative gene expression. Error bars represent ±SE (n = 3). One-way analysis of variance was conducted by Duncan’s new multiple-range test, n = 3. * indicates significant differences from the mock control at p ≤ 0.05 by Fisher’s least significant difference tests.
Figure 7
Figure 7
The expression pattern of OsOTU genes under different hormone treatments. Plants were treated with BL (10 μM) (A), ABA (50 μM) (B). Samples were collected at 0, 3, 6, and 12 h. The OsUBQ5 gene was the reference gene used to calibrate the relative gene expression. Error bars represent ±SE (n = 3). One-way analysis of variance was conducted by Duncan’s new multiple-range test, n = 3. * indicates significant differences from the mock control at p ≤ 0.05 by Fisher’s least significant difference tests.
Figure 8
Figure 8
The expression of OsOTU genes in response to RSV (A) and RBSDV (B) infection. Three biological replicate experiments were performed for each treatment and gene expression was detected by RT-qPCR. Samples were collected at 25 days post-inoculation (dpi) from RSV-infected plants and at 45 dpi from RBSDV-infected plants. The OsUBQ5 gene was used to normalize the relative gene expression. Error bars represent ±SE (n = 3). * indicates significant differences from the mock control at p ≤ 0.05 by Fisher’s least significant difference tests.
Figure 9
Figure 9
The expression of OsOTU genes in response to SRBSDV (A) and RSMV (B) infection. Three biological replicate experiments were performed for each treatment and gene expression was detected by RT-qPCR. Samples were collected at 40 dpi from RSV-infected plants and at 45 dpi from RSMV-infected plants. The OsUBQ5 gene was used to normalize the relative gene expression. Error bars represent ±SE (n = 3). * indicates significant differences from the mock control at p ≤ 0.05 by Fisher’s least significant difference tests.
Figure 10
Figure 10
Differential expression analysis of resistant ZH5 and susceptible ZS97 plants after RBSDV infection. (A) RT-qPCR results showing the relative expression of viral RNA (RBSDV genomic RNA segments S2, S4, and S6) in RBSDV-infected ZH11, ZS97, and ZH5 plants. (B) RT-qPCR verification of the expression of OsOTU genes between resistant ZH5 and susceptible ZS97 after RBSDV infection. Three biological replicate experiments were performed. Samples were collected at 30 dpi from RBSDV-infected ZH5 and ZS97 plants. The OsUBQ5 gene was used to normalize the relative gene expression level. Error bars represent ±SE (n = 3). * indicates significant differences from the mock control at p ≤ 0.05 by the Fisher’s least significant difference tests.
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