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

ZmSIDP1, a DUF1644 gene from the halophyte Zoysia matrella, positively regulates salt tolerance in rice

As a detrimental abiotic stressor, salinity affects plant growth and yield. Domain of unknown function 1644 (DUF1644) is a large plant-specific DUF protein family that is predicted to be involved in abiotic stress responses in plants. However, the biological functions of DUF1644 genes in plants remain largely unexplored, especially in halophytes. Here, we investigated the function of the DUF1644 gene, ZmSIDP1, from the halophyte Zoysia matrella. ZmSIDP1 could enhance the salt tolerance of yeast. Furthermore, the heterologous transformation of the ZmSIDP1 gene in rice demonstrated that transgenic rice plants exhibited better growth under NaCl treatment. The Na + content was lower in ZmSIDP1 transgenic rice than in wild-type rice under salt stress. ZmSIDP1 transgenic rice showed stronger resistance to oxidative stress induced by salt stress. Further investigation indicated that ZmSIDP1 could interact with an HD-Zip transcription factor, ZmROC1. These results suggest that the ZmSIDP1 gene from the halophyte Z. matrella can positively regulate salt resistance in rice, laying a foundation for the application of salt tolerance genes from halophytes to enhance salt tolerance in rice.

Genome-wide investigation of HD-ZIP gene family and functional characterization of BnaHDZ149 and BnaHDZ22 in salt and drought response in Brassica napus L

HD-ZIP proteins comprise a plant-specific transcription factor family, which play pivotal roles in plant development and adaptation to ever-changing environment. Although HD-ZIP family members have been identified in some plant species, so far our knowledge about HD-ZIP genes in rapeseed is still limited. In this study, 178 Brassica napus HD-ZIP (BnaHDZ) family members were identified in the rapeseed genome. The phylogenetic relationship, chromosomal locations, intron-exon structures, motif composition, and expression patterns of the BnaHDZ members were analyzed. The BnaHDZ family can be phylogenetically divided into four categories (Ⅰ, Ⅱ, Ⅲ and Ⅳ). Genome-wide transcriptome analysis revealed that most of the HD-ZIP I members respond to at least one abiotic stress. Two closely homologous stress-responsive HD-ZIP Ⅰ genes, BnaHDZ22 and BnaHDZ149, were identified to be involved in drought and salt responses, and selected for further functional characterization. Overexpressing BnaHDZ149 in rapeseed increased salt sensitivity of the transgenic plants, whereas overexpressing BnaHDZ22 increased sensitivity of the transgenic plants to polyethylene glycol (PEG)-simulated drought stress. This research provides not only a comprehensive landscape of BnaHDZ genes, but also a theoretical basis for elucidating the molecular mechanism of the abiotic stress responses of the HD-ZIP family in rapeseed.

Transcription factor CaHDZ15 promotes pepper basal thermotolerance by activating HEAT SHOCK FACTORA6a

High temperature stress (HTS) is a serious threat to plant growth and development and to crop production in the context of global warming, and plant response to HTS is largely regulated at the transcriptional level by the actions of various transcription factors (TFs). However, whether and how homeodomain-leucine zipper (HD-Zip) TFs are involved in thermotolerance are unclear. Herein, we functionally characterized a pepper (Capsicum annuum) HD-Zip I TF CaHDZ15. CaHDZ15 expression was upregulated by HTS and abscisic acid in basal thermotolerance via loss- and gain-of-function assays by virus-induced gene silencing in pepper and overexpression in Nicotiana benthamiana plants. CaHDZ15 acted positively in pepper basal thermotolerance by directly targeting and activating HEAT SHOCK FACTORA6a (HSFA6a), which further activated CaHSFA2. In addition, CaHDZ15 interacted with HEAT SHOCK PROTEIN 70-2 (CaHsp70-2) and glyceraldehyde-3-phosphate dehydrogenase1 (CaGAPC1), both of which positively affected pepper thermotolerance. CaHsp70-2 and CaGAPC1 promoted CaHDZ15 binding to the promoter of CaHSFA6a, thus enhancing its transcription. Furthermore, CaHDZ15 and CaGAPC1 were protected from 26S proteasome-mediated degradation by CaHsp70-2 via physical interaction. These results collectively indicate that CaHDZ15, modulated by the interacting partners CaGAPC1 and CaHsp70-2, promotes basal thermotolerance by directly activating the transcript of CaHSFA6a. Thus, a molecular linkage is established among CaHsp70-2, CaGAPC1, and CaHDZ15 to transcriptionally modulate CaHSFA6a in pepper thermotolerance.

