Abstract
BackgroundIn plants, the basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Genome-wide comprehensive and systematic analyses of bHLH proteins have been well conducted in Arabidopsis, rice, tomato and other plant species. However, only few of bHLH family genes have been functional characterized in maize.ResultsIn this study, our genome-wide analysis identified 208 putative bHLH family proteins (ZmbHLH proteins) in maize (Zea mays). We classified these proteins into 18 subfamilies by comparing the ZmbHLHs with Arabidopsis thaliana bHLH proteins. Phylogenetic analysis, conserved protein motifs, and exon-intron patterns further supported the evolutionary relationships among these bHLH proteins. Genome distribution analysis found that the 208 ZmbHLH loci were located non-randomly on the ten maize chromosomes. Further, analysis of conserved cis-elements in the promoter regions, protein interaction networks, and expression patterns in roots, leaves, and seeds across developmental stages, suggested that bHLH family proteins in maize are probably involved in multiple physiological processes in plant growth and development.ConclusionWe performed a genome-wide, systematic analysis of bHLH proteins in maize. This comprehensive analysis provides a useful resource that enables further investigation of the physiological roles and molecular functions of the ZmbHLH transcription factors.
Highlights
In plants, the basic helix-loop-helix transcription factors play key roles in diverse biological processes
Identification and classification of basic helix-loop-helix (bHLH) family proteins in maize Examination of the maize genome sequence identified 208 Zea mays basic helix-loop-helix (ZmbHLH) family proteins in the maize inbred line B73 (Additional file 2: Table S2). This indicates that maize has more bHLH transcription factor family members than other plant species (166 bHLH family members in Arabidopsis, 166 in rice, 159 in tomato) [19,20,21]
ZmbHLH family proteins were classified into 18 subfamilies according to multiple alignments and phylogenetic analysis, and the classification of bHLH family proteins in Arabidopsis and rice (Additional file 3 and Additional file 4: Figure S1)
Summary
The basic helix-loop-helix (bHLH) transcription factors play key roles in diverse biological processes. Maize (Zea mays) is an important crop plant and the question of how to effectively increase maize production and improve other key agronomic traits (nitrogen use efficiency, disease resistance, etc.) remains a major challenge in functional genomics and modern agriculture. Members of the bHLH superfamily of eukaryotic transcription factors act as important transcriptional regulators in many organisms. In these transcription factors, the conserved bHLH domain contains a basic region and a HLH region. The basic region is generally located at the N-terminus of the bHLH domain and binds to a consensus hexanucleotide E-box (CANNTG) [2]. The HLH region is located at the C-terminus of the bHLH domain, contains about 50 amino acids, and is composed of two alpha helixes separated by a loop of variable length. The HLH region mediates interactions with other bHLH proteins to form homodimeric or heterodimeric complexes [3]
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