Genomic Organization, Phylogenetic and Expression Analysis of the B-BOX Gene Family in Tomato.

Zhuannan Chu,Jinhua Li,Ying Li,Bo Ouyang,Hanxia Li,Xin Wang,Yongen Lu,Huiyang Yu

doi:10.3389/fpls.2016.01552

Abstract

The B-BOX (BBX) proteins encode a class of zinc-finger transcription factors possessing one or two B-BOX domains and in some cases an additional CCT (CO, CO-like and TOC1) motif, which play important roles in regulating plant growth, development and stress response. Nevertheless, no systematic study of BBX genes has undertaken in tomato (Solanum lycopersicum). Here we present the results of a genome-wide analysis of the 29 BBX genes in this important vegetable species. Their structures, conserved domains, phylogenetic relationships, subcellular localizations, and promoter cis-regulatory elements were analyzed; their tissue expression profiles and expression patterns under various hormones and stress treatments were also investigated in detail. Tomato BBX genes can be divided into five subfamilies, and twelve of them were found to be segmentally duplicated. Real-time quantitative PCR analysis showed that most BBX genes exhibited different temporal and spatial expression patterns. The expression of most BBX genes can be induced by drought, polyethylene glycol-6000 or heat stress. Some BBX genes were induced strongly by phytohormones such as abscisic acid, gibberellic acid, or ethephon. The majority of tomato BBX proteins was predicted to be located in nuclei, and the transient expression assay using Arabidopsis mesophyll protoplasts demonstrated that all the seven BBX members tested (SlBBX5, 7, 15, 17, 20, 22, and 24) were localized in nucleus. Our analysis of tomato BBX genes on the genome scale would provide valuable information for future functional characterization of specific genes in this family.

Highlights

Transcription factors are a class of proteins that regulate every aspect of plant life
To obtain a global view of the BBX genes in tomato genome, keyword and BLAST searches were performed at Sol Genomics Network database (SGN), NCBI, and other public databases
For the sake of consistency, we named these genes as SlBBX1 to SlBBX29 according to their homology to the BBX members of Arabidopsis firstly, and the rest members were named depending on their homology to the newly named tomato BBX genes

Summary

Introduction

Transcription factors are a class of proteins that regulate every aspect of plant life. They are usually composed of at least four discrete domains: DNA binding site, transcription activation domain, oligomerization site, and nuclear localization signal. All of these domains work together to control specific physiological and biochemical processes (Diao et al, 2016). Dozens of transcription factor families exist in a plant genome, such as tomato (Solanum lycopersicum), which represents an economically important crop and a model species for fleshy-fruit study (Tomato Genome Consortium, 2012). The BBX proteins are a class of zinc-finger transcription factors possessing one or two

Methods

Results

Conclusion