Pentatricopeptide repeat proteins in maize

Abstract

Nucleus-encoded pentatricopeptide repeat proteins (PPRs) are a superfamily of ubiquitous RNA-binding factors involved in organellar gene expression. To date, a large number of PPR genes have been identified and some of them have been functionally analyzed in higher plants, while the family in maize [Zea mays (Zm)] has long been unknown. In this study, a genome-scale analysis was conducted to identify all ZmPPR gene members, and exon/intron structure, chromosomal mapping and gene duplication events were analyzed. Then, homology modeling was used to explore structure-function relationships. Finally, publically transcriptome data and real-time PCR were used for studying gene expression. A total of 521 PPR-encoding genes were predicted to occur in the maize genome and unevenly distributed on ten chromosomes. More than 66% PPR genes rarely contain introns and similar exon/intron structural patterns were observed in the same classes/subclasses. Three-dimensional (3D) structural modeling of ZmPPR479 provided insights into the mechanism of RNA recognition. The transcript abundance of 471 genes detected in 60 different developmental stages reveled that some members exhibit tissue-specific expression. Under salt stress, five significantly differentially expressed genes were found in crown root (CR) and ten detected in primary root (PR) and seminal root (SR), respectively. For drought stress, the expressions of seven ZmPPRs showed obvious upregulation in leaf, whereas ten genes were significantly downregulated. Additionally, the expression of 25 and 145 genes were evidently increased and decreased in cob, respectively. Furthermore, the expression patterns of 18 ZmPPRs were confirmed using quantitative real-time PCR.