Genome-wide identification and expression analysis of the BTB domain-containing protein gene family in tomato

Abstract

BTB (broad-complex, tramtrack, and bric-a-brac) family proteins are characterized by the presence of a protein-protein interaction BTB domain. BTB proteins have diverse functions, including transcriptional regulation, protein degradation, chromatin remodeling, and cytoskeletal regulation. However, little is known about this gene family in tomato (Solanum lycopersicum), the most important model plant for crop species. In this study, 38 BTB genes were identified based on tomato whole-genome sequence. Phylogenetic analysis of BTB proteins in tomato revealed that SlBTB proteins could be divided into at least 4 subfamilies. The SlBTB proteins contains 1-3 BTB domains, and several other types of functional domains, including KCTD (Potassium channel tetramerization domain-containing), the MATH (meprin and TRAF homology), ANK (Ankyrin repeats), NPR1 (nonexpressor of pathogenesis-related proteins1), NPH3 (Nonphototropic Hypocotyl 3), TAZ zinc finger, C-terminal Kelch, Skp1 and Arm (Armadillo/beta-catenin-like repeat) domains are also found in some tomato BTB proteins. Moreover, their expression patterns in tissues/stages, in response to different abiotic stress treatments and hormones were also investigated. This study provides the first comprehensive analysis of BTB gene family in the tomato genome. The data will undoubtedly be useful for better understanding the potential functions of BTB genes, and their possible roles in mediating hormone cross-talk and abiotic stress in tomato as well as in some other relative species.

Genome-Wide Identification and Expression Analysis of the Protease Inhibitor Gene Families in Tomato

“…Untreated plants were used as controls to avoid the effects of biological clock on differential gene expression. After 0, 1, 4, 6, 12, and 24 h of treatment, the materials of leaves were immediately frozen in liquid nitrogen and stored at −80 • C. The RNA isolation and real-time PCR was performed as described previously [39] with gene-specific primers ( Supplementary Table S1).…”

Contribution of CaBPM4, a BTB Domain–Containing Gene, to the Response of Pepper to Phytophthora capsici Infection and Abiotic Stresses

“…Utilizing available whole genome sequences, 80 and 149 members of the BTB gene superfamily have been identified in Arabidopsis thaliana and rice, respectively [44,45]. Moreover, 38 BTB members were found in the tomato plant [26]. Furthermore, six BPMs (BTB-MATH) in Arabidopsis have been observed to assemble with cullins to form complexes [29].…”

“…The tissue-specific expression patterns of BPM genes have been reported in various species, such as Arabidopsis [48], tomato [26], and rice [49]. However, there is no uniform pattern of gene expression for these BPM genes [17,31].…”

“…Furthermore, the BTB-containing protein ARIA also affected the abscisic acid (ABA)-mediated signaling pathway through interactions with a transcription factor ABF2 [25]. The BTB domain-containing protein gene family of tomato was also well-known to be related closely to abiotic stresses [26].Many BTB/POZ proteins contain a secondary protein domain, such as a meprin and TRAF (tumor necrosis factor receptor associated factor) homology (MATH) domain, a tumor necrosis factor receptor-associated element [27]. A previous study suggested that MATH domain-containing proteins positively regulate defense responses to abiotic stresses in Arabidopsis and rice [28].…”

“…Furthermore, the BTB-containing protein ARIA also affected the abscisic acid (ABA)-mediated signaling pathway through interactions with a transcription factor ABF2 [25]. The BTB domain-containing protein gene family of tomato was also well-known to be related closely to abiotic stresses [26].…”