Evolutionary Consequences of Functional and Regulatory Divergence of HD-Zip I Transcription Factors as a Source of Diversity in Protein Interaction Networks in Plants

The HD superfamily has been studied in detail for several decades. The plant-specific HD-Zip I subfamily attracts the most attention because of its involvement in plant development and stress responses. In this review, we provide a comprehensive insight into the evolutionary events responsible for the functional redundancy and diversification of the HD-Zip I genes in regulating various biological processes. We summarized the evolutionary history of the HD-Zip family, highlighting the important role of WGDs in its expansion and divergence of retained duplicates in the genome. To determine the relationship between the evolutionary origin and functional conservation of HD-Zip I in different species, we performed a phylogenetic analysis, compared their expression profiles in different tissues and under stress and traced the role of orthologs and paralogs in regulating developmental processes. We found that HD-Zip I from different species have similar gene structures with a highly conserved HD and Zip, bind to the same DNA sequences and are involved in similar biological processes. However, they exhibit a functional diversity, which is manifested in altered expression patterns. Some of them are involved in the regulation of species-specific leaf morphology and phenotypes. Here, we discuss the role of changes in functional domains involved in DNA binding and protein interaction of HD-Zip I and in cis-regulated regions of its target genes in promoting adaptive innovations through the formation of de novo regulatory systems. Understanding the role of the HD-Zip I subfamily in organism-environment interactions remains a challenge for evolutionary developmental biology (evo-devo).

Analysis of the HD-Zip I transcription factor family in Salvia miltiorrhiza and functional research of SmHD-Zip12 in tanshinone synthesis

Background

The homeodomain-leucine zipper I (HD-Zip I) transcription factor is a plant-specific protein that plays an essential role in the abiotic stress response of plants. Research on the HD-Zip I family in Salvia miltiorrhiza is still lacking.

Methods and Results

In this study, a total of 25 SmHD-Zip I proteins were identified. Their characterizations, phylogenetic relationships, conserved motifs, gene structures, and cis-elements were analyzed comprehensively using bioinformatics methods. Expression profiling revealed that SmHD-Zip I genes exhibited distinctive tissue-specific patterns and divergent responses to ABA, PEG, and NaCl stresses. SmHD-Zip12 responded the most strongly to ABA, PEG, and NaCl, so it was used for transgenic experiments. The overexpression of SmHD-Zip12 significantly increased the content of cryptotanshinone, dihydrotanshinone I, tanshinone I, and tanshinone IIA by 2.89-fold, 1.85-fold, 2.14-fold, and 8.91-fold compared to the wild type, respectively. Moreover, in the tanshinone biosynthetic pathways, the overexpression of SmHD-Zip12 up-regulated the expression levels of SmAACT, SmDXS, SmIDS, SmGGPPS, SmCPS1, SmCPS2, SmCYP76AH1, SmCYP76AH3, and SmCYP76AK1 compared with the wild type.

Conclusions

This study provides information the possible functions of the HD-Zip I family and lays a theoretical foundation for clarifying the functional mechanism of the SmHD-Zip12 gene in regulating the synthesis of tanshinone in S. miltiorrhiza.

Genome-Wide Identification of Homeodomain Leucine Zipper (HD-ZIP) Transcription Factor, Expression Analysis, and Protein Interaction of HD-ZIP IV in Oil Palm Somatic Embryogenesis

Understanding the molecular mechanisms underlying somatic embryogenesis is essential for resolving the problems related to the long duration of the process and a low rate of somatic embryo induction in oil palm tissue culture. In this study, we conducted genome-wide identification of the oil palm homeodomain leucine zipper (EgHD-ZIP) family, which is one of the plant-specific transcription factors reported to be involved in embryogenesis. EgHD-ZIP proteins can be divided into four subfamilies, which have similarities in gene structure and protein-conserved motifs within a group. In silico expression analysis showed that the expression of EgHD-ZIP gene members in the EgHD-ZIP I and II families, as well as most members in the EgHD-ZIP IV family, were up-regulated during the zygotic and somatic embryo developmental stages. In contrast, the expression of EgHD-ZIP gene members in the EgHD-ZIP III family was down-regulated during zygotic embryo development. Moreover, the expression of EgHD-ZIP IV genes was validated in the oil palm callus and at the somatic embryo stages (globular, torpedo, and cotyledon). The results revealed that EgHD-ZIP IV genes were up-regulated at the late stages of somatic embryogenesis (torpedo and cotyledon). While BABY BOOM (BBM) gene was up-regulated at the early stage of somatic embryogenesis (globular). In addition, the Yeast-two hybrid assay revealed the direct binding between all members of the oil palm HD-ZIP IV subfamily (EgROC2, EgROC3, EgROC5, EgROC8, and EgBBM). Our findings suggested that the EgHD-ZIP IV subfamily and EgBBM work together to regulate somatic embryogenesis in oil palms. This process is important because it is widely used in plant biotechnology to produce large quantities of genetically identical plants, which can be used for oil palm tissue culture improvement.

