Promoter Cis-Element Analyses Reveal the Function of αVPE in Drought Stress Response of Arabidopsis

SIMPLE SUMMARY: Vacuolar processing enzyme (VPE) is a cysteine protease responsible for vacuolar proteins’ maturation and regulation of programmed cell death in plants. Among four isoforms of Arabidopsis thaliana VPEs, only the functions of βVPE, γVPE, and δVPE were determined. Hence, to investigate the possible function of αVPE, promoter analysis, co-expression network, gene expression profiling, and loss of function studies were performed. Repetitive drought-related cis-elements such as ABRE, MBS, MYC, and MYB were successfully identified with the aid of PlantCARE and PLACE databases. Similarly, the co-expression network also revealed that genes interacting with αVPE were involved in drought-regulation-related function. In addition, A. thaliana under drought treatment recorded an upregulation of αVPE expression (2.7-fold). Loss of function study through αvpe knockout mutants showed that αvpe mutants remained viable with 22% higher water retention as compared with wild-type after drought treatment. Biochemical analyses recorded a 47% reduction in proline activity, 70% decrease in sucrose content, and 39% lower MDA content, but 50% increased photosynthetic pigments in αvpe mutants. Altogether, our study provided important proof and a foundation for understanding the involvement of αVPE in modulating drought tolerance in A. thaliana. ABSTRACT: Vacuolar processing enzyme (VPE) is a cysteine protease responsible for vacuolar proteins’ maturation and regulation of programmed cell death (PCD). Four isoforms of Arabidopsis thaliana VPEs were identified previously, but only the functions of βVPE, γVPE, and δVPE were determined. The specific function of a gene is linked to the cis-acting elements in the promoter region. A promoter analysis found repetitive drought-related cis-elements in αVPE, which highlight its potential involvement in drought regulation in A. thaliana. The further co-expression network portraying genes interacting with αVPE substantiated its drought-regulation-related function. Expression of αVPE was upregulated after drought treatment in A. thaliana. To confirm the role of αVPE, a loss of function study revealed that αVPE knockout mutants remained green compared with WT after drought treatment. The mutants had reduced proline activity, decreased sucrose content, and lower MDA content, but increased photosynthetic pigments, indicating that αVPE negatively regulates drought tolerance in A. thaliana. Taken together, our findings serve as important evidence of the involvement of αVPE in modulating drought tolerance in A. thaliana.