Genome-wide identification and characterization of the RPA gene family in maize

TL;DR

This study identifies and characterizes the RPA gene family in maize, revealing their roles in growth, development, and stress responses.

Contribution

The study provides the first comprehensive analysis of the RPA gene family in maize, including phylogeny, expression patterns, and protein interactions.

Findings

Thirteen ZmRPA genes were identified and classified into three subgroups based on phylogenetic analysis.

ZmRPA genes are highly conserved and associated with light-responsive and developmental processes.

Some ZmRPA genes show stress-responsive expression and are highly expressed in meristems and reproductive tissues.

Abstract

The Replication Protein A (RPA) is a highly conserved heterotrimeric complex that binds single-stranded DNA and interacts with multiple proteins, playing essential roles in DNA replication, repair, and homologous recombination, thereby maintaining genome stability and supporting normal development. However, the specific members and functions of the RPA gene family remain uncharacterized in maize.

In this study, 13 ZmRPA members in maize were identified, which exhibited a wide range of protein lengths, from 86 to 876 amino acids. A phylogenetic analysis of these ZmRPA genes revealed their classification into three distinct subgroups: RPA1, RPA2, and RPA3. Notably, within each subgroup, the motifs of ZmRPA proteins were similar, although variations were observed among different subfamilies. An analysis of gene duplication events suggests that RPA genes have remained highly conserved in maize. Furthermore, the analysis of cis-elements indicated that RPA genes are associated with light-responsive, as well as plant growth and development. RNA-seq analysis revealed that some ZmRPA genes exhibited pronounced expression changes under cold and drought stresses, while the results of tissue-specific expression analysis showed that most ZmRPA genes were highly expressed in the actively dividing meristems and reproductive primordia. Protein interaction and yeast two-hybrid assays revealed that ZmRPA family members interact with each other to perform their biological functions.

Collectively, these findings suggest that ZmRPA family subunits may play important roles in plant growth and development, as well as stress responses, by forming various types of heteromeric complexes through protein interactions. This study provides a comprehensive understanding of the RPA gene family in maize and will facilitate further effective characterization of the RPA genes.

The online version contains supplementary material available at 10.1186/s12870-026-08280-9.

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