Genome-wide identification, characterization, and expression analysis unveil the roles of pseudouridine synthase (PUS) family proteins in rice development and stress response

Dhingra, Yashika; Lahiri, Milinda; Bhandari, Nikunj; Kaur, Inderjit; Gupta, Shitij; Agarwal, Manu; Katiyar-Agarwal, Surekha (2023). Genome-wide identification, characterization, and expression analysis unveil the roles of pseudouridine synthase (PUS) family proteins in rice development and stress response. Physiology and Molecular Biology of Plants, 29(12), pp. 1981-2004. Springer 10.1007/s12298-023-01396-4

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Pseudouridylation, the conversion of uridine (U) to pseudouridine (Ѱ), is one of the most prevalent and evolutionary conserved RNA modifications, which is catalyzed by pseudouridine synthase (PUS) enzymes. Ѱs play a crucial epitranscriptomic role by regulating attributes of cellular RNAs across diverse organisms. However, the precise biological functions of PUSs in plants remain largely elusive. In this study, we identified and characterized 21 members in the rice PUS family which were categorized into six distinct subfamilies, with RluA and TruA emerging as the most extensive. A comprehensive analysis of domain structures, motifs, and homology modeling revealed that OsPUSs possess all canonical features of true PUS proteins, essential for substrate recognition and catalysis. The exploration of OsPUS promoters revealed presence of cis-acting regulatory elements associated with hormone and abiotic stress responses. Expression analysis of OsPUS genes showed differential expression at developmental stages and under stress conditions. Notably, OsTruB3 displayed high expression in salt, heat, and drought stresses. Several OsRluA members showed induction in heat stress, while a significant decline in expression was observed for various OsTruA members in drought and salinity. Furthermore, miRNAs predicted to target OsPUSs were themselves responsive to variable stresses, adding an additional layer of regulatory complexity of OsPUSs. Study of protein–protein interaction networks provided substantial support for the potential regulatory role of OsPUSs in numerous cellular and stress response pathways. Conclusively, our study provides functional insights into the OsPUS family, contributing to a better understanding of their crucial roles in shaping the development and stress adaptation in rice.

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