Decoding rice seed storage proteins: From gene identification to structural prediction

Abstract

Background and Aims: Rice seed storage proteins (SSPs) are major determinants of grain nutritional quality, serving as primary sources of dietary protein, energy, and essential nutrients. However, limited understanding of their diversity, evolution, and regulation constrains efforts to improve grain quality. This study aimed to perform a comprehensive genome-wide characterization of SSPs in rice. Methods: A combined homology- and domain-based approach was employed to identify SSP-encoding genes in the rice genome. These proteins were further analysed through phylogenetic reconstruction, domain and motif characterization, promoter cis-element analysis, expression profiling across seed developmental stages, and three-dimensional structural modelling. Key Results: A total of 65 SSP genes were identified, including 19 previously uncharacterized members. Phylogenetic and domain analyses revealed evolutionary relationships between albumins and prolamins, and between globulins and glutelins. Tandem clustering of albumins, glutelins, and prolamins suggested gene duplication as a major driver of SSP family expansion. Expression profiling indicated that albumins, globulins, and glutelins were transcriptionally active from the S2 stage, whereas prolamins were predominantly expressed from the S3 stage onwards. Promoter analysis identified several seed-specific cis-regulatory elements, including CAATBOX1, EBOXBNNAPA, and DOFCOREZM. Structural modelling showed that albumins and prolamins are primarily composed of α-helices, while globulins and glutelins are enriched in β-strands and coils. Conclusions: This integrative analysis provides comprehensive insights into the classification, evolution, regulatory mechanisms, and structural features of rice SSPs. The findings establish a valuable resource for future functional studies and offer a foundation for strategies aimed at improving grain nutritional quality.