Genome-wide identification and systematic analysis of the HD-Zip gene family and its roles in response to pH in Panax ginseng Meyer

BACKGROUND

Ginseng, Panax ginseng Meyer, is a traditional herb that is immensely valuable both for human health and medicine and for medicinal plant research. The homeodomain leucine zipper (HD-Zip) gene family is a plant-specific transcription factor gene family indispensable in the regulation of plant growth and development and plant response to environmental stresses.

RESULTS

We identified 117 HD-Zip transcripts from the transcriptome of ginseng cv. Damaya that is widely grown in Jilin, China where approximately 60% of the world's ginseng is produced. These transcripts were positioned to 64 loci in the ginseng genome and the ginseng HD-Zip genes were designated as PgHDZ genes. Identification of 82 and 83 PgHDZ genes from the ginseng acc. IR826 and cv. ChP genomes, respectively, indicated that the PgHDZ gene family consists of approximately 80 PgHDZ genes. Phylogenetic analysis showed that the gene family originated after Angiosperm split from Gymnosperm and before Dicots split from Monocots. The gene family was classified into four subfamilies and has dramatically diverged not only in gene structure and functionality but also in expression characteristics. Nevertheless, co-expression network analysis showed that the activities of the genes in the family remain significantly correlated, suggesting their functional correlation. Five hub PgHDZ genes were identified that might have central functions in ginseng biological processes and four of them were shown to be actively involved in plant response to environmental pH stress in ginseng.

CONCLUSIONS

The PgHDZ gene family was identified from ginseng and analyzed systematically. Five potential hub genes were identified and four of them were shown to be involved in ginseng response to environmental pH stress. The results provide new insights into the characteristics, diversity, evolution, and functionality of the PgHDZ gene family in ginseng and lay a foundation for comprehensive research of the gene family in plants.

Discovering favorable genes, QTLs, and genotypes as a genetic resource for sesame (Sesamum indicum L.) improvement

Sesame (Sesamum indicum L.) is an ancient diploid oilseed crop with high oil content, quality protein, and antioxidant characteristics that is produced in many countries worldwide. The genes, QTLs, and genetic resources of sesame are utilized by sesame researchers and growers. Researchers have identified the many useful traits of this crop, which are available on different platforms. The genes, genotypes, QTLs, and other genetic diversity data of sesame have been collected and stored in more than nine genomic resources, and five sesame crop marker databases are available online. However, data on phenotypic and genotypic variability, which would contribute to sesame improvements, are limited and not yet accessible. The present study comprehensively reviewed more than 110 original published research papers and scientifically incorporated the results. The candidate genes, genotypes, and QTLs of significantly important traits of sesame were identified. Genetic resources related to grain yield and yield component traits, oil content and quality, drought tolerance, salt tolerance, waterlogging resistance, disease resistance, mineral nutrient, capsule shattering resistance, and other agronomic important traits of sesame were studied. Numerous candidate genotypes, genes, QTLs, and alleles associated with those traits were summarized and discovered. The chromosome regions and linkage groups, maps associated with the best traits, and candidate genes were also included. The variability presented in this paper combined with sesame genetic information will help inform further sesame improvement.

The roles of HD-ZIP proteins in plant abiotic stress tolerance

Homeodomain leucine zipper (HD-ZIP) proteins are plant-specific transcription factors that contain a homeodomain (HD) and a leucine zipper (LZ) domain. The highly conserved HD binds specifically to DNA and the LZ mediates homodimer or heterodimer formation. HD-ZIP transcription factors control plant growth, development, and responses to abiotic stress by regulating downstream target genes and hormone regulatory pathways. HD-ZIP proteins are divided into four subclasses (I-IV) according to their sequence conservation and function. The genome-wide identification and expression profile analysis of HD-ZIP proteins in model plants such as Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) have improved our understanding of the functions of the different subclasses. In this review, we mainly summarize and discuss the roles of HD-ZIP proteins in plant response to abiotic stresses such as drought, salinity, low temperature, and harmful metals. HD-ZIP proteins mainly mediate plant stress tolerance by regulating the expression of downstream stress-related genes through abscisic acid (ABA) mediated signaling pathways, and also by regulating plant growth and development. This review provides a basis for understanding the roles of HD-ZIP proteins and potential targets for breeding abiotic stress tolerance in plants.

