Genome-wide identification of growth-regulating factors in moso bamboo (Phyllostachys edulis): in silico and experimental analyses.

Yanan Shi,Yan Xiang,Huanlong Liu,Yujiao Wang,Min Wu,Yameng Gao

doi:10.7717/peerj.7510

Yanan Shi, Yan Xiang + Show 4 more

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https://doi.org/10.7717/peerj.7510

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Abstract

Growth-regulating factor (GRF), a small plant-specific transcription factor (TF) family, is extensively involved in the regulation of growth and developmental processes. However, the GRF family has not been comprehensively studied in moso bamboo (Phyllostachys edulis), a typical non-timber forest member. Here, 18 GRF genes were identified and characterized from the moso bamboo genome, and they clustered into three subfamilies (A, B and C). PeGRF genes were analyzed to determine their gene structures, conserved motifs and promoter. The non-synonymous/synonymous substitution ratios of paralogous and orthologous were less than 1, indicating that the GRF family mainly experienced purifying selection during evolution. According to the analysis of tissue-specific expression patterns, the participation of moso bamboo GRFs might be required during the formation and development of these five tissues. Moreover, PeGRF proteins might be involved in the regulation of plant development in biological processes. The qRT-PCR analysis demonstrated that PeGRF genes played essential roles in combating hormonal stresses and they might be involved in hormone regulation. PeGRF11, a nuclear localized protein as assessed by a subcellular localization assay, could interact with PeGIF3 in yeast and in planta according to yeast two-hybridization and bimolecular fluorescence complementation assays (BiFC) assays. But PeGRF11, as a TF, had no transcriptional activity in yeast. These results provide useful information for future functional research on the GRF genes in moso bamboo.

Highlights

Bamboo is an important non-timber forest product worldwide, that financially supports nearly 250 million people (Peng et al, 2013)
Identification and sequence analyses of moso bamboo Growth-regulating factor (GRF) genes A BLASTP analysis-based search was performed against the moso bamboo genome database using the consensus protein sequences from the Hidden Markov Model profile as a query
We identified 18 PeGRF genes from moso bamboo genome, which were further classified into three subfamilies based on phylogenetic relationship analysis

Summary

Introduction

Bamboo is an important non-timber forest product worldwide, that financially supports nearly 250 million people (Peng et al, 2013). The QLQ conserved region is found in the yeast SWI2/SNF2 protein, which interacts with SNF11 to form a complex that participates in chromatin remodeling (Ma et al, 2017; Zhang et al, 2018) This protein–protein interaction domain, combines with the SNH domain of the GRF–interacting factor (GIF) family, which leads to the formation of the GRF–GIF complex involved in transcriptional activation (Kim, Choi & Kende, 2003). Less-conserved motifs including FFD (Phe, Phe, Asp) and TQL (Thr, Gln, Leu) are remained in the C-termini of several GRF proteins (Kim, Choi & Kende, 2003; Ma et al, 2017)

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