Genome-Wide Identification and Characterization of the <i>PPPDE</i> Gene Family in Rice
Wangmin Lian,
Xiaodeng Zhan,
Daibo Chen,
Weixun Wu,
Qunen Liu,
Yinxing Zhang,
Shihua Cheng,
Xiangyang Lou,
Liyong Cao,
Yongbo Hong
Affiliations
Wangmin Lian
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Xiaodeng Zhan
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Daibo Chen
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Weixun Wu
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Qunen Liu
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Yinxing Zhang
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Shihua Cheng
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Xiangyang Lou
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Liyong Cao
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Yongbo Hong
China National Center for Rice Improvement, State Key Laboratory of Rice Biology and Breeding, Zhejiang Key Laboratory of Super-Rice, China National Rice Research Institute, Hangzhou 311401, China
Protein ubiquitination is common and crucial in cellular functions, however, little is known about how deubiquitinating enzymes (DUBs) reverse regulate the ubiquitination signaling process. PPPDE family proteins are a novel class of deubiquitinating peptidases with demonstrated deubiquitination/deSUMOylating activities. In this study, we identified 10 PPPDE genes from the rice (Oryza sativa L.) genome unevenly distributed on five chromosomes, where most of these members have not been reported to date. Based on the gene structure, the OsPPPDE family consists of three distinct subgroups within the phylogenetic tree. Cis-element analysis identified light/phytohormone-responsive, development, and abiotic stress-related elements in the promoters of OsPPPDE. Furthermore, we conducted and analyzed the transcript abundance of OsPPPDE under various tissues and stresses using the transcriptome data of 352 samples from the Rice Expression Database and GEO datasets. Moreover, OsPPPDE5 showed differential regulation of its transcript abundance during Cd and drought stress. Collinearity and syntenic analysis of 101 PPPDEs and PPPDE-like proteins in 10 plant genomes indicated that this family is evolutionarily conserved. Domestication analysis suggests that OsPPPDEs may contribute to indica–japonica divergence using the data from the 3K Rice Genome Project. Our study provides a foundation for further study on the function and molecular mechanism of the OsPPPDE gene family.
