Genome-wide investigation of pentatricopeptide repeat gene family in poplar and their expression analysis in response to biotic and abiotic stresses

Haitao Xing,Li Guo,Xiaofeng Tang,Chen Yang,Changzheng Xu,Xiaokang Fu,Keming Luo,Chaofeng Li

doi:10.1038/s41598-018-21269-1

Abstract

Pentatricopeptide repeat (PPR) proteins, which are characterized by tandem 30–40 amino acid sequence motifs, constitute of a large gene family in plants. Some PPR proteins have been identified to play important roles in organellar RNA metabolism and organ development in Arabidopsis and rice. However, functions of PPR genes in woody species remain largely unknown. Here, we identified and characterized a total of 626 PPR genes containing PPR motifs in the Populus trichocarpa genome. A comprehensive genome-wide analysis of the poplar PPR gene family was performed, including chromosomal location, phylogenetic relationships and gene duplication. Genome-wide transcriptomic analysis showed that 154 of the PtrPPR genes were induced by biotic and abiotic treatments, including Marssonina brunnea, salicylic acid (SA), methyl jasmonate (MeJA), mechanical wounding, cold and salinity stress. Quantitative RT-PCR analysis further investigated the expression profiles of 11 PtrPPR genes under different stresses. Our results contribute to a comprehensive understanding the roles of PPR proteins and provided an insight for improving the stress tolerance in poplar.

Highlights

The pentatricopeptide repeat (PPR) proteins are characterized by an assembly of 2 to about 30 degenerate tandem repeats of approximately 35 amino acid residues that mediate their RNA-binding activities[1,2]
626 PPR proteins, of which 346 members belong to the P subfamily and 280 ones belong to the PLS subfamily, were identified in P. trichocarpa (Supplemental Table 1)
A previous study has shown that seven PtrPPR genes have complementary sites of PtrmiR474, PtrmiR475 and PtrmiR47634

Summary

Introduction

The pentatricopeptide repeat (PPR) proteins are characterized by an assembly of 2 to about 30 degenerate tandem repeats of approximately 35 amino acid residues that mediate their RNA-binding activities[1,2]. The P subfamily proteins with orthodox 35 amino acid PPR motifs participate in a wide range of organelle RNA-processing activities, including determination and stabilization of 50 and/or 30 termini, RNA splicing and translation initiation[3]. Another PLS subfamily of PPR proteins, which is specific to land plants, generally contain the P motif and two P motif-derived variants, including the short (S) and the long (L) motifs[1]. The Arabidopsis mutant of Slow Growth 1 (slg1) affected shoot growth and negatively regulated drought stress and ABA signaling[24] Another PPR protein SLO2 was identified to regulate plant growth. Our results provide an insight on the molecular mechanisms of these PtrPPR genes in response to environmental stresses in poplar

Methods

Results

Conclusion