Abstract
BackgroundPentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. A large majority of the PPR genes in the higher plants are localized in organelles. Their functions remain as yet largely unknown. The majority of characterized PPR proteins have been found to function in modulating the expression plastid and mitochondrial genes in plants.ResultsHere, a genome-wide identification and comparison of the PPR genes from 5 organisms was performed, including the moss Physcomitrella patens, the lycophyte Selaginella moellendorffii, the eudicot Arabidopsis, and the monocots rice and foxtail millet. It appears that the expansion of this gene family prior to the divergence of the euphyllophytes and the lycophytes in land plants. The duplication and divergence rates of the foxtail millet PPR genes (SiPPRs) showed that the expansion period of this gene family around 400 Mya, and indicated that genome segmental duplication was very likely the primary mechanism underlying the expansion of the PPR gene family in vascular plants. An analysis of a complete set of SiPPR genes/proteins that included classification, chromosomal location, orthologous relationships, duplication analysis, and auxiliary motifs is presented. Expression analysis of the SiPPR genes under stress conditions revealed that the expression of 24 SiPPR genes was responsive to abiotic stress. Subcellular localization analysis of 11 PPR proteins indicated that 5 proteins were localized to chloroplasts, that 4 were localized to mitochondria, and that 2 were localized to the cytoplasm.ConclusionsOur results contribute to a more comprehensive understanding the roles of PPR proteins and will be useful in the prioritization of particular PPR proteins for subsequent functional validation studies in foxtail millet.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3184-2) contains supplementary material, which is available to authorized users.
Highlights
Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs
While subsequent analysis revealed that the pentatricopeptide repeat (PPR) proteins are found in a few animal and fungal proteins, but it is clear that the family has expanded greatly in land plants; there are with 450 PPR genes in Arabidopsis and 477 PPR genes in rice (Oryza sativa) [6,7,8, 15]
In order to investigate the functional conservation of the PPR proteins in foxtail millet, we examined the presence of PPR-LAGLIDADG proteins in a broad range of species to explore their origins and diversification
Summary
Pentatricopeptide repeat (PPR) proteins are encoded by a large gene family of approximately 450 members in Arabidopsis and 477 in rice, which characterized by tandem repetitions of a degenerate 35 amino acid characteristic sequence motifs. The pentatricopeptide repeat (PPR) proteins represent one of the largest protein families in land plants (450 members in Arabidopsis and 477 members in rice) This family was identified serendipitously over a decade ago as a result of bioinformatics analyses of the incomplete Arabidopsis genome sequence [6]. Most of the functional analyses of PPR proteins have been performed Arabidopsis, rice, or maize (Zea mays), and these studies revealed that they participate in various post-transcriptional processes related to gene expression in plant organelles [11,12,13,14, 19,20,21,22]. Functional studies of PPR proteins relating to biotic and abiotic stress response mechanisms in higher plants remain very sparse, and the characterization of these proteins remains one a major challenge in plant science
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