The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

Bin Huang,Zhijun Zhang,Ruifang Ma,Zhinuo Huang,Jialu Chen

doi:10.1186/s12864-021-07821-w

Abstract

BackgroundThe BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown.ResultIn the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis.ConclusionsIn conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

Highlights

The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses
In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family
Identification and characterization of PeBBX genes in P. edulis Putative BBX candidate genes were obtained from an HMMER3 search of the bamboo protein database using the plant BBX-type model (Pfam PF00643) with an Evalue threshold of ≤ 10− 5

Summary

Introduction

The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Transcription factors (TFs) are essential regulatory proteins that can activate or repress the expression of their target genes and play an important regulatory role in all eukaryotes [1]. This regulation is achieved through specific interactions between the DNA-binding domain of the TF and the promoter of the target gene. These interactions are affected by TF transcriptional activation. The zinc finger type of B1 is C-X2-C-X7-8-C-X2D-X-A-X-L-C-X2-C- D-X3-HB, while the zinc finger type of B2 is C-X2-C-X3-P-X4-C-X2-D-X3-L-C-X2-CD-X3-H [7, 8]

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