Abstract
The homeodomain-leucine zipper (HD-Zip) gene family, whose members play vital roles in plant growth and development, and participate in responding to various stresses, is an important class of transcription factors currently only found in plants. Although the HD-Zip gene family, especially the HD-Zip I subfamily, has been extensively studied in many plant species, the systematic report on HD-Zip I subfamily in cultivated tobacco (Nicotiana tabacum) is lacking. In this study, 39 HD-Zip I genes were systematically identified in N. tabacum (Nt). Interestingly, that 64.5% of the 31 genes with definite chromosome location information were found to originate from N. tomentosoformis, one of the two ancestral species of allotetraploid N. tabacum. Phylogenetic analysis divided the NtHD-Zip I subfamily into eight clades. Analysis of gene structures showed that NtHD-Zip I proteins contained conserved homeodomain and leucine-zipper domains. Three-dimensional structure analysis revealed that most NtHD-Zip I proteins in each clade, except for those in clade η, share a similar structure to their counterparts in Arabidopsis. Prediction of cis-regulatory elements showed that a number of elements responding to abscisic acid and different abiotic stresses, including low temperature, drought, and salinity, existed in the promoter region of NtHD-Zip I genes. The prediction of Arabidopsis ortholog-based protein–protein interaction network implied that NtHD-Zip I proteins have complex connections. The expression profile of these genes showed that different NtHD-Zip I genes were highly expressed in different tissues and could respond to abscisic acid and low-temperature treatments. Our study provides insights into the evolution and expression patterns of NtHD-Zip I genes in N. tabacum and will be useful for further functional characterization of NtHD-Zip I genes in the future.
Highlights
As regulatory proteins for the transcriptional activation or repression of target genes, transcription factors (TFs) are the main players in development and differentiation in eukaryotic organisms [1].The TFs regulate gene expression by interacting with cis-regulatory regions [2].The homeodomain-leucine zipper (HD-Zip) gene family is a relatively pivotal class of TFs, presentGenes 2019, 10, 575; doi:10.3390/genes10080575 www.mdpi.com/journal/genesGenes 2019, 10, 575 only in the plant kingdom [3,4]
To identify the NtHD-Zip I subfamily gene in N. tabacum, a BLASTP search was implemented against the tobacco genome database using HD-Zip I protein sequences from multiple plants, and conserved HD and leucine zipper (LZ) domains were further analyzed following BLASTP search
39 NtHD-Zip I genes were identified in this study
Summary
Genes 2019, 10, 575 only in the plant kingdom [3,4] This gene family has been identified in multiple plant species, such as soybean (Glycine max), tomato (Solanum lycopersicum), grape (Vitis vinifera), rice (Oryza sativa), maize (Zea mays), and wheat (Triticum aestivum) [5,6,7,8,9,10]. Based on their corresponding gene structure, including some specific cis-elements, conserved sequences, and biological function, they can be divided into four subfamilies: HD-Zip I to HD-Zip IV [4]. The HD can bind to DNA, and the LZ can act as a dimerization motif
Sign-in/Register to view highlights & summary 
Published Version (
Free)
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call