Genome-wide characterization of homeodomain-leucine zipper genes reveals RsHDZ17 enhances the heat tolerance in radish (Raphanus sativus L.)

Homeodomain-leucine zipper (HD-Zip) transcription factors are involved in various biological processes of plant growth, development, and abiotic stress response. However, how they regulate heat stress (HS) response remains largely unclear in plants. In this study, a total of 83 RsHD-Zip genes were firstly identified from the genome of Raphanus sativus. RNA-Seq, RT-qPCR and promoter activity assays revealed that RsHDZ17 from HD-Zip Class I was highly expressed under heat, salt, and Cd stresses. RsHDZ17 is a nuclear protein with transcriptional activity at the C-terminus. Ectopic overexpression (OE) of RsHDZ17 in Arabidopsis thaliana enhanced the HS tolerance by improving the survival rate, photosynthesis capacity, and scavenging for reactive oxygen species (ROS). In addition, transient OE of RsHDZ17 in radish cotyledons impeded cell injury and augmented ROS scavenging under HS. Moreover, yeast one-hybrid, dual-luciferase assay, and electrophoretic mobility shift assay revealed that RsHDZ17 could bind to the promoter of HSFA1e. Collectively, these pieces of evidence demonstrate that RsHDZ17 could play a positive role in thermotolerance, partially through up-regulation of the expression of HSFA1e in plants. These results provide novel insights into the role of HD-Zips in radish and facilitate genetical engineering and development of heat-tolerant radish in breeding programs.

Genome-Wide Characterization and Anthocyanin-Related Expression Analysis of the B-BOX Gene Family in Capsicum annuum L

The transcription factors, B-box (BBX), belong to a subfamily of the zinc finger family of proteins and exhibit multiple biological functions in plant growth, development, and abiotic stress response pathways. In this study, a total of 23 CaBBX members were identified using the pepper reference genome database. According to the gene structure, conserved domains, and the phylogenetic tree, 23 CaBBX genes were divided into four groups, wherein the analysis of the promoter region indicated the presence of cis-acting elements related to plant development, hormones, and stress response. Interspecies collinearity analysis showed that the CaBBXs had three duplicated gene pairs, and the highest gene density was found on chromosomes 2 and 7. Transcriptome RNA-seq data and quantitative polymerase chain reaction (qRT-PCR) analysis of pepper plants spanning the entire period showed that more than half of the CaBBX genes were widely expressed in diversity tissues of pepper. Co-expression network analysis indicated that the CaBBXs and the anthocyanin structural genes had a close co-expression relationship. Thus, it was reasonably speculated that the CaBBX genes may be involved in the regulation of anthocyanin biosynthesis. Overall, this study involved the genome-wide characterization of the CaBBX family and may serve as a solid foundation for further investigations on CaBBX genes involved in the anthocyanin synthesis mechanisms and development in pepper.

Genome-wide analysis of poplar HD-Zip family and over-expression of PsnHDZ63 confers salt tolerance in transgenic Populus simonii × P.nigra

HD-Zip is a plant-specific HB transcription factor, which participates in plant development and stress response. In this study, we identified 63 poplar HD-Zip transcription factors, which were randomly distributed on 19 chromosomes of poplar. Based on the gene structure and phylogenetic relationship, these members are divided into four groups, which have a variety of collinear evolutionary relationships. They also have rich segmental replication events and experienced strong purification selection. Based on RNA-seq analysis, we profiled the expression pattern of the 63 HD-Zip members under salt stress. Subsequently, we carried out in-depth study on the significantly up-regulated PsnHDZ63 in the stems and leaves. The transgenic Populus simonii × P.nigra plants over-expressing PsnHDZ63 displayed better morphological and physiological indexes than WT under salt stress. In addition, PsnHDZ63 enhanced salt stress tolerance of transgenic lines by combining effective stress-resistant elements to improve reactive oxygen species scavenging ability. These studies laid a foundation for a comprehensive understanding of poplar HD-Zip family members, and revealed the important role of PsnHDZ63 in plant salt tolerance.