Genome-wide identification and expression profile of HD-ZIP genes in physic nut and functional analysis of the JcHDZ16 gene in transgenic rice

Abstract

Background: Homeodomain-leucine zipper (HD-ZIP) transcription factors play important roles in the growth, development and stress responses of plants, including (presumably) physic nut (Jatropha curcas), which has high drought and salinity tolerance. However, although physic nut's genome has been released, there is little knowledge of the functions, expression profiles and evolutionary histories of the species' HD-ZIP genes. Results: In this study, 32 HD-ZIP genes were identified in the physic nut genome (JcHDZs) and divided into four groups (I-IV) based on phylogenetic analysis with homologs from rice, maize and Arabidopsis. The analysis also showed that most of the JcHDZ genes were closer to members from Arabidopsis than to members from rice and maize. Of the 32 JcHDZ genes, most showed differential expression patterns among four tissues (root, stem cortex, leaf, and seed). Expression profile analysis based on RNA-seq data indicated that 15 of the JcHDZ genes respond to at least one abiotic stressor (drought and/or salinity) in leaves at least at one time point. Transient expression of a JcHDZ16-YFP fusion protein in Arabidopsis protoplasts cells showed that JcHDZ16 is localized in the nucleus. In addition, rice seedlings transgenically expressing JcHDZ16 had lower proline contents and activities of antioxidant enzymes (catalase and superoxide dismutase) together with higher relative electrolyte leakage and malondialdehyde contents under salt stress conditions (indicating higher sensitivity) than wild-type plants. The transgenic seedlings also showed increased sensitivity to exogenous ABA, and increases in the transcriptional abundance of several salt stress-responsive genes were impaired in their responses to salt stress. Further data on JcHDZ16-overexpressing plants subjected to salt stress treatment verified the putative role of JcHDZ genes in salt stress responses. Conclusion:Our results may provide foundations for further investigation of functions of JcHDZ genes in responses to abiotic stress, and promote application of JcHDZ genes in physic nut breeding.

Promoter Architecture and Transcriptional Regulation of Genes Upregulated in Germination and Coleoptile Elongation of Diverse Rice Genotypes Tolerant to Submergence

“…The enrichment of this element is most probably associated with the activities of a number of HD-ZIP genes such as Os06g014040 (Homeobox protein knotted-1-like 10), Os05g0129700 (Homeobox-leucine zipper protein HOX28), Os03g0198600 (Homeodomain-leucine zipper transcription factor), Os06g0140700 (Homeobox-leucine zipper protein HOX2), Os03g0188900 (Homeobox-leucine zipper protein HOX13), and Os09g0528200 (Similar to Homeobox-leucine zipper protein HOX6) ( Table 4 ). HD-ZIP is involved in the regulation of many developmental processes and response to different abiotic stresses in many plants ( Annapurna et al, 2016 ; Tang et al, 2019 ; Zhao et al, 2019 ). However, the role of HD-ZIP in response to submergence stress is not known yet.…”

Genome-Wide Characterization and Expression Analysis of the HD-ZIP Gene Family in Response to Salt Stress in Pepper

“…The phylogenetic tree was constructed using HDZ proteins of pepper, rice, and Arabidopsis . HDZ proteins of pepper can be divided into four categories (HD-ZIP I-IV), and the number of HD-ZIP I, II, III, and IV are 14, 10, and 5, respectively, 11, and 17, 10, 5, and 16 in Arabidopsis [ 58 ]; 12, 9, 4, and 7 in physic nut [ 59 ]; 11, 7, 5, and 8 in grape [ 60 ]; 16, 10, 9, and 10 in sesame [ 53 ]. These results suggested that the HD-ZIPI protein was the most abundant type of pepper HD-ZIP transcription factor, and the amount of HD-ZIPIII protein in pepper was the same as that of most plants.…”

“…These results suggested that the HD-ZIPI protein was the most abundant type of pepper HD-ZIP transcription factor, and the amount of HD-ZIPIII protein in pepper was the same as that of most plants. In addition, the phylogenetic tree also showed that most CaHDZ proteins were closer to members of Arabidopsis thaliana than members from rice [ 59 ] ( Figure 7 . Motif analysis also demonstrated that CaHDZ protein motifs distributed differently with subfamilies, and genes of the same family had similar structure and function ( Figure 1 , S2 ), which provided a powerful guarantee for the evolution of pepper.…”

Genome-wide analysis of Jatropha curcas MADS-box gene family and functional characterization of the JcMADS40 gene in transgenic rice

“…Subcellular localization of the control YFP and JcMADS40-YFP fusion proteins was observed under a confocal laser scanning microscope. Arabidopsis protoplasts were obtained following Tang [5].…”

“…These mechanisms are under the control of many related genes acting through complex regulatory networks. In these processes, transcription factor (such as members of the MYB, HD-Zip, ARF, NAC, MADSbox, and ERF gene families) specifically recognize cisregulatory elements present in the promoter regions of these genes, and regulate their expression so as to modulate a wide range of biochemical, physiological and developmental processes [1][2][3][4][5][6].…”